Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Shewanella Federation
37
Functional Analysis of Shewanella, A Cross Genome Comparison
Margrethe H. Serres* (mserres@mbl.edu) and Monica Riley
Marine Biological Laboratory, Woods Hole, MA
The genome sequence of Shewanella oneidensis MR-1, a microbe with unique metabolic and respiratory properties including the use of metals as electron acceptors, has been published (Heidelberg et al. 2002). Recently six additional Shewanella genomes; S. putrefaciens CN-32, S. alga PV-4, S. amazonensis SB2B, S. baltica OS155, S. frigidimarina NCIMB400, and S. denitrificans OS2717 have been sequenced at the Joint Genome Institute. The new strains were selected as representatives of different ecological niches and redox environments ranging from terrestrial to marine and freshwater sediments. We are making use of the new sequences to do a comparative analysis between the protein coding sequences of S. oneidensis and MR-1 and those of the newly available Shewanella strains. In addition we are including the genomes of Escherichia coli, an experimentally well studied organism, and Geobacter sulfurreducens, an organism with metal reducing capabilities. Our aim is to detect variations in the protein content that may be related to differences in metabolic properties and environmental adaptation for the organisms.
In our previous work we have assembled groups of sequence similar proteins of S. oneidensis MR-1. We initially identified fused proteins (155) as these complicate the grouping process and separated them into stand-alone functional entities. The Darwin algorithm was used to detect sequence similarity among the protein sequences. A transitive grouping process was applied to generate sequence similar groups containing both closely related as well as more distantly related members. We also restrict the membership of a protein to one sequence similar group. As a result we identified 406 paralogous or sequence similar groups with memberships ranging from 2 to 64. The largest paralogous groups were found to encode for response regulators, ATP-binding component of the ABC superfamily transporters, transcriptional regulators of the LysR family, regulatory proteins, and sensory histidine kinases. The group sizes show a power-law distribution with most of the groups having few members and few groups having many members. The paralogous groups represent ancestral genes which have gone through duplication and divergence to generate today’s gene families. These gene families encode for proteins with related functions. Gene duplication and divergence is thought of as an important means by which an organism may specialize or generate functions.
We are making use of the paralogous group data for the S. oneidensis MR-1 genome to search for sequence matches in the newly sequenced Shewanella genomes and in E. coli and G. sulfurreducens. Data will be presented on the distribution of homologs to the members of the S. oneidensis MR-1 paralogous groups. The data will be analyzed to identify differences or similarities between the organisms and further use this information to shed light on functions that may be of importance to the metabolic properties and environmental fitness of the organisms.
One of the larger S. oneidensis MR-1 paralogous groups was found to contain a family of 27 methyl-accepting chemotaxis proteins (MCPs). These proteins are located in the membrane where they serve as signal receptors for the chemotaxis apparatus. Five MCPs are encoded in the E. coli genome and they are known to bind specific attractants or repellants. The expanded repertoire of MCPs in S. oneidensis MR-1 suggests that the chemotactic response and environmental sensing is highly specialized in this organism. Sequence similarity between the S. oneidensis MR-1 MCPs and the proteins encoded in the newly sequenced Shewanella strains shows an expansion of the MCPs versus that of E. coli for all the strains. Interestingly the number of proteins with sequence matches varies widely in the different genomes from 19 to 40. G. sulfurreducens appears to contain 33 homologs of the S. oneidensis MR-1 MCP group. The sequence similarity and distribution of other chemotaxis related proteins will be presented.
* Presenting author
