Plant sensor TWA1 as molecular thermogenetic control switch and for improvement of thermotolerance and modifying of senescence
Field of the invention
The present invention relates to the use of TWA1 or a homolog thereof for modifying thermotolerance and/or senescence in plants or plant cells, and further to the use of TWA1 or a homolog thereof as a molecular thermosensitive genetic control switch for gene expression. The present invention further relates to a method of modifying thermotolerance and/or senescence in a plant or plant cell, comprising:
I) modifying the TWA1 locus or a homolog thereof in a plant or plant cell; and/or
II) introducing into a plant or plant cell an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and/or
III) introducing into a plant or plant cell a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences; and/or
IV) introducing an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) into a plant or plant cell, wherein expression of the gene product of the modified TWA1 locus or the homolog thereof and/or of the nucleic acid sequence as defined in any one of items i) to iv), or presence of the introduced polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) results in modified thermotolerance and/or senescence in said plant or plant cell. The present invention further relates to a method of producing a transgenic plant or plant cell using such a nucleic acid as defined in any one of items i)-iv) or a recombinant nucleic acid comprising said elements a)-c) in 5'-3' orientation; to a transgenic cell comprising a such a recombinant nucleic acid molecule; to a transgenic plant comprising such a transgenic cell or produced by such a method, and parts of these plants, transgenic harvest products and transgenic propagation material of these plants, such as protoplasts, plant cells, calli, seeds, tubers, cuttings, and the transgenic progeny of this plant; and to the use of the TWA1 locus or a homolog thereof for the production of transgenic plants or transgenic plant cells with modified thermotolerance and/or modified senescence.
Background of the invention
Climatic temperature gradients constrain growth and fitness of plants. Plant species have preferred temperatures with daytime optima that vary substantially from 10 °C, for instance, for the cool-preferring Viola to 35 °C, for instance, for the tropical kapok tree. Temperatures substantially exceeding the optimum trigger acclimation responses that involve the heat stress response (HSR). Several plant thermosensors that regulate temperature-induced developmental processes are known, such as Camchannels, transcriptional regulators, and light receptors. However, the sensing mechanism initiating basal and acquired thermotolerance of plants are yet unknown. In metazoans, fungi and plants, heat triggers the HSR via heat shock factor 1 (HSF1) transcription factors. After release from inhibitory molecular chaperones HSF1 induces expression of heat shock proteins (HSPs) and initiates adaptation. In plants, HSR further involves several phytohormone pathways. Arabidopsis mutants deficient in biosynthesis or signaling of abscisic acid (ABA) are more sensitive in basal and acquired thermotolerance while ethylene appears to play a more specific role in establishing basal thermotolerance. ABA is the key signal to regulate the water status of plants by adjusting transpiration and water resorption to the demand of atmospheric CO2 for photosynthesis. Under water deficit, ABA levels increase and induce protective measures including stomatai closing, differential gene expression, downregulation of chlorophylls, and biosynthesis of osmolytes such as proline. Excessive stimulation of ABA signaling targets and activates key regulators of plant senescence inducing leaf chlorosis. Heat frequently leads to increases in ABA because of the higher water vapour gradient between plant and a warmer atmosphere (less water saturation) and the concomitant constrain on the water status of plants. Hence, ABA functions under heat as a mediator of thermotolerance and as a stimulant of senescence. In natural environments, heat and drought occur often combined and are the cause of major crop losses.
Senescence is a stress-induced process and a developmental program during which chlorophyll is catabolized, and nitrogen-containing compounds are mobilized to other organs. A stay-green phenotype of plants in which chlorophyll catabolism is altered is caused either by a lesion in the senescence pathway or, if the pathway is functional, by delayed or slow onset of the process (ref45). The functional stay-green trait (SG) attracted much attention among breeders after a positive correlation between yield increases and stay-green scores of crop varieties was uncovered. SG phenotypes were found to provide improved drought tolerance that was associated with reduced ABA and ABA catabolite levels and changes in plant architecture by optimizing the post-anthesis balance between supply and demand of water. ABA is known to trigger senescence. Major genetic determinants responsible for SG traits include genes for PIN proteins involved in auxin transport, genes of the vernalization response, and in the magnesium dechelatase required for chlorophyll catabolism. Senescence is counterbalanced by the phytohormone cytokinin and enhancing cytokinin levels provided a SG trait and improved abiotic stress resilience. SG varieties extend the grain-filling period which is associated with higher yield, even under drought and heat stress. Global temperature increase will shorten the grain filling period. The trend negatively impacts on yield and imposes urgency on identifying genes associated with SG and heat tolerance. Breeders developed rice varieties more tolerant to heat-induced sterility and wheat lines have been generated with improved heat tolerance by introgression of chromosomal segments of Aegilops tauschii.
Various technologies and approaches are already being used to improve the thermotolerance of plants. Some of the best known of these encompass genetic engineering and gene editing, marker-assisted selection (MAS), hormone-based approaches, biofortification as well as breeding techniques. MAS, biofortification, and breeding techniques have been in use for many years. They are less precise than gene editing, but also less expensive and time-consuming.
In analogy to optogenetics, thermogenetics refers to the control of biological processes by temperature including infrared light. Thermogenetics is an emerging field that uses molecular temperature switches to control physiological processes such as gene expression, protein translation, or protein-protein interaction as successfully applied by optogenetics. There are parallels between thermogenetics and optogenetics. The latter uses electric magnetic waves in the visible and near-visible range while thermogenetics uses temperature changes. The advantage of using light instead of chemical inducers to activate biological processes is the fast on/off dynamic and reduced cell toxicity. Thermogenetics holds promise to complement the toolbox of optogenetics by offering the advantage that thermal changes such as by infrared light or microwave penetrate deeper into the tissue than the visible spectrum of electromagnetic waves.
The inventors of the present invention identified a specific gene locus of the plant Arabidopsis thaliana encoding a protein termed TWA1 (for Thermo-With ABA-response 1 ; amino acid sequence set forth in SEQ ID NO: 106; encoded by the nucleic acid sequence set forth in SEQ ID NO: 105) that confers thermotolerance in Arabidopsis and plant cells in acting as a thermosensor, more specifically as a temperature-sensitive transcription co-regulator for temperature-induced transcription regulation within the plant or plant cell. As discovered by the inventors, TWA1 (AT5G13590) interacts with JASMONATE- ASSOCIATED MYC-LIKE (JAM) transcription factors and TOPLESS/TOPLESS-related proteins (TPL/TPRs) to form a transcriptional repressor complex, and operates within a certain temperature range, acting as a temperature-sensitive control switch. The conformational switch of TWA1 occurs approximately within a 10 °C temperature window with half-maximum response (IT50) at 26 °C ±1 °C. However, said temperature range differs across different types of plant species. For instance, the IT50 values of the TWA1 ortholog of Arabidopsis lyrata and white mustard (Sinapis alba) was found to be about 20 °C and about 30 °C, respectively. TWA1 is expressed throughout the plant. The TWA1 locus encodes a 130 kDa intrinsically disordered protein with a thermosensory key function of an aminoterminally located highly variable region (HVR) among orthologs. Exchange of this HVR with the HVR of the A. lyrata homolog conferred the temperature responsiveness of the A. lyrata thermosensor. Exchange of TWA1 by the orthologs from Arabidopsis lyrata and white mustard in Arabidopsis plants changed the temperature dependence of gene expression for the ABA-regulated gene RD29B (AT5G52300) and early heat shock-responsive genes such as heat shock transcription factor A2 (HSF2A, AT2G26150), heat shock protein 21 (HSP21, AT4G27670) and HSP26.5 (AT1 G52560). In response to elevated temperatures, green fluorescent protein (GFP)-tagged TWA1 was found by the present inventors to accumulate in nuclear subdomains to which physical interaction with JAM2 (AT1 G01260) or TPL (AT1 G15750) appeared to be restricted. Functional inactivation of TWA1 , JAMs, or TPL/TPRs was found to increase heat sensitivity of Arabidopsis, while ectopic TWA1 expression was found to improve basal and acquired thermotolerance in a JAM-dependent manner. The transcriptional upregulation of the HSFA2 transcription factor and heat shock proteins by temperature rise was found to depend on TWA1 consistent with its sensor function in early signaling of heat stress. Ectopic TWA1 expression also suppressed chlorosis/senescence of leaves and ion leakage of plants induced by heat. The identification of the thermosensor TWA1 and its orthologs from other plant species, as herein described and defined, supplies molecular tools and prototypes for adjusting thermal acclimation and senescence responses of crops by breeding and biotechnology, and sensitive tools and prototypes for temperature switches in thermogenetics.
Summary of the invention
In a first aspect, provided herein is therefore the use of TWA1 or a homolog thereof for modifying thermotolerance and/or senescence in plants or plant cells.
In some embodiments, the modifying of thermotolerance is increasing thermotolerance and/or the modifying of senescence is reducing senescence.
In some embodiments of said use, the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
In a further aspect, the present invention also provides a method of modifying thermotolerance and/or senescence in a plant or plant cell, comprising:
I) modifying the TWA1 locus or a homolog thereof in a plant or plant cell; and/or
II) introducing into a plant or plant cell an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and/or
III) introducing into a plant or plant cell a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences; and/or
IV) introducing an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) into a plant or plant cell, wherein expression of the gene product of the modified TWA1 locus or the modified homolog thereof and/or of the nucleic acid sequence as defined in any one of items i) to iv), or presence of the introduced polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) results in modified thermotolerance and/or senescence in said plant or plant cell.
In some embodiments, said method further comprises the step of growing the plant or keeping the plant cell under conditions, wherein the expression product of the nucleic acid molecule as defined in any one of items i) to iv) or the polypeptide introduced into the plant or plant cell is able to act, in the plant or plant cell, as a thermosensor.
In some embodiments, said method comprises exposure of the plant or plant cell to temperatures in the range of about 7 to 60 °C, such as temperatures of about 10 °C, 15 °C, 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45, 50, 55, or 60 °.
In some embodiments, the nucleic acid sequence is derived from Arabidopsis, preferably Arabidopsis thaliana or Arabidopsis lyrata; Brassica, preferably Brassica oleracea; Sinapis, preferably Sinapis alba; Gossypium; Glycine max; Nelumbo nucifera; Phoenix dactylifera; Zea mays; or Triticum aestivum.
In some embodiments, the isolated polypeptide confers thermotolerance in plants or plant cells.
In some embodiments, the isolated polypeptide confers protection against senescence in plants or plant cells.
In some embodiments of said method, the modifying of thermotolerance is increasing thermotolerance and/or wherein the modifying of senescence is reducing senescence. In some embodiments of said method, the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
In another aspect, the present invention further provides a method of producing a transgenic plant or plant cell, said method comprising the steps of: a) introducing into a plant or plant cell, optionally integrating it into the plant genome, an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and/or b) introducing into a plant or plant cell, optionally integrating it into the plant genome, a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences.
In various embodiments, said method is not a non-technical, i.e., essentially biological method or process. Thus, in various embodiments, said method is a biotechnological method. In some embodiments, said method further comprises a step of expressing the nucleic acid sequence as defined in any one of items i) to iv) in said plant or plant cell.
In some embodiments, said method further comprises a step of regenerating a transgenic plant from a transgenic plant cell thus obtained. In yet another aspect, the present invention provides a transgenic cell comprising a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and optionally c) operatively linked thereto, one or more additional expression control sequences.
In some embodiments, the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell, or a plant cell.
In some embodiments, said transgenic cell has, relative to the wild-type cell and/or a control cell, an increased content of a polypeptide encoded by a nucleic acid sequence according to any one of items i) to iv).
In some embodiments, the transgenic cell is a transgenic plant cell, wherein optionally said transgenic plant cell is obtainable by a method of producing a transgenic plant cell according to the present invention.
In some embodiments, said transgenic plant cell has, relative to the wild-type plant cell and/or a control plant cell, a modified thermotolerance and/or senescence.
In some embodiments, the modified thermotolerance is an increased thermotolerance and/or the modified senescence is a reduced senescence.
In a still further aspect, the present invention also provides a transgenic plant comprising a transgenic cell according to the present invention or produced by a method according to the present invention, and parts of these plants, transgenic harvest products and transgenic propagation material of these plants, such as protoplasts, plant cells, calli, seeds, tubers, cuttings, and the transgenic progeny of this plant. In some embodiments, the transgenic plant is a monocotyledonous plant, preferably a plant belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; or a dicotyledonous plant, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
In yet another aspect, the present invention provides for the use of the TWA1 locus or a homolog thereof for the production of transgenic plants or transgenic plant cells with modified thermotolerance and/or modified senescence.
In a final aspect, the present invention provides the use of TWA1 or a homolog thereof as a molecular thermosensitive genetic control switch for gene expression.
In some embodiments, TWA1 or a homolog thereof acts, in a temperature-dependent manner, in conjunction with one or more TWA1 -binding proteins.
In various embodiments, the one or more TWA1 -binding proteins are selected from the JAM transcription factors and the corepressors TPL/TPRs, preferably JAM2 and its orthologs and TPL and its orthologs.
In various embodiments, TWA1 or a homolog thereof and the TWA1 -binding proteins form a protein complex of TWA1 -JAM-TPL/TPRs.
In various embodiments, the protein complex of TWA1 -JAM-TPL/TPRs acts as a transcriptional repressor complex.
Brief description of the drawings
Figure 1 shows a graphic evaluation of the inhibition of root growth by heat stress in the dark. 4 day-old Arabidopsis thaliana wild type seedlings, seedlings of the triple mutants pp2c_a (abi1 ,abi2,hab1) and pp2c_b (abi1,hab1,pp2ca) with deficiencies in ABA-coreceptors encoded by protein phosphatase 2Cs ABI1 (AT4G26080), ABI2 (AT5G57050), HAB1 (AT1 G72770),and PP2CA (AT3G11410), and of lines overexpressing ABA receptors RCAR6 (AT5G45870) and RCAR1 (AT 1 G01360) were cultivated at 22°C under continuous light (50 pE nr2 s1). The seedlings were acclimated to elevated temperatures by exposure to 38 °C for 2 h followed by 2h at ambient temperature (22°C) und subsequently exposed to 45 °C heat stress for the indicated times in the dark. Root extension was measured 5 days after treatment. Mean ± SD (n=6).
Figure 2 depicts a graphic evaluation of TWA1 expression in various plant tissues. TWA1 protein and TWA1 transcript abundance according to Mergner et al. (Mass-spectrometry-based draft of the Arabidopsis proteome, Nature 579, 409-414 (2020)) in the ATHENA proteomics database. TPM, transcripts per kilobase and million reads; iBAQ are summed peptide intensity per protein normalized to the number of expected peptides.
Figure 3 depicts a graphic evaluation of the acquired thermotolerance (acclimation scheme as in Figure 1) of twa1-1, twa1-2, and two twa1-2 lines complemented with the TWA1 wildtype gene. In the twa1-1 allele, a point mutation generates a premature stop codon terminating translation of the mutant twa1 protein after 247 amino acids. The T-DNA knockout line twa1-2 with disrupted TWA1 in the second exon (GabiKat GK_476GH03). 5 day-old acclimated seedlings were exposed to 45 °C heat stress for the indicated times. Root extension was measured 5 days after treatment. Mean ± SD (n=6). Both twa1-1 and twa1-2 were found to be heat-sensitive, while transfer of a genomic fragment encompassing the TWA1 gene complemented the thermosensitivity of both mutants comparable to wild type.
Figure 4 depicts a graphic evaluation of the prediction of intrinsically disordered regions (via https://metapredict.net/) with maximum score of 1 and domain structure of TWA1 with the highly variable region (HVR, black framed box) and two EAR protein interaction domains (grey dashes). Arrowheads indicate the sites of protein disruption in twa1-1 and twa1-2. Bottom, amino acid identity within the HVR between Arabidopsis thaliana (A.t.) and the A. lyrata (A. I.) homolog.
Figure 5 depicts a graphic evaluation of the inhibition of the ABA-responsive pRD29B:LUC reporter, in which a 2 kb promoter fragment of the ABA-responsive RD29B gene controls luciferase (LUC) expression (Christmann, 2005. Plant Physiol 137, 209-219, doi : 10.1104/pp.104.053082), by expression of TWA1 and variants in leaf protoplasts. Analysis of TWA1 in leaf protoplasts of wild type plants, and from the mutants twa1-1 and twa1-2 in the presence of 10 pM exogenous ABA. DNA of a TWA1 ortwal expression cassette (0.3 pg/105 protoplasts) were transfected, incubated for 16h at 25 °C, and the reporter activity (RLU) determined and normalized to a cotransfected control (RFU). The mutant twa1 (truncated protein from twa1-1 allele, aa 1-247 of TWA1) was analysed in twa1-2 protoplasts (dashed line).
Figure 6 depicts a graphic evaluation of the temperature-sensitive inhibition of ABA-responsive pRD29B:LUC reporter by expression of TWA1 in leaf protoplasts with TWA1 (0.3 pg) at different exogenous ABA levels in twa1-2 protoplasts. The experiment was conducted as mentioned in the legend of Fig. 5, however, at different incubation temperatures as indicated.
Figure 7 depicts a graphic evaluation of the inhibition of ABA-responsive pRD29B:LUC reporter by expression of TWA1 and variants in leaf protoplasts with TWA1 and TWA1 variants (0.3 pg effector DNA/105 protoplasts) at different incubation temperatures. The analysis included orthologs from A. lyrata and Sinapis alba (AITWA1 and SaTWAI , respectively), TWA1_AN, in which 554 aminoterminal amino acid residues were truncated, and TWA1_AIHVR, in which the HVR of TWA1 was replaced by the A. lyrata domain. Conditions as described in Fig. 6. Figure 8 depicts a graphic evaluation of temperature-dependent gene regulation in yeast by the thermogenetic control switches TWA1 , TWA1 orthologs of other plant species, and a TWA1 variant with exchanged HVR sensor domain, g) The Yeast-Two-Hybrid (YTH) system was used to evaluate the temperature control exerted by TWA1 and variants thereof. Temperature-induced conformational changes of TWA1 and variants allow binding of JAM2. The plant transcription factor JAM2 was fused to the activation domain (AD) of the yeast GAL4 transcription factor and TWA1 or JAM2 was fused to the Gal 4-DNA binding domain (BD). The fusion proteins were expressed in yeast deficient in histidine biosynthesis. JAM2-AD binding to TWA1 -BD at 30 °C restores a functional GAL4 transcription factor (AD-BD), which can then bind to and activate a gene required for histidine biosynthesis and thus allows histidine autotrophic growth. This histidine autotrophy was not observed at 20 °C. JAM2 forms a homodimer and coexpression of JAM2-AD and JAM2-BD served as a positive control. Yeasts were grown in the absence of leucine and tryptophan (-L-W) as control, or in the absence of leucine, tryptophan, and histidine (-L-W-H) (mean ± SD, n = 3, two repetitions). h,i) Growth rate p of TWA1 , TWA1 functional orthologs, and TWA1 variants fused to BD (labelled as in Fig. 7) using the YTH assay for histidine autotrophy with JAM2-AD. The JAM2-AD-JAM2-BD combination (JAM2) served as positive control. Growth rates were calculated by the cell density increase within 24 h after inoculation with respective yeast suspension at a logarithmic growth phase to an optical density at 600 nm of 0.02. Yeasts were grown at the temperature indicated under histidine-autotroph selective conditions (-L-W-H) (mean ± SD, n = 3).
Figure 9 depicts data showing the physical interaction of TWA1 and the transcriptional corepressor Topless (TPL) and TPL-related (TPR) homologs. Top: TPL and TPR homologs bind to TWA1 in a YTH assay at 30 °C. Bottom: the interaction of TPL with the thermosensor is temperature dependent and JAM2 does not directly bind to TPL. Yeasts were grown at the indicated temperatures in the absence of leucine and tryptophan (-L-W) or in the absence of leucine, tryptophan, and histidine (-L-W-H) using serial tenfold culture dilutions. Controls are yeasts with empty expression cassettes (LV).
Figure 10 depicts data obtained in the context of evaluation of the molecular mechanism of TWA1- mediated transcriptional repression. TPL and TPRs are required for TWA1 -mediated inhibition of ABA- dependent reporter expression. Arabidopsis protoplasts from the triple tpr mutant with deficiency in TPL, TPR2 (AT3G16830), and TPR4 (AT3G15880) were transfected with TWA1 effector DNA in the presence or absence of co-transfected DNA of TPL or TPR2 expression cassette (3 pg/105 protoplasts) and incubated at 25 °C and 10 pM exogenous ABA for 16h. Mean ± SD, n = 3 per data point.
Figure 11 depicts data obtained in the context of evaluation of the molecular mechanism of TWA1- mediated transcriptional repression. JAM1 and JAM2 coexpression rescues the TWA1 response in the jam triple mutant with JAM1 (AT2G46510), JAM2, and JAM3 (AT4G16430) deficiency. Arabidopsis protoplasts from the jam triple mutant were transfected with TWA1 effector DNA in the presence or absence of co-transfected JAM1 , JAM2 or JAM3 DNA (3 pg/105 protoplasts) and incubated at 25 °C and 10 pM exogenous ABA for 16h. Mean ± SD, n = 3 per data point. Figure 12 depicts a simplified model of repressor complex formation at permissive temperatures. Temperature transition from 20 °C to 30 °C unfolds TWA1 that allows access of JAM2 and TPL to interact with the carboxyterminal and aminoterminal part of TWA1 , respectively. JAM2 are binding as dimers to the core G-Box motif or G-box related cis elements of promoters, that is to imperfect G-boxes with one nucleotide deviation from the core CACGTG motif (Song, 2016. Science 354, doi:10.1126/science.aag1550). TPL is tetrameric and physically interacts by the EAR-motifs (Causier, 2012. Plant Physiol 158, 423-438, doi:10.1104/pp.111.186999) of TWA1 (striped sections in the TWA1 model) and binds to subunits of the mediator complex (Leydon, 2021 . Elife 10, doi:10.7554/eLife.66739). The temperature sensing HVR (see Fig. 4) domain is indicated by a bold-lined box within the TWA1 model.
Figure 13 depicts data obtained in the context of evaluation of thermotolerance controlled by TWA1 . a) Enhanced acquired thermotolerance of two independently generated TWA1 overexpressing lines (TWAl oe) assayed by determining the inhibition of root growth in TWAl oe lines compared to wild type in response to various 45 °C exposure times (after a 2 h priming exposure to 38 °C, see Fig. 1). The TWAl oe lines express the coding sequence (CDS) of TWA1 under the viral 35S promoter with the nopaline synthase terminator in the twa1-2 genotype, b) The TWA1 expression in TWA1 oe lines resulted in elevated transcript levels compared to wild type (wt) and the twa1 mutants. Analysis by Realtime- Quantitative Polymer Chain Reaction (RT-qPCR) of 5-day-old seedlings with the ubiquitin-conjugating enzyme 9 (UBC9, AT4G27960), UBI10 (At4g05320), and TIP41 L (At4g34270) transcripts as combined references (Mean ± SD, n=3 per data point with 10 seedlings per n).
Figure 14 depicts data obtained in the context of evaluation of thermotolerance by TWAI . Basal thermotolerance is improved in TWAl oe lines and impaired in twa1-1 and twa1-2. Chlorophyll a content per fresh weight of 5d-old seedlings one day after exposure to 37 °C as indicated (mean ± SD, n = 15 from three repetitions). The respective method is described in Example 8 herein below.
Figure 15 depicts data obtained in the context of evaluation of thermotolerance controlled by TWAI . Basal thermotolerance is improved in TWAl oe lines and impaired in twa1-1 and twa1-2. Root growth inhibition by heat stress at 45 °C for different periods without a priming period (details see Fig. 1 but without the 2h priming at 38 °C), (mean ± SD, n = 6 per data point).
Figure 16 depicts data obtained in the context of evaluation of thermotolerance controlled by TWAI . Ion leakage assay of three-weeks-old plantlets exposed to 37 °C for 24h or kept at 22 °C. Ion leakage was determined one day after heat treatment and expressed relative to maximum leakage after boiling (mean ± SD, n = 6 per data point). The respective method is described in Example 8 herein below.
Figure 17 depicts data obtained in the contexfof evaluation of thermotolerance and the transcript level of the key heat shock factor HSFA2 controlled by TWAI . Temperature- and TWA1 -dependent induction of the HSFA2 promoter driving LUC reporter expression in leaf protoplasts from six different lines, TWA1 oe1 , twa1-1, twa1-2, wild type (HB6:LUC of Col-0 genotype), and from Arabidopsis plants that stably expressed the TWA1 orthologs AITWA1 and SaTWAI under the control of the 35S promoter in the twa1-2 background. (Details of the analysis see Fig. 1 but protoplasts of different genotype were kept prior to transfection at 20 °C and then incubated at different temperatures as indicated for 16 h). Mean ± SD, n = 3 per data point.
Figure 18 depicts data obtained in the context of evaluation of thermotolerance and level of early heat shock transcripts controlled by TWA1 . Transcript changes of HSFA2, HSP21, and HSP26.5 affected by TWA1 and orthologs in 5-day old seedlings from ten different lines grown at 20 °C and exposed for 1 h to 25 °C, or kept at 20 °C, with 0.5 h recovery period at 20 °C prior to RT-qPCR analysis. Lines were TWA1 oe1 and TWA1 oe2, twa1-1, twa1-2, wild type (Col-0 accession, and HB6:LUC reporter line in Col- 0 background labelled as WT), and two arabidopsis lines that stably expressed the TWA1 orthologs AITWA1 and SaTWAI under the control of the 35S promoter in the twa1-2 background. (Mean ± SD, n=3 per data point with 10 seedlings per n).
Figure 19 depicts data obtained in the context of evaluation of thermotolerance and level of early heat shock transcripts controlled by TWA1 . HSFA2 transcripts in the arabidopsis lines shifted from 20 °C to 35 °C for 1 h with 0.5h recovery at 20 °C prior to RT-qPCR analysis. Lines and analysis as in Fig. 18 with the variance of the temperature.
Figure 20 depicts data obtained in the context of evaluation of thermotolerance conferred by enhanced TWA1 expression. TWA1 does not affect growth and photosynthesis, a, Improved thermotolerance of TWAl oe lines without tradeoffs in growth and changes in apparent photosynthetic parameters. Comparison of leaf area, leaf temperature, and net photosynthesis of plants grown for 38 days at short day conditions with 22 °C daytime temperature and 150 pmol nr2 s1 photosynthetic active radiation (n = 7, ± SEM). b, 20-day-old plantlets analyzed for maximum quantum yield of photosystem II (®max). photosynthetic yield of photosystem II (®psn), and non-photochemical quenching (NPQ). No significant differences (P < 0.05, one-way ANOVA). Values from 0 to 1 are expressed in false colors.
Figure 21 depicts the Alignment of TWA1 homologs. Homologs of TWA1 were identified through BLASTp searches, as herein defined, against genomes on NCBI. Amino acid sequences of TWA1 and representative proteins were aligned with NCBI’s COBALT alignment tool. Alignment positions with no gaps are colored with red, indicating highly conserved positions and blue, indicating lower conservation. E-values were calculated by comparison of the protein sequences to TWA1 or to lotus NnTWAI using the FASTA program (https://fasta.bioch.virginia.edu). Sequences from dicots were: TWA1 - NP_001331741 .1 , Arabidopsis lyrata - XP_002873619.1 , white mustard Sinapis alba - AF8055519.1 , soybean Glycine max - KAG5128726.1 , lotus Nelumbo nucifera - A0A1 U7ZPG7 and from monocots: date palm Phoenix dactylifera - A0A8B7BGH8, maize Zea mays - XP_035823187.1 , bread wheat Triticum aestivum - XP_044429385.1 .
Figure 22 depicts data obtained for the temperature-induced intramolecular domain movement of TWA1 revealed by Forster resonance energy transfer-fluorescence lifetime imaging (FRET-FLIM). Shifts of temperature from 17 °C up to 35 °C moves the aminoterminal and carboxyterminal domain of TWA1 apart as indicated by the increase of fluorescence lifetime of mCherry-TWA1-GFP. The mCherry-GFP protein served as a control in this yeast analysis. FRET requires the proximity of fluorophores in the nanometer range (< 10 nm). FRET reduces the fluorescence lifetime of the excited donor fluorophore GFP. Changes of fluorophore distance affects the FRET signal by the power of six (Algar,2019. Nature Methods 16, 815-829, doi:10.1038/s41592-019-0530-8).
Detailed description
Before describing in detail exemplary embodiments of the present invention, definitions which are important for understanding the present invention are given.
The present invention as illustratively described in the following may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein.
The present invention will be described with respect to particular embodiments and with reference to certain figures, but the invention is not limited thereto but only by the claims.
As used in this specification and in the appended claims, the singular forms of "a" and "an" also include the respective plurals unless the context clearly dictates otherwise.
In the context of the present invention, the terms "about" and "approximately" denote an interval of accuracy that a person skilled in the art will understand to still ensure the technical effect of the feature in question. The term typically indicates a deviation from the indicated numerical value of ±20 %, preferably ±15 %, more preferably ±10 %, and even more preferably ±5 %.
It is to be understood that the term "comprising" is not limiting, i.e., it does not exclude other elements. For the purposes of the present invention the term "consisting of is considered to be a preferred embodiment of the term "comprising of. If hereinafter a group is defined to comprise at least a certain number of embodiments, this is meant to also encompass a group which preferably consists of these embodiments only.
It is to be understood that this invention is not limited to the particular methodology, protocols, reagents etc. described herein as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art.
The present invention is concerned with the inventor’s finding that a specific gene locus encoding a temperature-responsive protein (TWA1) confers thermotolerance in plants and plant cells. TWA1 acts as a thermosensor, and certain temperature ranges activate its transcription co-regulator function. Thus, in a first aspect, the present invention relates to the use of TWA1 or a homolog thereof for modifying thermotolerance and/or senescence in plants or plant cells.
In the context of the present invention, the term “homolog of TWA1 ” refers to an entity with similar protein sequence to TWA1 of Arabidopsis thaliana (SEQ ID NO: 106) and/or to such homologs identified in reiterated homology searches as defined herein below. TWA1 and TWA1 homologs evolved during plant evolution in a highly dynamic manner compared to plant house-keeping genes, which necessitates the reiterated homology searches for the identification of thermosensory TWA1 homologs of plant species more distantly related to Arabidopsis thaliana, i.e., outside the order of Brassicales.
Thus, in the context of the present invention, the term “homolog of a nucleic acid sequence”, e.g., “homolog of a nucleic acid sequence according to item i)” and “homolog of a nucleic acid sequence according to item ii)”, respectively, referto a nucleic acid sequence encoding an entity with similar protein sequence to TWA1 of Arabidopsis thaliana (SEQ ID NO: 106) and/or to such homologs identified in reiterated homology searches as defined herein below. In other words, in the context of the present invention, a TWA1 polynucleotide sequence homolog is defined as the polyribonucleotide and/or polydesoxyribonucleotide sequences encoding the TWA1 polypeptide homologs.
In embodiments of the present invention, the term “similar protein sequence to TWA1 of Arabidopsis thaliana" refers to an entity defined in a pairwise comparison to TWA1 of Arabidopsis thaliana (NP_001331741 .1 ; SEQ ID NO: 106) using National Centre for Biotechnology Innovation (NCBI) BLASTp (https://blast.ncbi. nlm.nih.gov/Blast.cgi?PAGE=Proteins) with likelihood value of <108, <109, <10'10, <10-15, <10-20, <1025, <10-30, <1035, <10'40, <1045, <1050 <1055, <1060 <1065, <1070 <10 75, <i o-8o < 0-85, <10-90 <i o-95, <1 Q-ioo <i o-io5 or <1 O '110, preferably >10-120, more preferably >10-110, >10- 100, >10-90, >10-80, or >10-7°,and a query cover >30%, such as >35%, >40%, >45%, >50%, >55%, >60%, >65%, >70%, >75%, >80%, >85%, >95%, or >95%, preferably >40%, >45% or >50%, in deduced proteins from wild type genomes of the respective plant species. In some other embodiments of the present invention, the term “similar protein sequence to TWA1 of Arabidopsis thaliana" refers to an entity defined in a pairwise comparison to the TWA1 homolog from Glycine max (KAG5128726.1), or to the TWA1 homolog from Nelumbo nucifera (A0A1 U7ZPG7) using National Centre for Biotechnology Innovation (NCBI) BLASTp (https://blast.ncbi. nlm.nih.gov/Blast.cgi?PAGE=Proteins) with likelihood value of <108 and a query cover >30%, such as >35%, >40%, or >45%, in wild type genomes and/or proteomes of the respective plant species, preferably in deduced proteins from the respective plant species. The Glycine max TWA1 homolog has a likelihood value of <1 O'50 and a query cover >80% to Arabidopsis TWA1 . The Nelumbo nucifera TWA1 homolog (A0A1 U7ZPG7) has a likelihood value of <10'30 and a query cover >50% to Glycine max T\NM homolog (KAG5128726.1). In the context of the present invention, a TWA1 polynucleotide sequence homolog is defined as the polyribonucleotide and/or polydesoxyribonucleotide sequences encoding the TWA1 polypeptide homologs.
The search for homologs of TWA1 may be performed using the database “Non-redundant protein sequences (nr)” of NCBI, the algorithm blastp (protein-protein BLAST), matrix BLOSUM62, gap cost parameters “Existence: 11 Extension: 1”, conditional compositional score matrix adjustment and no filters or masking. Non-limiting examples of TWA1 homologs are indicated in tables 1-3 below.
Table 1. Selected Homologs of TWA1
Table 2. Selected Homologs of TWA1
Table 3. Selected Homologs of TWA1
In some embodiments of said use, the modifying of thermotolerance is increasing thermotolerance and/or wherein the modifying of senescence is reducing senescence.
In various embodiments, TWA1 comprises or consists of the amino acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 %, preferably 70 to 100 %, more preferably 80 to 100 %, still more preferably 90 to 100 %, particularly 95 to 100 %, more particularly 99 to 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106.
In various embodiments, a homolog of the TWA1 locus is selected from orthologs and paralogs thereof, preferably orthologs thereof.
In the context of the present invention, the term “homolog” refers to evolutionary-related polynucleotide sequences and evolutionary-related polypeptide sequences and is a general term for “paralog” and “ortholog”, respectively. Homologs, i.e., orthologs and paralogs, have similar sequence and similar functions. Orthologs are structurally related genes in different species that are derived by a speciation event and have a common function. Paralogs are structurally related genes within a single species that are derived by a duplication event and can have evolved overlapping or different functions. Sequences that are sufficiently similar to one another will be appreciated by those of skill in the art and may be based upon percentage identity of the complete sequences, percentage identity of q conserved domain or sequence within the complete sequence, percentage similarity to the complete sequence, percentage similarity to a conserved domain or sequence within the complete sequence, and/or an arrangement of contiguous nucleotides or peptides particular to a conserved domain or complete sequence, which is reflected in the low likelihood value (threshold I O10 ) used for the definition of TWA1 homologs for the independent evolution of similar sequences by chance. Sequences that are sufficiently similar to one another will also share the encoded function such that proteins bind to similar interacting proteins and regulate as protein complex shared transcriptional targets using methods well known to those of skill in the art.
In various embodiments, the modifying of thermotolerance is increasing thermotolerance. In some embodiments, the modifying of senescence is reducing senescence. In the context of the present invention, the term “thermotolerance” refers to a plant’s or plant cell’s ability to cope with and/or adapt to temperature-induced environmental stress, particularly heat stress. For instance, an “increased thermotolerance” manifests itself preferably in a reduced manifestation of symptoms of heat stress upon exposure to temperatures, at which the respective wildtype plant (i.e., control plant) typically manifests such symptoms. For instance, but without limitation, an increased thermotolerance in a plant manifests itself after exposure to elevated temperatures in reduced bleaching of the leaves of said plant, relative to the wildtype, with the wildtype showing bleaching, such as of the leaves, under the same conditions. For instance, but without limitation, an “elevated temperature” may be a temperature of about 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49 or 50 °C, particularly within the range of about 20 to 50 °C, for instance for a duration of about 0.1 hours to 3 months, such as about 0.5 to 240 hours, or 1 to 48 hours, or 1 to 12 hours, such as 2, 4, or 6 hours. For instance, but without limitation, symptoms such as bleaching (chlorophyll loss), inhibition of root growth, ion leakage, induction of heat shock transcription factors (HSFs) and heat shock proteins (HSPs) and other symptoms typical for heat stress like impaired hypocotyl elongation, reduced germination rates or inhibition of seedling greening, or diminished maximum photosystem II activity are reduced by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant,. In various embodiments, increased thermotolerance manifests itself in elevated transcript levels of HSPs, particularly small HSPs such as sHSPs 18.2, 21 and 26.5, and/or of the major ATP-dependent chaperone HSP70. In various such embodiments, transcript levels of HSPs are elevated by at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. The sHSPs associate as oligomers (often homodimers) with destabilized protein structures and form a first defense line against heat-evoked protein denaturation (Haslbeck, M., Weinkauf, S. & Buchner, J. Small heat shock proteins: Simplicity meets complexity. J Biol Chem 294, 2121-2132, doi:10.1074/jbc.REV118.002809 (2019)).
“Senescence”, in the context of the present invention, refers to the aging of a plant or plant cell. A “reduced senescence”, therefore, refers to reduced aging, in other words, to a process within a plant or plant cell that protects the plant or plant cell from aging and senescence or that results in delayed aging or senescence of the plant or plant cell. In some embodiments, reduced senescence or anti-aging effects of the present invention are characterized by decreased levels of nitric oxide (NO) or hydrogen peroxide or reduced ABA stress levels within the plant or plant cell, for example as a result of a change in the expression of certain genes involved in NO or hydrogen peroxide production or breakdown or signaling. For instance, but without limitation, reduced senescence or anti-aging effects are characterized by decreased levels or signaling of NO or hydrogen peroxide within the plant or plant cell, wherein levels or signaling of NO or hydrogen peroxide within the plant or plant cell are reduced by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In some embodiments, reduced senescence or anti-aging effects of the present invention may be characterized by a change in levels of certain phytohormones. In some embodiments, this change may be associated with decreased levels of abscisic acid (ABA) or ABA signaling, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant; increased levels of gibberellins (GA), for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant; or increased levels of auxins, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In some embodiments, the levels of expression of the gibberellin (GA) biosynthetic genes, such as GA3-oxidase 2, RSG, KAO, and 14-3-3 genes may be increased, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In other embodiments, the levels of expression of the genes that are regulated by GAs, such as ent-kaurenoic (KAO) and repression of shoot growth (RSG), are increased, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In other embodiments, the levels of expression of the GA degradation genes or negative regulators of the GA biosynthesis pathway, for example 14- 3-3 genes, are decreased, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In still other embodiments, reduced senescence or antiaging effects of the present invention may be characterized by decreased levels of expression of the genes involved in the ABA biosynthesis pathway, for example the 9-cis-epoxycarotenoid dioxygenase (NCED) gene, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. In some embodiments, the expression of the genes involved in the ABA catabolic pathway, for example the 8'-hydroxylase gene, are increased, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant.
In some embodiments, the expression of the genes involved in ABA signal transduction pathway and the targeted ABA-responsive genes, for example the ABA- and drought-upregulated gene Responsive to Drought 29B are downregulated, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant.
In further embodiments, modified senescence, such as reduced senescence, may be manifested in increased (crop) yields, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95%, in comparison with the control plant. Reduced senescence manifests itself in the so called ‘staygreen trait’ known to the person skilled in the field, which is associated with a longer growth phase, and/or a longer flowering phase, and/or a longer seed setting and seed ripening period, for instance by preferably at least 10% or at least 20%, especially preferably by at least 40% or 60%, particularly preferably by at least 70% or 80%, most preferably by at least 90% or 95% longer, in comparison with the control plant. Reduced senescence may be manifested in delayed chlorophyll breakdown, delayed for instance by preferably at least 1 % of the vegetative growth phase, especially preferably by at least 4% or 10%, particularly preferably by at least 10% or 20%, most preferably by more than 20%, in comparison with the control plant.
The term “plant”, as used herein, includes whole plants, plant parts (e.g., leaves, stems, flowers, roots, etc.), plant tissue, plant protoplasts, and progeny thereof. The classes of plants that can be used to practice this invention can be as broad as the class of higher plants, including plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), as well as gymnosperms, also including plants of a variety of ploidy levels, including polyploid, diploid, haploid and hemizygous states.
The term “plant cell” as used herein refers to protoplasts, gamete producing cells and cells which regenerate to whole plants. Accordingly, a seed comprising multiple plant cells capable of regenerating into a whole plant, is included in the definition of “plant cell”.
In another aspect, the present invention relates to a method of modifying thermotolerance and/or senescence in a plant or plant cell, comprising:
I) modifying the TWA1 locus or a homolog thereof in a plant or plant cell; and/or
II) introducing into a plant or plant cell an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and/or
III) introducing into a plant or plant cell a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences; and/or
IV) introducing an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) into a plant or plant cell, wherein expression of the gene product of the modified TWA1 locus or the modified homolog thereof and/or of the nucleic acid sequence as defined in any one of items i) to iv), or presence of the introduced polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) results in modified thermotolerance and/or senescence in said plant or plant cell.
In various embodiments, said method is not a non-technical method or process, i.e., said method is not an essentially biological method or process. In various embodiments, said method is a biotechnological method.
In some embodiments, a homolog of the TWA1 locus is selected from orthologs and paralogs thereof, preferably orthologs thereof.
Thus, in some embodiments, the method of modifying thermotolerance and/or senescence in a plant or plant cell comprises modifying the TWA1 locus or a homolog thereof in a plant or plant cell.
In the context of the present invention, “modifying the TWA1 locus” relates to the modification of the TWA1 -promoter-encoding sequence and/orthe natural TWA1-encoding sequence present at the natural chromosomal locus of a plant cell. In the context of the present invention, said modification leads to whole, sexually competent viable plants.
Accordingly, in some embodiments, the method of modifying thermotolerance and/or senescence in a plant or plant cell encompasses genome editing, i.e., genome editing of the TWA1 locus or of a homolog thereof. In the context of the present invention, the term “genome editing” encompasses insertions, deletions or point mutations or combinations thereof. Molecular instruments having the required nuclease activity and which can be guided to the respective target sequence to be modified to program and carry out the respective specific and site-directed mutagenesis are generally known in the art, examples of which include zinc finger nucleases (ZFNs) or “transcription activator-like effector nucleases” (TALENs), as well as the CRISPR nuclease-based system, including, inter alia, Cas (CRISPR associated gene) nuclease or Cpf1 nucleases, known in the art as “CRISPR SPR” systems (clustered regularly interspaced short palindromic repeat), typically referred to by its acronym “CRISPR”. Five types (l-V) of CRISPR systems have been described so far (Barrangou et al., 2007, Science, 315(5819):1709-12; Bouns et al., 2008, Science, 321 (5891): 960-4; Marraffini and Sontheimer, 2008, Science, 322(5909): 1843-5; Makarova et al., Nature Rev. Microbiol., 13, 722-736, 2015), wherein each system comprises a cluster of CRISPR SPR-associated genes (Cas or others) and a CRISPR array belonging thereto. A recombinant CRISPR SPR/Cas system, or in general, a CRISPR SPR/nuclease system, enables a targeted DNA recognition and/or bonding through a small, individually tailored, nonencoding RNA (guide RNA or gRNA) in combination with a possibly modified nuclease, and the optional generation of a single- or double-strand break. Recombinant gRNA molecules can comprise both the variable DNA recognition region and also the nuclease interaction region and thus can be specifically designed, independently of the specific target nucleic acid and the desired nuclease (Jinek et. al., Science 2012, 337: 816-821). As a further safety mechanism, PAMs (protospacer adjacent motifs) must be present in the target nucleic acid region; these are DNA sequences which in type II CRISPR system follow on directly from the Cas9/RNA complex-recognized DNA. The PAM sequence for the Cas9 from Streptococcus pyogenes is in fact “NGG” or “NAG” (Standard IUPAC nucleotide code) (Jinek etal.). The PAM sequence for Cas9 from Staphylococcus aureus is “NNGRRT” or “NNGRR(N)”. Further variant CRISPR SPR/Cas9 systems are known. Thus, a Neisseria meningitidis Cas9 cleaves at the PAM sequence NNNNGATT. A Streptococcus thermophilus Cas9 cleaves at the PAM sequence NNAGAAW. Furthermore, by using modified Cas polypeptides, specific single-stranded breaks can be obtained. The combined use of Cas nickases with various recombinant gRNAs can also induce highly specific DNA double-stranded breaks by means of double DNA nicking. By using two gRNAs, moreover, the specificity of the DNA binding and thus the DNA cleavage can be optimized. Further Reference in this context may be made to WO 2015/026885 A1 and Bortesi & Fischer (“The CRISPR SPR/Cas9 system for plant genome editing and beyond”, Biotechnology Advances, 33, pages 41-52, 2014).
Alternatively or additionally, modification of thermotolerance and/or senescence in a plant or plant cell can also be achieved by manipulating the expression of the plant-intrinsic endogenous protein TWA1 or a homolog thereof. Manipulation of the protein expression can be achieved for example by modifying the promoter DNA sequence of the protein-encoding gene. Such a modification, which results in a modified, preferably increased, expression rate of the respective endogenous gene can be generated by deleting or inserting DNA sequences. A modification of the promoter sequence of endogenous genes will, as a rule, lead to a modification of the expressed amount of the gene and thus, for example, also to a modification of the thermosensor activity, which can be detected in the cell, or in the plants by standard techniques. Particularly, the modification of the promoter sequence of the endogenous gene can also lead to a modification of the amount of TWA1 protein or a homolog thereof in the cell.
In some embodiments, a further possibility for increasing the activity of the endogenous protein TWA1 is changing, preferably enhancing, the abundance and/or activity of the TWA1-binding proteins, i.e., the JAM transcription factors and the corepressors TPL/TPRs, preferably JAM2 and its orthologs and TPL and its orthologs, respectively. Means for changing abundance and/or activity of said TWA1-binding proteins are generally known in the art and encompass, for instance but without limitation, transcriptional up-regulation thereof.
In some embodiments, a further possibility for increasing the activity and the content of the endogenous protein TWA1 is the regulation of transcription factors that are involved in the transcription of the TWA1 gene, for instance by overexpression. Means for overexpressing transcription factors are known to the person skilled in the field. Furthermore, an increased expression of the endogenous TWA1 gene can be achieved using a regulator protein that does not occur in the untransformed organism interacting with the promoter of said gene. Such a regulator can take the form of a chimeric protein, which consists of a DNA binding domain and a transcription activator domain, as described, for example, in WO 96/06166.
In other embodiments, the method of modifying thermotolerance and/or senescence in a plant or plant cell comprises, additionally or alternatively, the introduction of an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii) into a plant or plant cell.
In some embodiments, a homolog of a nucleic acid sequence according to item i) or ii) is selected from orthologs and paralogs thereof, preferably orthologs thereof.
The terms “nucleic acid” or “nucleic acid sequence” or “nucleotide sequence” as used herein refer to an oligonucleotide, nucleotide, polynucleotide, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin. The phrases “nucleic acid” or “nucleic acid sequence” includes oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), orto any DNA-like or RNA-like material, natural or synthetic in origin, including, e.g., iRNA, ribonucleoproteins (e.g., double stranded iRNAs, e.g., iRNPs). The term encompasses nucleic acids, /.e., oligonucleotides, containing known analogues of natural nucleotides. The term also encompasses nucleic-acid-like structures with synthetic backbones, see, e.g., Mata (1997) Toxicol. Appl. Pharmacol. 144:189-197; Strauss-Soukup (1997) Biochemistry 36:8692-8698; Samstag (1996) Antisense Nucleic Acid Drug Dev 6:153-156. “Oligonucleotide” includes either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands that may be chemically synthesized. Such synthetic oligonucleotides have no 5' phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide can ligate to a fragment that has not been dephosphorylated. A “coding sequence of’ or a “nucleotide sequence encoding” a particular polypeptide or protein is a nucleic acid sequence, which is transcribed and translated into a polypeptide or protein when placed under the control of appropriate regulatory sequences.
The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (introns) between individual coding segments (exons).
As used herein, the term “isolated” means that the material (e.g., a nucleic acid, a polypeptide, a cell) is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition and still be isolated in that such vector or composition is not part of its natural environment. Thus, an “isolated” nucleic acid molecule is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid, in the context of the present invention, an isolated nucleic acid preferably does not have any sequences which naturally flank the nucleic acid in the genomic DNA of the organism from which the nucleic acid originates (for example sequences located at the 5'- and 3'-termini of the nucleic acid). In various embodiments, the isolated molecule may comprise for example fewer than approximately 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb nucleotide sequences which naturally flank the nucleic acid molecule in the genomic DNA of the cell from which the nucleic acid originates.
The nucleic acid molecules as herein defined and described herein, for example a nucleic acid molecule with a nucleotide sequence of SEQ ID NO. 105 or a part thereof, can be isolated using standard techniques of molecular biology and the sequence information provided herein. Also, it is possible to identify for example a homologous sequence, or homologous, conserved sequence regions, at the DNA or amino acid level using comparative algorithms as can be found for example on the NCBI homepage at http://www.ncbi.nlm.nih.gov. Essential parts of this sequence, or the entire homologous sequence, can be used as hybridization probe using standard hybridization techniques (such as, for example, described in Sambrook et al.). Moreover, a nucleic acid molecule comprising a complete sequence as shown in SEQ ID NO. 105 or a part thereof can be isolated by a polymerase chain reaction, where oligonucleotide primers based on the sequences stated herein or of parts thereof are used (for example, a nucleic acid molecule comprising the complete sequence or a part thereof can be isolated by a polymerase chain reaction using oligonucleotide primers which have been generated on the basis of the same sequence). For example, mRNA can be isolated from cells (for example by the guanidinium thiocyanate extraction method by Chirgwin et al. (1979) Biochemistry 18; 5294-5299), and cDNA can be generated therefrom by means of reverse transcriptase (for example Moloney MLV reverse transcriptase, obtainable from Gibco/BRL, Bethesda, Md. or AMV reverse transcriptase, obtainable from Seikagaku Amerika, Inc., St. Petersburg, Fla.). Synthetic oligonucleotide primers for amplification by means of a polymerase chain reaction can be generated on the basis of the nucleic acid sequence shown in SEQ ID NO. 105 or with the aid of the amino acid sequence shown in SEQ ID NO. 106. A nucleic acid according to the invention can be amplified by means of standard PCR amplification techniques using cDNA or alternatively using genomic DNA as the template and suitable oligonucleotide primers. The nucleic acid thus amplified can be cloned into a suitable vector and characterized by means of DNA sequence analysis. Oligonucleotides which correspond to a nucleotide sequence which codes for a protein according to the invention can be generated by standard synthetic methods, for example using an automatic DNA synthesizer.
The term “sequence identity” between two nucleic acid sequences is understood as meaning the identity of the nucleic acid sequence over the entire sequence length in each case, in a preferred embodiment over the entire expressed sequence length, preferably cDNA, even more preferably over the coding sequence, preferably CDS. The term “sequence identity” in the context of polypeptides is understood as meaning the identity of the amino acids over a specific protein region, preferably over the entire protein length, in particular the identity which is calculated by comparison with the aid of software.
Various sequence comparison programs are particularly contemplated for use in this aspect of the invention. Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA and CLUSTALW (Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85(8):2444-2448, 1988; Altschul et al., J. Mol. Biol. 215(31:403-410. 1990; Thompson et al., Nucleic Acids Res. 22(21:4673-4680. 1994; Higgins et al., Methods Enzymol. 266:383- 402, 1996; Altschul et al., J. Mol. Biol. 215(31:403-410. 1990; Altschul et al., Nature Genetics 3:266-272, 1993).
Homology or identity is often measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wl 53705). Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions, and other modifications. Thus, the terms “homology” and “identity” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection.
In the context of the present invention, the term “fragments”, e.g., “functional fragments”, as used in the context of nucleic acid sequences is understood as meaning portions of a nucleic acid sequence which code for the TWA1 protein or a homolog thereof, whose biological activity consists in that it alters thermotolerance and/or senescence in plants or plant cells and acts as a thermogenetic control switch. Thus, nucleic acid fragments described and defined herein code for a portion of a protein that senses temperature in plants or plant cells, wherein said portion is necessary for conferring thermotolerance. In some embodiments, such a fragment codes for the aminoterminal HVR (highly variable region) of the TWA1 protein or a homolog thereof. In some embodiments, the HVR of the TWA1 protein or a homolog thereof comprises or consists of an amino acid sequence having at least 30, 31 , 32, 33, 34, 35, 36, 37,
38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64,
65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 ,
92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ
ID NO: 107 (SEQ ID NO: 107 = amino acid sequence of HVR of Arabidopsis thaliana-V M).
However, as the HVR is highly variable and diverse across different types of plants, in particular embodiments, a functional fragment of a nucleic acid sequence according to item i) or ii), as herein defined above, can be defined as a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, wherein SEQ ID NO: 106 does not comprise the HVR. In some such embodiments, said HVR comprises or consists of an amino acid sequence having at least 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 107.
Without wishing to be bound by theory, it is presumed that thermal activation of the TWA1 sensor involves HVR by contributing to domain rearrangements within the unstructured protein that changes the accessibility of its interaction domains for JAM transcription factors and repressor proteins. Thus, in some embodiments, an altered thermotolerance can be conferred by introducing or generating these fragments or structurally related fragments in plants.
The term “fragments” as used in the context of the polypeptides described and defined herein is understood as meaning protein portions whose biological activity consists in that it alters thermotolerance and/or senescence in plants or plant cells. The protein fragments preferably comprise an HVR, more preferably an aminoterminal HVR. Fragments can have the same or substantially the same amino acid sequence as the naturally occurring protein. “Substantially the same” means that an amino acid sequence is largely, but not entirely, the same, but retains at least one functional activity of the sequence to which it is related.
In particular embodiments, a fragment of the TWA1 protein or a homolog thereof comprises or consists of an amino acid sequence having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65,
66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92,
93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof. In general, two amino acid sequences are “substantially the same” or “substantially homologous” if they are at least about 85% identical, such as about 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 % identical. Fragments which have different primary structures as the naturally occurring protein are also included. An example of this, is a “pro-form” molecule, such as a low activity proprotein that can be modified by cleavage to produce a mature enzyme with significantly higher activity.
As the HVR, however, is highly variable and diverse across different types of plants, in particular embodiments, the protein fragments comprise an HVR, but the amino acid sequence of the fragment is substantially the same, as herein defined, as the corresponding amino acid sequence set forth in SEQ ID NO: 106 excluding the HVR, in other words, sequence identity is determined without taking into account the respective HVRs. In some such embodiments, said HVR comprises or consists of an amino acid sequence having at least 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 , 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 107.
Particularly, thermotolerance and/or senescence can be modified in transgenic plants using the fragments of polypeptides as described and defined herein, such as of a polypeptide having the amino acid sequence set forth in SEQ ID NO: 106.
“Hybridization” refers to the process by which a nucleic acid strand joins with a complementary strand through base pairing. Hybridization reactions can be sensitive and selective so that a particular sequence of interest can be identified even in samples in which it is present at low concentrations. Suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature and are well known in the art. In particular, stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature. In some embodiments, nucleic acids of the invention are defined by their ability to hybridize under various stringency conditions (e.g., high, medium, and low), as set forth herein.
The terms “stringent” or “stringent condition” refer to conditions that permit hybridization of DNA strands whose sequences are complementary, wherein these same conditions exclude hybridization of significantly mismatched DNAs. Polynucleotide sequences capable of hybridizing under stringent conditions with the polynucleotides of the present invention may be, for example, variants of the disclosed polynucleotide sequences, including allelic or splice variants, or sequences that encode orthologs or paralogs of presently disclosed polypeptides. Nucleic acid hybridization methods are disclosed in detail by Kashima et al. (1985) Nature 313:402-404, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual. 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (“Sambrook”), and by Hames and Higgins, “Nucleic Acid Hybridisation: A Practical Approach”, IRL Press, Washington, D.C. (1985). For example, hybridization under high stringency conditions could occur in about 50 % formamide at about 37 °C to 42 °C. Hybridization could occur under reduced stringency conditions in about 35 % to 25 % formamide at about 30 °C to 35 °C. In particular, hybridization could occur under high stringency conditions at 42 °C in 50 % formamide, 5X SSPE, 0.3 % SDS and 200 ug/ml sheared and denatured salmon sperm DNA. Hybridization could occur under reduced stringency conditions as described above, but in 35 % formamide at a reduced temperature of 35 °C. The temperature range corresponding to a particular level of stringency can be further narrowed by calculating the purine to pyrimidine ratio of the nucleic acid of interest and adjusting the temperature accordingly. Variations on the above ranges and conditions are well known in the art.
In this context, the term “standard hybridization conditions” means, depending on the application, stringent or less stringent hybridization conditions. Such hybridization conditions are described, for instance, in Sambrook and Russell, Molecular Cloning, A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory Press, 2001) or in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
Nucleic acid sequences which deviate from the nucleic acid sequence set forth in SEQ ID NO: 105 can be generated for example by introducing one or more nucleotide substitutions, additions or deletions into a nucleotide sequence of SEQ ID NO: 105 so that proteins are generated into which one or more amino acid substitutions, additions or deletions have been introduced in comparison with the sequence shown in SEQ ID NO: 106. Mutations can be introduced into the sequence of SEQ ID NO: 105 by means of standard techniques, such as, for example, site-specific mutagenesis and PCR-mediated mutagenesis. It is preferred to generate conservative amino acid substitutions on one or more of the predicted nonessential amino acid residues, that is to say on amino acid residues which have no effect on the thermosensor activity. In a “conservative amino acid substitution”, an amino acid residue is exchanged for an amino acid residue with a similar side chain. Families of amino acid residues with similar side chains have been defined in the art. These families comprise amino acids with basic side chains (for example lysine, arginine, histidine), acidic side chains (for example aspartic acid and glutamic acid), uncharged polar side chains (for example glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), unpolar side chains (for example alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (for example threonine, valine, isoleucine) and aromatic side chains (for example tyrosine, phenylalanine, tryptophan). A predicted nonessential amino acid residue in the protein used in accordance with the invention is thus preferably exchanged for another amino acid residue from the same side-chain family. As an alternative, it is possible, in another embodiment, to introduce the mutations randomly over the entire sequence, or part of the sequence, which codes for the protein according to the invention, for example to screen for their ability of conferring thermotolerance in plants or plant cells.
In various embodiments, the nucleic acid sequence as defined herein above under items i), ii), iii), and iv) is derived from Arabidopsis, preferably Arabidopsis thaliana or Arabidopsis lyrata; Brassica, preferably Brassica oleracea; Sinapis, preferably Sinapis alba’ Gossypiurrr, Glycine max, Nelumbo nucifera; Phoenix dactylifera; Zea mays; or Triticum aestivum.
Alternatively or additionally, the method of modifying thermotolerance and/or senescence in a plant or plant cell comprises introduction of a recombinant nucleic acid molecule into a plant or plant cell, said recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation:
- a promoter, and
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences, i.e., one or more further expression control sequences present in addition to the promoter.
As used herein, the term “recombinant” in the context of polypeptides or proteins means that the respective polypeptide or protein has been produced via biomolecular engineering, e.g., in a biotechnological process, and has not been isolated from its natural environment, i.e., the environment in which it is naturally occurring, said biotechnological process encompassing use of one or more genetically modified organism and/or transient transfected cell culture(s). In other words, recombinant polypeptides or proteins refer to polypeptides or proteins produced by recombinant DNA techniques; i.e., produced from cells transformed by an exogenous DNA construct encoding the desired polypeptide or protein. Particularly, in various embodiments, the term “recombinant” in the context of nucleic acid sequences means that the nucleic acid is adjacent to a “backbone” nucleic acid to which it is not adjacent in its natural environment. In this context, “backbone molecules” include nucleic acids such as expression vectors, self-replicating nucleic acids, viruses, integrating nucleic acids and other vectors or nucleic acids used to maintain or manipulate a nucleic acid insert of interest.
As used herein, the term “promoter” refers to a sequence of DNA capable of driving/initiating transcription of a coding sequence in a cell, typically located near the transcription start sites of genes, upstream on the DNA (towards the 5' region of the sense strand), to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter.
The term “operatively linked” refers to a functional relationship between two or more nucleic acid (e.g., DNA) segments. Typically, it refers to the functional relationship of transcriptional regulatory sequence to a transcribed sequence. For example, a promoter is operatively linked to a coding sequence, such as a nucleic acid sequence as defined in any one of items i) to iv), if it stimulates or modulates the transcription of the coding sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operatively linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. However, some transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance. In other words, the promoter and the nucleic acid sequence to be expressed and, optionally, further expression control elements are arranged in such a way that each of the regulatory elements can fulfill its function when the nucleic acid sequence is expressed, and direct linkage in the chemical sense is not necessarily required. Genetic control sequences such as, for example, enhancer sequences, can also exert their function on the target sequence from positions which are further away, or indeed from other DNA molecules. In various embodiments, preferred arrangements are those in which the nucleic acid sequence to be expressed is positioned behind the sequence acting as the promoter, so that the two sequences are linked covalently to each other. The distance between the promoter sequence and the nucleic acid sequence to be expressed recombinantly is, in some embodiments, less than 200 base pairs, preferably less than 100 base pairs and particularly less than 50 base pairs.
Such an operable linkage, and a recombinant nucleic acid molecule as herein described, can be generated by means of customary recombination and cloning techniques as are described, for example, in Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor (NY), in Silhavy T J, Berman M L and Enquist L W (1984) Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor (NY), in Ausubel F M et al. (1987) Current Protocols in Molecular Biology, Greene Publishing Assoc, and Wiley Interscience and in Gelvin et al. (1990) In: Plant Molecular Biology Manual. However, further sequences which, for example, act as a linker with specific cleavage sites for restriction enzymes, or as a signal peptide, may also be positioned between the promoter nucleic acid molecule to be expressed. The insertion of sequences may also lead to the expression of fusion proteins. Preferably, the recombinant nucleic acid molecule, comprising an operable linkage of at least a promoter and the nucleic acid sequence to be expressed, can exist in a vector-integrated form and be inserted into a plant genome, for example by transformation.
As used herein, the term “expression control sequences” refers to transcriptional and/or translational control or regulatory sequences, e.g., promoters or enhancers, to direct or modulate RNA synthesis/ expression such as sequences that can act as transcription, termination and/or polyadenylation signals.
In various embodiments, the one or more additional expression control sequences, i.e., one or more further expression control sequences present in addition to the promoter, are selected from transcription, termination and/or polyadenylation signals.
In various embodiments, the recombinant nucleic acid molecule described and defined herein is an expression cassette.
As used herein, the term "expression cassette" refers to a nucleotide sequence which is capable of affecting expression of a structural gene (i.e., a protein coding sequence, such as a polypeptide of SEQ ID NO: 106) in a host compatible with such sequences.
In various such embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences, wherein said nucleic acid molecule is a nucleic acid sequence having at least 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof.
In various other embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences, wherein said nucleic acid molecule is a nucleic acid sequence encoding a polypeptide having at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof.
In various other embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences, wherein said nucleic acid molecule is a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence, which is a nucleic acid sequence having at least 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof.
In various other embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences, wherein said nucleic acid molecule is a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence, which is a nucleic acid sequence encoding a polypeptide having at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof.
Particularly, in various embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter functional in plants,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, one or more additional expression control sequences functional in plants. As used herein, the term “functional in plants” in the context of promotors and other expression control sequences refers to any such element, which is capable of governing the expression of genes, in particular foreign genes, in plants or plant parts, plant cells, plant tissues, or plant cultures.
In some further embodiments, a recombinant nucleic acid molecule as described and defined herein comprises the following elements in 5'-3' orientation:
- a promoter functional in plants,
- operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and
- optionally, operatively linked thereto, a terminator sequence functional in plants.
In various embodiments, the promoter is a constitutive promoter.
“Constitutive” promoters are those that drive expression continuously under most environmental conditions and states of development or cell differentiation.
In some embodiments, the promoter is a constitutive promoter functional in plant cells.
Examples of constitutive promoters functional in plants include the cauliflower mosaic virus (CaMV) 35S transcription initiation region, the 1 '- or 2'- promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes known to those of skill. Such genes include, e.g., ACT11 from Arabidopsis (Huang (1996) Plant Mol. Biol. 33:125-139); Cat3 from Arabidopsis (GenBank No. U43147, Zhong (1996) Mol. Gen. Genet. 251 :196-203); the gene encoding stearoyl-acyl carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe (1994) Plant Physiol. 104:1167-1176); GPc1 from maize (GenBank No. X15596; Martinez (1989) J. Mol. Biol 208:551-565); the Gpc2 from maize (GenBank No. U45855, Manjunath (1997) Plant Mol. Biol. 33:97- 112); plant promoters described in U.S. Patent Nos. 4,962,028; 5,633,440; the promoters of the vacuolar ATPase subunits or the promoter of a proline-rich protein from wheat (WO 91/13991), the ubiquitin promoter (Holtorf S et al. (1995) Plant Mol Biol 29: 637-649); the ubiquitin 1 promoter (Christensen et al. (1992) Plant Mol Biol 18: 675-689; Bruce et al. (1989) Proc. Natl. Acad. Sci. USA 86: 9692-9696); the Smas promoter; and the cinnamyl alcohol dehydrogenase promoter (U.S. Pat. No. 5,683,439).
In some embodiments, the promoter is a constitutive promoter functional in plant cells selected from the cauliflower mosaic virus 35S or ubiquitin promoter.
In some other embodiments, the promoter is a tissue-specific promoter.
“Tissue-specific” promoters are transcriptional control elements that are only active in particular cells or tissues or organs, e.g., in plants or animals. Tissue-specific regulation may be achieved by certain intrinsic factors that ensure that genes encoding proteins specific to a given tissue are expressed. Such factors are known to exist in mammals and plants so as to allow for specific tissues to develop. In some embodiments, the promoter is a tissue-specific promoter functional in plants. Non-limiting examples of tissue-specific promotors functional in plants include those with specificity for the anthers, ovaries, flowers, leaves, stems, roots and seeds. In some such embodiments, the tissue-specific promoter is an epidermis-, mesophyll-, seed- or leaf-specific promoter.
Seed-specific promoters are such as, for example, the phaseolin promoter (U.S. Pat. No. 5,504,200; Bustos et al. (1989) Plant Cell 1 (9): 839-53), the 2S albumin gene promoter (Joseffson et al. (1987) J. Biol. Chem. 262: 12196-12201), the legumin promoter (Shirsat et al. (1989) Mol. Gen. Genet. 215(2): 326-331), the USP (unknown seed protein) promoter; Baumlein et al. (1991) Mol. Gen. Genet. 225(3): 459-67), the napin gene promoter (U.S. Pat. No. 5,608,152; Stalberg et al. (1996) L. Planta 199: SI S- 519), the promoter of the gene coding for sucrose binding protein (WO 00/26388) or the legumin B4 promoter (LeB4; Baumlein et al. (1991) Mol. Gen. Genet. 225: 121-128; Baumlein et al. (1992) Plant Journal 2(2): 233-9; Fiedler et al. (1995) Biotechnology (NY3) 13(10): 1090f), the Arabidopsis oleosin promoter (WO 98/45461), the Brassica Bce4 promoter (WO 91/13980). Further suitable seed-specific promoters are those of the genes coding for the high-molecular-weight glutenin (HMWG), gliadin, branching enzyme, ADP glucose pyrophosphatase (AGPase). Further preferred promoters are those which permit seed-specific expression in monocots such as maize, barley, wheat, rye, rice and the like. The following can be employed advantageously: the promoter of the Ipt2 or Ipt1 gene (WO 95/15389, WO 95/23230) or the promoters described in WO 99/16890 (promoters of the hordein gene, the glutelin gene, the oryzin gene, the prolamin gene, the gliadin gene, the zein gene, the kasirin gene, orthe secalin gene).
Tuber-, storage-root- or root-specific promoters are, for example, the patatin promoter class I (B33), the potato cathepsin D inhibitor promoter. Another example of a root-specific promoter is the promoter from the alcohol dehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. 123:39-60).
Leaf-specific promoters are, for example, the potato cytosolic FBPase promoter (WO 97/05900), the SSU promoter (small subunit) of Rubisco (ribulose-1 ,5-bisphosphate carboxylase) or the ST-LSI promoter from potato (Stockhaus et al. (1989) EMBO J 8: 2445-2451).
Epidermis-specific promoters are, for example, the OXLP gene (oxalate-oxidase-like protein) promoter (Wei et al. (1998) Plant Mol Biol 36: 101 -112), a promoter consisting of the GSTA1 promoter and WIR1 a intron (WO 2005/035766); WIR5(=GstA1), acc. X56012 (Dudler & Schweizer, unpublished); GLP4, acc. AJ310534 (Wei (1998) Plant Molecular Biology 36. 101 -112); GLP2a, acc. AJ237942 (Schweizer (1999). Plant J 20: 541-552); Prx7, acc. AJ003141 (Kristensen (2001) Molecular Plant Pathology 2(6); 311-317); GerA, acc. AF250933 (Wu (2000) Plant Phys. Biochem. 38: 685-698); OsROCI , acc. AP004656; RTBV, acc. AAV62708, AAV62707 (Klbti (1999) PMB 40: 249-266); and Cer3 (Hannoufa (1996) Plant J. 10 (3): 459-467).
Mesophyll-specific promoters include the promoter of the wheat germin 9f-3.8 gene (GenBank Acc.-No.:
M63224) or the barley GerA promoter (WO 02/057412); Arabidopsis CAB-2 promoter (Genrank Acc.- No.: X15222) and the Zea mays PPCZml promoter (GenBank Acc.-No.: X63869) or homologues thereof; PPCZml (=PEPC; Kausch (2001) Plant Mol. Biol. 45: 1-15); OsrbcS (Kyozuka et al. (1993) Plant Phys. 102: 991-1000); OsPPDK, ace. AC099041 ; TaGF-2.8, acc. M63223 (Schweizer (1999) Plant J. 20: 541-552); TaFBPase, acc. X53957; TaWISI , acc. AF467542 (US 2002/115849); HvBISI , acc. AF467539 (US 2002/115849); ZmMISI , acc. AF467514 (US 2002/115849); HvPRI a, acc. X74939 (Bryngelsson et al. (1994) Molecular Plant-Microbe Interactions 7(2): 267-75; HvPRI b, acc. X74940 (Bryngelsson et al. (1994) Molecular Plant-Microbe Interactions 7(2): 267-75); HvB1 ,3gluc; acc. AF479647; HvPrx8, acc. AJ276227 (Kristensen et al (2001) Molecular Plant Pathology 2(6); 311-317; and HvPAL, acc. X97313 (Wei (1998) Plant Molecular Biology 36: 101-112).
Other tissue-specific promoters are, for example, flower-specific promoters such as, for example, the phytoen synthase promoter (WO 92/16635) or the promoter of the Prr gene (WO 98/22593), and antherspecific promoters such as the 5126 promoter (U.S. Pat. No. 5,689,049, U.S. Pat. No. 5,689,051), the global promoter and the y-zein promoter.
In various other embodiments, the promoter is an inducible promoter.
“Inducible” or “regulatable” promoters direct expression of the nucleic acid of the invention under the influence of environmental conditions or developmental conditions. Examples of environmental conditions that may affect transcription by inducible promoters functional in plants include anaerobic conditions, wounding, temperature changes, drought, the presence of light, and exposure to chemicals or hormones, such as auxins.
In some embodiments, the promoter is an inducible promoter functional in plants.
For example, the auxin-response elements E1 promoter fragment (AuxREs) in the soybean (Glycine max L.) (Liu (1997) Plant Physiol. 115:397-407); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen (1996) Plant J. 10: 955-966); the auxininducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit (1997) Mol. Plant Microbe Interact. 10:933-937); the promoter responsive to the stress hormone abscisic acid (Sheen (1996) Science 274:1900-1902); or ethanol- or cyclohexanone-inducible promoters (WO 93/21334) may be used in the context of the present invention. Other examples of inducible promotors functional in plants include, without limitation, the maize ln2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder (1997) Plant Cell Physiol. 38:568-577); a tetracycline-inducible promoter, e.g., as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11 :465-473); or a salicylic acid-responsive element (Stange (1997) Plant J. 11 :1315-1324). Examples of woundinducible promoters include promoters such as that of the pinll gene (Ryan (1990) Ann. Rev. Phytopath 28: 425-449; Duan et al. (1996) Nat. Biotech. 14: 494-498), of the wun1 and wun2 gene (U.S. Pat. No. 5,428,148), of the win1 and win2 gene (Stanford et al. (1989) Mol. Gen. Genet. 215: 200-208), of the systemin gene (McGurl et al. (1992) Science 225: 1570-1573), of the WIP1 gene (Rohmeier et al. (1993) Plant Mol. Biol. 22: 783-792; Eckelkamp et al. (1993) FEBS Letters 323: 73-76), and of the MPI gene (Corderok et al. (1994) Plant J 6(2): 141 -150).
Further examples of inducible promotors useful in the context of the present invention include the heatinducible hsp70 or hsp80 promoter from tomato (U.S. Pat. No. 5,187,267), the chill-inducible alphaamylase promoter from potato (WO 96/12814), and the light-inducible PPDK promoter.
In principle, it is possible to use all natural promoters together with their regulatory sequences, such as those mentioned above, for the method according to the invention. Moreover, it is also possible advantageously to use synthetic promoters.
Genetic control sequences furthermore also comprise the 5'-untranslated regions, introns or the noncoding 3' region of genes such as in plants, for example, the actin-1 intron, or the Adh1-S introns 1 , 2 and 6 (The Maize Handbook, Chapter 116, Freeling and Walbot, Eds., Springer, New York (1994)). It has been demonstrated that 5'-untranslated sequences are capable of enhancing the transient expression of heterologous genes. An example of translation enhancers which may be mentioned is the 5'-leader sequence from the tobacco mosaic virus and the like. They can furthermore promote tissue specificity.
In some embodiments, the recombinant nucleic acid molecule as described and defined herein can comprise one or more enhancer sequences, operatively linked to the promoter, which enable enhanced transgenic expression of the nucleic acid sequence. Additional advantageous sequences may also be inserted at the 3' end of the nucleic acid sequences to be expressed recombinantly, such as further regulatory elements or terminators. It is further envisaged that, in some embodiments, the nucleic acid sequences to be expressed recombinantly may be present in the gene construct as one or more copies.
In some embodiments, proper polypeptide expression may require polyadenylation region at the 3'-end of the coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant (or animal or other) genes, or from genes in the Agrobacterial T-DNA. Non-limiting examples include T-DNA polyadenylation signals from Agrobacterium tumefaciens, in particular of gene 3 of the T-DNA (octopine synthase) of the Ti plasmid pTiACHS or functional equivalents thereof.
Control sequences are furthermore to be understood as meaning those which allow for homologous recombination or insertion into the genome of the host organism, or which permit the removal from the genome. In the case of homologous recombination, it is possible, for example, to replace the natural promoter of a specific gene with a promoter with specificity for the embryonal epidermis and/or the flower.
In various embodiments, the recombinant nucleic acid molecule as described and defined herein may comprise further functional elements, non-limiting examples of which include selection markers, reporter genes, origins of replication, and elements that are necessary for Agrobacterium-mediated plant transformation, such as, for example, the right or left border of the T-DNA or the vir region.
In particular embodiments, the recombinant nucleic acid molecule as described and defined herein is a vector.
A “vector” comprises a nucleic acid that can infect, transfect, transiently or permanently transduce a cell. A vector can be a naked nucleic acid, or a nucleic acid complexed with protein or lipid. The vector may comprise viral or bacterial nucleic acids and optionally proteins and/or membranes (e.g., a cell membrane, a viral lipid envelope, etc.). Vectors include, but are not limited to, replicons (e.g., RNA replicons, bacteriophages) to which fragments of DNA may be attached and become replicated. Vectors thus include, but are not limited to RNA, autonomous self-replicating circular or linear DNA or RNA (e.g. , plasmids, viruses, and the like), and include both the expression and non-expression plasmids. Where a recombinant microorganism or cell culture is described as hosting an expression vector, this includes both extra-chromosomal circular and linear DNA and DNA that has been incorporated into the host chromosome(s). Where a vector is being maintained by a host cell, the vector may either be stably replicated by the cells during mitosis as an autonomous structure or is incorporated within the host's genome.
The vectors may take the form of, for example, plasmids, cosmids, fosmids, phages, phagemids, viruses or else agrobacteria. In various other embodiments, the vector is a viral vector comprising an adenovirus vector, a retroviral vector or an adeno-associated viral vector.
In various other embodiments, the recombinant nucleic acid molecule as described and defined herein is an artificial chromosome comprising a bacterial artificial chromosome (BAC), a bacteriophage P1- derived vector (PAC), a yeast artificial chromosome (YAC), or a mammalian artificial chromosome (MAC).
Thus, in the context of the present invention, the recombinant nucleic acid molecule as described and defined herein may be referred to as an expression construct.
Alternatively or additionally, the method of modifying thermotolerance and/or senescence in a plant or plant cell comprises introduction of an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) into a plant or plant cell. In various embodiments, the isolated polypeptide of the invention comprises a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof. In various embodiments, the isolated polypeptide has the amino acid sequence set forth in SEQ ID NO: 106. In various embodiments, said polypeptide affects the temperature range of the thermosensor and of the onset of thermotolerance mechanisms induced by TWA1 and its homologs in plants or plant cells.
In some embodiments, said polypeptide affects the temperature range of the thermosensor and of the onset of senescence suppressing mechanisms induced by TWA1 and its homologs in plants or plant cells.
In various embodiments, said polypeptide is derived from is derived from Arabidopsis, preferably Arabidopsis thaliana or Arabidopsis lyrata; Brassica, preferably Brassica oleracea; Sinapis, preferably Sinapis alba; Gossypium; Glycine max; Nelumbo nucifera; Phoenix dactylifera; Zea mays; or Triticum aestivum.
In various embodiments of the method of modifying thermotolerance and/or senescence in a plant or plant cell, the method further comprises the step of growing the plant or keeping the plant cell under conditions, wherein the expression product of the nucleic acid molecule as defined in any one of items i) to iv) or the polypeptide introduced into the plant or plant cell, as herein defined and described, is able to act, in the plant or plant cell, as a thermosensor to modify thermotolerance and/or senescence, as herein described.
In various such embodiments, particularly, said step of growing the plant or keeping the plant cell comprises exposure of the plant or plant cell to elevated temperatures, such as temperatures of about 10 °C, 15 °C, 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45, 50, 55, or 60 °, preferably temperatures such as 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45, or 50 °C. In some such embodiments, exposure to elevated temperatures is imposed for a duration of at least minutes, to days or up to several weeks. 0.1 , 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1 .5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10.0, 10.5, 11 .0, 11 .5, or 12 hours, preferably for a duration of about 1 to 24 hours, or 1 day to 6 days, or 1 to 4 weeks.
In this context, the term “growing” means growing a whole plant, a plant cell, a group of plant cells, a plant part (including seeds), or a plant piece (e.g., from a protoplast, callus, or tissue parts).
In some embodiments, the method of the present invention is characterized in that the modifying of thermotolerance is increasing thermotolerance, as herein defined. In some embodiments, the method of the present invention is characterized in that the modifying of senescence is reducing senescence, as herein defined.
In further embodiments, the method of the present invention is characterized in that the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
Particularly, in various embodiments, increased thermotolerance conferred to a plant or plant cell in accordance with the methods of the present invention is not accompanied by detectable alterations in terms of plant growth, plant physiognomy, photosynthesis, and/or leaf gas exchange, relative to a control plant, wherein relative to a control plant refers to a control plant grown or kept under conditions that do not elicit environmental stress in said plant, e.g. conditions that are generally considered as optimal growth conditions for the respective plant. In various embodiments, the methods of the present invention do not result in thermo-morphogenesis (morphological acclimation responses, which include the elongation of hypocotyls, stems, petioles and roots, leaf hyponasty and a reduction in leaf blade size) of the plant, into which a nucleic acid sequence as defined in any one of items i) to iv) or a recombinant nucleic acid molecule as herein described and defined has been introduced and in which the respective nucleic acid sequence has been expressed, or into which an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) has been introduced.
In a further aspect, the present invention provides for a method of producing a transgenic plant or plant cell, said method comprising the step of: a) introducing into a plant or plant cell, optionally integrating it into the plant genome, an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); or b) introducing into a plant or plant cell, optionally integrating it into the plant genome, a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences.
In various embodiments, said method is not a non-technical method or process, i.e., said method is not an essentially biological method or process. In various embodiments, said method is a biotechnological method.
In some embodiments, a homolog of a nucleic acid sequence according to item i) or ii) is selected from orthologs and paralogs thereof, preferably orthologs thereof.
In some embodiments, the method further comprises a step of expressing the nucleic acid sequence as defined in any one of items i) to iv) in said plant or plant cell.
In some embodiments, the method further comprises a step of regenerating a transgenic plant from a transgenic plant cell thus obtained. Methods for regenerating plants from plant cells have been discussed herein above.
In the context of the present invention, the term “transgenic” refers to constructs or organisms which exist as a result of recombinant methods and in which either a) the nucleic acid sequence as defined in any one of items i)-iv), or b) a genetic control sequence, for example a promoter, which is operably linked with the nucleic acid sequence as defined in any one of items i)-iv), or c) a) and b) has been introduced. Accordingly, as used herein, the terms “transgenic plant” and “transgenic plant cells” include plants or plant cells, respectively, into which a heterologous nucleic acid sequence has been inserted, e.g., the isolated nucleic acids and various recombinant constructs as described and defined herein.
Consequently, in a further aspect, the present invention also provides a transgenic cell comprising a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto, a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and optionally c) operatively linked thereto, one or more additional expression control sequences.
In some embodiments, a homolog of a nucleic acid sequence according to item i) or ii) is selected from orthologs and paralogs thereof, preferably orthologs thereof.
In some embodiments, the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell, or a plant cell.
In various embodiments, the transgenic cell is a transgenic plant cell, and optionally said transgenic plant cell is obtainable in a method of producing a transgenic plant or plant cell according to the present invention, i.e., as herein described and defined.
In some embodiments, said transgenic cell has, relative to the wild-type cell, an increased content of a polypeptide encoded by a nucleic acid sequence according to any one of items i) to iv).
In some embodiments, said transgenic plant cell has, relative to the wild-type plant cell, a modified thermotolerance and/or senescence. In some such embodiments, the modified thermotolerance is an increased thermotolerance and/or the modified senescence is a reduced senescence.
In a further aspect, provided herein is a transgenic plant comprising a transgenic cell according to the present invention or produced by a method according to the present invention, and parts of these plants, transgenic harvest products and transgenic propagation material of these plants, such as protoplasts, plant cells, calli, seeds, tubers, cuttings, and the transgenic progeny of this plant. Accordingly, the invention also provides transgenic plant products or byproducts, e.g., fruits, oils, seeds, leaves, extracts and the like, which comprise a nucleic acid sequence according to any one of items i) to iv) or a recombinant nucleic acid molecule comprising a nucleic acid sequence according to any one of items i) to iv). The invention also provides methods of using these transgenic plants and seeds. The transgenic plant or plant cell may be constructed in accordance with any method known in the art. See, for example, U.S. Patent No. 6,309,872.
In some embodiments, the transgenic plant is a monocotyledonous plant, preferably a plant belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like.
In other embodiments, the transgenic plant is a dicotyledonous plant, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees. Useful plants may be fruit (in particular apples, pears, cherries, grapes, citrus, pineapples and bananas), oil palms, tea bushes, cocoa bushes and coffee bushes, sisal and, among medicinal plants, Rauwolfia and Digitalis.
Thus, the transgenic plants of the invention include a broad range of plants, including, but not limited to, species from the genera Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Coffea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannisetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solanum, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and Zea. In some embodiments, the transgenic plants of the invention may be selected from fiber-containing plants, such as cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, ramie, kenaf, hemp, roselle, jute, sisal abaca and flax.
The specific expression ofthe TWAI protein or a homolog thereof in the plants according to the invention or in the plant cells according to the invention can be detected, and monitored, with the aid of traditional methods of molecular biology and biochemistry. The skilled worker is familiar with these techniques, and he is easily capable of selecting a suitable detection method, for example a Northern Blot analysis for detecting protein-specific RNA or for determining the accumulation level of protein-specific RNA, or a Southern Blot analysis or PCR analysis for detecting DNA sequences which code for the TWA1 protein or a homolog thereof. The probe or primer sequences used for this purpose can either be identical to the sequence shown in SEQ ID NO. 105 or can feature a small number of deviations from this sequence.
In a further aspect, the present invention also provides for the use of the TWA1 locus or a homolog thereof for the production of transgenic plants or transgenic plant cells with modified thermotolerance and/or modified senescence.
In some such embodiments, the modified thermotolerance is increased thermotolerance and/or the modified senescence is reduced senescence.
The present invention further relates to the use of the transgenic organisms according to the invention and of the cells, cell cultures, parts, such as, for example, in the case of transgenic plant organisms, roots, leaves and the like, and transgenic propagation material such as seeds or fruits for the preparation of foodstuffs or feeding stuffs, pharmaceuticals or fine chemicals.
As discovered by the present inventors, TWA1 or a homolog thereof, upon thermal activation, unfolds to allow access of JAM2 and TPL to interact with the carboxyterminal and aminoterminal part of TWA1 , respectively. An illustrative scheme of this mechanism is depicted in Figure 12. JAM2 are binding to G- box cis elements (G-box nucleotide sequence CACGTG) and to related cis elements (G-box with one nucleotide deviation from CACGTG) as dimers. TPL is tetrameric and physically interacts by the ethylene-responsive element binding factor-associated amphiphilic repression (EAR)-motifs of TWA1 (striped sections in the TWA1 model) and binds to subunits of the mediator complex. In view of this thermosensitive gene expression-regulative property of TWA1 and homologs thereof, the present invention is, in yet another aspect, directed to the use of TWA1 or a homolog thereof as a molecular thermosensitive genetic control switch for gene expression. A non-limiting example of this aspect is depicted in Figure 8. Means for coupling of TWA1 -binding proteins such as JAM2 or TPL/TPR, or fragments thereof, to target cis elements of specific promoters and one or more target genes the expression of which is to be regulated by TWA1 or a homolog thereof, as herein defined, are generally known to a person skilled in the field.
In the context of the present invention, the term “homolog of TWA1 ” refers to an entity with similar protein sequence to TWA1 of Arabidopsis thaliana (SEQ ID NO: 106) and/or to such homologs identified in reiterated homology searches as defined herein above. In the context of the present invention, a TWA1 polynucleotide sequence homolog is defined as the polyribonucleotide and/or polydesoxyribonucleotide sequences encoding the TWA1 polypeptide homologs.
In various embodiments of this aspect, TWA1 or a homolog thereof acts, in a temperature-dependent manner, in conjunction with one or more TWA1 -binding proteins.
In various embodiments, the one or more TWA1 -binding proteins are selected from the JAM transcription factors and the corepressors TPL/TPRs, preferably JAM2 and its orthologs and TPL and its orthologs.
In various embodiments, TWA1 or a homolog thereof and the TWA1 -binding proteins form a protein complex of TWA1 -JAM-TPL/TPRs.
In various embodiments, the protein complex of TWA1 -JAM-TPL/TPRs acts as a transcriptional repressor complex.
Specific items of the present invention
Item 1) Use of TWA1 or a homolog thereof for modifying thermotolerance and/or senescence in plants or plant cells.
Item 2) The use according to item 1 , wherein the modifying of thermotolerance is increasing thermotolerance and/or wherein the modifying of senescence is reducing senescence.
Item 3) The use according to item 1 or 2, wherein the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees. Item 4) A method of modifying thermotolerance and/or senescence in a plant or plant cell, comprising:
I) modifying the TWA1 locus or a homolog thereof in a plant or plant cell; and/or
II) introducing into a plant or plant cell an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); and/or
III) introducing into a plant or plant cell a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences; and/or
IV) introducing an isolated polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) into a plant or plant cell, wherein expression of the gene product of the modified TWA1 locus or the homolog thereof and/or of the nucleic acid sequence as defined in any one of items i) to iv), or presence of the introduced polypeptide comprising an amino acid sequence encoded by a nucleic acid sequence as defined in any one of items i) to iv) results in modified thermotolerance and/or senescence in said plant or plant cell.
Item 5) The method according to item 4, further comprising the step of growing the plant or keeping the plant cell under conditions, wherein the expression product of the nucleic acid molecule as defined in any one of items i) to iv) or the polypeptide introduced into the plant or plant cell is able to act, in the plant or plant cell, as a thermosensor.
Item 6) The method according to item 5, comprising exposure of the plant or plant cell to temperatures in the range of about 7 to 60 °C, such as temperatures of about 10 °C, 15 °C, 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45, 50, 55, or 60 °. Item 7) The method according to any one of items 4 to 6, wherein the nucleic acid sequence is derived from Arabidopsis, preferably Arabidopsis thaliana or Arabidopsis lyrata; Brassica, preferably Brassica oleracea; Sinapis, preferably Sinapis alba; Gossypium; Glycine max; Nelumbo nucifera; Phoenix dactylifera; Zea mays; or Triticum aestivum.
Item 8) The method according to any one of items 4 to 7, wherein the isolated polypeptide confers thermotolerance in plants or plant cells.
Item 9) The method according to any one of items 4 to 8, wherein the isolated polypeptide confers protection against senescence in plants or plant cells.
Item 10) The method according to any one of items 4 to 9, wherein the modifying of thermotolerance is increasing thermotolerance and/or wherein the modifying of senescence is reducing senescence.
Item 11) The method according to any one of items 4 to 10, wherein the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
Item 12) A method of producing a transgenic plant or plant cell, said method comprising the steps of: a) introducing into a plant or plant cell, optionally integrating it into the plant genome, an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii); or b) introducing into a plant or plant cell, optionally integrating it into the plant genome, a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto a nucleic acid sequence as defined in any one of items i) to iv), and c) optionally, operatively linked thereto, one or more additional expression control sequences.
Item 13) The method of item 12, wherein said method is not a non-technical method or process, i.e., said method is not an essentially biological method or process; and/or said method is a biotechnological method; and/or said method further comprises a step of expressing the nucleic acid sequence as defined in any one of items i) to iv) in said plant or plant cell.
Item 14) The method according to item 12 or 13, further comprising a step of regenerating a transgenic plant from a transgenic plant cell thus obtained.
Item 15) A transgenic cell comprising a recombinant nucleic acid molecule comprising the following elements in 5'-3' orientation: a) a promoter, and b) operatively linked thereto, a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii), and optionally, c) operatively linked thereto, one or more additional expression control sequences.
Item 16) The transgenic cell according to item 15, wherein the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell, or a plant cell. Item 17) The transgenic cell according to item 15 or 16, wherein said transgenic cell has, relative to the wild-type cell and/or a control cell, an increased content of a polypeptide encoded by a nucleic acid sequence according to any one of items i) to iv).
Item 18) The transgenic cell according to any one of items 15 to 17, wherein the transgenic cell is a transgenic plant cell, wherein optionally said transgenic plant cell is obtainable by a method according to any one of items 12 to 14.
Item 19) The transgenic cell according to item 18, wherein said transgenic plant cell has, relative to the wild-type plant cell and/or a control plant cell, a modified thermotolerance and/or senescence.
Item 20) The transgenic cell according to item 19, wherein the modified thermotolerance is an increased thermotolerance and/or the modified senescence is a reduced senescence.
Item 21) A transgenic plant comprising a transgenic cell according to any one of items 15 to 20 or produced by a method according to any one of items 12 to 14, and parts of these plants, transgenic harvest products and transgenic propagation material of these plants, such as protoplasts, plant cells, calli, seeds, tubers, cuttings, and the transgenic progeny of this plant.
Item 22) The transgenic plant according to item 21 , wherein the transgenic plant is a monocotyledonous plant, preferably a plant belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; or a dicotyledonous plant, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
Item 23) Use of the TWA1 locus or a homolog thereof for the production of transgenic plants or transgenic plant cells with modified thermotolerance and/or modified senescence.
Item 24) Use of TWA1 or a homolog thereof as a molecular thermosensitive genetic control switch for gene expression.
Item 25) The use according to item 24, wherein TWA1 or a homolog thereof acts, in a thermosdependent manner, in conjunction with one or more TWA1 -binding proteins.
Item 26) The use according to item 25, wherein the one or more TWA1 -binding proteins are selected from the JAM transcription factors and the corepressors TPL/TPRs, preferably JAM2 and its orthologs and TPL and its orthologs.
Item 27) The use according to item 25 or claim 26, wherein TWA1 or a homolog thereof and the TWA1- binding proteins form a protein complex of TWA1-JAM-TPL/TPRs. Item 28) The use according to item 27, wherein the protein complex of TWA1-JAM-TPL/TPRs acts as a transcriptional repressor complex.
Further embodiments of the present invention
1 . An isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of: i) a nucleic acid sequence having at least 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the nucleic acid sequence set forth in SEQ ID NO: 105, or fragments thereof; and/or ii) a nucleic acid sequence encoding a polypeptide having at least 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 98, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99 or 100 % sequence identity to the amino acid sequence set forth in SEQ ID NO: 106, or fragments thereof; and/or iii) a nucleic acid sequence, which hybridizes under stringent conditions with a complementary strand of a nucleic acid sequence according to item i) or ii); and/or iv) a homolog or functional fragment of a nucleic acid sequence according to item i) or ii), encoding a polypeptide or a fragment thereof, which confers thermotolerance in plants or plant cells.
2. The isolated nucleic acid molecule according to embodiment 1 , wherein the nucleic acid sequence is derived from Arabidopsis, preferably Arabidopsis, preferably Arabidopsis thaliana or Arabidopsis lyrata; Brassica, preferably Brassica oleracea; Sinapis, preferably Sinapis alba; Gossypium; Glycine max; Nelumbo nucifera; Phoenix dactylifera; Zea mays; or Triticum aestivum.
3. An isolated polypeptide, said polypeptide conferring thermotolerance in plants or plant cells, comprising an amino acid sequence encoded by a nucleic acid sequence according to embodiment 1 .
4. An isolated polypeptide, said polypeptide conferring altered thermotolerance in plants or plant cells, comprising an amino acid sequence encoded by a nucleic acid sequence according to embodiment 1 .
5. An isolated polypeptide, said polypeptide conferring protection against senescence in plants or plant cells, comprising an amino acid sequence encoded by a nucleic acid sequence according to embodiment 1 .
6. An isolated polypeptide, said polypeptide being able to sense temperature and/or temperature shifts in plants or plant cells, comprising an amino acid sequence encoded by a nucleic acid sequence according to embodiment 1 . 7. A recombinant nucleic acid molecule, comprising the following elements in 5'-3' orientation:
- a promoter,
- operatively linked thereto a nucleic acid sequence according to embodiment 1 , and
- optionally, operatively linked thereto, one or more additional expression control sequences.
8. The recombinant nucleic acid molecule according to embodiment 7, wherein said recombinant nucleic acid molecule is an expression cassette.
9. The recombinant nucleic acid molecule according to embodiment 7 or 8, wherein the promoter is a constitutive promoter, preferably the cauliflower mosaic virus 35S or ubiquitin promoter.
10. The recombinant nucleic acid molecule according to embodiment 7 or 8, wherein the promoter is a tissue-specific promoter.
11 . The recombinant nucleic acid molecule according to embodiment 10, wherein the tissue-specific promoter is an epidermis, mesophyll, seed, root, or leaf-specific promoter.
12. The recombinant nucleic acid molecule according to embodiment 7 or 8, wherein the promoter is an inducible promoter.
13. A method for modifying thermotolerance in a plant or plant cell, comprising introducing a nucleic acid sequence according to embodiment 1 or a recombinant nucleic acid molecule according to any one of embodiment 7 to 12 into a plant or plant cell and expressing the nucleic acid sequence in said plant or plant cell, or modifying the TWA1 locus in a plant or plant cell, or introducing an isolated polypeptide according to any one of embodiments 3 to 6 into a plant or plant cell.
14. The method according to embodiment 13, further comprising the step of growing the plant or keeping the plant cell under conditions wherein the expression product of the nucleic acid molecule according to embodiment 1 or the polypeptide according to any one of embodiments 3 to 6 is able to act, in the plant or plant cell, as a thermosensor.
15. The method according to embodiment 14, comprising exposure of the plant or plant cell to elevated temperatures, such as temperatures of about 10 °C, 15 °C, 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45, 50, 55, or 60 °.
16. A method of producing a transgenic plant or plant cell, said method comprising introducing a nucleic acid sequence according to embodiment 1 or a recombinant nucleic acid molecule according to any one of embodiment 7 to 12 into a plant or plant cell, optionally integrating it into the plant genome, and expressing the nucleic acid sequence in said plant or plant cell, wherein preferably said method is not a non-technical method or process and/or is not an essentially biological method or process, wherein more preferably said method is a biotechnological method. 17. The method according to embodiment 16, further comprising a step of regenerating a transgenic plant from a transgenic plant cell thus obtained.
18. A transgenic cell comprising a nucleic acid sequence according to embodiment 1 or comprising the recombinant nucleic acid molecule according to any one of embodiment 7 to 12, wherein optionally the cell is a bacterial cell, a mammalian cell, a fungal cell, a yeast cell, an insect cell or a plant cell.
19. The transgenic cell according to embodiment 18, wherein said transgenic cell has, relative to the wild-type cell, an increased content of a polypeptide encoded by a nucleic acid sequence according to embodiment 1 .
20. The transgenic cell according to embodiment 18 or 19, wherein the transgenic cell is a transgenic plant cell, wherein optionally said transgenic plant cell is obtained in a method according to embodiment 16 or 17.
21 . The transgenic cell according to embodiment 20, wherein said transgenic plant cell has, relative to the wild-type plant cell, a modified thermotolerance.
22. The transgenic cell according to embodiment 20 or 21 , wherein said transgenic plant cell has, relative to the wild-type plant cell, an increased thermotolerance.
23. A transgenic plant comprising a transgenic cell according to any one of embodiments 18 to 22 or produced by a method according to embodiment 16 or 17, and parts of these plants, transgenic harvest products and transgenic propagation material of these plants, such as protoplasts, plant cells, calli, seeds, tubers, cuttings, and the transgenic progeny of this plant.
24. The transgenic plant according to embodiment 23, wherein the transgenic plant is a monocotyledonous plant, preferably a plant belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like.
25. The transgenic plant according to embodiment 23, wherein the transgenic plant is a dicotyledonous plant, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees.
26. Use of a nucleic acid sequence according to embodiment 1 for the production of transgenic plants or transgenic plant cells with modified thermotolerance.
27. The Use according to embodiment 26, wherein the modified thermotolerance is increased thermotolerance. 28. Use of an isolated polypeptide according to any one of embodiments 3 to 6 as a thermosensor in plants or plant cells.
29. The use according to claim 28, wherein the thermosensor is a thermogenetic control switch.
30. Use of TWA1 for modifying thermotolerance and/or senescence in a plant or plant cell.
31 . The use according to embodiment 30, wherein the modifying of thermotolerance is increasing thermotolerance.
32. The use according to embodiment 30, wherein the modifying of senescence is reducing senescence.
33. The use according to any one of embodiments 30 to 32, wherein the plant is selected from monocotyledonous plants, preferably plants belonging to the genera Avena, Triticum, Secale, Hordeum, Oryza, Panicum, Pennisetum, Phoenix, Setaria, Sorghum, and the like; and dicotyledonous plants, preferably selected from the group consisting of alfalfa, beans, broccoli, cabbage, capsicum, carrot, cauliflower, celery, cotton, cucumber, eggplant, lettuce, lotus, melon, mustard, ornamental plants, pea, potato, pumpkin, radish, rapeseed, spinach, soybean, squash, sugar beet, sunflower, tobacco, tomato, and trees
Examples
Example 1 : Plant materials and growth conditions
Plants of Arabidopsis thaliana (L.) Heynh. ecotype Columbia (Col-0) and accession Landsberg erecta (Ler-0) were grown in pots on a perlite/soil mixture at 22 °C under long day conditions with 16 h light (150 pE nr2 s1). The plants were used for stable transformation, protoplast preparation and DNA extraction. Arabidopsis seedlings were grown on agar plates with half strength Murashige and Skoog agar medium for physiological assays as previously described (Tischer, S. V. et al. Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 114, 10280-10285, doi:10.1073/pnas.1706593114 (2017)). For thermotolerance tests, Arabidopsis seeds were plated on Murashige and Skoog agar medium under sterile conditions and stratified at 4 °C for 2 d in the dark. The plates were then transferred to a culture room with continuous light (~50 pE nrr2 S"1) at 22 °C and 5-day-old seedlings were used for assessment of basal or acquired thermotolerance (see below: Example 7). T-DNA knockout lines of the GABI-Kat collection (Rosso, M. G. et al. An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol 53, 247-259, doi:10.1023/B:PLAN.0000009297.37235.4a (2003)) including GK-476H03 (At5g13590; twa1-2) and SALK collection (Alonso, J. M. et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301 , 653-657, doi:10.1126/science.1086391 (2003)) including SALK_143411 (At2g33540; designated cpl3-10) were obtained from The European Arabidopsis Stock Centre.
The JAM2/bHLH013 (At1g01260) gene was inactivated in pHB6:LUC line using the CRISPR/Cas9 system (Ordon, J. et al. Generation of chromosomal deletions in dicotyledonous plants employing a user-friendly genome editing toolkit. The Plant Journal 89, 155-168, doi:https://doi.org/10.1111/tpj.13319 (2017); Labun, K., Krause, M., Torres Cleuren, Y. & Valen, E. CRISPR Genome Editing Made Easy Through the CHOPCHOP Website. Current Protocols 1 , e46, doi:https://doi.org/10.1002/cpz1 .46 (2021)) and vector pDGE63, (Addgene plasmid #79445; http://n2t.net/addgene:79445; RRID:Addgene_79445). Two independent jam2 isolates harboured a frameshift, which resulted in early termination of translation after 12 aa and we designated them as jam2-2. DNA sequence analysis revealed the absence of off-target mutations in the closely related genes JAM1/bHLH017 (At2g46510) and JAM3/bHLH003 (At4g16430). The triple mutant jam1-2 jam2- 2 jam3-2 (jam) was generated by crossing jam2-2, jam1-2 (GK_285E09) and jam3-2 (GK_301 G05) (Sasaki-Sekimoto, Y. et al. Basic Helix-Loop-Helix Transcription Factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 Are Negative Regulators of Jasmonate Responses in Arabidopsis. Plant Physiology 163, 291-304, doi:10.1104/pp.113.220129 (2013)) and selecting for the homozygous jam mutant in the offspring. Similarly, the tpl-8 tpr2-2 tpr4-2 triple mutant (tpr) was obtained by crossing tpl-8 (SALK_036566) with SALK_112730 (tpr2-2) and SALK_002209 (designated tpr4-2). The generation of RCAR1 and RCAR6 overexpressing lines has been reported (Tischer, S. V. et al. Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 114, 10280-10285, doi:10.1073/pnas.1706593114 (2017)). Quadruple RCAR knockout lines were obtained by combining the multiple PYR/PYL knockout line pyr1 pyl1 pyl2 pyl4 pyl5 pyl8 (Gonzalez-Guzman, M. et al. Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatai aperture and transcriptional response to abscisic acid. The Plant Cell 24, 2483-2496, doi:10.1105/tpc.112.098574 (2012)), the rcar9 mutant (Fuchs, S., Tischer, S. V., Wunschel, C., Christmann, A. & Grill, E. Abscisic acid sensor RCAR7/PYL13, specific regulator of protein phosphatase coreceptors. Proceedings of the National Academy of Sciences of the United States of America 111 , 5741-5746, doi:10.1073/pnas.132208511 1 (2014)), and lines SALK_083621 (rcarT) and GK-012D02 (rcar13). The triple mutants abi1-2 abi2-2 hab1-1 and abi1-2 hab1-1 pp2ca1 (Rubio, S. et al. Triple Loss of Function of Protein Phosphatases Type 2C Leads to Partial Constitutive Response to Endogenous Abscisic Acid. Plant Physiology 150, 1345-1355, doi:10.1104/pp.109.137174 (2009)) were a gift of Pedro L. Rodriguez together with the multiple PYR/PYL knockout. Mutants were crossed to the ABA reporter lines pRD29B:LUC and pHB6:LUC (Christmann, A., Hoffmann, T., Teplova, I., Grill, E. & Muller, A. Generation of active pools of abscisic acid revealed by in vivo imaging of water-stressed Arabidopsis. Plant Physiol 137, 209-219, doi:10.1104/pp.104.053082 (2005)). Lines homozygous for reporter constructs and for mutant alleles were used throughout the experiments.
Example 2: Mutant isolation and ABA exposure
Mutants with ABA-hypersensitive reporter activation were recovered from a screen of the maternal second generation (M2) of EMS-mutagenized Arabidopsis seeds of the ABA reporter line pHB6:LUC (Christmann, A., Hoffmann, T., Teplova, I., Grill, E. & Muller, A. Generation of active pools of abscisic acid revealed by in vivo imaging of water-stressed Arabidopsis. Plant Physiol 137, 209-219, doi:10.1104/pp.104.053082 (2005)) in the Col-0 background. Briefly, the M2 seedlings were grown on solidified half-strength MS medium for five days prior transfer to medium supplemented with 3 pM (+) cis-trans-ABA (Chemos GmbH, www.chemos-group.com) or 0.3 M mannitol for 24 h followed by life luciferase imaging (Christmann, A., Hoffmann, T., Teplova, I., Grill, E. & Muller, A. Generation of active pools of abscisic acid revealed by in vivo imaging of water-stressed Arabidopsis. Plant Physiol 137 , 209- 219, doi:10.1104/pp.104.053082 (2005)). Among the mutants recovered, certain mutants were hypersensitive to exogenously applied ABA while mutants with an unaltered response to ABA were considered to carry lesions in drought stress signalling upstream of the canonical ABA signalling pathway. About 115,000 seedlings were screened and 109 putatively hypersensitive mutants were selected. Candidates showing a hypersensitive reporter response were propagated and the progeny reexamined. Finally, 24 mutants were confirmed among which 16 were found to be ABA-hypersensitive and 8 to be affected in early drought stress signalling upstream of ABA. We selected mutants with a robust phenotype for map-based cloning in combination with Next Generation Sequencing and identified twa1-1 together with mutants allelic to cp!1 and cp!3. The twa1-1 mutant was backcrossed to pHB6:LUC for four times.
Example 3: Gene identification
The 7WA1 locus has been identified by bulked segregant analysis (Nordstrom, K. J. V. et al. Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nature Biotechnology 31 , 325-330, doi:10.1038/nbt.2515 (2013)). Briefly, approximately 50 homozygous mutant seedlings were pooled and subjected to next generation DNA sequencing for identifying single nucleotide polymorphisms (SNPs) compared to the reference genome Col-0. The analysis confined the location of the target gene within a 180 kb genomic fragment on chromosome 5. In this fragment, four SNPs were found within genes, two of them were synonymous. The nonsynonymous mutations generated a premature TGA stop codon in At5g13590 at nt 744 of CDS and the other caused a conservative amino acid exchange in At5g13930. The identity of TWA1 (At5g13590) was confirmed by complementation of the ABA-hypersensitive phenotype by gene transfer of a 7 kb genomic fragment encompassing 1.1 kb of the promoter region, the structural gene, and the terminator (see Table 1 for primers and restriction sites used for cloning).
Example 4: Effector constructs and analysis of gene expression
Plant RNA extraction, cDNA synthesis, and construction of plasmids for effector expression have been described (Tischer, S. V. et al. Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proc Natl Acad Sci USA 114, 10280-10285, doi:10.1073/pnas.1706593114 (2017)). Briefly, cDNA had been generated from mRNA isolated from leaves of Arabidopsis Col-0, A. lyrata, and Sinapis alba. Total RNA was purified from leaves using the analytik jena-innuPREP Plant RNA Kit (Analytik Jena GmbH, http:// /www. analytik-jena.de) and cDNA was synthesized using RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, https://www.thermofisher.com). The coding sequences of effectors were integrated into a modified Bluescript vector with an expression cassette consisting of the 35S promoter, followed by the CDS, and the NOS terminator (Tischer, S. V. et al. Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proc Natl Acad Sci USA 114, 10280-10285, doi:10.1073/pnas.1706593114 (2017)). Primers and restriction sites used for cloning are listed in Table 1 . The 363 bp Avrl l-Hind 111 DNA fragment of AITWA1 gene encompassing the HVR was exchanged with the Avrll-Hindlll fragment of TWA1 to yield TWA1-AIHVR. Constructs used for FRET-FLIM analysis were cloned using the Golden-gate system (Chiasson, D. et al. A unified multi-kingdom Golden Gate cloning platform. Sc/ Rep 9, 10131 , doi:10.1038/s41598-019-46171-2 (2019)). cDNAs for TWA1 , twa1 , JAM2 and JAM3 were cloned into level I vector (LI_Bpil) first and afterwards into LII expression vectors (JAM2 and JAM3: LII_3-4_CEN_LEU with promoter pTDH3 and terminator tDH1, plus the N-terminal mCherry tag; TWA1 and twa1 : LII_1-2_CEN_LEU with pTDH3 and tDH1 , plus N-terminal GFP tag). For intramolecular FRET in yeast, 71/I/A7 was cloned into LII_3-4_CEN_LEU with pTDH3 and tDH1, including a C-terminal GFP tag and N-terminal mCherry (GFP used in all constructs was monomeric enhanced GFP, meGFP) tag linked to TWA1 via a ten amino acid-long glycine, serine linker (GGSGGGGSGG). As a control, both fluorophores were fused with the glycine, serine linker and expressed using the LII_3-4_LEU expression cassette. The GFP_AIHVR_TWA1 construct was cloned into pGREG574 (Jansen, G., Wu, C., Schade, B., Thomas, D. Y. & Whiteway, M. Drag&Drop cloning in yeast. Gene 344, 43-51 , doi:10.1016/j.gene.2004.10.016 (2005)) using the TWA1-AIHVR cassette (see above) and Sall restriction enzyme. The reporter construct pHSFA2:LUC was generated by replacing the RD29B promoter in pRD29B:LUC with an amplified 2 kb fragment of the HSFA2 promoter region according to Nishizawa et al. (Nishizawa, A. et al. Arabidopsis heat shock transcription factor A2 as a key regulator in response to several types of environmental stress. Plant J 48, 535-547, doi:10.11 11/j.1365-313X.2006.02889.x (2006)). Correctness of all constructs was verified by DNA sequence analysis. Quantitative gene expression was monitored with BRYT Green® Dye-based qPCR (GoTaq qPCR Master Mix kit, Promega) using a LightCycler 480 instrument (Roche) and gene specific primers. TIP41 L (AT3G54000), UBC9 (AT4G27960), and UBI10 (AT4G05320) were used for normalization. Primers used for quantitative RT-PCR are listed in Table 2. Reference in this context is made to Figures 13, 17, 18 and 19.
Example 5: Protein sequence alignments
Homologs of TWA1 were identified, as herein described and defined, through BLASTp searches against genomes on NCBI and amino acid sequences of TWA and representative proteins were aligned with NCBI’s COBALT alignment btool (Papadopoulos, J. S. & Agarwala, R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics (Oxford, England) 23, 1073-1079, doi:10.1093/bioinformatics/btm076 (2007)). Reference in this context is made to Figures 4 and 21.
Example 6: Protoplast assays and transgenic plants
Transient expression analysis in Arabidopsis protoplasts and expression cassettes for pRD29B::L UCa nd effectors have been described (Moes, D., Himmelbach, A., Korte, A., Haberer, G. & Grill, E. Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis. Plant J 54, 806-819, doi:10.1 111/j.1365-313X.2008.03454.X (2008)). Protoplasts were isolated from leaves of Columbia wild-type accession (Col-0) or from mutant lines of Col-0 background. Briefly, approximately 105 protoplasts were transfected with DNA of different expression cassettes including the ABA-responsive pRD29B::LUC reporter (5 pg), the p35S::GUS control reporter (3 pg) for expression normalization and 0.1 pg to 3 pg of various effector plasmids and incubated at 25°C (or - if to be tested - at a certain temperature within a temperature range from 15 °C to 37 °C) for 16h prior to assessment of luciferase and glucuronidase activity. Ectopic expression of TWA1 and twa1 (mutant allele of twa1-1), AITWA1 , and SaTWAI in Arabidopsis plants was under the 35S promoter in the twa1-2 background. Primers for DNA amplification and restriction sites used for generation of effector constructs are listed (Table 1). Protoplasts were isolated from leaves of Columbia wild-type accession (Col-0) or from mutant lines of Col-0 background. Briefly, approximately 105 protoplasts were transfected with DNA of different expression cassettes including the ABA-responsive pRD29B::LUC reporter (5 pg), the p35S::GUS control reporter (3 pg) for expression normalization and indicated amounts of various effector plasmids and incubated at 25 °C, unless otherwise stated, for 16h prior to assessment of luciferase and glucuronidase activity. Ectopic expression of TWA1 and twa1 (mutant allele of twa1-1), AITWA1 , and SaTWAI in arabidopsis plants was under the 35S promoter in the twa1-2 background. The cDNA expression cassettes of the TWA1 variants and orthologs were inserted as an Asci DNA fragment into the pGreenll 0179 vector (Hellens, R. P., Edwards, E. A., Leyland, N. R., Bean, S. & Mullineaux, P. M. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Molecular Biology 42, 819-832 (2000)) modified with an Asci cloning site in the T-DNA region. Transgenic plants were generated by Agrobacterium tumefaciens-mediated gene transfer as described (Meyer, K., Leube, M. P. & Grill, E. A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana. Science 264, 1452-1455 (1994)). Arabidopsis seeds planted in soil-containing pots (12 x12 cm) were allowed to germinate and grow under long day condition (16 h 120 pE m-2 s-1 light, 22 °C and approximately 50-70% relative humidity, during daytime, night 18 °C, 70-80 % relative humidity) for approximately 3 weeks until inflorescences were visible but flowers not yet open. The Agrobacterium tumefaciens strains (GV3101 , MP90) carrying the desired plasmid were cultivated O/N in 200 ml standard Luria Broth media, pelleted for 10 min at 5000 x g and resuspended in 300 ml infiltration medium (5 % sucrose [w/v], 0,5 % [v/v] Silwet L-77). The plasmid carried the gene of interest together with a selectable marker such as providing resistance to kanamycin or hygromycin within the confines of the T-DNA that is transferred into the plant host. Plant inflorescences were submerged in the bacterial suspension for 30 sec assuring complete wetting. After dipping, inflorescences of a single pot were carefully tied together and kept under well-watered conditions for allowing seed set. To increase transformation rates, the dipping procedure was repeated 3 days after the first dipping. Harvested seeds were subsequently screened for successful T-DNA transfer by virtue of a co-transferred resistance marker on, for instance, kanamycin- or hygromycin-containing solidified medium. Reference in this context is made to Figures 5, 6, 7, 10, 11 and 17.
Example 7: Thermotolerance evaluation
Thermotolerance was analyzed as reported (Larkindale, J., Hall, J. D., Knight, M. R. & Vierling, E. Heat stress phenotypes of Arabidopsis mutants implicate multiple signaling pathways in the acquisition of thermotolerance. Plant Physiology 138, 882-897, doi:10.1 104/pp.105.062257 (2005)). Briefly, 5-d light grown Arabidopsis seedlings (22 °C) were exposed to heat stress at 45 °C for 90 to 180 min with 15- minute intervals for assessment of basal thermotolerance in the light. For heat stress in the darkness, seedlings were 4-days old. For analysis of acquired thermotolerance, seedlings had a preceding 90 min acclimation period at 38 °C followed by a 120 min recovery phase (22 °C) prior heat stress at 45 °C for up to 180 min. For root growth assays, seedlings were allowed to recover for 5 days in continuous light (22 °C) and the root extension after heat stress was determined. Reference in this regard is made to Figures 1 , 3, 13, and 15.
Example 8: Determination of chlorophyll content and of electrolyte leakage
For chlorophyll analysis, seedlings were frozen in liquid nitrogen after their fresh weight had been determined, homogenized using a TissueLyser II (Qiagen) and extracted with methanol for determination of photosynthetic pigments on ice in the dark for 10 min with mixing every 1 min Absorption of extracts cleared by centrifugation (20.000 xg, 5 min, 4 °C) was recorded at 665nm, 652nm and 470nm to allow for calculation of chlorophyll and carotenoid content (Lichtenthaler, H. K. Chlorophylls and Carotenoids: Piments of photosynthetic biomembranes. Methods in Enzymology 148, 350-382 (1987)). In the electrolyte leakage assay, leaves of 3-week-old Arabidopsis plants were placed in Petri dishes containing 25 ml water and were incubated at 37 °C or 22 °C in the light (65 pmol nr2 s-1) for 24 h. Thereafter, single leaves were immersed in 1 mL of double-distilled water in Eppendorf tubes and incubated for 30 min with gentle shaking (Clarke, S. M. et al. Jasmonates act with salicylic acid to confer basal thermotolerance in Arabidopsis thaliana. New Phytol 182, 175-187, doi:10.11 11/j.1469-8137.2008.02735.x (2009)). Conductivity was measured using a Conductivity Meter (Seven Easy Mettler Toledo, InLab 752-6mm conductivity sensor). Electrolyte leakage was normalized to the conductivity after heating the samples to 99 °C for 10 min. Reference in this context is made to Figures 14 and 16.
Example 9: Photosynthetic parameters and thermoimaqinq
Gas exchange measurements and thermoimaging were carried out as described (Yang, Z. et al. Leveraging abscisic acid receptors for efficient water use in Arabidopsis. Proc Natl Acad Sci U S A 113, 6791-6796, doi:10.1073/pnas.16019541 13 (2016)). For thermoimaging, wild type and TWAl oe lines were grown for 38 days in single pots (12x12 cm) under short-day conditions (8 h 120 pE m-2 s-1 light, 22 °C and approximately 50-70% relative humidity, during daytime, night 18 °C, 70-80% relative humidity). Thermal imaging was carried out on whole plant trays containing 24 pots at randomized positions and within the environmentally controlled plant growth cabinets (E15 chamber, Conviron Inc., Canada) by using the ImageIR thermoimaging system (InfraTec, Dresden, Germany). Thermal images were taken 2 hours after illumination onset and the recorded temperature integrated over the leaf area to determine the mean. For quantifying An, C,, and stomatai conductance gs of the whole rosette, the GFS-3000 gas exchange system was equipped with custom-built whole plant cuvettes (Heinz Walz, Effeltrich). The analyses were conducted at 150 pmol nr2 s1 PAR, 400 mmol mol1 external CO2, and a water vapor deficit (VPD) of 19 ± 1 Pa kPa1 using the software of the instrument supplier. PAM imaging was performed by using a MAXI version of IMAGING PAM (Heinz Walz, Effeltrich, Germany). The operation of the PAM imaging system was according to the manufacture’s instruction. In brief, plants were dark adapted for 30 min followed by a saturating light pulse and maximum quantum efficiency of photosystem II ( PSI lmax) was calculated from basic (Fo) and maximum level of fluorescence (Fm). Actinic light was then applied (150 pmol nr2 s1 PAR) and after 1 h of illumination, a saturating light pulse was triggered to determine transient fluorescence (Ft) and maximal fluorescence (Fm). The corresponding quantum efficiency of photosystem II (<|)PSI I) was calculated as (Fm - Ft) I Fm . The non-photochemical quenching (NPQ) was determined as the ratio of (Fm - Fm ) I Fm . The images of NPQ are presented using the standard false color code, with rescaled values (original values divided by 4) ranging from 0 to 1 . As a result, we found that gas exchange parameters and function of the photosynthetic machinery as characterized by <|)PSIImax, <|)PSII, and nonphotochemical quenching (NPQ) remained statistically unaltered when TWA1 was overexpressed in Arabidopsis. Reference in this context is made to Figure 20.
Example 10: Confocal microscopy
Confocal microscopy and FRET-FLIM analyses were performed as described (Ruschhaupt, M. et al. Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeast. The EMBO Journal 38, e101859, doi:10.15252/embj.2019101859 (2019)). Briefly, leaves of 5 week-old tobacco (A/. benthamiana) were infiltrated with a suspension of Agrobacterium tumefaciens GV3101 (MP90) for expression of the viral p19 protein and Arabidopsis proteins. The bacteria contained binary level II plasmids (Binder, A. et al. A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants. PLOS ONE 9, e88218, doi: 10.1371 /journal. pone.0088218 (2014)) for the expression of GFP:TWA1/twa1 , and mCherrry fusions with JAM2, JAM3, and TPL under the control of the viral 35S promoter in plant leaves. Infiltrated plants were incubated for 2 days at 20 °C and exposed for 2h to 37 °C or 20 °C. For analysis of yeasts, freshly transformed yeast cells of strain AH 109 (MATa, obtained from Uhrig, Kbln) were cultivated overnight in 1 ml synthetic dextrose medium (SD) at different temperatures as indicated prior to confocal analysis. Confocal analysis was conducted using an Olympus FluoView™ 3000 inverse laser scanning confocal microscope with an UPLSAPO 60XW 60x/NA 1.2/WD 0.28 water immersion objective (Olympus, Hamburg, Germany). For imaging of the GFP and mCherry fluorophore, tissue samples were excited at 488 and 561 nm, respectively. Specific GFP fluorescence in the nucleus was calculated by subtracting background fluorescence (Carrillo, R. & Christopher, D. A. Development of a GFP biosensor reporter for the unfolded protein response-signaling pathway in plants: incorporation of the bZIP60 intron into the GFP gene. Plant Signaling & Behavior 'l l, 2098645, doi:10.1080/15592324.2022.2098645 (2022)). For Forster resonance energy transferfluorescence lifetime imaging (FRET-FLIM) data acquisition, the PicoQuant advanced FCS/FRET FLIM/rapidFLIM upgrade kit (PicoQuant, Berlin, Germany) was used. FRET requires the proximity of fluorophores in the nanometer range (< 10 nm) and it reduces the fluorescence lifetime (FL) of the excited donor fluorophore. Changes of fluorophore distance affects the FRET signal by the power of six (Algar,2019. Nature Methods 16, 815-829, doi:10.1038/s41592-019-0530-8). GFP was excited at 485 nm with a pulsed laser (pulse rate 40 MHz, laser driver: PDL 828 SEPIA II, laser: LDH-D-C-485, PicoQuant), and fluorescence emission was collected by Hybrid Photomultiplier Detector Assembly 40 (PicoQuant) and processed by a TimeHarp 260 PICO Time-Correlated Single Photon Counting module (resolution 25 ps, PicoQuant). At least 250 photons per pixel were recorded for each analysed sample. Data were fitted to a bi-exponential decay function and convoluted using SymPhoTime 64 software (PicoQuant). Reference in this context is made to Figures 22.
Example 11 : Yeast constructs and growth analyses
Yeast growth and Yeast-Two-Hybrid (YTH) assays were carried out as reported (Fuchs, S., Tischer, S. V., Wunschel, C., Christmann, A. & Grill, E. Abscisic acid sensor RCAR7/PYL13, specific regulator of protein phosphatase coreceptors. Proc Natl Acad Sci USA 111 , 5741-5746, doi:10.1073/pnas.1322085111 (2014)), unless otherwise stated, by using pGAD424 (GenBank Accession #1107647) and pBRIDGE vectors for expression of Arabidopsis proteins (Clontech Inc.). Briefly, for YTH analysis for histidine-autotrophic growth, yeasts were grown at 30°C, unless otherwise stated, in standard synthetic dextrose (SD) medium supplemented with amino acids either without supplementation of the amino acids leucine and tryptophan (-L-W) for selection of introduced expression plasmids, or without leucine, tryptophan, and histidine (-L-W-H) for additional selection of protein-protein interaction that restores histidine autotrophy in the YTH system. Yeast cell suspensions successively diluted tenfold were also plated as droplets on SD medium solidified with 15 grams of agar per liter for growth assessment at indicated temperatures ranging from 15 °C to 37 °C for two to four days. Controls were yeast cells with an empty expression cassette or cassettes (LV). A screen for proteins interacting with TWA1 was performed with Arabidopsis Y2H libraries (Arabidopsis Interactome Mapping, C. Evidence for network evolution in an Arabidopsis interactome map. Science 333, 601-607, doi:10.1126/science.1203877 (2011); Altmann, M. et al. Extensive signal integration by the phytohormone protein network. Nature 583, 271-276, doi:10.1038/S41586-020-2460-0 (2020)). CDSs of TWA1 and homologs were expressed as fusions with the GAL4-activation domain (AD), while JAM, MYC2, TPL and TPRs were fused to the GAL4-DNA binding domain (BD). For analysis of yeast growth in liquid culture, precultures of three independently transformed yeast colonies per construct were used for inoculation of 1 .5 ml SD medium containing 2 % glucose supplemented with 20 mg/L uracil, 20 mg/L methionine, and as indicated in Figures 8 and 9 with 20 mg/L histidine (H), 60 mg/L leucine (L), and 50 mg/L tryptophan (W). After growth over night in a gyratory shaker at 200 rpm and 30°C, 13.5 ml supplemented SD was added, and the suspension culture further cultivated until the beginning of the exponential growth phase was reached at optical densities GD600 between 0.6 and 0.8. Subsequently, cells were sedimented (1.500 g, 5 min), resuspended in selective SD media (without leucine and tryptophan [-L-W] and with or without histidine [H]) to test for histidine autotrophy and used to inoculate 20 ml fresh selective SD to a final GD600 of 0.020 for monitoring growth at different temperatures (200 rpm). The apparent growth rate p was calculated in the first 24h of culturing by using the formula p = (In OD24h/ODoh)/24h. The growth rate in yeast was used to approximate the Q10 temperature coefficient of TWA1 response as Q10 = [pT2/ pTi]10/(T2 T1) where T is temperature in Celsius and pTi and pT2 the rates at T1 and T2, respectively. Q10 value of ~150 was estimated using the measured rates at 25 and 20°C, 0.138 and 0.011 h1, respectively. Reference in this context is made to Figures 8 and 9.
Example 12: Identification of TWA1 homologs
A search for homologs of TWA1 was performed using BLASTP of NCBI (Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402; Stephen F. Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.;

and the database “Non-redundant protein sequences (nr)”, the algorithm blastp (protein-protein BLAST), matrix BLOSUM62, gap cost parameters “Existence: 11 Extension: 1 ”, conditional compositional score matrix adjustment and no filters or masking. Similar protein sequence of a TWA1 homolog is defined in a pairwise comparison to TWA1 of Arabidopsis thaliana (NP_001331741 .1), to the TWA1 homolog from Glycine max (KAG5128726.1), or to the TWA1 homolog from Nelumbo nucifera (A0A1 U7ZPG7) using NCBI-BLASTp
with likelihood value of <10
8 and a query cover >45% in wild type genomes of the respective plant species. The Glycine max TWA1 homolog has a likelihood value of <1 O'
50 and a query cover >80% to Arabidopsis TWA1 . The Nelumbo nucifera TWA1 homolog has a likelihood value of <1 O'
30 and a query cover >50% to Glycine max TWA1. The results are indicated in tables 1 -3 of the present invention.
Statistics
Data were analyzed using the Mann-Whitney U test, One-way ANOVA or Student's t-test. Table 4. Primers used for genotyping and cloning
Table 5. Primers used for qPCR expression analysis.