In silico analysis on promoter sequences of protein-coding genes from Xylella fastidiosa

• Grant number: 10/03382-3
• Support Opportunities: Scholarships in Brazil - Master
• Start date: August 01, 2010
• End date: April 30, 2012
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Aline Maria da Silva
• Grantee: Fernando Domingues Kummel Tria
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Xylella fastidiosa is a xylem limited bacteria that colonizes a wide variety of plants and is the causal agent of diseases in economically important crops, such as coffee, wine and orange trees. Different strains of X. fastidiosa were identified and the genomic sequence for some of them is already known. The comparative analysis of genomic sequences of X. fastidiosa , associated with wet-lab analysis, enabled the proposal of virulence mechanisms. The biofilm formation, for example, is thought to occlude the xylem vessel causing water and nutrients stress in infected plants. Nevertheless, it is hypothesized that other important mechanisms remain to be unraveled. Although some regulons of X. fastidiosa have been characterized there are no comparative studies of promoter regions among different genomes of X. fastidiosa or large-scale identification of cis-regulatory elements in these genomes. Our goal in this research project is to perform in silico analysis on promoters regions of protein-coding genes from Xylella fastidiosa in order to raise new evidence to better understand the dynamics of transcriptional regulation of its genes, including those involved in mechanisms of pathogenicity and virulence. In a first stage we will analyze promoter regions of the reference strain 9a5c to predict regulatory elements in a genome- wide perspective. In a second stage we plan to conduct comparative analyzes involving corresponding promoter sequences from different X. fastidiosa strains. We expect to identify differences in regulatory regions possibly associated to phenotypic variation.

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

TRIA, Fernando Domingues Kummel. In silico analysis on promoter sequences of protein-coding genes from Xylella fastidiosa. 2013. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.