毛竹CCR基因家族成员生物信息学和表达模式分析
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摘要
肉桂酰辅酶A还原酶(CCR)是木质素生物合成的关键酶之一,对木质素生物合成途径的碳流具有重要的调控作用。研究毛竹(Phyllostachys edulis) CCR基因的分子特征和表达模式对于揭示影响竹子材性的木质素调控机制具有重要意义。采用同源序列比对的方法在毛竹基因组中获取13个CCR基因同源序列,其中9个具有完整的保守结构域,依次命名为PeCCR1～PeCCR9。PeCCRs基因的内含子数量、长度和位置均存在较大差异,如PeCCR2有5个内含子,而PeCCR5没有内含子;内含子最长的为4 090 bp,最短的仅为89 bp。PeCCRs编码的氨基酸序列长度范围为136～391 aa,推测分子量在14.97～43.05 kD之间,理论等电点介于5.60～8.31之间。PeCCRs的氨基酸序列在N-端和C-端均存在明显的差异,二级、三级结构进一步显示了其差异,但中部序列具有很高的一致性,都含有肉桂酰辅酶A还原酶家族蛋白特有的保守结构域和催化位点,表明其进化上是比较保守的。基于转录组数据的基因组织表达特异性分析表明,PeCCRs在各组织中的表达量差异明显,如PeCCR6在盛花期花序、鞭和笋中均未检测到基因表达,PeCCR9在盛花期花序中的表达是所有PeCCRs最高的,而PeCCR5在50 cm笋中则是所有检测到PeCCRs中最低的。本研究为进一步研究毛竹CCR基因家族成员的功能提供了参考,为利用基因工程调控竹子木质素提供了依据。
Cinnamoyl-CoA reductase(CCR) is one of key enzymes involved in lignin biosynthesis, which plays a vital role in the regulation of carbon flow in lignin biosynthetic pathway. Study on the molecular characteristics and expression patterns of the CCR gene in Phyllostachys edulis is of great significance to reveal the regulatory mechanism of lignin affecting bamboo properties. By using the method of homologous sequence alignment,thirteen homologous sequences of CCR gene in moso bamboo genome were obtained, among which nine had the complete conserved domain, and were named as PeCCR1～PeCCR9 respectively. There were significant differences in the number, length and location of the introns of PeCCRs, for example, PeCCR2 had five introns while PeCCR5 had no intron. The longest intron was 4 090 bp, and the shortest one was 89 bp. The length of amino acid sequences encoded by PeCCRs ranged from 136 to 391 aa, with the predicted molecular weight of4.971～43.05 kD and the isoelectric point of 5.60～8.31. The amino acid sequences of PeCCRs were significantly different at the N-terminus and C-terminus consistent with their secondary and tertiary structures, but the central sequences were highly consistent, containing the conserved domain and catalytic sites specific to the cinnamoyl-CoA reductase family proteins, which indicated CCRs were relatively conservative in evolution.Based on transcriptome data, the tissue specific expression analysis showed that the expression levels of PeCCRs in tissues were significantly different, for example, the expression of PeCCR6 was not detected in flowering inflorescence, rhizome and shoot, the expression of PeCCR9 in flowering inflorescence was the highest of all the PeCCRs, and the expression of PeCCR5 in 50 cm shoot was the lowest of all detected PeCCRs. This study could provide a reference for the further study on the function of CCR gene family members in bamboo and lay the foundation for the regulation of bamboo lignin synthesis by genetic engineering.
Cinnamoyl-CoA reductase(CCR) is one of key enzymes involved in lignin biosynthesis, which plays a vital role in the regulation of carbon flow in lignin biosynthetic pathway. Study on the molecular characteristics and expression patterns of the CCR gene in Phyllostachys edulis is of great significance to reveal the regulatory mechanism of lignin affecting bamboo properties. By using the method of homologous sequence alignment,thirteen homologous sequences of CCR gene in moso bamboo genome were obtained, among which nine had the complete conserved domain, and were named as PeCCR1～PeCCR9 respectively. There were significant differences in the number, length and location of the introns of PeCCRs, for example, PeCCR2 had five introns while PeCCR5 had no intron. The longest intron was 4 090 bp, and the shortest one was 89 bp. The length of amino acid sequences encoded by PeCCRs ranged from 136 to 391 aa, with the predicted molecular weight of4.971～43.05 kD and the isoelectric point of 5.60～8.31. The amino acid sequences of PeCCRs were significantly different at the N-terminus and C-terminus consistent with their secondary and tertiary structures, but the central sequences were highly consistent, containing the conserved domain and catalytic sites specific to the cinnamoyl-CoA reductase family proteins, which indicated CCRs were relatively conservative in evolution.Based on transcriptome data, the tissue specific expression analysis showed that the expression levels of PeCCRs in tissues were significantly different, for example, the expression of PeCCR6 was not detected in flowering inflorescence, rhizome and shoot, the expression of PeCCR9 in flowering inflorescence was the highest of all the PeCCRs, and the expression of PeCCR5 in 50 cm shoot was the lowest of all detected PeCCRs. This study could provide a reference for the further study on the function of CCR gene family members in bamboo and lay the foundation for the regulation of bamboo lignin synthesis by genetic engineering.
引文
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Lauvergeat V.,Lacomme C.,Lacombe E.,Lasserre E.,Roby D.,and Grima-Pettenati J.,2001,Two cinnamoyl-coa reductase(CCR)genes from Arabidopsis thaliana are differentially expressed during development and in response to infection with pathogenic bacteria,Phytochemistry,57(7):1187-1195
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Li B.,Liang Y.,and Chai Y.R.,2006,Achievements in research on plant cinnamoyl-coa reductase(CCR)genes,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),4(3):55-65(李波,梁颖,柴友荣,2006,植物肉桂酰辅酶A还原酶(CCR)基因的研究进展,分子植物育种,4(3):55-65)
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Ma Q.H.,2007,Characterization of a cinnamoyl-CoA reductase that is associated with stem development in wheat,Journal of Experimental Botany,58(8):2011-2021
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Chao N.,Li N.,Qi Q.,Li S.,Lv T.,Jiang X.N.,and Gai Y.,2017,Characterization of the cinnamoyl-CoA reductase(CCR)gene family in(Populus tomentosa)reveals the enzymatic active sites and evolution of CCR,Planta,245(1):61-75
Chou K.C.,and Shen H.B.,2010,Plant-mPLoc:a top-down strategy to augment the power for predicting plant protein subcellular localization,PLo S One,5(6):e11335
Deb A.,Grewal R.K.,and Kundu S.,2016,Regulatory cross-talks and cascades in rice hormone biosynthesis pathways contribute to stress signaling,Front.Plant Sci.,26(7):1303
Deng X.B.,Hu S.L.,Cao Y.,Lu X.Q.,Ren P.,and Duan N.,2011,Bioinformatics analysis of cellulose synthase(CesA)of Bambusa oldhamii and Phyllostachys edulis,Fujian Linxueyuan Xuebao(Journal of Fujian College of Forestry),31(1):84-90(邓小波,胡尚连,曹颖,卢学琴,任鹏,段宁,2011,绿竹与毛竹纤维素合成酶(CesA)的生物信息学分析,福建林学院学报,31(1):84-90)
Fan F.F.,Li J.Q.,Zhan Q.W.,Wang L.H.,and Liu Y.L.,2015,Research progress of cinnamoyl-CoA reductase(CCR)gene in plants,Zhongguo Shengwu Gongcheng Zazhi(China Biotechnology),35(12):96-102(樊飞飞,李杰勤,詹秋文,王丽华,刘言龙,2015,植物肉桂酰辅酶A还原酶基因克隆研究进展,中国生物工程杂志,35(12):96-102)
Gao Z.M.,Wang X.C.,Peng Z.H.,Zheng B.,and Liu Q.,2012,Characterization and primary functional analysis of phenylalanine ammonia-lyase gene from Phyllostachys edulis,Plant Cell Rep.,31(7):1345-1356
Goujon T.,Ferret V.,Mila I.,Pollet B.,Ruel K.,Burlat V.,Joseleau J.P.,Barriere Y.,Lapierre C.,and Jouanin L.,2003,Down-regulation of the AtCCR1 gene in Arabidopsis thaliana:effects on phenotype,lignins and cell wall degradability,Planta,217(2):218-228
Gu Z.Z.,Zhang D.Q.,and Huang Q.Y.,2010,Transgenic modification on pulp plants by key genes regulating lignin biosynthesis,Zhongnan Linye Keji Daxue Xuebao(Central South University of Forestry and Technology),30(3):68-75(谷振军,张党权,黄青云,2010,木质素合成关键酶基因与造纸植物转基因改良应用研究,中南林业科技大学学报,30(3):68-75)
Gui R.Y.,Shao J.F.,Yu Y.M.,Zhu Y.J.,Dong D.Y.,and Fang W.,2011,Influence of obtruncation on physical and mechanical properties of 5 years old culms of Phyllostachys edulis,Linye Kexue(Scientia Silvae Sinicae),47(6):194-198(桂仁意,邵继锋,俞友明,朱永军,董墩义,方伟,2011,钩梢对5年生毛竹竹材物理力学性质的影响,林业科学,47(6):194-198)
He X.,Hall M.B.,Gallo-Meagher M.,and Smith R.L.,2003,Improvement of forage quality by downregulation of maize O-Methyltransferase,Crop Sci.,43(6):2240-2251
Hu X.S.,Han Y.F.,and Qiu D.Y.,1999,Research progress on genetic variation in lignin content of trees,Linye Kexue Yanjiu(Forest Research),12(6):563-571(胡新生,韩一凡,邱德有,1999,树木木质素含量的遗传变异研究进展,林业科学研究,12(6):563-571)
Hua X.W.,2015,Paper industry:the different paper kinds developed differently,Zhonghua Zhiye(China Pulp&Paper Industry),36(15):48-53(花小伟,2015,造纸业底部趋稳弱势向上,纸种分化显著,中华纸业,36(15):48-53)
Jiang W.X.,2013,Population structure and phylogenetic relationships of Phyllostachys edulis(Poaceae)in China,Dissertation for Ph.D.,Nanjing Forestry University,Supervisor:Ding Y.L.,pp.56-79(蒋维昕,2013,毛竹的遗传结构及群体演化,博士学位论文,南京林业大学,导师:丁雨龙,pp.56-79)
Kawasaki T.,Koita H.,Nakatsubo T.,Hasegawa K.,Wakabayashi K.,Takahashi H.,Umemura K.,Umezawa T.,and Shimamoto K.,2006,Cinnamoyl-coa reductase,a key enzyme in lignin biosynthesis,is an effector of small gtpase rac in defense signaling in rice,Proc.Natl.Acad.Sci.USA,103(1):230-235
Kelley L.A.,Mezulis S.,Yates C.M.,Wass M.N.,and Sternberg M.J.,2015,The Phyre2 web portal for protein modeling,prediction and analysis,Nat.Protoc.,10(6):845-858
Lacombe E.,Hawkins S.,Van Doorsselaere J.,Piquemal J.,Goffner D.,Poeydomenge O.,Boudet A.M.,and Grima-Pettenati J.,1997,Cinnamoyl coa reductase,the first committed enzyme of the lignin branch biosynthetic pathway:cloning,expression and phylogenetic relationships,Plant Journal,11(3):429-441
Lauvergeat V.,Lacomme C.,Lacombe E.,Lasserre E.,Roby D.,and Grima-Pettenati J.,2001,Two cinnamoyl-coa reductase(CCR)genes from Arabidopsis thaliana are differentially expressed during development and in response to infection with pathogenic bacteria,Phytochemistry,57(7):1187-1195
Leple J.C.,Dauwe R.,Morreel K.,Storme V.,Lapierre C.,Pollet B.,Naumann A.,Kang K.Y.,Kim H.,Ruel K.,Lefèbvre A.,Joseleau J.P.,Grima-Pettenati J.,Rycke R.D.,AnderssonGunneras S.,Erban A.,Fehrle I.,Petit-Conil M.,Kopka J.,Polle A.,Messens E.,Sundberg B.,Mansfield S.D.,Ralph J.,Pilate G.,and Boerjan W.,2007,Downregulation of cinnamoyl-coenzyme A reductase in poplar:multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure,The Plant Cell,19(11):3669-3691
Li B.,Liang Y.,and Chai Y.R.,2006,Achievements in research on plant cinnamoyl-coa reductase(CCR)genes,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),4(3):55-65(李波,梁颖,柴友荣,2006,植物肉桂酰辅酶A还原酶(CCR)基因的研究进展,分子植物育种,4(3):55-65)
Li B.Y.,Hu S.L.,Cao Y.,and Xu G.,2015,Bioinformatics analysis of NAC gene family in moso bamboo,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(8):1769-1777(黎帮勇,胡尚连,曹颖,徐刚,2015,毛竹NAC转录因子家族生物信息学分析,基因组学与应用生物学,34(8):1769-1777)
Li X.P.,Gao Z.M.,Peng Z.H.,and Yue Y.D.,2008,Cloning and characterization of CCoAOMT gene from Bambusa oldhamii,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(3):587-592(李雪平,高志民,彭镇华,岳永德,2008,绿竹咖啡酰辅酶A-O-甲基转移酶基因CCoAOMT的克隆与分析,分子植物育种,6(3):587-592)
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