Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development

BMC Genomic Data - Tập 23 Số 1 - 2022
Xiaoqing Liu1, Hongmei Zhang1, Wei Zhang1, Wenjing Xu1, Songsong Li1, Xin Chen1, Huatao Chen1
1Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China

Tóm tắt

Abstract Background CesA and Csl gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. Results In this study, we identified 39 putative cellulose synthase genes from the common bean genome sequence. Then, we performed a bioinformatics analysis of this gene family involving sequence alignment, phylogenetic analysis, gene structure, collinearity analysis and chromosome location. We found all members possess a cellulose_synt domain. Phylogenetic analysis revealed that these cellulose synthase genes may be classified into five subfamilies, and that members in the same subfamily share conserved exon-intron distribution and motif compositions. Abundant and distinct cis-acting elements in the 2 k basepairs upstream regulatory regions indicate that the cellulose synthase gene family may plays a vital role in the growth and development of common bean. Moreover, the 39 cellulose synthase genes are distributed on 10 of the 11 chromosomes. Additionally expression analysis shows that all CesA/Csl genes selected are constitutively expressed in the pod development. Conclusions This research reveals both the putative biochemical and physiological functions of cellulose synthase genes in common bean and implies the importance of studying non-model plants to understand the breadth and diversity of cellulose synthase genes.

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Tài liệu tham khảo

Richmond TA, Somerville CR. The cellulose synthase superfamily. Plant Physiol. 2000;124(2):495–8. https://doi.org/10.1104/pp.124.2.495.

Hazen SP, Scott-Craig JS, Walton JD. Cellulose synthase-like genes of rice. Plant Physiol. 2002;128(2):336–40. https://doi.org/10.1104/pp.010875.

Pear JR, Kawagoe Y, Schreckengost WE, Delmer DP, Stalker DM. Higher plants contain homologs of the bacterial CslA genes encoding the catalytic subunit of cellulose synthase. Proc Natl Acad Sci. 1996;93(22):12637–42. https://doi.org/10.1073/pnas.93.22.12637.

Arioli T, Peng L, Betzner AS, Burn J, Wittke W, Herth W, et al. Molecular analysis of cellulose biosynthesis in Arabidopsis. Science. 1998;279:717–20. https://doi.org/10.1126/science.279.5351.717.

Yin Y, Huang J, Xu Y. The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biol. 2009;9:99–113. https://doi.org/10.1186/1471-2229-9-99.

Appenzeller L, Doblin M, Barreiro R, Wang H, Ni X, Kollipara K, et al. Cellulose synthesis in maize isolation and expression analysis of the cellulose synthase (CesA) gene family. Cellulose. 2004;11(3–4):287–99. https://doi.org/10.1023/B:CELL.0000046417.84715.27.

Burton RA, Shirley NJ, King BJ, Harvey AJ, Fincher GB. The CESA gene family of barley. Quantitative analysis of transcripts reveals two groups of co-expressed genes. Plant Physiol. 2004;134:224–36. https://doi.org/10.1104/pp.103.032904.

Kaur S, Dhugga KS, Gill K, Singh J. Novel structural and functional motifs in cellulose synthase (CesA) genes of bread wheat (Triticum aestivum L.). PLoS One. 2016;11:e0147046. https://doi.org/10.1371/journal.pone.0147046.

Li S, Lei L, Gu Y. Functional analysis of complexes with mixed primary and secondary cellulose synthases. Plant Signal Behav. 2013;8(3):e23179. https://doi.org/10.4161/psb.23179.

Taylor NG, Laurie S, Turner SR. Multiple cellulose synthase catalytic subunits are required for cellulose synthesis in Arabidopsis. Plant Cell. 2000;12(12):2529–40. https://doi.org/10.1105/tpc.12.12.2529.

Persson S, Paredes A, Carroll A, Palsdottir H, Doblin M, Poindexter P, et al. Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis. Proc. Natl. Acad. Sci. 2007;104(39):15566–71. https://doi.org/10.1073/pnas.0706592104.

Zou XY, Zhen Z, Ge Q, Fan SM, Liu AY, Gong WK, et al. Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species. Gene. 2018;646:28–38. https://doi.org/10.1016/j.gene.2017.12.043.

Fincher GB. Revolutionary times in our understanding of cell wall biosynthesis and remodeling in the grasses. Plant Physiol. 2009;149(1):27–37. https://doi.org/10.1104/pp.108.130096.

Doblin MS, Pettolino F, Bacic A. Plant cell walls: the skeleton of the plant world. Funct Plant Biol. 2010;37(5):357–81. https://doi.org/10.1071/FP09279.

Goubet F, Barton CJ, Mortimer JC, Yu X, Dupree P. Cell wall glucomannan in Arabidopsis is synthesized by CSLA glycosyltransferases, and influences the progression of embryogenesis. Plant J. 2009;60(3):527–38. https://doi.org/10.1111/j.1365-313X.2009.03977.x.

Liepman AH, Wilkerson CG, Keegstra K. Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases. Proc Natl Acad Sci. 2005;102(6):2221–6. https://doi.org/10.1073/pnas.0409179102.

Dhugga KS, Barreiro R, Whitten B, Stecca K, Hazebroek J, Randhawa GS, et al. Guar seed beta-mannan synthase is a member of the cellulose synthase super gene family. Science. 2004;303(5656):363–6. https://doi.org/10.1126/science.1090908.

Liepman AH, Cavalier DM. The Cellulose synthase-like A and cellulose synthase-like C families: recent advances and future perspectives. Front Plant Sci. 2012;3:109. https://doi.org/10.3389/fpls.2012.00109.

Dwivany FM, Yulia D, Burton RA, Shirley NJ, Wilson SM, Fincher GB, et al. The cellulose-synthase like c (CSLC) family of barley includes members that are integral membrane proteins targeted to plasma membrane. Mol Plant. 2009;2(5):1025–39. https://doi.org/10.1093/mp/ssp064.

Cocuron JC, Lerouxel O, Drakakaki G, Alonso AP, Liepman AH, Keegstra K, et al. A gene from the cellulose synthase-like C family encodes a beta-1,4 glucan synthase. Proc Natl Acad Sci. 2007;104(20):8550–5. https://doi.org/10.1073/pnas.0703133104.

Bernal AJ, Jensen JK, Harholt J, Sørensen S, Moller I, Blaukopf C, et al. Disruption of AtCslD5 results in reduced growth, reduced xylan and homogalacturonan synthase activity and altered xylan occurrence in Arabidopsis. Plant J. 2007;52(5):791–802. https://doi.org/10.1111/j.1365-313X.2007.03281.x.

Bernal AJ, Yoo CM, Mutwil M, Jensen JK, Hou GC, Blaukopf C, et al. Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells. Plant Physiol. 2008;148(3):1238–53. https://doi.org/10.1104/pp.108.121939.

Li M, Xiong G, Li R, Cui J, Ding T, Zhang B, et al. Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth. Plant J. 2009;60(6):1055–69. https://doi.org/10.1111/j.1365-313X.2009.04022.x.

Verhertbruggen Y, Yin L, Oikawa A, Scheller HV. Mannan synthase activity in the CslD family. Plant Signal Behav. 2011;6(10):1620–3. https://doi.org/10.4161/psb.6.10.17989.

Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, et al. Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1,3;1,4)-beta-D-glucans. Science. 2006;311(5769):1940–2. https://doi.org/10.1126/science.1122975.

Burton RA, Jobling SA, Harvey AJ, Shirley NJ, Mather DE, Bacic A, et al. The genetics and transcriptional profiles of cellulose synthase-like HvCslF gene family in barley. Plant Physiol. 2008;146(4):1821–33. https://doi.org/10.1104/pp.107.114694.

Schmutz J, McClean PE, Mamidi S, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46(7). https://doi.org/10.1038/ng.3008.

Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711–6. https://doi.org/10.1038/nature11543.

Li Y, Yang T, Dai D, Hu Y, Guo X, Guo H. Evolution, gene expression profifiling and 3D modeling of CSLD proteins in cotton. BMC Plant Biol. 2017;17:119. https://doi.org/10.1186/s12870-017-1063-x.

Shu O, Wei Z, John H, Lin H, Matthew C, Kevin C, et al. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 2007;35:D883–7. https://doi.org/10.1093/nar/gkl976.

Song XM, Xu L, Yu JW, Tian P, Hu X. Genome-wide characterization of the cellulose synthase gene superfamily in Solanum lycopersicum. Gene. 2019;688:71–83. https://doi.org/10.1016/j.gene.2018.11.039.

Nawaz MA, Rehman HM, Baloch FS, Ijaz B, Ali MA, Khan IA, et al. Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean. J Plant Physiol. 2017;215:163–75. https://doi.org/10.1016/j.jplph.2017.04.009.

Schwerdt JG, MacKenzie K, Wright F, Oehme D, Wagner JM, Harvey AJ, et al. Evolutionary dynamics of the cellulose synthase gene superfamily in grasses. Plant Physiol. 2015;168:968–83. https://doi.org/10.1104/pp.15.00140.

Farrokhi N, Burton RA, Brownfield L, Hrmova M, Wilson SM, Bacic A, et al. Plant cell wall biosynthesis: Genetic, biochemical and functional genomics approaches to the identification of key genes. Plant Biotechnol J. 2006;4(2):145–67. https://doi.org/10.1111/j.1467-7652.2005.00169.x.

Yin Y, Johns MA, Cao H, Rupani M. A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. BMC Genomics. 2014;15:260. https://doi.org/10.1186/1471-2164-15-260.

Suzuki S, Li L, Sun YH, Chiang VL. The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa. Plant Physiol. 2006;142(3):1233–45. https://doi.org/10.1104/pp.106.086678.

Ermawar RA, Collins HM, Byrt CS, Henderson M, Donovan LAO, Shirley NJ, et al. Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp. BMC Plant Biol. 2015;15:236. https://doi.org/10.1186/s12870-015-0624-0.

Betts MJ, Guigo R, Agarwal P, Russell RB. Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? EMBO J. 2001;20:5354–60. https://doi.org/10.1093/emboj/20.19.5354.

Worberg A, Quandt D, Barniske AM, Löhne C, Hilu KW, Borsch T. Phylogeny of basal eudicots: insights from non-coding and rapidly evolving DNA. Org Divers Evol. 2008;7:55–77. https://doi.org/10.1016/j.ode.2006.08.001.

Xu G, Guo C, Shan H, Kong H. Divergence of duplicate genes in exon-intron structure. Proc Natl Acad Sci. 2012;109:1187–92. https://doi.org/10.1073/pnas.1109047109.

Liepman AH, Wightman R, Geshi N, Turner SR, Scheller HV. Arabidopsis - a powerful model system for plant cell wall research. Plant J. 2010;61:1107–21. https://doi.org/10.1111/j.1365-313X.2010.04161.x.

Artimo P. ExPASy: SIB bioinformatics resource portal. Nucl. Acids Res. 2012;40(Web Server issue):W597–603. https://doi.org/10.1093/nar/gks400.

Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics. 2015;31:1296–7. https://doi.org/10.1093/bioinformatics/btu817.

Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77–8. https://doi.org/10.1093/jhered/93.1.77.

Darzentas N. Circoletto: visualizing sequence similarity with circos. Bioinformatics. 2010;2010(26):2620–1. https://doi.org/10.1093/bioinformatics/btq484.

Borges A, Tsai SM, Caldas DGG. Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses. Plant Cell Rep. 2012;31:827–38. https://doi.org/10.1007/s00299-011-1204-x.

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