Project Number: 1907-21000-035-00
Project Type: Appropriated

Start Date: Feb 26, 2012
End Date: Feb 25, 2017

Objective:
1: Describe key bacterial pathways involved in disease establishment and progression. 1A: Characterize the role of ncRNAs and the RNA binding proteins Crc and Hfq in pathogenesis. 1B: Identify ECF sigma factor regulons and determine their role(s) in plant interactions. 2: Identify bacterial transcriptional responses to plant signals and defense systems in planta. 2A: In vitro, examine bacterial transcriptional responses to conditions thought to be relevant in planta. 2B: Examine bacterial transcription during plant infection. 2C: Evaluate each gene in P. syringae for its contribution to fitness in plants. 2D: Develop systems models of pathogen-plant interactions.

Approach:
Bacterial plant pathogens are responsible for major losses in nearly all crops. Attempts to develop resistance in host plant species have been hindered by a lack of understanding of the complex network of plant-microbe interactions. A central problem is that the pathways used by bacteria to sense and respond to the environment inside the plant are largely unknown. Building upon our previous work in Pseudomonas syringae pv. tomato DC3000, we will address this problem by analyzing non-coding RNAs and ECF sigma factors, two classes of regulatory factors that are known linchpins of gene regulation. We will use established deep sequencing methods, such as ChIP-Seq, RNA-Seq and RNA 5'-end capture, and novel methods, such as genomic footprinting and in planta RNA-Seq, to monitor bacterial gene expression as it occurs during infection. The synthesis of the data sets from these experiments will reveal many key regulatory pathways involved in pathogenesis and virulence.