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Volumn 17, Issue 1, 2016, Pages

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

Author keywords

Bacteroidales; Gut microbiota; ICE integrative and conjugative element; T6SS; Type VI secretion system

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTEROIDALES; BACTEROIDES FRAGILIS; BIOINFORMATICS; CONTROLLED STUDY; GENE LOCUS; GENE STRUCTURE; GENETIC ANALYSIS; HIDDEN MARKOV MODEL; INTEGRATIVE CONJUGATIVE ELEMENT; INTESTINE FLORA; MICROBIAL DIVERSITY; NONHUMAN; ORTHOLOGY; POPULATION ABUNDANCE; PROTEOBACTERIA; TRANSCRIPTION REGULATION; TYPE VI SECRETION SYSTEM; GENETICS; HUMAN; INTERSPERSED REPEAT;

EID: 84954321839     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2377-z     Document Type: Article
Times cited : (118)

References (51)
  • 1
    • 79955603120 scopus 로고    scopus 로고
    • Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut
    • Zitomersky NL, Coyne MJ, Comstock LE. Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut. Infect Immun. 2011;79(5):2012-20. doi: 10.1128/IAI.01348-10.
    • (2011) Infect Immun , vol.79 , Issue.5 , pp. 2012-2020
    • Zitomersky, N.L.1    Coyne, M.J.2    Comstock, L.E.3
  • 3
    • 38449088143 scopus 로고    scopus 로고
    • Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
    • Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14(4):169-81. doi: 10.1093/dnares/dsm018.
    • (2007) DNA Res , vol.14 , Issue.4 , pp. 169-181
    • Kurokawa, K.1    Itoh, T.2    Kuwahara, T.3    Oshima, K.4    Toh, H.5    Toyoda, A.6
  • 5
    • 84859925158 scopus 로고    scopus 로고
    • How glycan metabolism shapes the human gut microbiota
    • Koropatkin NM, Cameron EA, Martens EC. How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol. 2012;10(5):323-35. doi: 10.1038/nrmicro2746.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.5 , pp. 323-335
    • Koropatkin, N.M.1    Cameron, E.A.2    Martens, E.C.3
  • 6
    • 84891789294 scopus 로고    scopus 로고
    • An ecological network of polysaccharide utilization among human intestinal symbionts
    • Rakoff-Nahoum S, Coyne MJ, Comstock LE. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr Biol. 2014;24(1):40-9. doi: 10.1016/j.cub.2013.10.077.
    • (2014) Curr Biol , vol.24 , Issue.1 , pp. 40-49
    • Rakoff-Nahoum, S.1    Coyne, M.J.2    Comstock, L.E.3
  • 9
    • 84867899841 scopus 로고    scopus 로고
    • Structure and regulation of the type VI secretion system
    • Silverman JM, Brunet YR, Cascales E, Mougous JD. Structure and regulation of the type VI secretion system. Annu Rev Microbiol. 2012;66:453-72. doi: 10.1146/annurev-micro-121809-151619.
    • (2012) Annu Rev Microbiol , vol.66 , pp. 453-472
    • Silverman, J.M.1    Brunet, Y.R.2    Cascales, E.3    Mougous, J.D.4
  • 10
    • 84884556983 scopus 로고    scopus 로고
    • TssK is a trimeric cytoplasmic protein interacting with components of both phage-like and membrane anchoring complexes of the type VI secretion system
    • Zoued A, Durand E, Bebeacua C, Brunet YR, Douzi B, Cambillau C, et al. TssK is a trimeric cytoplasmic protein interacting with components of both phage-like and membrane anchoring complexes of the type VI secretion system. J Biol Chem. 2013;288(38):27031-41. doi: 10.1074/jbc.M113.499772.
    • (2013) J Biol Chem , vol.288 , Issue.38 , pp. 27031-27041
    • Zoued, A.1    Durand, E.2    Bebeacua, C.3    Brunet, Y.R.4    Douzi, B.5    Cambillau, C.6
  • 11
    • 33744974779 scopus 로고    scopus 로고
    • A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus
    • Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, Gifford CA, et al. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science. 2006;312(5779):1526-30. doi: 10.1126/science.1128393.
    • (2006) Science , vol.312 , Issue.5779 , pp. 1526-1530
    • Mougous, J.D.1    Cuff, M.E.2    Raunser, S.3    Shen, A.4    Zhou, M.5    Gifford, C.A.6
  • 12
    • 84881666828 scopus 로고    scopus 로고
    • PAAR-repeat proteins sharpen and diversify the type VI secretion system spike
    • Shneider MM, Buth SA, Ho BT, Basler M, Mekalanos JJ, Leiman PG. PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature. 2013;500(7462):350-3. doi: 10.1038/nature12453.
    • (2013) Nature , vol.500 , Issue.7462 , pp. 350-353
    • Shneider, M.M.1    Buth, S.A.2    Ho, B.T.3    Basler, M.4    Mekalanos, J.J.5    Leiman, P.G.6
  • 13
    • 84883776001 scopus 로고    scopus 로고
    • Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates
    • Silverman JM, Agnello DM, Zheng H, Andrews BT, Li M, Catalano CE, et al. Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates. Mol Cell. 2013;51(5):584-93. doi: 10.1016/j.molcel.2013.07.025.
    • (2013) Mol Cell , vol.51 , Issue.5 , pp. 584-593
    • Silverman, J.M.1    Agnello, D.M.2    Zheng, H.3    Andrews, B.T.4    Li, M.5    Catalano, C.E.6
  • 14
    • 84899656771 scopus 로고    scopus 로고
    • Genetically distinct pathways guide effector export through the type VI secretion system
    • Whitney JC, Beck CM, Goo YA, Russell AB, Harding BN, De Leon JA, et al. Genetically distinct pathways guide effector export through the type VI secretion system. Mol Microbiol. 2014;92(3):529-42. doi: 10.1111/mmi.12571.
    • (2014) Mol Microbiol , vol.92 , Issue.3 , pp. 529-542
    • Whitney, J.C.1    Beck, C.M.2    Goo, Y.A.3    Russell, A.B.4    Harding, B.N.5    Leon, J.A.6
  • 15
    • 84903434335 scopus 로고    scopus 로고
    • The VgrG proteins are "a la carte" delivery systems for bacterial type VI effectors
    • Hachani A, Allsopp LP, Oduko Y, Filloux A. The VgrG proteins are "a la carte" delivery systems for bacterial type VI effectors. J Biol Chem. 2014;289(25):17872-84. doi: 10.1074/jbc.M114.563429.
    • (2014) J Biol Chem , vol.289 , Issue.25 , pp. 17872-17884
    • Hachani, A.1    Allsopp, L.P.2    Oduko, Y.3    Filloux, A.4
  • 16
    • 84923345050 scopus 로고    scopus 로고
    • Structure of the type VI secretion system contractile sheath
    • Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, et al. Structure of the type VI secretion system contractile sheath. Cell. 2015;160(5):952-62. doi: 10.1016/j.cell.2015.01.037.
    • (2015) Cell , vol.160 , Issue.5 , pp. 952-962
    • Kudryashev, M.1    Wang, R.Y.2    Brackmann, M.3    Scherer, S.4    Maier, T.5    Baker, D.6
  • 17
    • 84923361694 scopus 로고    scopus 로고
    • Atomic structure of T6SS reveals interlaced array essential to function
    • Clemens DL, Ge P, Lee BY, Horwitz MA, Zhou ZH. Atomic structure of T6SS reveals interlaced array essential to function. Cell. 2015;160(5):940-51. doi: 10.1016/j.cell.2015.02.005.
    • (2015) Cell , vol.160 , Issue.5 , pp. 940-951
    • Clemens, D.L.1    Ge, P.2    Lee, B.Y.3    Horwitz, M.A.4    Zhou, Z.H.5
  • 18
    • 84865067839 scopus 로고    scopus 로고
    • Type 6 secretion dynamics within and between bacterial cells
    • Basler M, Mekalanos JJ. Type 6 secretion dynamics within and between bacterial cells. Science. 2012;337(6096):815. doi: 10.1126/science.1222901.
    • (2012) Science , vol.337 , Issue.6096 , pp. 815
    • Basler, M.1    Mekalanos, J.J.2
  • 19
    • 84858002430 scopus 로고    scopus 로고
    • Type VI secretion requires a dynamic contractile phage tail-like structure
    • Basler M, Pilhofer M, Henderson GP, Jensen GJ, Mekalanos JJ. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature. 2012;483(7388):182-6. doi: 10.1038/nature10846.
    • (2012) Nature , vol.483 , Issue.7388 , pp. 182-186
    • Basler, M.1    Pilhofer, M.2    Henderson, G.P.3    Jensen, G.J.4    Mekalanos, J.J.5
  • 20
    • 84904198712 scopus 로고    scopus 로고
    • Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta
    • Ma LS, Hachani A, Lin JS, Filloux A, Lai EM. Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe. 2014;16(1):94-104. doi: 10.1016/j.chom.2014.06.002.
    • (2014) Cell Host Microbe , vol.16 , Issue.1 , pp. 94-104
    • Ma, L.S.1    Hachani, A.2    Lin, J.S.3    Filloux, A.4    Lai, E.M.5
  • 21
    • 84862602464 scopus 로고    scopus 로고
    • Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
    • Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct. 2012;7:18. doi: 10.1186/1745-6150-7-18.
    • (2012) Biol Direct , vol.7 , pp. 18
    • Zhang, D.1    Souza, R.F.2    Anantharaman, V.3    Iyer, L.M.4    Aravind, L.5
  • 22
    • 84906934947 scopus 로고    scopus 로고
    • VgrG, Tae, Tle, and beyond: the versatile arsenal of Type VI secretion effectors
    • Durand E, Cambillau C, Cascales E, Journet L. VgrG, Tae, Tle, and beyond: the versatile arsenal of Type VI secretion effectors. Trends Microbiol. 2014;22(9):498-507. doi: 10.1016/j.tim.2014.06.004.
    • (2014) Trends Microbiol , vol.22 , Issue.9 , pp. 498-507
    • Durand, E.1    Cambillau, C.2    Cascales, E.3    Journet, L.4
  • 23
    • 84903978009 scopus 로고    scopus 로고
    • Evidence of extensive DNA transfer between Bacteroidales species within the human gut
    • Coyne M, Zitomersky N, McGuire A, Earl A, Comstock L. Evidence of extensive DNA transfer between Bacteroidales species within the human gut. mBio. 2014;5(3):e1305-14.
    • (2014) mBio , vol.5 , Issue.3 , pp. e1305-e1314
    • Coyne, M.1    Zitomersky, N.2    McGuire, A.3    Earl, A.4    Comstock, L.5
  • 24
    • 84921894836 scopus 로고    scopus 로고
    • A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism
    • Russell AB, Wexler AG, Harding BN, Whitney JC, Bohn AJ, Goo YA, et al. A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism. Cell Host Microbe. 2014;16(2):227-36. doi: 10.1016/j.chom.2014.07.007.
    • (2014) Cell Host Microbe , vol.16 , Issue.2 , pp. 227-236
    • Russell, A.B.1    Wexler, A.G.2    Harding, B.N.3    Whitney, J.C.4    Bohn, A.J.5    Goo, Y.A.6
  • 25
    • 84922640624 scopus 로고    scopus 로고
    • Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms
    • Wilson MM, Anderson DE, Bernstein HD. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms. PLoS One. 2015;10(2):e0117732. doi: 10.1371/journal.pone.0117732.
    • (2015) PLoS One , vol.10 , Issue.2 , pp. e0117732
    • Wilson, M.M.1    Anderson, D.E.2    Bernstein, H.D.3
  • 26
    • 63049098068 scopus 로고    scopus 로고
    • Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?
    • Boyer F, Fichant G, Berthod J, Vandenbrouck Y, Attree I. Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? BMC Genomics. 2009;10:104. doi: 10.1186/1471-2164-10-104.
    • (2009) BMC Genomics , vol.10 , pp. 104
    • Boyer, F.1    Fichant, G.2    Berthod, J.3    Vandenbrouck, Y.4    Attree, I.5
  • 27
    • 84858163374 scopus 로고    scopus 로고
    • Structural biology of type VI secretion systems
    • Cascales E, Cambillau C. Structural biology of type VI secretion systems. Philos Trans R Soc Lond B Biol Sci. 2012;367(1592):1102-11. doi: 10.1098/rstb.2011.0209.
    • (2012) Philos Trans R Soc Lond B Biol Sci , vol.367 , Issue.1592 , pp. 1102-1111
    • Cascales, E.1    Cambillau, C.2
  • 28
    • 84892577859 scopus 로고    scopus 로고
    • A View to a Kill: The Bacterial Type VI Secretion System
    • Ho BT, Dong TG, Mekalanos JJ. A View to a Kill: The Bacterial Type VI Secretion System. Cell Host Microbe. 2014;15(1):9-21. doi: 10.1016/j.chom.2013.11.008.
    • (2014) Cell Host Microbe , vol.15 , Issue.1 , pp. 9-21
    • Ho, B.T.1    Dong, T.G.2    Mekalanos, J.J.3
  • 29
    • 84903302259 scopus 로고    scopus 로고
    • Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK-TssFG subcomplex
    • English G, Byron O, Cianfanelli FR, Prescott AR, Coulthurst SJ. Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK-TssFG subcomplex. Biochem J. 2014;461(2):291-304. doi: 10.1042/BJ20131426.
    • (2014) Biochem J , vol.461 , Issue.2 , pp. 291-304
    • English, G.1    Byron, O.2    Cianfanelli, F.R.3    Prescott, A.R.4    Coulthurst, S.J.5
  • 30
    • 69349101612 scopus 로고    scopus 로고
    • Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes
    • Blondel CJ, Jimenez JC, Contreras I, Santiviago CA. Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes. BMC Genomics. 2009;10:354. doi: 10.1186/1471-2164-10-354.
    • (2009) BMC Genomics , vol.10 , pp. 354
    • Blondel, C.J.1    Jimenez, J.C.2    Contreras, I.3    Santiviago, C.A.4
  • 31
    • 84877317320 scopus 로고    scopus 로고
    • The underling mechanism of bacterial TetR/AcrR family transcriptional repressors
    • Deng W, Li C, Xie J. The underling mechanism of bacterial TetR/AcrR family transcriptional repressors. Cell Signal. 2013;25(7):1608-13. doi: 10.1016/j.cellsig.2013.04.003.
    • (2013) Cell Signal , vol.25 , Issue.7 , pp. 1608-1613
    • Deng, W.1    Li, C.2    Xie, J.3
  • 32
    • 83755172749 scopus 로고    scopus 로고
    • Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
    • Iyer LM, Zhang D, Rogozin IB, Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res. 2011;39(22):9473-97. doi: 10.1093/nar/gkr691.
    • (2011) Nucleic Acids Res , vol.39 , Issue.22 , pp. 9473-9497
    • Iyer, L.M.1    Zhang, D.2    Rogozin, I.B.3    Aravind, L.4
  • 34
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40(Database issue):D130-5. doi: 10.1093/nar/gkr1079.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. D130-D135
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 35
    • 84891787231 scopus 로고    scopus 로고
    • Ribosomal Database Project: data and tools for high throughput rRNA analysis
    • Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D633-D642
    • Cole, J.R.1    Wang, Q.2    Fish, J.A.3    Chai, B.4    McGarrell, D.M.5    Sun, Y.6
  • 39
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2012;9(2):173-5. doi: 10.1038/nmeth.1818.
    • (2012) Nat Methods , vol.9 , Issue.2 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 40
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292(2):195-202. doi: 10.1006/jmbi.1999.3091.
    • (1999) J Mol Biol , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 41
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21(7):951-60. doi: 10.1093/bioinformatics/bti125.
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 951-960
    • Soding, J.1
  • 45
  • 46
    • 80054078476 scopus 로고    scopus 로고
    • Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
    • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539. doi: 10.1038/msb.2011.75.
    • (2011) Mol Syst Biol , vol.7 , pp. 539
    • Sievers, F.1    Wilm, A.2    Dineen, D.3    Gibson, T.J.4    Karplus, K.5    Li, W.6
  • 47
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9. doi: 10.1101/gr.074492.107.
    • (2008) Genome Res , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 48
    • 40849101515 scopus 로고    scopus 로고
    • Type VI secretion: a beginner's guide
    • Bingle LE, Bailey CM, Pallen MJ. Type VI secretion: a beginner's guide. Curr Opin Microbiol. 2008;11(1):3-8. doi: 10.1016/j.mib.2008.01.006.
    • (2008) Curr Opin Microbiol , vol.11 , Issue.1 , pp. 3-8
    • Bingle, L.E.1    Bailey, C.M.2    Pallen, M.J.3
  • 49
    • 48649107476 scopus 로고    scopus 로고
    • The type VI secretion toolkit
    • Cascales E. The type VI secretion toolkit. EMBO Rep. 2008;9(8):735-41. doi: 10.1038/embor.2008.131.
    • (2008) EMBO Rep , vol.9 , Issue.8 , pp. 735-741
    • Cascales, E.1
  • 50
    • 84879880852 scopus 로고    scopus 로고
    • The Type VI secretion system - a widespread and versatile cell targeting system
    • Coulthurst SJ. The Type VI secretion system - a widespread and versatile cell targeting system. Res Microbiol. 2013;164(6):640-54. doi: 10.1016/j.resmic.2013.03.017.
    • (2013) Res Microbiol , vol.164 , Issue.6 , pp. 640-654
    • Coulthurst, S.J.1


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