水稻扩展蛋白家族的生物信息学分析

doi:10.3724/SP.J.1005.2014.0809

遗传 ›› 2014, Vol. 36 ›› Issue (8): 809-820.doi: 10.3724/SP.J.1005.2014.0809

水稻扩展蛋白家族的生物信息学分析

施杨, 徐筱, 李昊阳, 徐倩, 徐吉臣

北京林业大学,林木育种国家工程实验室,北京100083

收稿日期:2014-01-14 出版日期:2014-08-20 发布日期:2013-07-19
通讯作者: 徐吉臣,教授,研究方向：植物抗逆分子生物学。E-mail:jcxu282@sina.com
作者简介:施杨,硕士研究生,专业方向：植物抗逆分子生物学。Tel: 010-62336628; E-mail: xiandao_shiyang@126.com
基金资助:
国家自然科学基金项目(编号：31128016)资助

Bioinformatics analysis of the expansin gene family in rice

Yang Shi, Xiao Xu, Haoyang Li, Qian Xu, Jichen Xu

National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China

Received:2014-01-14 Online:2014-08-20 Published:2013-07-19

摘要/Abstract

摘要： 扩展蛋白是植物细胞壁的重要组成部分,具有松驰细胞壁和增加细胞壁柔韧性的作用,在植物的生长发育及抗性等方面起到重要的作用。水稻的全基因组序列统计分析显示,水稻扩展蛋白基因家族包含58个成员,分属于A(34)、B(19)、LA(4)和LB(1)4个亚家族,分布在水稻10条染色体上的58个位点,且同一亚家族成员有成簇存在的现象。扩展蛋白基因长度范围为687~1128 bp,编码蛋白质具有保守的结构域,以及保守的半胱氨酸和色氨酸残基。多数情况下,亚家族成员之间的氨基酸一致率小于35%,而同一亚家族成员之间的氨基酸一致率大于35%。在内含子、外显子组成模式上,水稻扩展蛋白呈现明显的亚家族特异性,除个别基因以外,A类基因含有1或2个内含子,B类含有3个内含子,LA和LB类含有4个内含子。密码子使用统计显示,与其他物种相比,水稻中的扩展蛋白具有更多的密码子使用偏好性,有26个高频密码子存在。研究结果展示了水稻扩展蛋白基因家族的基本信息,为深入研究扩展蛋白基因的功能、探讨物种间的进化关系奠定基础。

关键词: 水稻, 扩展蛋白, 细胞壁, 基因家族, 生物信息学

Abstract: Expansin refers to a family of nonenzymatic proteins found in the plant cell wall with important roles in plant cell growth, developmental processes, and resistance to stress. Whole rice genome sequencing revealed that it contains 58 expansin genes, which belong to 4 subfamilies (A (34), B (19), LA (4) and LB (1)). All the genes were located on 10 of 12 rice chromosomes where several subfamily members clustered. Each of expansin genes ranged from 687 bp to 1128 bp in size. Sequence alignment showed that all expansins had three structural domains with two conserved amino acids of cystine in N-terminus and tryptophan in C-terminus. The amino acid identity of members among different subfamilies was less than 35%, while that among the same subfamily was more than 35%. Most genes of A subfamily had 1 or 2 introns, while genes of B, LA and LB subfamily had 3, 4 and 4 introns, respectively. Statistics analysis of codon usage showed that expansins in rice have 26 high-frequency codons which are more biased than those in other species. These bioinformatics findings will be helpful for the further study of the function and evolution of expansin genes.

Key words: rice, expansin, cell wall, gene family, bioinformatics

施杨, 徐筱, 李昊阳, 徐倩, 徐吉臣. 水稻扩展蛋白家族的生物信息学分析[J]. 遗传, 2014, 36(8): 809-820.

Yang Shi, Xiao Xu, Haoyang Li, Qian Xu, Jichen Xu. Bioinformatics analysis of the expansin gene family in rice[J]. HEREDITAS(Beijing), 2014, 36(8): 809-820.

参考文献

[1] DJ. Loosening of plant cell walls by expansins. Nature , 2000, 407(6802): 321-326.
[2] DJ. Growth of the plant cell wall. Nat Rev Mol Cell Biol , 2005, 6(11): 850-861.
[3] HT, Kende H. Expansins and internodal growth of deepwater rice. Plant Physiol , 2001, 126(4): 1471-1479.
[4] HT, Kende H. Expansins in deepwater rice internodes. Plant Physiol , 1997, 113(4): 1137-1143.
[5] DJ. Characterization of long-term extension of isolated cell walls from growing cucumber hypocotyls. Planta , 1989, 177(1): 121-130.
[6] Y, Kende H. Expression of β-expansins is correlated with elongation of internodes in deepwater rice. Plant Physiol , 2001, 127(2): 645-654.
[7] S, Durachko DM, Cosgrove DJ. Two endogenous proteins that induce cell wall extension in plant. Plant Cell , 1992, 4(11): 1425-1433.
[8] HT, Kende H. Expression of expansin genes is correlated with growth in deepwater rice. Plant Cell , 1997, 9(9): 1661-1671.
[9] DJ, Li LC, Cho HT, Hoffmann-Benning S, Moore RC, Blecker D. The growing world of expansins. Plant Cell Physiol , 2002, 43(12): 1436-1444.
[10] WG, Tao J, Zhou XR, Yang WY. Characteristics of expansins insoybean ( Glycine max ) internodes and responses to shade stress. Asian J Crop Science , 2011, 3(1): 26-34.
[11] Y, Kende H. Expression of α-expansin and expansin-like genes in deepwater rice. Plant Physiol , 2002, 130(3): 1396-1405.
[12] D, Lee Y, Cho HT, Kende H. Regulation of expansin gene expression affects growth and development in transgenic rice plants. Plant Cell , 2003, 15(6): 1386-1398.
[13] J, Takano T, Akita S. Expression of α-expansin genes in young seedlings of rice ( Oryza sativa L.). Planta , 2000, 211(4): 467-473.
[14] Y, Choi D. Biochemical properties and localization of the β-expansin OsEXPB3 in rice ( Oryza sativa L.). Mol Cell , 2005, 20(1): 119-126.
[15] L, Kudahettige RL, Alpi A, Perata P. Expansin gene expression and anoxic coleoptile elongation in rice cultivars. J Plant Physiol , 2009, 166(14): 1576-1580.
[16] HT, Cosgrove DJ. Regulation of root hair initiation and expansin gene expression in Arabidopsis . Plant Cell , 2002, 14(12): 3237-3253.
[17] ZM, Kang B, He XW, Lv SL, Bai YH, Ding WN, Chen M, Cho HT, Wu P. Root hair-specific expansins modulate root hairelongation in rice. Plant J , 2011, 66(5): 725-734.
[18] HT, Kende H. Tissue localization of expansins in deepwater rice. Plant J , 1998, 15(6): 805-812.
[19] W, Zhao J, Li X, Qin L, Yan X, Liao H. A soybean β-expansin gene GmEXPB2 intrinsically involved in root system architecture responses to abiotic stresses. Plant J , 2011, 66(3): 541-552.
[20] JH, Jeong DH, Park MC, An G. Characterization and transcriptional expression of the α-expansin gene family in rice. Mol Cells , 2005, 20(2): 210-218.
[21] L, Zheng B, Mao C, Qi X, Liu F, Wu P. Analysis of transcripts that are differentially expressed in three sectors of the rice root system under water deficit. Mol Genet Genomics , 2004, 272(4): 433-442.
[22] YJ, Thorne ET, Sharp RE. Modification of expansin transcript levels in the maize primary root at low water potentials. Plant Physiol , 2001, 126(4): 1471-1479
[23] AJ, McQueen-Mason S, Mandel T, Kuhlemeier C. Induction of leaf primordia by the cell wall protein expansin. Science , 1997, 276(5317): 1415-1418.
[24] HT, Cosgrove DJ. Altered expression of expansin modulates leaf growth and pedicel abscission in Arabidopsis th a liana . Proc Natl Acad Sci USA , 2000, 97(17): 9783-9788.
[25] E, Cosgrove DJ. Expansins in growing tomato leaves. Plant J , 1995, 8(6): 795-802.
[26] GM, Mellerowicz EJ, Abe H, Schrader J, Winzéll A, Sterky F, Blomqvist K, McQueen-Mason S, Teeri TT, Sundberg B. Expansins abundant in secondary xylem belong to subgroup a of the α-expansin gene family. Plant Physiol , 2004, 135(3): 1552-1564.
[27] MC, Pombo MA, Martínez GA, Civello PM. Heat treatments and expansin gene expression in strawberry fruit. Sci Hortic , 2011, 130(4): 775-780.
[28] JKC, Lee HH, Bennett AB. Expression of a divergent expansin gene is fruit-specific and ripening-regulated. Proc Natl Acad Sci USA , 1997, 94(11): 5955-5960.
[29] N, Kerim T, Rolfe B, Weinman JJ. Effect of early cold stress on the maturation of rice anthers. Proteomics , 2004, 4(7): 1873-1882.
[30] M, Feron R, Mariani C. Pollination modulates expression of the PPAL gene, a pistil-specific β-expansin. Plant Mol Biol , 2002, 49(2): 187-197.
[31] X, Cao Y, Huang L, Zhao J, Xu C, Li X, Wang S. Activation of the indole-3-acetic acid-amido synthetase GH3-8 suppresses expansin expression and promotes salicylate- and jasmonate-independent basal immunity in rice. Plant Cell , 2008, 20(1): 228-240.
[32] H, Gu G, Longa J, Yin Q, Wu T, Song T, Zhang S, Chen Z, Dong H. Combinative effects of a bacterial type-III effector and a biocontrol bacterium on rice growth and disease resistance. J Biosci , 2006, 31(5): 617-27.
[33] CM, Zoerb C, Muhling KH. Salt stress differentially affects growth-mediating β-expansins in resistant and sensitive maize ( Zea mays L.). Plant Physiol Bi o chem , 2010, 48(12): 993-998.
[34] YY, Li AX, Li F, Zhao MR, Wang W. Characterizaition of a wheat ( Triticum aestivum L.) expansin gene, TaEXPB23, involved in the abiotic stress response and phytohormone regulation. Plant Physiol Biochem , 2012, 54(5): 49-58.
[35] JC, Tian J, Belanger FC, Huang B. Identification and characterization of an expansin gene AsEXP1 associated with heat tolerance in C3 Agrostis grass species. J Exp Bot , 2007, 58(13): 3789-3796.
[36] MR, Han YY, Feng YN, Li F, Wang W. Expansins are involved in cell growth mediated by abscisic acid and indole-3-acetic acid under drought stress in wheat. Plant Cell Rep , 2012, 31(4): 671-685.
[37] 孙涛, 赵会君, 柴团耀. 商陆扩展蛋白基因PaEXP1在逆境胁迫下的表达. 中国科学院研究生院学报, 2010, 27(4): 448-455.
[38] D, Cho HT, Lee Y. Expansins: expanding importance in plant growth and development. Physiol Plant , 2006, 126(4): 511-518.
[39] SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong JP, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. A draft sequence of the rice genome ( Oryza sativa L. ssp. indica). Science , 2002, 296(5565): 92-100.
[40] 孟金陵. MapDraw, 在Excel中绘制遗传连锁图的宏. 遗传, 2003, 25(3): 317-321.
[41] O, Steel M. Neighbor-joining revealed. Mol Biol Evol , 2006, 23(11): 1997-2000.
[42] JF. Analysis of Codon Usage. Nottingham: University of Nottingham, 1999, 101: 13951-13956.
[43] GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Res , 2004, 14(6): 1188-1190.
[44] JM. The proteomics protocols handbook. New York City: Humana Press, University of Hertfordshire, Hatfield, 2005.
[45] H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T. Rice annotation project database (RAP-DB): An integrative and interactive database for rice genomics. Plant Cell Physiol , 2013, 54(2): e6.
[46] J, Cosgrove DJ. The expansin superfamily. Genome Biol , 2005, 6(12): 242.
[47] 沈文涛, 周鹏. Expansin超级家族的进化与命名. 广东农业科学, 2007, (8): 133-135.
[48] 王学臣. 扩张蛋白(Expansin)研究进展. 农业生物技术科学, 2005, 21(7): 82-86.
[49] 徐倩, 张楷, 徐吉臣. 植物扩展蛋白基因的研究进展. 北京林业大学学报, 2010, 32(5): 154-161.
[50] 范晓军, 付月君, 梁爱华. 二硫键的形成与蛋白质的氧化折叠. 中国生物工程杂志, 2008, 28(S6): 259-264.
[51] 倪志华, 沈明山, 陈亮. 高频密码子分析法及其在烟草密码子分析中的应用. 厦门大学学报(自然科学版), 2002, 41(5): 551-554.
[52] 辛培尧, 许玉兰, 刘岩, 韦援教, 董娇, 曹有龙, 周军. 几种经济植物UFGT基因的生物信息学分析. 基因组学与应用生物学, 2010, 30(1): 92-102.
[53] A. Thermostability and aliphatic index of globular proteins. J Biochem , 1980, 88(6): 1895-1898.
[54] 冯英, 董辉. 20个物种同义密码子偏性的比较分析. 西北农林科技大学学报(自然科学版), 2004, 32(7): 67-71.
[55] 马文丽, 郑文岭. SARS冠状病毒的密码子偏爱性分析. 生命科学研究, 2003, 7(3): 219-223.
[56] 薛庆中. 拟南芥及水稻转录因子MADS密码子的偏好性比较. 浙江大学学报(农业与生命科学版), 2005, 31(5): 513-517.
[57] 陈乃芝, 熊艳梅, 王学臣. 扩张蛋白在旱稻根的免疫组化定位及对旱稻抗旱性的表达分析. 自然科学进展, 2006, 16(4): 475-479.
[58] SD, Bhalla PL, Singh MB. Transcriptome-based examination of putative pollen allergens of rice ( Oryza sativa ssp. japonica). Mol Plant , 2008, 1(5): 751-759.
[59] A, Li LC, Cosgrove DJ. Matrix solubilization and cell wall weakening by β-expansin (group-1 allergen) from maize pollen. Plant J , 2011, 68(3): 546-559.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

水稻扩展蛋白家族的生物信息学分析

Bioinformatics analysis of the expansin gene family in rice

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	张桂权. 基于SSSL文库的水稻设计育种平台[J]. 遗传, 2019, 41(8): 754-760.
[2]	卢涣滋,王迪侃,王智. HPV阳性口咽癌患者预后与T细胞浸润和新抗原负荷相关性分析[J]. 遗传, 2019, 41(8): 725-735.
[3]	孟玉,杨若林. 基于基因家族大小的比较研究脊椎动物的适应性进化[J]. 遗传, 2019, 41(2): 158-174.
[4]	李明,程飞跃,龚路遥,向华. 微生物新型防御系统的系统性发现与展望[J]. 遗传, 2018, 40(4): 259-265.
[5]	刘次桃, 王威, 毛毕刚, 储成才. 水稻耐低温逆境研究：分子生理机制及育种展望[J]. 遗传, 2018, 40(3): 171-185.
[6]	杨德卫, 郑向华, 程朝平, 叶宁, 黄凤凰, 叶新福. 基于CSSLs群体定位和图位克隆水稻长芒基因GAD1-2[J]. 遗传, 2018, 40(12): 1101-1111.
[7]	辛高伟, 胡熙璕, 王克剑, 王兴春. Cas9蛋白变体VQR高效识别水稻NGAC前间区序列邻近基序[J]. 遗传, 2018, 40(12): 1112-1119.
[8]	张源笙,夏琳,桑健,李漫,刘琳,李萌伟,牛广艺,曹佳宝,滕徐菲,周晴,章张. 生命与健康大数据中心资源[J]. 遗传, 2018, 40(11): 1039-1043.
[9]	吴比, 胡伟, 邢永忠. 中国水稻遗传育种历程与展望[J]. 遗传, 2018, 40(10): 841-857.
[10]	李佳,刘运华,张余,陈晨,余霞,余舜武. 干旱对水稻生物钟基因和干旱胁迫响应基因每日节律性变化的影响[J]. 遗传, 2017, 39(9): 837-846.
[11]	徐宗昌,孔英珍. 普通烟草CESA基因家族成员的鉴定、亚细胞定位及表达分析[J]. 遗传, 2017, 39(6): 512-524.
[12]	韩晓斌, 徐冉, 段朋根, 于海跃, 罗越华, 李云海. 水稻斑点叶突变体spl101和spl102的筛选及候选基因鉴定[J]. 遗传, 2017, 39(4): 346-353.
[13]	朱帅旗,龚一富,章丽,俞凯,王何瑜,严小军. 绿色杜氏藻不同β-胡萝卜素羟化酶基因家族胁迫应答模式研究[J]. 遗传, 2017, 39(2): 156-165.
[14]	何一旻, 顾鸣敏. 肌球蛋白重链基因在人类遗传性疾病中的研究进展[J]. 遗传, 2017, 39(10): 877-887.
[15]	向小华, 吴新儒, 晁江涛, 杨明磊, 杨帆, 陈果, 刘贯山, 王元英. 普通烟草WRKY基因家族的鉴定及表达分析[J]. 遗传, 2016, 38(9): 840-856.