Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

BioMed Central full text link BioMed Central Free PMC article
Full text links

Actions

Share

.2014 Dec 16;15(1):1116.
doi: 10.1186/1471-2164-15-1116.

Genome-wide and molecular evolution analysis of the subtilase gene family in Vitis vinifera

Affiliations

Genome-wide and molecular evolution analysis of the subtilase gene family in Vitis vinifera

Jun Cao et al. BMC Genomics..

Abstract

Background: Vitis vinifera (grape) is one of the most economically significant fruit crops in the world. The availability of the recently released grape genome sequence offers an opportunity to identify and analyze some important gene families in this species. Subtilases are a group of subtilisin-like serine proteases that are involved in many biological processes in plants. However, no comprehensive study incorporating phylogeny, chromosomal location and gene duplication, gene organization, functional divergence, selective pressure and expression profiling has been reported so far for the grape.

Results: In the present study, a comprehensive analysis of the subtilase gene family in V. vinifera was performed. Eighty subtilase genes were identified. Phylogenetic analyses indicated that these subtilase genes comprised eight groups. The gene organization is considerably conserved among the groups. Distribution of the subtilase genes is non-random across the chromosomes. A high proportion of these genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the subtilase gene family. Analyses of divergence and adaptive evolution show that while purifying selection may have been the main force driving the evolution of grape subtilases, some of the critical sites responsible for the divergence may have been under positive selection. Further analyses of real-time PCR data suggested that many subtilase genes might be important in the stress response and functional development of plants.

Conclusions: Tandem duplications as well as purifying and positive selections have contributed to the functional divergence of subtilase genes in V. vinifera. The data may contribute to a better understanding of the grape subtilase gene family.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Phylogenetic relationships and gene structures of grape subtilase genes. The numbers above branches show bootstrap values from maximum likelihood (PhyML) and distance analyses (PHYLIP), respectively. The model used for ML analysis was LG + G, which was selected by ModelGenerator (AIC1). Eight major groups, designated 1 to 8, are marked with different colored backgrounds. The exon/intron structures of the subtilase genes are shown in the right panel. Green boxes represent exons and black lines represent introns.
Figure 2
Figure 2
Multiple sequence alignment of the PA-subtilisin-like domain of grape subtilase group 1. The multiple alignment results clearly show the highly conserved PA-subtilisin-like domains among group 1 subtilase genes. The secondary structure elements of this domain are shown above the alignment. Cylindrical tubes represent α-helices and block arrows represent β-sheets.
Figure 3
Figure 3
Distribution of conserved motifs in the subtilase family members. All motifs were identified by MEME using the complete amino acid sequence of the 80 grape subtilases documented in Figure 1. The names of all members among the defined gene clusters and combinedP-values are shown on the left side of the figure; motif sizes are indicated at the bottom of the figure. Different motifs are indicated by different colors and are numbered 1–25. The same number in different proteins refers to the same motif. For details of the motifs refer to Table S3 (See Additional file3).
Figure 4
Figure 4
Chromosomal locations of the grape subtilase genes. The 71 subtilase genes mapping to 14 of the 19 grape chromosomes are shown. Paralogous regions in the putative ancestral constituents of the grape genome are depicted using the colors according to Jaillonet al. (2007)[48] and Licausiet al. (2010)[64].
Figure 5
Figure 5
Evolution of the one subgroup of grape subtilase genes.A. Phylogenetic relationships.B. Hypothetical origins of 19 grape subtilase genes by tandem duplication and retroposition. The letters R and T on the nodes of the phylogenetic tree indicate the positions where retroposition and tandem duplication have occurred, respectively.
Figure 6
Figure 6
Expression profiles of the grape subtilase gene family. For saline stress treatments, 3-week grape seedlings were treated with 100 mM NaCl for 6 h or 12 h; for cold and heat stress treatments, the 3-week seedlings were treated with 4°C or 42°C for 6 h and 12 h; for drought treatments, the 3-week seedlings were dried for 7 days or 12 days. Expression profiles of subtilase genes family in different tissues (roots, leaves, stems, floral buds and internodes) and in 2-month-old grapes were used. GHB, green hard berry; GSB, green soft berry; PSB, pink soft berry; RSB, red soft berry.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Siezen RJ, Leunissen JA. Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci. 1997;6:501–523. doi: 10.1002/pro.5560060301. - DOI - PMC - PubMed
    1. Antao CM, Malcata FX. Plant serine proteases: biochemical, physiological and molecular features. Plant Physiol Biochem. 2005;43:637–650. doi: 10.1016/j.plaphy.2005.05.001. - DOI - PubMed
    1. Dodson G, Wlodawer A. Catalytic triads and their relatives. Trends Biochem Sci. 1998;23:347–352. doi: 10.1016/S0968-0004(98)01254-7. - DOI - PubMed
    1. Siezen RJ, Renckens B, Boekhorst J. Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins. 2007;67(3):681–994. doi: 10.1002/prot.21290. - DOI - PubMed
    1. Fuller RS, Brake A, Thorner J. Yeast prohormone processing enzyme (KEX2 gene product) is a Ca2_-dependent serine protease. Proc Natl Acad Sci U S A. 1989;86:1434–1438. doi: 10.1073/pnas.86.5.1434. - DOI - PMC - PubMed

Publication types

MeSH terms

Substances

Related information

LinkOut - more resources

Full text links
BioMed Central full text link BioMed Central Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp