棉花病原菌碳水化合物酶类注释和比较分析

doi:10.3864/j.issn.0578-1752.2013.03.006

中国农业科学 ›› 2013, Vol. 46 ›› Issue (3): 496-506.doi: 10.3864/j.issn.0578-1752.2013.03.006

棉花病原菌碳水化合物酶类注释和比较分析

陈捷胤, 柳少燕, 李蕾, 戴小枫

1.中国农业科学院农产品加工研究所，北京100193
2.中国农业科学院作物科学研究所，北京 100081

收稿日期:2012-08-15 出版日期:2013-02-01 发布日期:2013-01-10
通讯作者: 通信作者戴小枫，Tel：010-62815976；E-mail：dxf@caas.net.cn
作者简介:陈捷胤，E-mail：chenjieyin@caas.net.cn
基金资助:
国家“973”计划项目（2011CB100700）、国家科技基础性工作专项（SB2007FY027）

Annotation and Comparative Analysis of the Carbohydrate-Active Enzymes in Cotton Pathogen

CHEN Jie-Yin, LIU Shao-Yan, LI Lei, DAI Xiao-Feng

1.Institite of Agro-products Processing Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193
2.Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081

Received:2012-08-15 Online:2013-02-01 Published:2013-01-10

摘要/Abstract

摘要： 【目的】预测并分析可侵染棉花的病原菌基因组编码的碳水化合物酶类CAZymes，以内生菌绿色木霉和枯草芽孢杆菌为对照，通过碳水化合物酶类家族比较分析确定与病原菌侵染相关的植物细胞壁降解酶类，为细胞壁降解酶参与病原菌侵染机理的研究提供理论依据。【方法】利用已公布的可侵染棉花的7个病原菌全基因组编码蛋白序列，以内生菌绿色木霉为参照，应用BLASTP方法确定共有的核心基因集并构建系统发育树；通过BLASTP方法对基因组编码蛋白的CAZymes进行注释，统计并比较分析病原菌与内生菌CAZymes各个家族基因的差异，获得病原菌相对于内生菌发生扩增的植物细胞壁降解酶类家族；应用MEGA 4.0构建CAZymes亚家族的系统发育树，确定与致病性或者侵染特性相关的CAZymes。【结果】根据共有核心基因集构建了棉花病原菌的系统发育树，初步明确了侵染棉花根部和地上组织病原菌在进化上的差异。CAZymes注释和比较分析表明，病原菌编码的果胶、纤维素、淀粉和木聚糖降解酶类的数量相对于内生菌均有扩增。进一步分析发现，6个果胶降解酶类亚家族（GH35、GH78、GH105、PL1、PL3和PL4）、2个纤维素降解酶类亚家族（GH61和CBM1）、淀粉降解酶类CBM20亚家族和木聚糖降解酶类GH43亚家族相对于内生菌发生了显著扩增；同时，系统发育树分析还发现病原菌PL1和PL3亚家族衍生出了与致病性或者侵染方式相关的基因。【结论】本研究通过7个棉花病原菌与2个内生菌CAZymes的比较分析，发现了棉花病原菌基因组中10个与植物细胞壁降解相关的CAZymes亚家族（GH35、GH43、GH61、GH78、GH105、PL1、PL3、PL4、CBM1和CBM20）显著扩增，它们参与了植物细胞壁组分果胶、纤维素、淀粉和木聚糖的降解作用，初步明确了与棉花病原菌侵染相关的植物细胞壁降解酶类家族及其与病原菌侵染特性的关系。

关键词: 棉花病原菌 , 碳水化合物酶类 , 植物细胞壁降解酶 , 基因家族扩增

Abstract: 【Objective】The objective of this study is to annotate and compare the carbohydrate-active enzymes (CAZymes) in seven cotton pathogens and two endophyte of Trichoderma viride and Bacillus subtilis, and identify plant cell wall degrading enzymes in cotton pathogen.【Method】The core gene set of cotton pathogen and endophytes were selected with BLASTP methods and the phylogenetic tree of nine microorganisms was analyzed. The CAZymes of nine microorganism genomes were annotated with CAZymes database by BLASP method and the CAZymes were classified into different sub-families. All sub-families of plant cell wall degrading enzymes were compared between cotton pathogen and endophyte, and the expansion subfamilies in cotton pathogen were obtained. The phylogenetic tree of expansion sub-families was described by MEGA4.0 and the CAZymes response to pathogenicity or invasion were confirmed.【Result】The phylogenetic analysis of cotton pathogen showed that there was a difference in invasion characteristics between root and shoot. With the CAZymes annotation and comparison, the plant cell wall degrading enzymes of pectin, cellulose, starch and xylan were increased in cotton pathogen genome compared to endophyte, including the pectin degrading sub-families of GH35, GH78, GH105, PL1, PL3 and PL4, cellulose degrading sub-families of GH61 and CBM1, starch degrading sub-families of CBM20, and xylan degrading subfamilies of GH43. Moreover, phylogenetic analysis showed that the pectin degrading genes related to different pathogenicities and invasion were found in PL1 and PL3 sub-families.【Conclusion】Ten expansion sub-families of plant cell wall degrading enzymes in cotton pathogen were found and compared to endophyte which including GH35, GH43, GH61, GH78, GH105, PL1, PL3, PL4, CBM1 and CBM20. These results indicated that the expansion sub-families of pathogen play an important role in plant cell wall degrading and response to the pathogenicity and invasion characteristics.

Key words: cotton pathogen , carbohydrate-active enzymes , plant cell wall degradation enzymes , gene family expansion

陈捷胤, 柳少燕, 李蕾, 戴小枫. 棉花病原菌碳水化合物酶类注释和比较分析[J]. 中国农业科学, 2013, 46(3): 496-506.

CHEN Jie-Yin, LIU Shao-Yan, LI Lei, DAI Xiao-Feng. Annotation and Comparative Analysis of the Carbohydrate-Active Enzymes in Cotton Pathogen[J]. Scientia Agricultura Sinica, 2013, 46(3): 496-506.

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参考文献

[1]van den Brink J, de Vries R P. Fungal enzyme sets for plant polysaccharide degradation. Applied Microbiology and Biotechnology, 2011, 91(6): 1477-1492.

[2]董金皋. 农业植物病理学. 北京: 中国农业出版社, 2001: 198-219.

Dong J G. Agricultural Plant Pathology. Beijing: China Agriculture Press, 2001: 198-219. (in Chinese)

[3]简桂良, 邹亚飞, 马存. 棉花黄萎病连年流行的原因及对策. 中国棉花, 2003, 30(3): 13-14.

Jian G L, Zou Y F, Ma C. Analysis and resolve of Verticillium wilt of cotton in China. Chinese Cotton, 2003, 30(3): 13-14. (in Chinese)

[4]Huang L K, Mahoney R R. Purification and characterization of an endo-polygalacturonase from Verticillium albo-atrum. Journal of Applied Micriobiology, 1999, 86: 145-156.

[5]Bidochka M J, Burke S, Ng L. Extracellular hydrolytic enzymes in the fungal genus Verticillium: adaptations for pathogenesis. Canadian Journal of Microbiology, 1999, 45: 856-864.

[6]Henrissat B, Davies G J. Glycoside hydrolases and glycosyltransferases. Families, modules, and implications for genomics. Plant Physiology, 2000, 124: 1515-1519.

[7]Campbell J A, Davies G J, Bulone V, Henrissat B. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochemistry Journal, 1997, 326: 929-942.

[8]Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho P M, Henrissat B. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochemistry Journal, 2010, 432: 437-444.

[9]Boraston A B, Bolam D N, Gilbert H J, Davies G J. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochemistry Journal, 2004, 382: 769-781.

[10]Ma L J, van der Does H C, Borkovich K A, Coleman J J, Daboussi M J, Galagan J, Cuomo C A, Kistler H C, Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, 2010, 464(7287): 367-373.

[11]Klosterman S J, Subbarao K V, Kang S, Veronese P, Gold S E, Thomma B P, Chen Z, Henrissat B, Lee Y H, Park J, Garcia-Pedrajas M D, Barbara D J, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte S G, Paz Z, Inderbitzin P, Hayes R J, Heiman D I, Young S, Zeng Q, Engels R, Galagan J, Cuomo C A, Dobinson K F, Ma L J. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathogens, 2011, 7(7): e1002137.

[12]Ospina-Giraldo M D, Griffith J G, Laird E W, Mingora C. The CAZyome of Phytophthora spp.: a comprehensive analysis of the gene complement coding for carbohydrate-active enzymes in species of the genus Phytophthora. BMC Genomics, 2010, 11: 525.

[13]Amselem J, Cuomo C A, van Kan J A, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, 2011, 7(8): e1002230.

[14]Coleman J J, Rounsley S D, Rodriguez-Carres M,Vanetten H D. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics, 2009, 5(8): e1000618.

[15]Altschul S F, Madden T L, Schäffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997, 25(17): 3389-3402.

[16]Cantarel B L, Coutinho P M, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Research, 2009, 37(Database issue): 233-238.

[17]Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 1997, 25(24): 4876-4882.

[18]Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 2007, 24: 1596-1599.

[19]Fradin E F, Thomma B P. Physiology and molecular aspects of Verticillium wilt diseases caused by V. dahliae and V. albo-atrum. Molecular Plant Pathology, 2006, 7(2): 71-86.

[20]Delannoy E, Lyon B R, Marmey P, Jalloul A, Daniel J F, Montillet J L, Essenberg M, Nicole M. Resistance of cotton towards Xanthomonas campestris pv. malvacearum. Annual Review of Phytopathology, 2005, 43: 63-82.

[21]Berg G, Ballin G. Bacterial antagonists to Verticillium dahliae Kleb. Journal of Phytopathology, 1994, 141(1): 99-110.

[22]Liu R J. Effect of vesicular-arbuscular mycorrhizal fungi on Verticillium wilt of cotton. Mycorrhiza, 1995, 5(4): 293-297.

[23]Walton J D. Deconstructing the cell wall. Plant Physiology, 1994, 104(4): 1113-1118.

[24]Kämper J, Kahmann R, Bölker M, Ma L J, Galagan J, Birren B W. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 2006, 444(7115): 97-101.

[25]Battaglia E, Benoit I, van den Brink J, Wiebenga A, Coutinho P M, Henrissat B, de Vries R P. Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics, 2011, 12: 38.

[26]Mohnen D. Pectin structure and biosynthesis. Current Opinion in Plant Biology, 2008, 11: 266-277.

棉花病原菌碳水化合物酶类注释和比较分析

Annotation and Comparative Analysis of the Carbohydrate-Active Enzymes in Cotton Pathogen

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