Ruegeria pomeroyi
| Silicibacter pomeroyi | |
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| Species: | Ruegeria pomeroyi (Gonzálezet al.2003) Yiet al.2007
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Ruegeria pomeroyiis a species ofGram-negative,rod-shaped, aerobicdimethylsulfoniopropionate-demethylatingbacterium. Its type strain is DSS-3T(=ATCC 700808T=DSM 15171T).[1]Its genome has been sequenced.[2]
Discovery
[edit]Ruegeria pomeroyiwas discovered off the coast of the Eastern United States in the laboratory of Mary Ann Moran, Ph.D.[3]at the University of Georgia.
R. pomeroyiwas named after Lawrence "Larry" Pomeroy, the marine microbial ecologist who notably established in 1974 thatmarine bacteriaplay a substantial and pivotal role inocean food webdynamics.[4]Pomeroy was also a researcher at the University of Georgia.
Genome
[edit]The genome of theRuegeria pomeroyitype 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.[5]
Ecology
[edit]Ruegeria pomeroyiis a coastal ocean bacterium in a lineage of bacteria commonly considered ecological "generalists."[5]The relatively large genome ofR. pomeroyi,as compared to other marine bacterial species, supports this concept. In line with this,R. pomeroyihas a highly versatile ability to utilize andsequester carbonand energy.[6]
R. pomeroyialso has the ability to degradedimethylsulfoniopropionate(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 inR. pomeroyithat Howard and colleagues discovered the first gene that degrades DMSP.[7]This gene (dmdA)[7]codes for a protein (DmdA) that removes a methyl group (-CH3) from DMSP. The DmdA protein has since been further characterized fromR. pomeroyi,[8]as well as the transcriptional response of thedmdAgene to the presence of DMSP[9]and the sequence diversity of thedmdAgene.[10]This demethylation process is the first step in the highly sought-after demethylation pathway of DMSP degradation in marine bacteria. Following the discovery of thedmdAgene, 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.[11]
Following the discovery of the demethylation pathway of DMSP degradation inR. pomeroyi,an alternative pathway of DMSP degradation was discovered in which DMSP is cleaved in half instead of demethylated, a process whichR. pomeroyialso is capable.[12]
References
[edit]- ^Gonzalez, J. M. (2003)."Silicibacter pomeroyisp. nov. andRoseovarius nubinhibenssp. 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.ISSN1466-5026.PMID13130004.
- ^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 ofSilicibacter pomeroyireveals adaptations to the marine environment ".Nature.432(7019): 910–913.Bibcode:2004Natur.432..910M.doi:10.1038/nature03170.ISSN0028-0836.PMID15602564.
- ^"Moran Lab".moranresearch.uga.edu.Retrieved2016-07-29.
- ^Pomeroy, Lawrence R. (1974-09-01). "The Ocean's Food Web, A Changing Paradigm".BioScience.24(9): 499–504.doi:10.2307/1296885.ISSN0006-3568.JSTOR1296885.
- ^abMoran, 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.ISSN0028-0836.PMID15602564.
- ^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.ISSN1751-7362.PMID20072162.
- ^abHoward, 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.ISSN0036-8075.PMID17068264.S2CID41199461.
- ^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.ISSN1098-5530.PMC2593244.PMID18849431.
- ^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.ISSN1462-2920.PMID17922758.
- ^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.Bibcode:2010ApEnM..76..609V.doi:10.1128/AEM.01258-09.ISSN0099-2240.PMC2805212.PMID19948858.
- ^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.ISSN1462-2920.PMID18510552.
- ^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.ISSN0036-8075.PMID17272727.S2CID22472634.
Further reading
[edit]- Helmut Burgmann, Erinn C. Howard, Wenying Ye, Feng Sun, Shulei Sun, Sarah Napierala &Mary Ann Moran(November 2007)."Transcriptional response ofSilicibacter pomeroyiDSS-3 to dimethylsulfoniopropionate (DMSP) ".Environmental Microbiology.9(11): 2742–2755.doi:10.1111/j.1462-2920.2007.01386.x.PMID17922758.
{{cite journal}}:CS1 maint: multiple names: authors list (link) - Reisch, C. R.; Moran, M. A.; Whitman, W. B. (2008)."Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) fromPelagibacter ubiqueandSilicibacter pomeroyi".Journal of Bacteriology.190(24): 8018–8024.doi:10.1128/JB.00770-08.ISSN0021-9193.PMC2593244.PMID18849431.