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Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: The class II cytokine receptors and their ligands in mammals and fish

Georges Lutfalla1,✉,Hugues Roest Crollius2,Nicole Stange-thomann3,Olivier Jaillon2,Knud Mogensen1,Danièle Monneron1
1Défenses antivirales et antitumorales, CNRS-UMR5124, 1919 route de Mende, 34293 Montpellier Cedex 5, France
2Genoscope-Centre National de Sequencage, CNRS UMR8030, 2 rue Gaston Cremieux, 91000, Evry, France
3Whitehead Institute MIT Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, U.S.A
✉

Corresponding author.

Received 2003 May 16; Accepted 2003 Jul 17; Collection date 2003.

Copyright © 2003 Lutfalla et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
PMCID: PMC179897  PMID:12869211

Abstract

Background

The high degree of sequence conservation between coding regions in fish and mammals can be exploited to identify genes in mammalian genomes by comparison with the sequence of similar genes in fish. Conversely, experimentally characterized mammalian genes may be used to annotate fish genomes. However, gene families that escape this principle include the rapidly diverging cytokines that regulate the immune system, and their receptors. A classic example is the class II helical cytokines (HCII) including type I, type II and lambda interferons, IL10 related cytokines (IL10, IL19, IL20, IL22, IL24 and IL26) and their receptors (HCRII). Despite the report of a near complete pufferfish (Takifugu rubripes) genome sequence, these genes remain undescribed in fish.

Results

We have used an original strategy based both on conserved amino acid sequence and gene structure to identify HCII and HCRII in the genome of another pufferfish,Tetraodon nigroviridisthat is amenable to laboratory experiments. The 15 genes that were identified are highly divergent and include a single interferon molecule, three IL10 related cytokines and their potential receptors together with two Tissue Factor (TF). Some of these genes form tandem clusters on the Tetraodon genome. Their expression pattern was determined in different tissues. Most importantly, Tetraodon interferon was identified and we show that the recombinant protein can induce antiviralMXgene expression in Tetraodon primary kidney cells. Similar results were obtained in Zebrafish which has 7MXgenes.

Conclusion

We propose a scheme for the evolution of HCII and their receptors during the radiation of bony vertebrates and suggest that the diversification that played an important role in the fine-tuning of the ancestral mechanism for host defense against infections probably followed different pathways in amniotes and fish.

Background

The increasing number of sequenced genomes provides molecular explanations for both the unity and diversity of living organisms. The more divergent the organisms, the less they share genes. This explains why annotation of genomes using genes with known functions in other organisms leaves a high number of predicted genes with no predicted function. For some prokaryotes, the percentage of genes with no predicted function rises to 65% but falls to 20% for the closely related vertebrate genomes [1-3].

The majority of genes with no assigned functions are those involved in the recent evolutionary success of the considered taxonomic group. This is both true for prokaryotes that develop original metabolisms allowing growth in special environments and for the vertebrate species that have developed original solutions in response to environmental pressures. Comparison of mammalian proteins show that host defense ligands and receptors make up the group of proteins that diverge the most rapidly [4]. According to the «red queen model» the pressure of pathogens is, at small time scales, the most drastic pressure for the evolution of vertebrate species.

At the genomic level, together with the mutation/modification of regulatory elements, three driving forces are instrumental for the diversification. The first is the emergence of new domain architecture through domain accretion and shuffling, the second is deletion of genes, and the third is the expansion of a gene family either by gene duplications or by retropositions. Lineage specific expansion (LSE) is the proliferation of a given gene family in a given lineage. Its description implies the comparison of sister lineages [5]. Using predicted proteomes, Lespinet et al. have recently performed a systematic comparative analysis of LSEs in the following eukaryotic genomes:Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogasterandArabidopsis thaliana. They reached the conclusion that «LSE seems to be one of the most important sources of structural and regulatory diversity in crown-group eukaryotes, which was critical for the tremendous exploration of the morphospace seen in these organisms» [6]. A good example for an LSE is the expansion of immunoglobulin genes in gnathostomes compared to other chordates. But LSEs also exist when comparing the different orders of mammals as exemplified by the expansion of the alpha interferons [7,8].

Vertebrate immunoglobulins (Ig) are built up from modules of one hundred amino acids. These modules are defined both by a common 3-D structure, by conserved disulfide bridges and by conserved amino acid positions. They share the same 3-D structure with the Fibronectin type III repeats (FNIII), but conserved amino acid positions are different in both groups of domains [9,10]. Genes coding for such modules were already present in the genomes of invertebrates [11]. The originality of the gnathostomes is the invention of rearranging antigen receptors by insertion of a transposable element in a gene coding for one of these Ig modules [3,12]. During the further diversification of the vertebrates, the different lineages (for example, condrychtians and osteichtians) have developed the system in different ways but the main difference consists in the maturation of the immune response that mainly takes place in the lymphoid organs. Cytokines that regulate the maturation of the immune response from antigen detection to clonal expansion of the one cell with better affinity mostly belong to the helical cytokine (HC) family [13]. They include interferons, most interleukins, LIF, CNTF, GCSF, GM-CSF, thrombopoïetine. These helical cytokines have no similarities at the level of primary amino acid sequences, but they are all structured around a similar four alpha helix bundle. They share this common 3-D structure with some hormones that for this reason are structurally described as helical cytokines: Growth Hormone (GH), Prolactin (PRL), Erythropoïetin (EPO) and Leptin [14]. These helical cytokines all bind to the extracellular binding domains of their cognate receptors (helical cytokines receptors: HCR) which all contain a 200 amino-acids (D200) domain that is the identification mark of theHCRgene family. These D200 domains are composed of two subdomains of 100 amino-acids (SD100A & SD100B) that are both structured like the basic Ig domains with two β sheets of respectively 3 and 4 strands (C type). Conserved amino-acid positions clearly distinguish these D200 domains from the Ig superfamily and from the FNIII family [9,10].

Whereas Ig and FNIII families have been expanded in invertebrates, a single gene with a D200 has been described in invertebrates: thedomegene in drosophila [15-17]. The HCR family is therefore an interesting example of a vertebrate specific LSE. Like other families of receptors involved in host defense, it mostly consists of highly diverging receptors (28% amino acids identities between the human and chicken IFNAR2 proteins) [4,18]. Together with the difficulty of predicting genes from genomic sequences, this explains why the comparison of the predicted human and Fugu proteomes did not allow the identification of the complete repertoire of HCR in Fugu [1]. Depending on the conserved amino acids residues, HCRs can be divided in two classes: Class I and Class II. Class II consists of the Tissue Factor, the receptors for interferons and the receptors for IL10 and its related cytokines(IL10, IL19, IL20, IL22, IL24 and IL26). Class I consists of all other HCRs [9,10]. Their cognate ligands have been called class I and class II helical cytokines. Genes for HCRI have been described in the major vertebrate groups including fish, birds and mammals, but HCRII have only been described in birds and mammals [10,18-21]. The question is therefore open as to whether the HCRII expansion is amniote specific or not. The recent efforts to sequence genomes from fish offer an interesting opportunity to answer this question.

Interestingly, the intron/exon structure of the vertebrateHCRgenes is strictly conserved in all the family: like the exons coding for the Igs and the FNIII, the exons coding each SD100 are bordered by phase 1 introns, but what is specific for D200s is that SD100As are encoded by two exons with an internal phase 2 intron falling at the level of the third β strand and that SD100Bs are encoded by two exons with an internal phase 0 intron falling at the level of the fourth β strand [22-24]. Intron/exon structures can thus be used as a criterion for the identification of homologs in distant species.

We decided to use the genomic data fromTetraodon nigroviridisto look for the genes coding the class II HCR (HCRII) and their ligands. The main interest ofT. nigroviridisis both its completely sequenced compact genome and the ease with which it can be maintained in the laboratory and used for experiments. We report here the complete description of theT. nigroviridisclass II HCR repertoire and show that its diversification from common ancestral elements has occurred independently in fish and mammalian lineages. We have also characterized two ligands for these receptors.

Results

Identification of HCRII genes inTetraodon nigroviridis

The starting point for the search was the alignment of the classII HCR D200 as reported in Uzé et al. (1995), extended to include the more recently described members IFNAR2 and CRF2-8 to CRF2-12 that allows the definition of a pattern of conserved positions. A conserved tryptophan in exon A1 (the first exon coding for SD100A), a conserved tryptophan and pair of cysteines in exon A2, a conserved serine and pair of cysteines in exon B2. All HCRII were tblastn against the 3 million genomic reads ofT. nigroviridis(see methods). Reads with e<0.1 were kept and assembled. Each contig was tested for the presence of correct potential exons: introns of the correct phase and predicted proteins compatible with HCRII. False positives were exons coding for FNIII repeats that do not have the D200 intron/exon structure. All matching contigs were further extended in order to reach sizes of contigs compatible with whole gene size in the compact genome ofT. nigroviridis: 5 contigs from 4 to 30 kb were obtained. Gene models were predicted in each contig and most probable exons were used to design oligonucleotides for 3' and 5' RACE. The full-length cDNAs were then aligned against the contigs to deduce gene structures and compared to Genscan predictionshttp://genes.mit.edu/GENSCAN.html. None of the 11 TnHCRII was correctly predicted by Genscan. The largest contig harbors 6 genes while the 5 others harbour a single HCRII gene. All genes are around 3 kb long. In agreement with the human nomenclature, they were named TnCRFB-1 to TnCRFB-11. All reading frames start with a leader peptide followed by a single D200. Except for TnCRFB-9 they all have a clear transmembrane (TM) domain after the D200. Expression patterns were determined for each of the 11 genes by Q-PCR using cDNAs reverse transcribed from RNAs of brain, spleen, cephalic kidney, gonads and intestine (figure2). Long open reading frames and high expression in at least one tissue were considered sufficient criteria to state that these genes code for receptors and are not pseudogenes.

Figure 2.

Figure 2

Expression pattern for the classII helical cytokine receptor genes.RNA samples were prepared from tissues, reverse transcribed and abundance of each cDNA was measured by QPCR using oligonucleotides listed in supplementary material. All data were normalized to the level of hnRNPA2 cDNA. 5% confidence in a student T test is shown. Orf4 stands for theT nigroviridishomologue of the human C21orf4 gene.

TheT. nigroviridisrepertoire of HCRII

Figure3 shows the comparison of theHCRIIgene repertoire in human andT. nigroviridis. As already described theHCRIIsare grouped in clusters on the human genome [18,19]. The largest cluster lies on human chromosome 21 (HSA21); it contains four genes (IFNAR2,IL10R2,IFNAR1andIFNGR2) and is linked to theC21orf4andGARTgenes. Two other clusters exist, one on HSA6q containing three genes (IFNGR1,IL22BPandIL20R1) and one on HSA1p containing two genes (IFNLR1andIL22R2). TheTFgene is also located on HSA1p but so distant that it cannot be considered as a member of the same cluster. TheIL20R2andIL10R1genes are isolated and therefore called outgroups. TheT. nigroviridisgenome harbors a singleHCRIIgene cluster. As proved by the presence and similar orientation of theTnC21orf4gene, this cluster is homologous to the HSA21 gene cluster. It contains six genes instead of the four genes present on the human homologous cluster. Interestingly, theTnGARTgene, is not linked to this cluster, but is adjacent to theTnMTgene (T nigroviridishomolog of the yeastYDR140wgene). The same organization of theGARTandMTgenes, has already been described in the Fugu genome [18]. The human homolog for thisMTgene (Acc nb of the cDNA:AF139682) is present on HSA21, 4.5 Mb centromeric to the cluster and transcribed toward the centromere [25]. The respective position of these genes indicates that an inversion has occurred since the divergence of the fish and mammalian ancestors. This inversion has involved a large chromosomal fragment covering genes fromC21orf4to theMThomolog of the yeastYDR140wgene. In one state, theC21orf4is adjacent to theGARTgene (amniotes), but in the other, theMTis next toGART.

Figure 3.

Figure 3

Comparative genomic mapping of the HCR genes in human and T. nigroviridisAll genes are represented by an arrow that indicates the orientation of transcription.A)Clusters of HCR in the human genome. Orientation of transcription is relative to the centromere indicated on the left of the figure. MT stands for the human homolog of the S cerevisiae YDR140w gene. All genes are around 30 kb long. The MT gene is approximately 4 Mb centromeric to the IFNAR2 gene.B)The uniqueT.nigroviridis HCR cluster. TnC21orf4 is for theT.nigroviridis homolog of the human C21orf4 gene. TnMT is for theT.nigroviridis homolog of the S cerevisiae YDR140w gene. All genes are around 3 kb long.

In order to determine if any of theTnHCRIIwould be the homolog of the functionally characterized human genes, the 13 human D200s (12 genes butIFNAR1with two D200) together with some of their mammalian or avian orthologs were aligned with the 11 D200s ofT. nigroviridis. The alignment was used to draw the phylogenetic tree that is depicted in figure4. Tree branches with bootstrap values over 80% are indicated in bold. The clearest result is the grouping of TnCRFB10 & 11 with the TFs. TnCRFB10 and TnCRFB11 therefore appear as homologous to the mammalian TFs. This is confirmed by the intron/exon structure of their genes.TnCRFB10&11, as the mammalianTFgenes, are unique among theHCRIIgenes coding for transmembrane proteins in that the same exon encodes the TM domain and the very short intracellular domain [26]. Except for the genes coding for soluble proteins, all the other HCRII genes have an exon that encode the TM domain plus the first amino acids of the intracellular domain separated from the last exon coding the intracellular domain by a phase 0 intron [27]. Interestingly,TnCRFB10&11are not expressed in the same tissues:TnCRFB11is specifically expressed in the brain (figure2).

Figure 4.

Figure 4

Phylogenetic tree (NJ) derived from the alignment of the Tn HCR D200 domains together with the human D200sDomains from other species have been included to allow better grouping.T. nigroviridisD200s are written in red italic in order to highlight them. Branching points with bootstrap values over 80% are shown in bold. h, human; Tn,T. nigroviridis; m, mouse; r, rat; b, bovine; o, ovine and c, chicken. Alignment inAdditional file: 2.

The phylogenetic tree derived from the alignment also reveals an interesting grouping of the TnCRFB4 and TnCRFB5 with the amniotes IL10R2. We can therefore postulate that the adjacent corresponding genes are derived from a recent tandem duplication and are homologs of the amniotesIL10R2. Furthermore the alignment derived grouping of TnCRFB1, 2 & 3 most probably reflects recent tandem duplications of their cognate genes but with no obvious amniote homologs. The otherTnHCRIIgenes do not appear robustly linked to mammalian genes.

Ligands for TnHCRII

The presence of so many HCRII raises the question of their ligands and more specifically, that of the existence of an interferon system in fish [1]. Clearly, as shown in figure4 (see alsoAdditional file: 2, tetraodons, contrarily to amniotes have no IFNAR1 receptor with its typical double D200 that has certainly been instrumental to the diversification of the type I IFNs [27]. But the question remains open whether or not fish have interferon related molecules with similar functions.

TheT. nigroviridisreads were searched for exons capable of coding for molecules structurally related to the IFNs and IL10 related cytokines (tblastn). Contrary to their receptors, these cytokines are not encoded by genes with similar intron/exon structures. Genes for type I IFNs (IFNI) have no introns, those for IFNII have three introns.[28], those for IFN lambda have four introns [29,30]and those for IL10 related cytokines have four common introns [19]. Therefore the intron/exon structure could not be used as a criterion for the search of homologs in distant species. Potential exons were used for 3' and 5' RACE and the genes for four helical cytokines could be cloned: three genes coding IL10 related cytokines with the four conserved phase 0 introns and an interestingTnIFNgene also interrupted by four phase 0 introns. This gene codes for an interferon structurally related to IFNI and IFN lambda. For this reason, we call itTnIFN. The same full-length cDNA was cloned both from a wild animal and from an animal from breeders.

In order to establish that this fishIFNgene is not specific for tetraodons, we also cloned the orthologous gene fromDanio rerio(zebrafish) using the trace repository reads to design oligonucleotides on potential exons for 3' and 5' RACE. The first four exons could easily be identifiedin silicousing theT. nigroviridissequence, but the last exon could be identified only by 3' RACE. The corresponding gene was calledzIFN. Full-length cDNAs were cloned from two individuals from different breeders: alleles A & B. Both zIFN sequences differed at four silent positions, two non silent positions and differed at their COOH terminus; allele B codes for two extra amino acids. Despite the report from Aparicio et al. (2002) that they could not identify a Fugu IFN gene, reexamination of the Fugu genomic data allowed the identification of a Fugu IFN gene.

Of the three IL10 related cytokines, one is clearly the homolog of mammalian IL10, it is therefore called TnIL10. The two others are so divergent that it is difficult to identify them as clear orthologs of mammalian genes. However, according to the identity of the most similar genes, one is called TnIL20, the other is called TnIL24 (not shown). InterestinglyTnIL10andTnIL20are in tandem (Acc NumberAY294557)

An alignment of amino acid sequences of some IFNI and IFN lambda with theT. nigroviridisandD rerioIFNs was used to draw a phylogenetic tree of these IFNs (Figure5, see alsoAdditional file: 3). Branchings with bootstrap values over 80% are shown in bold. This tree shows a clear grouping of IFNI with fish IFNs and IFN lambda. This is illustrated using the outgroup genes hIL10 and TnIL10. Similar results are obtained whichever IL10 related cytokine or IFNII is used as an outgroup. The trees with more of these IL10 related cytokines are not shown because the bootstrap values are too low to state phylogenetic relationships between them. This tree illustrates very well the independent diversification of alpha IFNs in the different mammalian orders [7,8]. Expression patterns for TnIL10 mRNA (figure6A) and for TnIFN mRNA in five tissues from animals treated or not by PolyI/PolyC intraperitoneal injection (figure6B) have been determined. PolyI/polyC injection induces a very high induction of TnIFN from more than 10 times in testis to more than 104times in kidney.

Figure 5.

Figure 5

Phylogenetic tree (NJ) derived from the alignment of the fish interferons with human IFN lambda and some typeI IFNsNumber and phase of introns in the corresponding genes are indicated. Symbols same as in figure4 plus: sh, sheep; ce,Cervus elaphus(red deer); f, Fugu; gc,Giraffa camelopardalis(giraffe) and z:Danio rerio(zebrafish). Alignment inAdditional file: 3.

Figure 6.

Figure 6

Expression pattern of the TnIFN and TnIL10 genes and accumulation of the TnMX mRNA after IFN treatment.Results are amounts of mRNA relative to the hnRNPA2 mRNA. 5% confidence in a student T test is shown.A)TnIL10 in different tissues.B)TnIFN in different tissues in animals injected by PolyI/PolyC or PBS(basal).C)TnMX in primary kidney cells treated either with PolyI/PolyC, recombinant GFP (Green Fluorescent Protein) or recombinant TnIFN with either Nterm or Cterm 6His tag.

Activity of the newly discovered fish interferon

To test the biological activity of this interferon we decided to produce recombinant IFN in order to treat cells and to use quantitative RT-PCR to test for the induction of an interferon inducible gene. For this purpose, we looked for theMXgenes both inT. nigroviridisand in zebrafish.MXgenes code for mechanoenzymes of the Dynamin family [31] and are typical interferon induced genes. We have identified sevenMXgenes in zebrafish (zMXAtozMXG) and have found evidence of expression for all of them exceptzMXF. ThezMXAgene corresponds to the already reported zebrafishMXgene [32]. In contrastT. nigroviridishas a singleMXgene. The amount ofTnMXmRNA was therefore used as a test for the biological activity of TnIFN. The TnIFN orf was cloned in either pIVEX2.3-MCS or pIVEX 2.4bNde (6HIS Cterm and Nterm fusions respectively) and the resulting plasmids were used to produce recombinant TnIFN. The recombinant protein was used to challenge primary cultures of cephalic kidneyT. nigroviridiscells. After a 6 hours treatment, cells were harvested for total RNA preparations and quantitative RT PCR was used for measuring the amount of TnMX mRNAs. TheT. nigroviridismRNA for hnRNPA2, a house keeping splicing regulator, was used as a reference. PolyI/PolyC treatment was used as a control of interferon induction. Results shown in figure6C show that the recombinant TnIFN molecule with a Nterm HIS tag can induce the expression of the TnMX mRNA to a level similar to PolyI/PolyC treatment.

We verified that, in contrast to the PolyI/PolyC treatment, recombinant TnIFN and GFP do not induce the TnIFN mRNA (not shown). Similar result were obtained with zebrafish cell lines ZF4/7 using zMXE as a reporter mRNA as it is thezMXgene the more induced by IFN (not shown).PKRis an other very well characterized IFN induced gene [33].T. nigroviridishas twoPKRgenes (PKR1andPKR2) which were used as reporters to confirm the results withTnMX: both are induced like the singleTnMXgene (not shown).

While this manuscript was in preparation, Altmann et al (2003) [32] have reported the molecular and functional analysis of zIFN and shown its antiviral activity and Yap et al. (2003) [34] have shown that the promoter of the single Fugu MX gene can be induced by human interferon when transfected in human cells.

Discussion

Rapidly evolving lineage specific gene families are intrinsically difficult to analyze by large scale comparative genomic analysis [35]. A good example of this difficulty is the recent report of the near complete sequence of the Fugu genome [1]. This report clearly stated that IFNs and their related IL10 family cytokines and most of their receptors could not be identified in the Fugu genomes. We show here that reexamination of the data leads to opposite conclusions. Careful analysis of the HCR family in amniotes reveals features that can be used as criteria for a specific search of their homologs in distant species. Both conserved positions in the amino acid sequence of the protein and conserved phase and positions of introns are instrumental for this search.

Receptor diversification

Using the strategy described in figure1, we have been able to describe 11TnHCRIIgenes inT. nigroviridis. Primary amino acid sequences are so divergent that the phylogenetic tree is poorly reliable. Only a limited number of branches have good bootstrap values. For this reason, we cannot make estimates of divergence time for the different family members. It also explains why the tree differs from that of Kotenko et al [19] and why it is difficult to distinguish between paralogy and orthology for those receptors. The clearest homology is forTnCRFB10&11that are paralogous and represent the homologs of the mammalianTFs. TF is an interesting member of the HCRII family in that it does not bind a helical cytokine, but a coagulation factor (VIIa) whose 3D structure is similar to that of a helical cytokine. It clearly is not involved in host defense against pathogens and as such is not diverging as rapidly as the other HCRII family members from one species to the other. Interestingly, the twoT. nigroviridisgenes are not expressed in the same tissues,TnCRFB11being specific for the brain. We see two reasons to postulate that these two genes have not been duplicated recently. The first is that the encoded proteins show only 35% amino acid identity and the second is that they do not lie in cluster on the genome ofT. nigroviridis. This could lead us to postulate that other teleost fish species also have twoTFgenes. Curiously the Fugu proteome deduced from the near complete sequence of the Fugu genome contains only the ortholog ofTnCRFB10(Scaffold8956, protein 61906). AOncorhynchus mykis TFgene has been cloned (Acc nbCAC82787) that is also the ortholog ofTnCRFB10. For this reason we propose thatTnCRFB10would be calledTnTF1andTnCRFB11be calledTnTF2. The absence ofTF2in other species could simply reflect lack of detection of the paralogousTF2gene. We therefore re-examined the Fugu genome for potential exons coding for a FuguTF2. Such exons could be found on Fugu-Scaffold 5445, but the Scaffold seems badly assembled as the exons are scrambled, therefore the correct gene model has escaped automatic detection. This proves that the Fugu genome has theTF2gene. TheO. mikis TF2gene has probably escaped cloning by classical means just by chance as investigators were probably looking for just one gene.

Figure 1.

Figure 1

Strategy for the characterization of the T. nigroviridis HCR genes

The other possible homology is between TnCRFB4 & 5 and IL10R2. The IL10R2 receptor is in fact a "common chain" as it is a necessary component of the receptors for IL10, IL22 and IFN lambda and it is (apart from TF) the HCRII with the lowest sequence divergence in amniotes. Its gene lies in the center of the HSA21HCRIIgene cluster. Interestingly,TnCRFB4&5also lie in a similar central position on the homologousTnC21orf4linked gene cluster. Finally, TnCRFB1, 2 & 3 are closely related to each other. Careful inspection of the data indicates that the three genes are also present in the Fugu genome, but because of assembly problems they appear on different contigs (Fugu Scaffolds 3897 & 6320). They seem to code for receptors distantly related to amniote's IFNAR2. This is in accordance with their mapping at the extremity of the C21orf4 linked cluster and could suggest a common ancestry. The successive tandem duplications that lead to the three fish genes could be fish specific. The vicinity of the unassigned outgroupsTnHCRIIdid not reveal genes whose homologs would be linked to humanHCRIIgenes, it is therefore not possible to state any clear homology to mammalian genes. Careful inspection of the Fugu genome reveals that the 11TnHCRIIs have homologs in Fugu.

Ligand diversification

The search for ligands has revealed only four classII helical cytokines (HCII): IFN and three IL10 related cytokines (IL10, IL20 and IL24). The present work allows the definition of two categories of classII cytokines. One category is made up in mammals of lambda IFN and typeI IFN, the other would be made up of IL10 related cytokines and gamma IFN (see below). In fish, the first category would be made up of only an ancestral interferon gene with four phase 0 introns that is homologous to the human IFN lambda genes. The three human IFN lambda genes are located on human chromosome 19 and their four phase 0 are perfectly conserved both amongst them [30] and withTnIFNandzIFN. The key element during the evolution of theIFNgenes has therefore been a retroposition event that occurred during evolution after the separation of sarcopterygians from actinopterygians and that created an intronless type IIFNgene. In the mammalian lineage, this gene then underwent successive duplications to generate first the alpha and the beta interferons and then during the mammalian radiation, the numerous alphaIFNgenes [7,8,36]. This key retroposition event has probably been associated with duplication of receptor genes that generated theIFNAR1andIFNAR2genes. TheIFNAR1gene that was present in amniote ancestors already had two D200 allowing the building of receptor complexes with different binding sites that could accommodate the diversification of the ligands [18,27,37,38]. The "IL10 related cytokines" category is represented in Tetraodon by three genes with four phase 0 introns (IL10, 20&24). If some have extra-introns, all genes coding for IL10 related cytokines have the same four phase 0 introns. The high expression of theTnIL10gene in the intestine (figure2) suggests that the encoded fish cytokine could play a role similar to that of mammalian IL10 whose function is to keep under strict control the balance between immune and inflammatory response especially in the bowels [39,40].

Interestingly these two categories of HCII, despite having no similarity at the amino acid level, are both encoded by genes with exactly the same intron/exon structure. The four phase 0 introns fall at similar positions. This suggests that both genes derive from a common ancestor harboring the same four phase 0 introns. As in figure7, we therefore postulate that the ancestor for classII helical cytokine was encoded by a gene with this intron/exon structure. The first duplications would have taken place before the osteichtian radiation and would have generated the ancestral IFN and an ancestor for the IL10 related genes. The different lineages having then expanded this gene family by different means of retrotransposition and duplication. In this context, the gene for amniote type II IFN (gamma IFN) poses an interesting problem. It has only three phase 0 introns that correspond to the first three introns of both the ancestral IFN and IL10 related genes. Is it derived from an IFN gene or from an IL10 related gene? The location of the human IFN gamma gene on a cluster of classII cytokine genes including two other genes for the IL10 related cytokines (IL22andIL26) [19] suggests that it is in fact derived from an IL10 related gene. Despite the functional similarities of type I and type II IFNs, receptor binding characteristics of the dimeric forms of IL10 and IFN gamma also favor a closer relationship between these ligands [41,42].

Figure 7.

Figure 7

Schematic drawing for the diversification of the helical cytokines and their receptors during the evolution of the osteichthians.Open boxes are for coding exons, black parts for 3' and 5' non coding regions. Broken lines are for introns; their phase is indicated. For the receptors, broken boxes indicate that all D200 part of larger proteins. Exons are numbered A1 (for the first exon coding the SD100A) to B2 (second exon coding the SD100B). Conserved cysteines are indicated as vertical bars over the exon boxes. The retroposition event leading to typeI IFNs has only been observed in amniotes and is therefore labeled "amniote specific". Data from other sarcopterygians could lead to a revision.

Conclusions

To the origins of a diversified ligand/receptor system

This work provides an interesting perspective on the evolution and diversification of the classII helical cytokines and their receptors during the radiation of the osteichtians. It shows that the fine tuning of the main mechanisms for host defense against infections has been performed independently in the different vertebrate lineages. This is both true for the non specific antiviral defenses mediated by interferons and for the regulation of the immune response invented by ancestors of the gnathostomes in which IL10 related cytokines play a major role.

The question remains open of what happened in other vertebrate lineages, but the most fascinating question is the origin of this ligand/receptor system. Both genetic (intron/exon structures) and structural data (conserved amino acid positions and/or common 3D structures) argue in favor of a common ancestry for all classII ligand/receptor systems. The fascinating quest is now to find organisms that would have retained this single ancestral ligand/receptor pair and the central question will be: what is its function? In this perspective, thedomegene of drosophila is intriguing. Primary amino acid sequence clearly indicates that it harbors a D200 domain but the intron/exon structure is not that of the vertebrateHCRgenes. Thedomegene has one D200 domain plus FNIII repeats in its extracellular domain, but none of the canonical introns that border such domains in vertebrate genes is conserved [17]. Thedomegene has lost the intron/exon «memory». Interestingly, it is the only invertebrate gene with a D200 described so far; the expansion of the HCR family has occurred only in vertebrates. Thedomegene could therefore testify for the presence of an HCR ancestor in invertebrates. The first step in the diversification of this gene family in deuterostomes or chordates has therefore been the duplication to generate class I and class II ancestors. We have started the quest for these classI and classII ancestors by searching homologs of these genes in animal groups branching close to the vertebrate ancestors. In the genome ofCiona Intestinalis, we have found just twoHCRgenes, one coding for a classI and the other for a classII receptor. We have started experiments in order to determine in which biological functions they are involved.

Methods

Fish samples and sequences

T nigroviridisimported from Thailand (wild animals) or from Indonesia (breeders) were purchased at local dealers. Average animal weight was 3 grams. Phenoxy 2 ethanol was used as an anesthetic prior injections or dissections. PolyI/PolyC treatment was an IP injection of 0.1 ml of a 2.2 mg/ml solution in PBS. RNAs were prepared using the High Pure RNA Tissue Kit from Roche. Primary cultures of Cephalic Kidney cells were prepared by scratching the organ in a 200 micron mesh nylon in DMEM/F12 medium supplemented with 10% fetal calf serum. The primary cells were either used as such or separated in heavy and light populations by centrifugation on a Ficoll cushion. Primary cultures were kept up to 4 days with 5% CO2 at 30°C.

D. reriofrom breeders were purchased at local dealers. The ZF4/7 (ATCC: CRL-2050) cell line was maintained in the same conditions as theT. nigroviridisprimary cells.

Genomic sequences for theT. nigroviridisgenes are assemblies of shotgun reads produced by the Genoscopehttp://www.genoscope.cns.fr and the Whitehead Institute Center for Genome Researchhttp://www.genome.wi.mit.edu. The shotgun reads are available through the Trace Repository athttp://trace.ensembl.org/. They represent a 8.3X genome coverage Assemblies of small sets of reads (up to a few hundred) were done using caphttp://www.infobiogen.fr. Sequence of the resulting contigs were finished by designing oligonucleotides and resequencing regions of problems.

Cloning and Quantitative-PCR

Oligonucleotides are listed inAdditional file: 1. 3' and 5'RACE were performed using the GeneRacer Kit from Invitrogen. Amplified products were tested for the presence of specific products using internal oligonucleotides, cloned using the Topo TA cloning kit from Invitrogen. Bacterial colonies were screened using the internal oligonucleotide and the plasmids were entirely sequenced. Oligonucleotides TnIFN.52 and TnIFN.32 were used to amplify the complete ORF of TnIFN. The resulting fragment was digested by NdeI and SacI and cloned in the pIVEX2.3-MCS vector (Roche) digested by the same enzymes for the production of recombinant TnIFN with a Cterm 6His tag. For the Nterm 6His tagging, amplification was with TnIFN52 and TnIFN33; cloning was in pIVEX2.4bNde. In vitro production of recombinant IFN was done using the RTS100E. coliHY kit from Roche using 300 ng of CsCl purified plasmid per 10 μl of reaction (3 h incubation at 30°C). Production was checked using SDS-PAGE.

Conventional PCR were performed using Platinium Taq DNA polymerase in a MJ Research PTC200 thermocycler. Real time Quantitative PCR (Q-PCR) were performed using SYBR GREEN technology in a LightCycler Instrument from Roche. RNA samples were reverse transcribed using Spl2XhoT18 as primer and M-MuLV Reverse Transriptase as an enzyme [18]. First strand cDNAs were purified using Quiaquick purification columns (Quiagen).

Phylogenetic analysis

Alignments were performed using Clustal and phylogenetic trees were calculated using the Phylo_win package (distance, PAM) [43]. Drawing of trees was done using TREEVIEW.

Authors' contributions

GL and DM did the search, assembly, predictions, cloning and sequencing of the cDNAs coding for the receptors and their ligands. They also finished the sequencing of the genes. GL did the biological work with Tetraodons and zebrafish and drafted the manuscript. KM did the analysis of the protein structures. HRC, NST and OJ did the shotgun sequencing of the Tetraodon genome and performed searches and assemblies. All authors read and approved the final manuscript.

Supplementary Material

Additional File 1

Oligonucleotides. All sequences are 5' to 3'

Click here for file (430.5KB, doc)
Additional file 2
Click here for file (39.5KB, doc)
Additional file 3
Click here for file (29.5KB, doc)

Acknowledgments

Acknowledgements

We are indebted to Gilles Uzé for his constant support and exciting discussions. We thank Dr C. Bonnerot and B. Philippi for their help and critical reading of the manuscript. We would like to thank the Genoscope and the Whitehead Institute MIT Center for Genome Research for their joined efforts in theTetraodon nigroviridissequencing program and for providing unpublished sequence data. We more specifically want to thank Jean Weissenbach and Eric S. Lander for their constant support. Many thanks to Christine Dambly-Chaudière and Nicolas Cubedo for their help at the fish facilities. We want to thank Mark Ekker for providing the zebrafish cell line. This work was supported by CNRS.

Contributor Information

Georges Lutfalla, Email: lutfalla@infobiogen.fr.

Hugues Roest Crollius, Email: hrc@genoscope.cns.fr.

Nicole Stange-thomann, Email: sthomann@genome.wi.mit.edu.

Olivier Jaillon, Email: ojaillon@genoscope.cns.fr.

Knud Mogensen, Email: knud@athos.igm.cnrs-mop.fr.

Danièle Monneron, Email: monneron@igm.cnrs-mop.fr.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Additional File 1

Oligonucleotides. All sequences are 5' to 3'

Click here for file (430.5KB, doc)
Additional file 2
Click here for file (39.5KB, doc)
Additional file 3
Click here for file (29.5KB, doc)

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