Why identify regulatory elements of Pseudomonas syringe?

Predicted structure of a small RNA involved in bacterial response to internal iron levels found in Pseudomonas species.

Pseudomonas syringae pv. tomato strain DC3000 is a bacterial plant pathogen mainly characterized as causing bacterial speck disease on tomato plants, and is well known as the model organism for the study of plant-pathogen interactions. This bacterium is a major problem for tomato growers and therefore is an agriculturally important plant pathogen.

Although the genome of this bacterium has been sequenced and annotated, information, such as where promoters and regulatory sites are located, and what genes are transcribed together is lacking. Elucidating this important information is essential to dissecting global gene regulatory pathways. Also, determining the location and function of small RNAs, which are a newly discovered class of regulators that have been shown to control expression of many factors involved in disease, is necessary to fully understand the virulence mechanisms employed by Pseudomonas syringae during infection. Development of high-throughput genome-scale strategies will help delineate promoter sequences, promoter classes, and identify those genes that are co-regulated. These studies will provide critical information for a more complete transcript analysis of P. syringae, which ultimately will help in understanding the pathogenesis of this bacterium and other plant pathogens. Also, determining the contribution of small RNAs in the biology of the organism and plant infection will assist us in finding new strategies to improve disease management.

How do we identify regulatory elements?

To better characterize the genome and to decipher mechanisms of global gene regulation of this pathogen, we are developing new cutting edge genomics-related techniques that have not been previously used to study bacterial gene expression. One high-throughput approach, RNA profiling, evaluates the RNA population (transcripts) of the bacteria and compares this with the sequenced genome (DNA). These experiments take advantage of the new generation sequencers. To analyze the high throughput sequencing data, computational algorithms and tools are being developed in our laboratory. By combining RNA profiling experiments with computational methods and molecular biology techniques, we are discovering and characterizing novel regulatory elements.

What will identifying regulatory elements tell us?

Establishing new high-throughput techniques for analyzing bacterial RNA will have a significant impact on genome annotation of bacteria as well as the study of bacterial gene regulation. These genomics-related techniques have the potential to be applied to other plant pathogens, including bacteria and fungi and therefore may impact entire research communities. The discovery of novel regulatory elements, combined with the other data generated from other projects in our laboratory will provide a more complete characterization of how the bacterium globally adapts to surrounding environmental conditions, grows, and causes disease in plants.

3D Model of a protein (Hfq) that has been shown to interact with many small RNAs. The protein is being isolated and used to identify novel small RNAs in P. syringae	Swarming ability of Pseudomonas syringae. This phenomena is important for the formation of environmental resistant bacterial populations and is controlled by a small RNA