Silicibacter pomeroyi

Silicibacter pomeroyi is a species of Gram-negative, rod-shaped, aerobic dimethylsulfoniopropionate-demethylating bacterium. Its type strain is DSS-3T (=ATCC 700808T =DSM 15171T).[1] Muramatsu et al. 2007 considered unifying Silicibacter with Ruegeria, however the species found in the former genus are considered phenotypically different enough to warrant their current taxonomic standing.[2] Its genome has been sequenced.[3]

Silicibacter pomeroyi
Scientific classification
Kingdom:
Bacteria
Phylum:
Proteobacteria
Class:
Alphaproteobacteria
Order:
Rhodobacterales
Family:
Rhodobacteraceae
Genus:
Silicibacter
Species:
Silicibacter pomeroyi

González et al. 2003

Discovery

Silicibacter pomeroyi was discovered off the coast of the Eastern United States in the laboratory of Mary Ann Moran, Ph.D.[4] at the University of Georgia.

S. pomeroyi was named after Lawrence "Larry" Pomeroy, the marine microbial ecologist who notably established in 1974 that marine bacteria play a substantial and pivotal role in ocean food web dynamics.[5] Pomeroy was also a researcher at the University of Georgia.

Genome

The genome of the Silicibacter pomeroyi type strain (DSS-3) was completed in 2004. The genome is 4,109,442 base pairs long with a megaplasmid that is 491,611 base pairs long.[6]

Ecology

Silicibacter pomeroyi is a coastal ocean bacterium in a lineage of bacteria commonly considered ecological "generalists."[6] The relatively large genome of S. pomeroyi, as compared to other marine bacterial species, supports this concept. In line with this, S.pomeroyi has a highly versatile ability to utilize and sequester carbon and energy.[7]

S. pomeroyi also has the ability to degrade dimethylsulfoniopropionate (DMSP), a sulfur-containing algal osmolyte and use the sulfur to synthesize sulfur-containing amino acids. Although many marine bacteria are capable of degrading DMSP, the genes and proteins used to do so were elusive to researchers for many years. It was in S. pomeroyi that Howard and colleagues discovered the first gene that degrades DMSP.[8] This gene (dmdA)[8] codes for a protein (DmdA) that removes a methyl group (-CH3) from DMSP. The DmdA protein has since been further characterized from S. pomeroyi,[9] as well as the transcriptional response of the dmdA gene to the presence of DMSP[10] and the sequence diversity of the dmdA gene.[11] This demethylation process is the first step in the highly sought-after demethylation pathway of DMSP degradation in marine bacteria. Following the discovery of the dmdA gene, the gene sequence was used to establish that over half of marine bacteria, including both open-ocean and coastal bacteria, are capable of demethylating DMSP.[12]

Following the discovery of the demethylation pathway of DMSP degradation in S. pomeroyi, an alternative pathway of DMSP degradation was discovered in which DMSP is cleaved in half instead of demethylated, a process which S. pomeroyi also is capable.[13]

References
  1. Gonzalez, J. M. (2003). "Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments". International Journal of Systematic and Evolutionary Microbiology. 53 (5): 1261–1269. doi:10.1099/ijs.0.02491-0. ISSN 1466-5026. PMID 13130004.
  2. MURAMATSU (Y.), UCHINO (Y.), KASAI (H.), SUZUKI (K.) and NAKAGAWA (Y.): Ruegeria mobilissp. nov., a member of the Alphaproteobacteria isolated in Japan and Palau. Int. J. Syst. Evol. Microbiol., 2007,57, 1304-1309.
  3. Moran, Mary Ann; Buchan, Alison; González, José M.; Heidelberg, John F.; Whitman, William B.; Kiene, Ronald P.; Henriksen, James R.; King, Gary M.; Belas, Robert; Fuqua, Clay; Brinkac, Lauren; Lewis, Matt; Johri, Shivani; Weaver, Bruce; Pai, Grace; Eisen, Jonathan A.; Rahe, Elisha; Sheldon, Wade M.; Ye, Wenying; Miller, Todd R.; Carlton, Jane; Rasko, David A.; Paulsen, Ian T.; Ren, Qinghu; Daugherty, Sean C.; Deboy, Robert T.; Dodson, Robert J.; Durkin, A. Scott; Madupu, Ramana; Nelson, William C.; Sullivan, Steven A.; Rosovitz, M. J.; Haft, Daniel H.; Selengut, Jeremy; Ward, Naomi (2004). "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment". Nature. 432 (7019): 910–913. Bibcode:2004Natur.432..910M. doi:10.1038/nature03170. ISSN 0028-0836. PMID 15602564.
  4. "Moran Lab". moranresearch.uga.edu. Retrieved 2016-07-29.
  5. Pomeroy, Lawrence R. (1974-09-01). "The Ocean's Food Web, A Changing Paradigm". BioScience. 24 (9): 499–504. doi:10.2307/1296885. ISSN 0006-3568. JSTOR 1296885.
  6. Moran, Mary Ann; Buchan, Alison; González, José M.; Heidelberg, John F.; Whitman, William B.; Kiene, Ronald P.; Henriksen, James R.; King, Gary M.; Belas, Robert (2004-12-16). "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment". Nature. 432 (7019): 910–913. Bibcode:2004Natur.432..910M. doi:10.1038/nature03170. ISSN 0028-0836. PMID 15602564.
  7. Newton, Ryan J.; Griffin, Laura E.; Bowles, Kathy M.; Meile, Christof; Gifford, Scott; Givens, Carrie E.; Howard, Erinn C.; King, Eric; Oakley, Clinton A. (2010-06-01). "Genome characteristics of a generalist marine bacterial lineage". The ISME Journal. 4 (6): 784–798. doi:10.1038/ismej.2009.150. ISSN 1751-7362. PMID 20072162.
  8. Howard, Erinn C.; Henriksen, James R.; Buchan, Alison; Reisch, Chris R.; Bürgmann, Helmut; Welsh, Rory; Ye, Wenying; González, José M.; Mace, Kimberly (2006-10-27). "Bacterial Taxa That Limit Sulfur Flux from the Ocean". Science. 314 (5799): 649–652. Bibcode:2006Sci...314..649H. doi:10.1126/science.1130657. ISSN 0036-8075. PMID 17068264.
  9. Reisch, Chris R.; Moran, Mary Ann; Whitman, William B. (2008-12-01). "Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi". Journal of Bacteriology. 190 (24): 8018–8024. doi:10.1128/JB.00770-08. ISSN 1098-5530. PMC 2593244. PMID 18849431.
  10. Bürgmann, Helmut; Howard, Erinn C.; Ye, Wenying; Sun, Feng; Sun, Shulei; Napierala, Sarah; Moran, Mary Ann (2007-11-01). "Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP)". Environmental Microbiology. 9 (11): 2742–2755. doi:10.1111/j.1462-2920.2007.01386.x. ISSN 1462-2920. PMID 17922758.
  11. Varaljay, Vanessa A.; Howard, Erinn C.; Sun, Shulei; Moran, Mary Ann (2010-01-15). "Deep Sequencing of a Dimethylsulfoniopropionate-Degrading Gene (dmdA) by Using PCR Primer Pairs Designed on the Basis of Marine Metagenomic Data". Applied and Environmental Microbiology. 76 (2): 609–617. doi:10.1128/AEM.01258-09. ISSN 0099-2240. PMC 2805212. PMID 19948858.
  12. Howard, Erinn C.; Sun, Shulei; Biers, Erin J.; Moran, Mary Ann (2008-09-01). "Abundant and diverse bacteria involved in DMSP degradation in marine surface waters". Environmental Microbiology. 10 (9): 2397–2410. doi:10.1111/j.1462-2920.2008.01665.x. ISSN 1462-2920. PMID 18510552.
  13. Todd, Jonathan D.; Rogers, Rachel; Li, You Guo; Wexler, Margaret; Bond, Philip L.; Sun, Lei; Curson, Andrew R. J.; Malin, Gill; Steinke, Michael (2007-02-02). "Structural and Regulatory Genes Required to Make the Gas Dimethyl Sulfide in Bacteria". Science. 315 (5812): 666–669. Bibcode:2007Sci...315..666T. doi:10.1126/science.1135370. ISSN 0036-8075. PMID 17272727.

Further reading
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