Intra-species proteome within a natural population of Shewanella baltica
EMSL Project ID
14094
Abstract
With the inability to easily distinguish morphological features of bacteria as with larger macro-organisms, rRNA gene surveys have been used to assess organismal diversity of bacteria. From the very first molecular approaches to quantify microbial diversity and community structure over 15 years ago, researchers have consistently recovered large clusters of closely related rRNA gene sequences from a majority of environments. Recent attempts to explain this long-observed phenomenon indicate that this rRNA sequence ‘micro-diversity’ is a real feature of bacterial populations, and not an artifact of PCR or a consequence of intragenomic rRNA gene redundancy. High-levels of genome sequence heterogeneity in metagenomics provide confirmation that bacterial species exist in nature as populations of diverse genomic compositions. It is unknown, however, whether these substantial intra-species genomic differences are translated by the cell and therefore part of the cell proteome. We will use the comparative proteomic analysis of twelve strains of S. baltica to determine the core proteome in a natural population of the same bacterial species, Shewanella baltica, and identify the evolutionary and ecological forces creating structuring the proteome within this population. The twelve strains of Shewanella baltica chosen for proteomic analysis were isolated from samples of the central Baltic Sea, where they were found to be the dominant cultivable population during two sampling trips (1986, 1987). These strains were isolated from three different ecological zones in the water column: the oxic zone, oxic-anoxic transition zone, and the anoxic zone. The S. baltica strains are identical in rRNA gene sequence, and we have strong evidence that they differ significantly in genome content and organization (differ by up to 30% at the DNA-DNA reassociation level). One strain of S. baltica, strain OS155, has been sequenced to 8X coverage (~200 contigs >2 kb) at JGI under the DOE Microbial Genomes program and has a genome size of 5.1 Mbp with 4734 ORFs, and a %G+C content of 46.2%. A complete genome sequence is available for S. oneidensis MR-1 that contains orthologs for 72.5% of the S. baltica OS155 genes, and these strains share 85% average nucleotide identity. To our knowledge, this will be the first application of whole proteome mass spectroscopy data to comparative microbial taxonomy.
Each S. baltica strain will be grown under aerobic conditions in Difco Marine Broth 2216 to mid-log phase and harvested for whole-cell protein. Samples harvested in mid-log phase will be harvested by centrifugation, washed in 1X PBS, and aliquoted in 10X 1 mL aliquots per strain. Approximately 30 LTQ runs per strain and 4 FTICR runs per strain will be required.
Project Details
Project type
Exploratory Research
Start Date
2005-04-20
End Date
2006-01-30
Status
Closed
Released Data Link
Team
Principal Investigator