title: A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution.
abstract: Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins.
authors.affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia ; Victorian Bioinformatics Consortium, Monash University Melbourne, VIC, Australia.
authors.forename: Eva
authors.initials: E
authors.lastname: Heinz
authors.affiliation: Department of Microbiology, Monash University Melbourne, VIC, Australia.
authors.forename: Trevor
authors.initials: T
authors.lastname: Lithgow
keywords: BamA; Omp85; Omp85/TpsB superfamily; outer membrane protein assembly; two-partner secretion
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15831-6
references.pmid: 9861056
references.citation: Trends Microbiol. 2007 Nov;15(11):508-15
references.pmid: 17988872
references.citation: Trends Genet. 2010 Feb;26(2):47-51
references.pmid: 20036437
references.citation: BMC Genomics. 2006 Jun 17;7:156
references.pmid: 16780600
references.citation: BMC Evol Biol. 2013 Jul 22;13:156
references.pmid: 23875653
references.citation: Nat Struct Mol Biol. 2012 Apr 01;19(5):506-10, S1
references.pmid: 22466966
references.citation: Genome Biol Evol. 2010;2:609-19
references.pmid: 20660109
references.citation: Nat Rev Mol Cell Biol. 2011 Jan;12(1):48-59
references.pmid: 21139638
references.citation: Trends Plant Sci. 1999 Aug;4(8):302-307
references.pmid: 10431219
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: Nat Rev Microbiol. 2011 Nov 08;10(1):13-26
references.pmid: 22064560
references.citation: Bioinformatics. 2010 Jul 1;26(13):1608-15
references.pmid: 20472543
references.citation: J Biol Chem. 2011 Aug 5;286(31):27792-803
references.pmid: 21586578
references.citation: J Mol Biol. 2011 Mar 25;407(2):248-60
references.pmid: 21277859
references.citation: Trends Microbiol. 2005 Dec;13(12):581-8
references.pmid: 16216510
references.citation: Environ Microbiol. 2010 Jun;12(6):1498-512
references.pmid: 20192961
references.citation: J Comput Chem. 2004 Oct;25(13):1605-12
references.pmid: 15264254
references.citation: Biochim Biophys Acta. 2014 Jul;1838(7):1978-84
references.pmid: 24589688
references.citation: Int J Syst Evol Microbiol. 2009 Nov;59(Pt 11):2894-8
references.pmid: 19628600
references.citation: J Mol Biol. 2011 Mar 11;406(5):659-66
references.pmid: 21236263
references.citation: Mol Microbiol. 2012 Jun;84(5):832-44
references.pmid: 22524202
references.citation: Trends Microbiol. 2010 Oct;18(10):464-70
references.pmid: 20637628
references.citation: Biol Rev Camb Philos Soc. 2013 Nov;88(4):955-87
references.pmid: 23551966
references.citation: Bioinformatics. 2000 Apr;16(4):404-5
references.pmid: 10869041
references.citation: Bioinformatics. 2009 Sep 1;25(17):2286-8
references.pmid: 19535536
references.citation: Structure. 1999 Oct 15;7(10):1291-300
references.pmid: 10545334
references.citation: J Biol Chem. 2010 Jun 4;285(23):18016-24
references.pmid: 20348103
references.citation: Trends Biochem Sci. 2003 Oct;28(10):523-6
references.pmid: 14559180
references.citation: Nature. 2013 Sep 19;501(7467):385-90
references.pmid: 23995689
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94
references.pmid: 15980472
references.citation: Mol Biol Evol. 2014 Feb;31(2):410-8
references.pmid: 24188869
references.citation: Annu Rev Genet. 2011;45:21-39
references.pmid: 21910630
references.citation: Microbiol Mol Biol Rev. 2009 Dec;73(4):775-808
references.pmid: 19946141
references.citation: J Mol Biol. 2011 Mar 11;406(5):667-78
references.pmid: 21168416
references.citation: Nature. 2007 Oct 18;449(7164):835-42
references.pmid: 17943120
references.citation: Science. 2007 Aug 17;317(5840):957-61
references.pmid: 17702945
references.citation: Bioinformatics. 2010 Oct 1;26(19):2460-1
references.pmid: 20709691
references.citation: PLoS Comput Biol. 2006 Aug 25;2(8):e114
references.pmid: 16933986
references.citation: Mol Biol Cell. 2011 Aug 15;22(16):2823-33
references.pmid: 21680715
references.citation: Open Biol. 2013 Jan 08;3(1):120143
references.pmid: 23303308
references.citation: J Am Chem Soc. 2007 Apr 18;129(15):4800-7
references.pmid: 17375930
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8
references.pmid: 21470960
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: J Bacteriol. 2001 Feb;183(4):1320-8
references.pmid: 11157945
references.citation: Protein Sci. 2012 Jun;21(6):751-68
references.pmid: 22549918
references.citation: J Cell Biol. 2004 Jan 5;164(1):19-24
references.pmid: 14699090
references.citation: FEMS Microbiol Rev. 2009 Jul;33(4):785-800
references.pmid: 19416363
references.citation: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references.pmid: 22039361
references.citation: PLoS One. 2010 Jan 08;5(1):e8619
references.pmid: 20062535
references.citation: Database (Oxford). 2011 Mar 29;2011:bar009
references.pmid: 21447597
references.citation: PLoS Genet. 2012 Sep;8(9):e1002983
references.pmid: 23028376
references.citation: Nat Rev Microbiol. 2003 Oct;1(1):45-54
references.pmid: 15040179
references.citation: Bioinformatics. 2009 Aug 1;25(15):1972-3
references.pmid: 19505945
references.citation: Annu Rev Biochem. 2011;80:189-210
references.pmid: 21370981
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references.pmid: 22127870
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: Sci Rep. 2013;3:2015
references.pmid: 23778980
references.citation: J Biol Chem. 2010 Jun 4;285(23):18003-15
references.pmid: 20351097
references.citation: Biol Direct. 2006 Jul 11;1:19
references.pmid: 16834776
references.citation: Nat Struct Mol Biol. 2013 Nov;20(11):1318-20
references.pmid: 24056943
references.citation: Biochim Biophys Acta. 2002 May 3;1562(1-2):6-31
references.pmid: 11988218
references.citation: FEBS J. 2005 Mar;272(6):1367-78
references.pmid: 15752354
references.citation: Protein Sci. 2003 Aug;12(8):1652-62
references.pmid: 12876315
references.citation: Res Microbiol. 2013 Jul-Aug;164(6):583-95
references.pmid: 23542425
references.citation: Annu Rev Microbiol. 2011;65:149-68
references.pmid: 21639788
references.citation: Biochim Biophys Acta. 2014 Aug;1843(8):1542-50
references.pmid: 24135059
references.citation: FEMS Microbiol Rev. 2011 Jul;35(4):652-80
references.pmid: 21361996
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12
references.pmid: 22096229