|
Special Issue:
园艺-分子生物合辑Horticulture — Genetics · Breeding
|
|
|
|
| Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.) |
| WANG Xi-cheng, WU Wei-min, ZHOU Bei-bei, WANG Zhuang-wei, QIAN Ya-ming, WANG Bo, YAN Li-chun |
Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, P.R.China
|
|
|
|
|
摘要
本研究从葡萄基因组中共鉴定出59个SCPL蛋白，并对该基因家族进行了染色体定位、序列比对、基因结构、系统进化，及保守结构域等生物信息学分析，该基因家族的鉴定严格按照SCPL结构域进行。系统进化分析结果表明，VvSCPL基因家族可被划分成3个亚家族，每个亚家族内的基因均具有高度保守的结构域。VvSCPL基因家族外显子数量介于1-19之间，表明葡萄SCPL基因存在较大的变异。转录组测序与qRT-PCR分析结果表明，VvSCPL基因的表达受干旱和淹水胁迫的诱导或抑制，表明该家族基因可能在应答非生物胁迫过程中发挥着一定的作用。本研究为深入了解葡萄VvSCPL基因的生理与生物学功能提供了有力参考。
Abstract Serine carboxypeptidase-like (SCPL) proteins are a group of acyltransferase enzymes that have important roles in plant growth, development, and stress responses. Although SCPL proteins have been studied in many plants, the biological functions of SCPL genes in grape are still unknown. In this study, 59 putative SCPL proteins were identified from the grape genome. A bioinformatics analysis, including chromosomal locations, exon/intron structures, phylogeny, cis-elements, and conserved motifs, was performed for the gene family. The phylogenetic analysis revealed that VvSCPL proteins could be classified into three groups, with the gene motifs in each group showing high similarity levels. The number of exons in the VvSCPL genes ranged from 1 to 19, suggesting significant variations among grape SCPL genes. The expression of the VvSCPL genes, as assessed by RNA sequencing (RNA-seq) and quantitative real-time PCR, showed that most VvSCPL genes responded to drought- and waterlogging-stress treatments, which indicated their roles in abiotic stress responses. The results provide useful information for further study of SCPL genes in grape.
|
|
Received: 10 April 2020
Accepted:
|
| Fund: This research was supported by the National Key Research and Development Program of China (2018YFD0201300), the Natural Science Funds of Jiangsu Province, China (BK20160587) and the China Agriculture Research System of MOF and MARA (CARS-29-11). |
|
Corresponding Authors:
Correspondence WU Wei-min, Tel/Fax: +86-25-84392902, E-mail: 5wm@163.com
|
| About author: WANG Xi-cheng, E-mail: wxcown@163.com; |
Cite this article:
WANG Xi-cheng, WU Wei-min, ZHOU Bei-bei, WANG Zhuang-wei, QIAN Ya-ming, WANG Bo, YAN Li-chun.
2021.
Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.). Journal of Integrative Agriculture, 20(10): 2666-2679.
|
ailey T L, Williams N, Misleh C, Li W W. 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34, 369–373.
Bienert M D, Delannoy M, Navarre C, Boutry M. 2012. NtSCP1 from tobacco is an extracellular serine carboxypeptidase III that has an impact on cell elongation. Plant Physiology, 158, 1220.
Bontpart T, Ferrero M, Khater F, Marlin T, Vialet S, Vallverdù-Queralt A, Pinasseau L, Ageorges A, Cheynier V, Terrier N. 2018. Focus on putative serine carboxypeptidase-like acyltransferases in grapevine. Plant Physiology and Biochemistry, 130, 356–366.
Cakir B, Kilickaya O. 2015. Mitogen-activated protein kinase cascades in Vitis vinifera. Frontiers in Plant Science, 6, 556.
Cercos M, Urbez C, Carbonell J. 2003. A serine carboxypeptidase gene (PsCP), expressed in early steps of reproductive and vegetative development in Pisum sativum, is induced by gibberellins. Plant Molecular Biology, 51, 165–174.
Chiu C, Chen G, Tzen J T C, Yang C. 2016. Molecular identi?cation and characterization of a serine carboxypeptidase-like gene associated with abiotic stress in tea plant, Camellia sinensis (L.). Plant Growth Regulation, 79, 345–353.
Ciarkowska A, Ostrowski M, Jakubowska A. 2018. A serine carboxypeptidase-like acyltransferase catalyzes synthesis of indole-3-acetic (IAA) ester conjugate in rice (Oryza sativa). Plant Physiology and Biochemistry, 125, 126–135.
Domínguez F, González M C, Cejudo F J. 2002. A germination-related gene encoding a serine carboxypeptidase is expressed during the differentiation of the vascular tissue in wheat grains and seedlings. Planta, 215, 727.
Du H, Yang S S, Liang Z, Feng B R, Liu L, Huang Y B, Tang Y X. 2012. Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biology, 12, 106.
Feng Y, Xue Q. 2006. The serine carboxypeptidase like gene family of rice (Oryza sativa L. ssp. japonica). Functional & Integrative Genomics, 6, 14–24.
Feng Y, Yu C. 2009. Genome-wide comparative study of rice and Arabidopsis serine carboxypeptidase-like protein families. Journal of Zhejiang University, 35, 1–15. (in Chinese)
FPCGGC (The French-Italian Public Consortium for Grapevine Genome Characterization). 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463–467.
Fraser C M, Thompson M G, Shirley A M, Ralph J, Schoenherr J A, Sinlapadech T, Hall M C, Chapple C. 2007. Related Arabidopsis serine carboxypeptidase-like sinapoylglucose acyltransferases display distinct but overlapping substrate specificities. Plant Physiology, 144, 1986.
Granat S J, Wilson K A, Tan-Wilson A L. 2003. New serine carboxypeptidase in mung bean seedling cotyledons. Journal of Plant Physiology, 160, 1263–1266.
Guo A Y, Zhu Q H, Chen X, Luo J C. 2007. GSDS: A gene structure display server. Hereditas, 29, 1023–1026. (in Chinese)
Haider M S, Zhang C, Kurjogi M M, Pervaiz T, Zheng T, Zhang C, Chen L, Shangguan L, Fang J. 2017. Insights into grapevine defense response against drought as revealed by biochemical, physiological and RNA-Seq analysis. Scientific Reports, 7, 13134.
Hause B, Meyer K, Viitanenm P V, Chapple C, Strack D. 2002. Immunolocalization of 1-O-sinapoylglucose: Malate sinapoyltransferase in Arabidopsis thaliana. Planta, 215, 26–32.
Hung J H, Weng Z. 2016. Sequence alignment and homology search with BLAST and ClustalW. Cold Spring Harbor Protocols, 11, pdb.top093070.
Ikegami A, Eguchi S, Kitajima A, Inoue K, Yonemori K. 2007. Identification of genes involved in proanthocyanidin biosynthesis of persimmon (Diospyros kaki) fruit. Plant Science, 172, 1037–1047.
Jiang P, Zhang K, Ding Z, He Q, Li W, Zhu S, Cheng W, Zhang K, Li K. 2018. Characterization of a strong and constitutive promoter from the Arabidopsis serine carboxypeptidase-like gene AtSCPL30 as a potential tool for crop transgenic breeding. BMC Biotechnology, 18, 59.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, R36.
Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.
Lee S, Kaminaga Y, Cooper B, Pichersky E, Dudareva N, Chapple C. 2012. Benzoylation and sinapoylation of glucosinolate R-groups in Arabidopsis. Plant Journal, 72, 411–422.
Lehfeldt C, Shirley A M, Meyer K, Ruegger M O, Cusumano J C, Viitanen P V, Strack D, Chapple C. 2000. Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell, 12, 1295–1306.
Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 43, 1266–1269.
Li Z, Tang L, Qiu J, Zhang W, Wang Y, Tong X, Wei X, Hou Y, Zhang J. 2016. Serine carboxypeptidase 46 regulates grain filling and seed germination in rice (Oryza sativa L.). PLoS ONE, 11, e0159737.
Liu H, Wang X, Zhang H, Yang Y, Ge X, Song F. 2008. A rice serine carboxypeptidase-like gene OsBISCPL1 is involved in regulation of defense responses against biotic and oxidative stress. Gene, 420, 57–65.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–ΔΔCt method. Methods, 25, 402–408.
Milkowski C, Strack D. 2004. Serine carboxypeptidase-like acyltransferases. Phytochemistry, 65, 517–524.
Moura D S, Bergey D R, Ryan C A. 2001. Characterization and localization of a wound-inducible type I serine-carboxypeptidase from leaves of tomato plants (Lycopersicon esculentum Mill.). Planta, 212, 222–230.
Mugford S T, Milkowski C. 2012. Serine carboxypeptidase-like acyltransferases from plants. Method in Enzymology, 516, 279–297.
Mugford S T, Qi X, Bakht S, Hill L, Wegel E, Hughes R K, Papadopoulou K, Melton R, Philo M, Sainsbury F, Lomonossoff G P, Roy A D, Goss R J, Osbourn A. 2009. A serine carboxypeptidase-like acyltransferase is required for synthesis of antimicrobial compounds and disease resistance in oats. Plant Cell, 21, 2473–2484.
Robinson M D, McCarthy D J, Smyth G K. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139–140.
Shangguan L, Fang X, Chen L, Cui L, Fang J. 2018. Genome?wide analysis of autophagy?related genes (ARGs) in grapevine and plant tolerance to copper stress. Planta, 247, 1449–1463.
Shirley A M, Mcmichael C M, Chapple C. 2001. The sng2 mutant of Arabidopsis is defective in the gene encoding the serine carboxypeptidase-like protein sinapoylglucose: Choline sinapoyltransferase. Plant Journal, 28, 83–94.
Stehle F, Brandt W, Milkowski C, Strack D. 2006. Structure determinants and substrate recognition of serine carboxypeptidase-like acyltransferases from plant secondary metabolism. FEBS Letters, 580, 6366–6374.
Stehle F, Brandt W, Schmidt J, Milkowski C, Strack D. 2008a. Activities of Arabidopsis sinapoylglucose: Malate sinapoyltransferase shed light on functional diversification of serine carboxypeptidase-like acyltransferases. Phytochemistry, 69, 1826–1831.
Stehle F, Stubbs M T, Strack D, Milkowski C. 2008b. Heterologous expression of a serine carboxypeptidase-like acyltransferase and characterization of the kinetic mechanism. FEBS Journal, 275, 775–787.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D R, Pimentel H, Salzberg S L, Rinn J L, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7, 562.
Wang G, Lovato A, Polverari A, Wang M, Liang Y H, Ma Y C, Cheng Z M. 2014. Genome-wide identification and analysis of mitogen activated protein kinase kinase kinase gene family in grapevine (Vitis vinifera). BMC Plant Biology, 14, 219.
Wang G, Wang T, Jia Z, Xuan J, Pan D, Guo Z, Zhang J. 2018. Genome-wide bioinformatics analysis of MAPK gene family in kiwifruit (Actinidia chinensis). International Journal of Molecular Sciences, 19, 2510.
Wen J, Li J, Walker J C. 2012. Overexpression of a serine carboxypeptidase increases carpel number and seed production in Arabidopsis thaliana. Food Energy Security, 1, 61–69.
Wickham H. 2009. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York.
Xu C, Liu Y, Li Y, Xu X, Xu C, Li X, Xiao J, Zhang Q. 2015. Differential expression of GS5 regulates grain size in rice. Journal of Experimental Botany, 66, 2611–2623.
Xu G X, Guo C C, Shan H Y, Kong H Z. 2012. Divergence of duplicate genes in exonintron structure. Proceedings of the National Academy of Sciences of the United States of America, 109, 1187–1192.
Zhang Y, Wang C, Yu H, Cai B, Fang J. 2010. Screening of RNA extraction methods for various grapevine organs and tissues. Acta Agriculturae Boreali-Occidentalis Sinica, 19, 135–140. (in Chinese)
Zhu D, Chu W, Wang Y, Yan H, Chen Z, Xiang Y. 2018. Genome-wide identification, classification and expression analysis of the serine carboxypeptidase-like protein family in poplar. Physiologia Plantarum, 162, 333–352.
|
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
