Project Number: 1907-21000-027-04
Project Type: Specific Cooperative Agreement

Start Date: Sep 30, 2006
End Date: Sep 29, 2008

Objective:
The objective of this research project is to analyze and summarize results obtained from previous experiments in which the proteome of Pseudomonas syringae pv. tomato DC3000 (hereafter DC3000) was examined. In particular, protein expression was examined using high-throughput mass spectrometry to examine gene expression at a global level. These data must now be thoroughly assessed in preparation for publication. In addition, we will use chemostats to generate data necessary to construct a coarse-grained metabolic model for DC3000. This will involve measuring the growth of DC3000 under carefully controlled conditions, especially with respect to iron bioavailability, and using analytical techniques to determine protein, nucleic acid, carbohydrate, iron and other cellular components at a gross level.

Approach:
The analysis of proteomics data will involve examination of the very large data set generated previously by mass spectrometry for proteins derived from DC3000. Individual ¿hits¿ must be triaged to determine whether protein identifications are reliable. The data set must be evaluated as a whole to determine what kinds of proteins have been captured and these observations linked to the specific conditions under which the cells were grown. Coarse-grained metabolic modeling will be approached using methods developed by one of our collaborators, Michael Shuler, for use in E. coli. Cells will be grown in chemostats and conditions carefully perturbed. Growth response will be monitored along with measurements of cellular contents. These data will be used to construct a mathematical model that reproduces the observed behavior. Since our research group is focused on iron and gene regulation, we will be particularly interested in experiments that probe the response DC3000 makes to this important micronutrient.