title: Tandem-repeat protein domains across the tree of life.
abstract: Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20-40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.
authors: Department of Cell and Developmental Biology, Vanderbilt University , Nashville, TN , USA.
authors: Kristin K
authors: KK
authors: Jernigan
authors: Department of Biological Sciences, Vanderbilt University , Nashville, TN , USA ; Department of Pathology, Microbiology, and Immunology, Vanderbilt University , Nashville, TN , USA.
authors: Seth R
authors: SR
authors: Bordenstein
keywords: Ankyrin repeat domains; Archaea; Armadillo repeat domain; Bacteria; Protein domains; Symbiosis; Tetratricopeptide repeat domains
references: Nat Genet. 1995 Oct;11(2):115-6
references: 7550332
references: BMC Microbiol. 2012 Jan 18;12 Suppl 1:S12
references: 22375862
references: J Mol Biol. 2001 May 25;309(1):1-18
references: 11491282
references: Mol Biol Evol. 2014 May;31(5):1132-48
references: 24497029
references: J Genet Genomics. 2007 Sep;34(9):765-76
references: 17884686
references: EMBO J. 2001 Nov 15;20(22):6203-12
references: 11707392
references: Infect Immun. 2009 Oct;77(10):4243-55
references: 19651857
references: Proc Natl Acad Sci U S A. 2005 Apr 19;102(16):5721-6
references: 15824314
references: Bioinformatics. 2003 Aug 12;19(12):1572-4
references: 12912839
references: Curr Opin Struct Biol. 2008 Aug;18(4):507-15
references: 18602006
references: Trends Biochem Sci. 2003 Dec;28(12):655-62
references: 14659697
references: PLoS One. 2013;8(2):e55390
references: 23390535
references: Curr Biol. 2004 Aug 24;14(16):R650-1; author reply R652-3
references: 15324679
references: J Mol Evol. 1985;22(2):160-74
references: 3934395
references: PLoS One. 2009 Sep 24;4(9):e7148
references: 19777061
references: Cell. 1990 Jan 26;60(2):319-28
references: 2297790
references: Infect Immun. 2013 Mar;81(3):629-35
references: 23264049
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6
references: 19036790
references: Cell. 1990 Jan 26;60(2):307-17
references: 2404612
references: Infect Immun. 2008 Jul;76(7):2852-61
references: 18426883
references: Proc Natl Acad Sci U S A. 2011 May 3;108(18):7368-72
references: 21502530
references: J Mol Biol. 2008 Mar 7;376(5):1282-304
references: 18222472
references: PLoS Comput Biol. 2006 Aug 25;2(8):e114
references: 16933986
references: Trends Biochem Sci. 2000 Oct;25(10):509-15
references: 11050437
references: Trends Biochem Sci. 1999 Aug;24(8):311-6
references: 10431175
references: Curr Opin Plant Biol. 2000 Aug;3(4):278-84
references: 10873844
references: PeerJ. 2014 Feb 06;2:e264
references: 24688847
references: Trends Cell Biol. 2010 Aug;20(8):470-81
references: 20688255
references: PLoS Pathog. 2008 Aug 01;4(8):e1000117
references: 18670632
references: Biochim Biophys Acta. 2010 Mar;1804(3):620-7
references: 19766738
references: Syst Biol. 2003 Oct;52(5):696-704
references: 14530136
references: J Mol Biol. 2001 Nov 2;313(4):903-19
references: 11697912
references: Science. 2003 Nov 28;302(5650):1571-5
references: 14645851
references: Nature. 1987 Oct 15-21;329(6140):651-4
references: 2821408
references: Structure. 2014 Jul 8;22(7):1047-54
references: 24954617
references: Curr Opin Struct Biol. 1998 Jun;8(3):338-45
references: 9666330
references: J Mol Biol. 1999 Oct 15;293(1):151-60
references: 10512723
references: Curr Opin Struct Biol. 2013 Aug;23(4):622-31
references: 23831287
references: FEMS Microbiol Lett. 2006 Mar;256(1):57-66
references: 16487320
references: Protein Sci. 2004 Jun;13(6):1435-48
references: 15152081
references: Proteins. 1993 Dec;17(4):363-74
references: 8108379
references: Cell Microbiol. 2007 May;9(5):1284-96
references: 17250594
references: Bioinformatics. 2001 Aug;17(8):754-5
references: 11524383
references: BMC Microbiol. 2009 Mar 16;9:56
references: 19291314
references: Trends Microbiol. 2010 Mar;18(3):132-9
references: 19962898
references: J Biol Chem. 1994 Mar 25;269(12):8686-94
references: 8132596
references: J Mol Biol. 1999 Jun 18;289(4):729-45
references: 10369758
references: Nature. 1999 May 20;399(6733):221-9
references: 10353244
references: Cell. 1994 Mar 11;76(5):789-91
references: 7907279
references: Nat Methods. 2012 Jul 30;9(8):772
references: 22847109
references: Science. 1996 Nov 8;274(5289):1001-5
references: 8875926
references: EMBO J. 1998 Mar 2;17(5):1192-9
references: 9482716