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United States Department of Agriculture

Agricultural Research Service

Research Project: PSEUDOMONAS SYRINGAE SYSTEMS BIOLOGY

Location: Plant-Microbe Interactions Research

Title: Ecf Sigma Factor Regulation in Pseudomonas Syringae

Author
item Swingle, Bryan

Submitted to: Molecular Genetics of Bacteria and Phage
Publication Type: Abstract Only
Publication Acceptance Date: August 6, 2008
Publication Date: August 20, 2008
Citation: Swingle, B.M. 2008. Ecf sigma factor regulation in pseudomonas syringae. Molecular Genetics of Bacteria and Phage. p. 139.

Technical Abstract: Pseudomanads are renowned for their capacity to adapt to diverse environments, a fact that is reflected by the proportion of their genomes dedicated to encoding transcription regulators. Members of the Pseudomonas genus include species that are adapted to pathogenic and symbiotic lifestyles in association with animals, plants and insects as well as free living in soil and water. With the recent completion of genome sequences from several pseudomonad species, we now have the ability to make global genome comparisons to examine how orthologous regulators have been adapted to solve niche specific challenges. Examination of pseudomonad genome sequences revealed that these organisms are endowed with overlapping sets of orthologous sigma factors. We are focused on the subset of sigma factors that have been classified as being involved with iron uptake or metaloregulation based on their sequence similarity to FecI, which regulates iron citrate uptake in Escherichia coli. These regulators are members of the group IV or extracytoplasmic function (ECF) sigma factors and function by altering the promoter specificity of RNA polymerase in response to specific environmental stimuli. We are currently working to characterize the promoter motifs recognized by several members of this class of sigma factors from Pseudomonas syringae pv. tomato DC3000. We are using combinations of conventional molecular and high throughput techniques to identify the nucleotides within promoters that are important for mediating differential regulation. This information is the basis for computational models that are used to (1) summarize the relative conservation of a 30 bp region of the promoter and (2) as a tool to identify other sequences with similarity to the characterized promoters. We are testing the hypothesis that some of the sequences identified by the computational models will function as bona fide promoters and will be useful to predict regulon members for orthologous sigma factors in related pseudomonads. Furthermore, comparison of the regulon members will then be used to generate predictions regarding the species-specific role of each sigma factor in the related pseudomonads.

Last Modified: 7/24/2014
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