title: Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus.
abstract: BACKGROUND
  The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).
  
  
  RESULTS
  A total of 1,007 PAS domains and 686 PDC domains distributed over 1,174 proteins were identified. For 28 Gram-positive bacteria, the distribution, organization, and molecular evolution of PDC/PAS domains were analyzed in greater detail, with a special emphasis on the genus Staphylococcus. Compared to other bacteria the staphylococci have relatively fewer proteins (6-9) containing PDC/PAS domains. As a general rule, the staphylococcal genomes examined in this study contain a core group of seven PDC/PAS domain-containing proteins consisting of WalK, SrrB, PhoR, ArlS, HssS, NreB, and GdpP. The exceptions to this rule are: 1) S. saprophyticus lacks the core NreB protein; 2) S. carnosus has two additional PAS domain containing proteins; 3) S. epidermidis, S. aureus, and S. pseudintermedius have an additional protein with two PDC domains that is predicted to code for a sensor histidine kinase; 4) S. lugdunensis has an additional PDC containing protein predicted to be a sensor histidine kinase.
  
  
  CONCLUSIONS
  This comprehensive analysis demonstrates that variation in PDC/PAS domains among bacteria has limited correlations to the genome size or pathogenicity; however, our analysis established that bacteria having a motile phase in their life cycle have significantly more PDC/PAS-containing proteins. In addition, our analysis revealed a tremendous amount of variation in the number of PDC/PAS-containing proteins within genera. This variation extended to the Staphylococcus genus, which had between 6 and 9 PDC/PAS proteins and some of these appear to be previously undescribed signaling proteins. This latter point is important because most staphylococcal proteins that contain PDC/PAS domains regulate virulence factor synthesis or antibiotic resistance.
authors.affiliation: Department of Computer Science and Engineering, University of Nebraska, Lincoln, NE 68588-0115, USA.
authors.forename: Neethu
authors.initials: N
authors.lastname: Shah
authors.forename: Rosmarie
authors.initials: R
authors.lastname: Gaupp
authors.forename: Hideaki
authors.initials: H
authors.lastname: Moriyama
authors.forename: Kent M
authors.initials: KM
authors.lastname: Eskridge
authors.forename: Etsuko N
authors.initials: EN
authors.lastname: Moriyama
authors.forename: Greg A
authors.initials: GA
authors.lastname: Somerville
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D008958:Models, Molecular; D013210:Staphylococcus / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins
references.citation: PLoS One. 2010 Jun 11;5(6):e11071
references.pmid: 20552019
references.citation: J Bacteriol. 2001 Feb;183(4):1113-23
references.pmid: 11157922
references.citation: Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8
references.pmid: 3162770
references.citation: Pediatrics. 2008 Feb;121(2):229-34
references.pmid: 18245412
references.citation: PLoS Pathog. 2011 Sep;7(9):e1002217
references.pmid: 21909268
references.citation: Future Microbiol. 2010 Sep;5(9):1383-402
references.pmid: 20860483
references.citation: J Bacteriol. 2002 Dec;184(23):6624-34
references.pmid: 12426351
references.citation: Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15251-6
references.pmid: 11734624
references.citation: Bioinformatics. 2005 Apr 1;21(7):951-60
references.pmid: 15531603
references.citation: Nat Struct Biol. 2003 Dec;10(12):980
references.pmid: 14634627
references.citation: Appl Environ Microbiol. 2010 Dec;76(24):8160-73
references.pmid: 20971871
references.citation: J Bacteriol. 1999 Apr;181(7):2059-66
references.pmid: 10094682
references.citation: PLoS Pathog. 2011 Nov;7(11):e1002359
references.pmid: 22102812
references.citation: Microbiol Mol Biol Rev. 1999 Jun;63(2):479-506
references.pmid: 10357859
references.citation: Microbiol Mol Biol Rev. 2009 Jun;73(2):233-48
references.pmid: 19487727
references.citation: Bioinformatics. 2009 Jan 15;25(2):288-9
references.pmid: 19033274
references.citation: Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
references.pmid: 12136088
references.citation: Mol Microbiol. 2001 Jul;41(1):247-61
references.pmid: 11454217
references.citation: Mol Microbiol. 1998 Sep;29(6):1522-3
references.pmid: 9781888
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: J Mol Biol. 1999 Sep 17;292(2):195-202
references.pmid: 10493868
references.citation: Eur J Biochem. 2004 Mar;271(6):1198-208
references.pmid: 15009198
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94
references.pmid: 15980472
references.citation: J Bacteriol. 2007 Nov;189(22):8257-69
references.pmid: 17827301
references.citation: Proc Natl Acad Sci U S A. 1979 Jan;76(1):260-4
references.pmid: 370826
references.citation: Environ Microbiol. 2004 Jun;6(6):552-67
references.pmid: 15142243
references.citation: J Biol Chem. 2003 Oct 3;278(40):39189-96
references.pmid: 12867417
references.citation: Microbiology (Reading). 2003 Jun;149(Pt 6):1423-1435
references.pmid: 12777483
references.citation: Trends Biochem Sci. 1997 Sep;22(9):331-3
references.pmid: 9301332
references.citation: Cell Host Microbe. 2007 Apr 19;1(2):109-19
references.pmid: 18005689
references.citation: Annu Rev Microbiol. 2011;65:261-86
references.pmid: 21663441
references.citation: N Engl J Med. 2006 Aug 17;355(7):666-74
references.pmid: 16914702
references.citation: J Bacteriol. 2003 Dec;185(24):7068-76
references.pmid: 14645265
references.citation: Biochem Biophys Res Commun. 2004 Jan 30;314(1):259-67
references.pmid: 14715274
references.citation: J Bacteriol. 1996 Jul;178(13):3796-802
references.pmid: 8682783
references.citation: J Bacteriol. 1996 Mar;178(5):1374-85
references.pmid: 8631715
references.citation: Curr Biol. 1997 Nov 1;7(11):R674-7
references.pmid: 9382818
references.citation: DNA Res. 2004 Apr 30;11(2):69-81
references.pmid: 15449540
references.citation: J Biol Chem. 2008 Oct 31;283(44):30256-65
references.pmid: 18701447
references.citation: Nat Methods. 2011 Dec 25;9(2):173-5
references.pmid: 22198341
references.citation: Bioinformatics. 1998;14(9):755-63
references.pmid: 9918945
references.citation: Biochim Biophys Acta. 2002 Jan 17;1553(1-2):39-56
references.pmid: 11803016
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: J Bacteriol. 2000 Jul;182(14):3955-64
references.pmid: 10869073
references.citation: J Bacteriol. 2006 Nov;188(21):7335-43
references.pmid: 17050921
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: J Bacteriol. 2010 Jan;192(1):86-93
references.pmid: 19854899
references.citation: Mol Microbiol. 2000 Nov;38(3):535-42
references.pmid: 11069677
references.citation: Emerg Infect Dis. 1998 Apr-Jun;4(2):239-49
references.pmid: 9621194
references.citation: J Mol Biol. 2000 Aug 11;301(2):415-31
references.pmid: 10926518
references.citation: J Bacteriol. 2004 Feb;186(4):1175-81
references.pmid: 14762013
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5891-6
references.pmid: 18408157
references.citation: J Mol Biol. 2001 Apr 13;307(5):1271-92
references.pmid: 11292341
references.citation: Structure. 2009 Oct 14;17(10):1282-94
references.pmid: 19836329
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Mol Microbiol. 2008 Dec;70(6):1307-22
references.pmid: 19019149
references.citation: Syst Biol. 2010 May;59(3):307-21
references.pmid: 20525638
references.citation: Mol Biol Evol. 2009 Jul;26(7):1641-50
references.pmid: 19377059
references.citation: Antimicrob Agents Chemother. 2006 Jun;50(6):2137-45
references.pmid: 16723576
references.citation: J Bacteriol. 2010 Feb;192(4):1156-9
references.pmid: 20008068
references.citation: J Bacteriol. 1994 Mar;176(5):1234-41
references.pmid: 8113162
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8
references.pmid: 15980471