title: The first genomic and proteomic characterization of a deep-sea sulfate reducer: insights into the piezophilic lifestyle of Desulfovibrio piezophilus.
abstract: Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
authors: Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM110, Marseille, France. nathalie.pradel@ird.fr
authors: Nathalie
authors: N
authors: Pradel
authors: Boyang
authors: B
authors: Ji
authors: Grégory
authors: G
authors: Gimenez
authors: Emmanuel
authors: E
authors: Talla
authors: Patricia
authors: P
authors: Lenoble
authors: Marc
authors: M
authors: Garel
authors: Christian
authors: C
authors: Tamburini
authors: Patrick
authors: P
authors: Fourquet
authors: Régine
authors: R
authors: Lebrun
authors: Philippe
authors: P
authors: Bertin
authors: Yann
authors: Y
authors: Denis
authors: Matthieu
authors: M
authors: Pophillat
authors: Valérie
authors: V
authors: Barbe
authors: Bernard
authors: B
authors: Ollivier
authors: Alain
authors: A
authors: Dolla
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000596:Amino Acids / Q000378:metabolism; D001274:Atmospheric Pressure; D003901:Desulfovibrio / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D004734:Energy Metabolism / Q000235:genetics; D006874:Hydrostatic Pressure; D008055:Lipids / Q000096:biosynthesis; D005810:Multigene Family / Q000235:genetics; D009792:Oceans and Seas; D010084:Oxidation-Reduction; D011312:Pressure; D040901:Proteomics; D013045:Species Specificity; D013431:Sulfates / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D008055:Lipids; D013431:Sulfates
references: Microbiology (Reading). 2008 Dec;154(Pt 12):3649-3658
references: 19047732
references: Gene. 2005 Feb 14;346:7-12
references: 15716095
references: Mar Biotechnol (NY). 2007 Jul-Aug;9(4):429-36
references: 17497195
references: Biosci Biotechnol Biochem. 2007 Oct;71(10):2347-57
references: 17928722
references: Res Microbiol. 1999 Jan-Feb;150(1):21-32
references: 10096131
references: J Bacteriol. 2009 Mar;191(6):1924-32
references: 19103920
references: Biochim Biophys Acta. 2002 Mar 25;1595(1-2):367-81
references: 11983409
references: Int J Syst Evol Microbiol. 2010 Jan;60(Pt 1):33-38
references: 19648352
references: J Bacteriol. 2011 Aug;193(16):4297-8
references: 21705594
references: J Biotechnol. 2006 Oct 20;126(1):11-25
references: 16780980
references: Philos Trans R Soc Lond B Biol Sci. 1982 Sep 13;298(1093):543-61
references: 6127739
references: J Biomol Struct Dyn. 2004 Oct;22(2):205-14
references: 15317481
references: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-8
references: 16043709
references: Res Microbiol. 2010 Dec;161(10):799-809
references: 21035541
references: J Bacteriol. 2009 Oct;191(20):6383-93
references: 19700526
references: FEMS Microbiol Lett. 2007 Feb;267(1):108-12
references: 17166225
references: PLoS One. 2009;4(1):e4192
references: 19145256
references: Environ Microbiol. 2010 Sep;12(9):2613-23
references: 20482588
references: Extremophiles. 2002 Dec;6(6):507-14
references: 12486460
references: Science. 2004 Dec 24;306(5705):2216-21
references: 15618510
references: Int J Syst Evol Microbiol. 2003 Sep;53(Pt 5):1585-1590
references: 13130052
references: Gene. 2005 Feb 14;346:1-6
references: 15716096
references: J Bacteriol. 2008 Mar;190(5):1699-709
references: 18156275
references: Nat Biotechnol. 2004 May;22(5):554-9
references: 15077118
references: FEMS Microbiol Ecol. 2012 Dec;82(3):616-28
references: 22703298
references: Int J Syst Bacteriol. 1997 Apr;47(2):515-21
references: 9103642
references: Int J Syst Evol Microbiol. 2011 Nov;61(Pt 11):2706-2711
references: 21169465
references: Front Microbiol. 2012 Jul 17;3:253
references: 22822404
references: Database (Oxford). 2009;2009:bap021
references: 20157493
references: Ann N Y Acad Sci. 2010 Feb;1189:143-8
references: 20233381
references: PLoS One. 2007 Sep 19;2(9):e914
references: 17878949
references: Front Microbiol. 2011 Jun 29;2:135
references: 21747813
references: Appl Environ Microbiol. 2004 Feb;70(2):1231-3
references: 14766611
references: Int J Syst Evol Microbiol. 2002 May;52(Pt 3):765-772
references: 12054236
references: Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):173-178
references: 12656169
references: FEBS Lett. 2004 Jan 2;556(1-3):153-60
references: 14706843
references: Front Microbiol. 2011 Apr 19;2:69
references: 21747791
references: Trends Microbiol. 2010 Aug;18(8):374-81
references: 20646925
references: Mar Biotechnol (NY). 2010 Nov;12(6):719-27
references: 20514504
references: Science. 2005 Mar 4;307(5714):1459-61
references: 15746425
references: Environ Microbiol. 2012 May;14(5):1333-46
references: 22404914
references: BMC Genomics. 2005 Sep 14;6:122
references: 16162277
references: Extremophiles. 2009 Jan;13(1):21-30
references: 18818866
references: Annu Rev Microbiol. 1995;49:777-805
references: 8561479
references: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references: 15034147