AtlasT4SS: A curated database for type IV secretion systems

BMC Microbiology

Volumn 12, Issue , 2012, Pages

  Souza, Rangel C ^a   Del Rosario Quispe Saji, Guadalupe ^a   Costa, Maiana Oc ^a   Netto, Diogo S ^a   Lima, Nicholas Cb ^a   Klein, Cecília C ^a   Vasconcelos, Ana Tereza R ^a   Nicolás, Marisa F ^a  

^a LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ARCHAEON; ARTICLE; CLASSIFICATION; DATA BASE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; NONHUMAN; PHYLOGENY; PROTEIN DOMAIN; RHIZOBIUM ETLI; TYPE IV SECRETION SYSTEM;

ARCHAEA; BACTERIA; BACTERIAL SECRETION SYSTEMS; DATABASES, GENETIC; MEMBRANE TRANSPORT PROTEINS; PLASMIDS;

AGROBACTERIUM TUMEFACIENS; EUKARYOTA; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 84864667438     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-12-172     Document Type: Article

References (44)

1. Multiple pathways allow protein secretion across the bacterial outer membrane. Thanassi DG, Hultgren SJ, Curr Opin Cell Biol 2000 12 4 420 430 10.1016/S0955-0674(00)00111-3 10873830 (Pubitemid 30453591)
2. Mechanisms of protein export across the bacterial outer membrane. Kostakioti M, Newman CL, Thanassi DG, Stathopoulos C, J Bacteriol 2005 187 13 4306 4314 10.1128/JB.187.13.4306-4314.2005 15968039 (Pubitemid 40880940)
3. Type VII secretion - mycobacteria show the way. Abdallah AM, van Pittius NC G, Champion PA, Cox J, Luirink J, Vandenbroucke-Grauls CM, Appelmelk BJ, Bitter W, Nat Rev Microbiol 2007 5 11 883 891 10.1038/nrmicro1773 17922044 (Pubitemid 47578389)
4. Type VI secretion is a major virulence determinant in Burkholderia mallei. Schell MA, Ulrich RL, Ribot WJ, Brueggemann EE, Hines HB, Chen D, Lipscomb L, Kim HS, Mrzek J, Nierman WC, Deshazer D, Mol Microbiol 2007 64 6 1466 1485 10.1111/j.1365-2958.2007.05734.x 17555434 (Pubitemid 46889897)
5. Bacterial contact-dependent delivery systems. Hayes CS, Aoki SK, Low DA, Annu Rev Genet 2010 44 71 90 10.1146/annurev.genet.42.110807.091449 21047256
6. New insights into the distribution of WXG100 protein secretion systems. Sutcliffe IC, Antonie Van Leeuwenhoek 2011 99 2 127 131 10.1007/s10482-010-9507- 4 20852931
7. The versatile bacterial type IV secretion systems. Cascales E, Christie PJ, Nat Rev Microbiol 2003 1 2 137 149 10.1038/nrmicro753 15035043
8. Essential components of the Ti plasmid trb system, a type IV macromolecular transporter. Li PL, Hwang I, Miyagi H, True H, Farrand SK, J Bacteriol 1999 181 16 5033 5041 10438776 (Pubitemid 29383535)
9. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Christie PJ, Mol Microbiol 2001 40 2 294 305 10.1046/j.1365-2958.2001.02302.x 11309113 (Pubitemid 32391625)
10. Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system. Hofreuter D, Odenbreit S, Haas R, Mol Microbiol 2001 41 2 379 391 10.1046/j.1365-2958.2001.02502.x 11489125 (Pubitemid 32730538)
11. Biogenesis, architecture, and function of bacterial type IV secretion systems. Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski S, Cascales E, Annu Rev Microbiol 2005 59 451 485 10.1146/annurev.micro.58.030603.123630 16153176 (Pubitemid 41507439)
12. Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Christie PJ, Vogel JP, Trends Microbiol 2000 8 8 354 360 10.1016/S0966-842X(00)01792-3 10920394 (Pubitemid 30628954)
13. Natural competence for DNA transformation in Helicobacter pylori: identification and genetic characterization of the comB locus. Hofreuter D, Odenbreit S, Henke G, Haas R, Mol Microbiol 1998 28 5 1027 1038 10.1046/j.1365-2958.1998.00879.x 9663688 (Pubitemid 28258999)
14. F factor conjugation is a true type IV secretion system. Lawley TD, Klimke WA, Gubbins MJ, Frost LS, FEMS Microbiol Lett 2003 224 1 1 15 10.1016/S0378-1097(03)00430-0 12855161 (Pubitemid 36830816)
15. Identification of a Legionella pneumophila locus required for intracellular multiplication in human macrophages. Marra A, Blander SJ, Horwitz MA, Shuman HA, Proc Natl Acad Sci USA 1992 89 20 9607 9611 10.1073/pnas.89.20. 9607 1409673
16. Coxiella burnetii express type IV secretion system proteins that function similarly to components of the Legionella pneumophila Dot/Icm system. Zamboni DS, McGrath S, Rabinovitch M, Roy CR, Mol Microbiol 2003 49 4 965 976 10.1046/j.1365-2958.2003.03626.x 12890021 (Pubitemid 36981342)
17. Novel type IV secretion system involved in propagation of genomic islands. Juhas M, Crook DW, Dimopoulou ID, Lunter G, Harding RM, Ferguson DJ, Hood DW, J Bacteriol 2007 189 3 761 771 10.1128/JB.01327-06 17122343 (Pubitemid 46183850)
18. Intergeneric transfer of the Enterococcus faecalis plasmid pIP501 to Escherichia coli and Streptomyces lividans and sequence analysis of its tra region. Kurenbach B, Bohn C, Prabhu J, Abudukerim M, Szewzyk U, Grohmann E, Plasmid 2003 50 1 86 93 10.1016/S0147-619X(03)00044-1 12826062 (Pubitemid 36765462)
19. Plasmids and viruses of the thermoacidophilic crenarchaeote Sulfolobus. Lipps G, Extremophiles 2006 10 1 17 28 10.1007/s00792-005-0492-x 16397749 (Pubitemid 43375559)
20. Biological diversity of prokaryotic type IV secretion systems. Alvarez-Martinez CE, Christie PJ, Microbiol Mol Biol Rev 2009 73 4 775 808 10.1128/MMBR.00023-09 19946141
21. Definition of a bacterial type IV secretion pathway for a DNA substrate. Cascales E, Christie PJ, Science 2004 304 5674 1170 1173 10.1126/science.1095211 15155952 (Pubitemid 38661856)
22. Relationships between a new type IV secretion system and the icm/dot virulence system of Legionella pneumophila. Segal G, Russo JJ, Shuman HA, Mol Microbiol 1999 34 4 799 809 10.1046/j.1365-2958.1999.01642.x 10564519
23. Environmental mimics and the Lvh type IVA secretion system contribute to virulence-related phenotypes of Legionella pneumophila. Bandyopadhyay P, Liu S, Gabbai CB, Venitelli Z, Steinman HM, Infect Immun 2007 75 2 723 735 10.1128/IAI.00956-06 17101653 (Pubitemid 46203434)
24. Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence. Juhas M, Crook DW, Hood DW, Cell Microbiol 2008 10 12 2377 2386 10.1111/j.1462-5822.2008.01187.x 18549454
25. NCBI ftp server ftp://ftp.ncbi.nih.gov/genomes
26. The use of gene clusters to infer functional coupling. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, Proc Natl Acad Sci USA 1999 96 6 2896 2901 10.1073/pnas.96.6.2896 10077608 (Pubitemid 29148815)
27. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410 2231712
28. A System for Automated Bacterial Integrated Annotation-SABIA. Almeida LG, Paixão R, Souza RC, Costa GC, Barrientos FJ, Santos MT, Almeida DF, Vasconcelos AT, Bioinformatics 2004 20 2832 2833 10.1093/bioinformatics/bth273 15087310 (Pubitemid 39530171)
29. Using CLUSTAL for multiple sequence alignments. Higgins DG, Thompson JD, Gibson TJ, Methods Enzymol 1996 266 383 402 8743695 (Pubitemid 26165878)
30. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic Acids Res 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
31. The Jalview Java alignment editor. Clamp M, Cuff J, Searle SM, Barton GJ, Bioinformatics 2004 20 3 426 427 10.1093/bioinformatics/btg430 14960472 (Pubitemid 38262778)
32. InterPro http://www.ebi.ac.uk/interpro
33. KEGG-Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/keg
34. COG-Clusters of Orthologous Groups of proteins http://www.ncbi.nlm.nih. gov/COG
35. GO-Gene Onthology www.geneontology.org
36. UniProtKB/Swiss-Prot http://www.uniprot.org
37. PSORT http://psort.nibb.ac.jp
38. A combined transmembrane topology and signal peptide prediction method. Käll L, Krogh A, Sonnhammer EL, J Mol Biol 2004 338 5 1027 1036 10.1016/j.jmb.2004.03.016 15111065 (Pubitemid 38542831)
39. AtlasT4SS-cluster AvhB11/VirB11/TrbB/GspE http://www.t4ss.lncc.br/ GenesByClusters?cluster=182
40. AtlasT4SS-cluster VirB4/AvhB4/TrbE/CagE http://www.t4ss.lncc.br/ GenesByClusters?cluster=520
41. Conjugative transfer of p42a from rhizobium etli CFN42, which is required for mobilization of the symbiotic plasmid, is regulated by quorum sensing. Tun-Garrido C, Bustos P, González V, Brom S, J Bacteriol 2003 185 5 1681 1692 10.1128/JB.185.5.1681-1692.2003 12591886 (Pubitemid 36245970)
42. Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system. Hubber A, Vergunst AC, Sullivan JT, Hooykaas PJ, Ronson CW, Mol Microbiol 2004 54 2 561 574 10.1111/j.1365-2958.2004.04292.x 15469524 (Pubitemid 39388296)
43. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW, J Bacteriol 2002 184 11 3086 3095 10.1128/JB.184.11.3086-3095.2002 12003951 (Pubitemid 34517833)
44. Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Schrammeijer B, Risseeuw E, Pansegrau W, Regensburg-Tunk TJ, Crosby WL, Hooykaas PJ, Curr Biol 2001 11 4 258 262 10.1016/S0960-9822(01)00069-0 11250154 (Pubitemid 32185328)