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PLOS ONE  2014 

Redefining the PF06864 Pfam Family Based on Burkholderia pseudomallei PilO2Bp S-SAD Crystal Structure

DOI: 10.1371/journal.pone.0094981

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Abstract:

Type IV pili are surface-exposed filaments and bacterial virulence factors, represented by the Tfpa and Tfpb types, which assemble via specific machineries. The Tfpb group is further divided into seven variants, linked to heterogeneity in the assembly machineries. Here we focus on PilO2Bp, a protein component of the Tfpb R64 thin pilus variant assembly machinery from the pathogen Burkholderia pseudomallei. PilO2Bp belongs to the PF06864 Pfam family, for which an improved definition is presented based on newly derived Hidden Markov Model (HMM) profiles. The 3D structure of the N-terminal domain of PilO2Bp (N-PilO2Bp), here reported, is the first structural representative of the PF06864 family. N-PilO2Bp presents an actin-like ATPase fold that is shown to be present in BfpC, a different variant assembly protein; the new HMM profiles classify BfpC as a PF06864 member. Our results provide structural insight into the PF06864 family and on the Type IV pili assembly machinery.

References

[1]  Schell MA, Lipscomb L, DeShazer D (2008) Comparative genomics and an insect model rapidly identify novel virulence genes of Burkholderia mallei. J Bacteriol 190: 2306–2313. doi: 10.1128/jb.01735-07
[2]  Craig L, Li J (2008) Type IV pili: paradoxes in form and function. Curr Opin Struct Biol 18: 267–277. doi: 10.1016/j.sbi.2007.12.009
[3]  Pelicic V (2008) Type IV pili: e pluribus unum? Mol Microbiol 68: 827–837. doi: 10.1111/j.1365-2958.2008.06197.x
[4]  Roux N, Spagnolo J, de Bentzmann S (2012) Neglected but amazingly diverse type IVb pili. Res Microbiol 163: 659–673. doi: 10.1016/j.resmic.2012.10.015
[5]  Sakai D, Komano T (2002) Genes required for plasmid R64 thin-pilus biogenesis: identification and localization of products of the pilK, pilM, pilO, pilP, pilR, and pilT genes. J Bacteriol 184: 444–451. doi: 10.1128/jb.184.2.444-451.2002
[6]  Stone KD, Zhang HZ, Carlson LK, Donnenberg MS (1996) A cluster of fourteen genes from enteropathogenic Escherichia coli is sufficient for the biogenesis of a type IV pilus. Mol Microbiol 20: 325–337. doi: 10.1111/j.1365-2958.1996.tb02620.x
[7]  Kim SR, Komano T (1997) The plasmid R64 thin pilus identified as a type IV pilus. J Bacteriol 179: 3594–3603.
[8]  Carter MQ, Chen J, Lory S (2010) The Pseudomonas aeruginosa pathogenicity island PAPI-1 is transferred via a novel type IV pilus. J Bacteriol 192: 3249–3258. doi: 10.1128/jb.00041-10
[9]  Pickard D, Wain J, Baker S, Line A, Chohan S, et al. (2003) Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol 185: 5055–5065. doi: 10.1128/jb.185.17.5055-5065.2003
[10]  Giron JA, Gomez-Duarte OG, Jarvis KG, Kaper JB (1997) Longus pilus of enterotoxigenic Escherichia coli and its relatedness to other type-4 pili—a minireview. Gene 192: 39–43. doi: 10.1016/s0378-1119(97)00039-5
[11]  Shinagawa H, Taniguchi T, Yamaguchi O, Yamamoto K, Honda T (1993) Cloning of the genes that control formation of the fimbrial colonization factor antigen III (CFA/III) from an enterotoxigenic Escherichia coli. Microbiol Immunol 37: 689–694. doi: 10.1111/j.1348-0421.1993.tb01693.x
[12]  Kirn TJ, Bose N, Taylor RK (2003) Secretion of a soluble colonization factor by the TCP type 4 pilus biogenesis pathway in Vibrio cholerae. Mol Microbiol 49: 81–92. doi: 10.1046/j.1365-2958.2003.03546.x
[13]  Skerker JM, Shapiro L (2000) Identification and cell cycle control of a novel pilus system in Caulobacter crescentus. EMBO J 19: 3223–3234. doi: 10.1093/emboj/19.13.3223
[14]  Kachlany SC, Planet PJ, Bhattacharjee MK, Kollia E, DeSalle R, et al. (2000) Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in bacteria and archaea. J Bacteriol 182: 6169–6176. doi: 10.1128/jb.182.21.6169-6176.2000
[15]  Yamagata A, Milgotina E, Scanlon K, Craig L, Tainer JA, et al. (2012) Structure of an essential type IV pilus biogenesis protein provides insights into pilus and type II secretion systems. J Mol Biol 419: 110–124. doi: 10.1016/j.jmb.2012.02.041
[16]  Xu Q, Christen B, Chiu HJ, Jaroszewski L, Klock HE, et al. (2012) Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization. Mol Microbiol 83: 712–727. doi: 10.1111/j.1365-2958.2011.07954.x
[17]  Essex-Lopresti AE, Boddey JA, Thomas R, Smith MP, Hartley MG, et al. (2005) A type IV pilin, PilA, Contributes To Adherence of Burkholderia pseudomallei and virulence in vivo. Infect Immun 73: 1260–1264. doi: 10.1128/iai.73.2.1260-1264.2005
[18]  Currie BJ, Dance DA, Cheng AC (2008) The global distribution of Burkholderia pseudomallei and melioidosis: an update. Trans R Soc Trop Med Hyg 102 Suppl 1S1–4. doi: 10.1016/s0035-9203(08)70002-6
[19]  Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290–301. doi: 10.1093/nar/gkr1065
[20]  Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205–217. doi: 10.1006/jmbi.2000.4042
[21]  Otwinowski Z, Minor W (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode: Academic Press.
[22]  Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64: 112–122. doi: 10.1107/s0108767307043930
[23]  Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213–221. doi: 10.1107/s0907444909052925
[24]  Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, et al. (2010) phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J Appl Crystallogr 43: 669–676. doi: 10.1107/s0021889810015608
[25]  Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126–2132. doi: 10.1107/s0907444904019158
[26]  Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240–255. doi: 10.1107/s0907444996012255
[27]  Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12–21. doi: 10.1107/s0907444909042073
[28]  Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486–501. doi: 10.1107/s0907444910007493
[29]  Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67: 235–242. doi: 10.1107/s0907444910045749
[30]  Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477–486. doi: 10.1007/bf00228148
[31]  Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235–242. doi: 10.1093/nar/28.1.235
[32]  Burrows LL (2012) Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu Rev Microbiol 66: 493–520. doi: 10.1146/annurev-micro-092611-150055
[33]  Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, et al. (2008) The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. Bioinformatics 24: 2803–2804. doi: 10.1093/bioinformatics/btn524
[34]  Morris C, Tam CK, Wallis TS, Jones PW, Hackett J (2003) Salmonella enterica serovar Dublin strains which are Vi antigen-positive use type IVB pili for bacterial self-association and human intestinal cell entry. Microb Pathog 35: 279–284. doi: 10.1016/j.micpath.2003.08.001
[35]  Dudley EG, Abe C, Ghigo JM, Latour-Lambert P, Hormazabal JC, et al. (2006) An IncI1 plasmid contributes to the adherence of the atypical enteroaggregative Escherichia coli strain C1096 to cultured cells and abiotic surfaces. Infect Immun 74: 2102–2114. doi: 10.1128/iai.74.4.2102-2114.2006
[36]  Collyn F, Lety MA, Nair S, Escuyer V, Ben Younes A, et al. (2002) Yersinia pseudotuberculosis harbors a type IV pilus gene cluster that contributes to pathogenicity. Infect Immun 70: 6196–6205. doi: 10.1128/iai.70.11.6196-6205.2002
[37]  (2013) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res.
[38]  Chen C, Natale DA, Finn RD, Huang H, Zhang J, et al. (2011) Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One 6: e18910. doi: 10.1371/journal.pone.0018910
[39]  Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755–763. doi: 10.1093/bioinformatics/14.9.755
[40]  Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785–786. doi: 10.1038/nmeth.1701
[41]  Buchan DW, Ward SM, Lobley AE, Nugent TC, Bryson K, et al. (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Research 38: W563–568. doi: 10.1093/nar/gkq427
[42]  Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, et al. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 32: D226–229. doi: 10.1093/nar/gkh039
[43]  Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology 372: 774–797. doi: 10.1016/j.jmb.2007.05.022
[44]  Holm L, Rosenstrom P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545–549. doi: 10.1093/nar/gkq366
[45]  Xu Q, Dunbrack RL Jr (2012) Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics 28: 2763–2772. doi: 10.1093/bioinformatics/bts533
[46]  Johnson LS, Eddy SR, Portugaly E (2010) Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11: 431. doi: 10.1186/1471-2105-11-431
[47]  Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739–747. doi: 10.1093/protein/11.9.739
[48]  Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, et al. (2008) Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics 9: 566. doi: 10.1186/1471-2164-9-566
[49]  Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211–222. doi: 10.1093/nar/gkp985
[50]  Crowther LJ, Anantha RP, Donnenberg MS (2004) The inner membrane subassembly of the enteropathogenic Escherichia coli bundle-forming pilus machine. Mol Microbiol 52: 67–79. doi: 10.1111/j.1365-2958.2003.03963.x
[51]  Abendroth J, Bagdasarian M, Sandkvist M, Hol WG (2004) The structure of the cytoplasmic domain of EpsL, an inner membrane component of the type II secretion system of Vibrio cholerae: an unusual member of the actin-like ATPase superfamily. J Mol Biol 344: 619–633. doi: 10.1016/j.jmb.2004.09.062
[52]  Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29: 221–222. doi: 10.1093/nar/29.1.221

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