(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Alphaproteobacteria: NE > Rhodobacterales: NE > Rhodobacteraceae: NE > Ruegeria: NE > Ruegeria pomeroyi: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Silicibacter pomeroyi: N, E.
Ruegeria pomeroyi DSS-3: N, E.
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MRRAAVLALLAGLWGQGAQAGCAAEAAPCETADGTYHIALPEAENPPVLI FLHGHGGEGAATLRNARLVAPLLARGWAVIAPDGQSRAPGRPRSWTFFPG WEGRDEPAFLAQVLGEASARFGLDADRAVLGGFSAGAFMVTYLACATPGA YRAYVPVSGGFWRPQPDRCAGPVHLFQTHGWADPVVPLEGRFLGGGRFQQ GDIFAGLELWRQTNGCVEHKPDGFDQTGPFLRRRWQGCSGGSLEFALFPG GHTVPEGWADMMADWVEALPAP
References
Title: An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3 Rivers AR, Smith CB, Moran MA Ref: Stand Genomic Sci, 9:11, 2014 : PubMed
When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome.
Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
