title: Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa.
abstract: Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce's disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties are sensitive to this Gammaproteobacteria. Differential expression of proteins in infected tissue is an established methodology to identify key elements involved in plant defense pathways. Methods. In the current work, we developed a methodology named CHURNER that emphasizes relevant protein functions from proteomic data, based on identification of proteins with similar structures that do not necessarily have sequence homology. Such clustering emphasizes protein functions which have multiple copies that are up/down-regulated, and highlights similar proteins which are differentially regulated. As a working example we present proteomic data enumerating differentially expressed proteins in xylem sap from grapevines that were infected with X. fastidiosa. Results. Analysis of this data by CHURNER highlighted pathogenesis related PR-1 proteins, reinforcing this as the foremost protein function in xylem sap involved in the grapevine defense response to X. fastidiosa. β-1, 3-glucanase, which has both anti-microbial and anti-fungal activities, is also up-regulated. Simultaneously, chitinases are found to be both up and down-regulated by CHURNER, and thus the net gain of this protein function loses its significance in the defense response. Discussion. We demonstrate how structural data can be incorporated in the pipeline of proteomic data analysis prior to making inferences on the importance of individual proteins to plant defense mechanisms. We expect CHURNER to be applicable to any proteomic data set.
authors.affiliation: Department of Plant Sciences, University of California, Davis (UC Davis) , CA , United States of America.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Chakraborty
authors.affiliation: Department of Plant Sciences, University of California, Davis (UC Davis), CA, United States of America; Institute of Genetics and Biochemistry, Federal University of Uberlândia, Campus Umuarama, Uberlândia Minas Gerais, Brazil.
authors.forename: Rafael
authors.initials: R
authors.lastname: Nascimento
authors.affiliation: Institute of Genetics and Biochemistry, Federal University of Uberlândia, Campus Umuarama , Uberlândia Minas Gerais , Brazil.
authors.forename: Paulo A
authors.initials: PA
authors.lastname: Zaini
authors.affiliation: Department of Plant Sciences, University of California, Davis (UC Davis) , CA , United States of America.
authors.forename: Hossein
authors.initials: H
authors.lastname: Gouran
authors.affiliation: Department of Biological Sciences, Tata Institute of Fundamental Research , Mumbai, Maharashtra , India.
authors.forename: Basuthkar J
authors.initials: BJ
authors.lastname: Rao
authors.affiliation: Institute of Genetics and Biochemistry, Federal University of Uberlândia, Campus Umuarama, Uberlândia Minas Gerais, Brazil; Department of Medical Microbiology and Immunology, University of California, Davis (UC Davis), CA, United States of America.
authors.forename: Luiz R
authors.initials: LR
authors.lastname: Goulart
authors.affiliation: Department of Plant Sciences, University of California, Davis (UC Davis) , CA , United States of America.
authors.forename: Abhaya M
authors.initials: AM
authors.lastname: Dandekar
keywords: Functional enrichment; Plant defense; Plant-pathogen interaction; Proteome; Secreted effectors