Scientia Agricultura Sinica ›› 2013, Vol. 46 ›› Issue (3): 496-506.doi: 10.3864/j.issn.0578-1752.2013.03.006

• PLANT PROTECTION • Previous Articles     Next Articles

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

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

  1. 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

PDF

793

Cited

1

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

[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.
No related articles found!
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd