Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin

BMC Structural Biology

Volumn 11, Issue , 2011, Pages

  Arenas, Nelson E ^a,d,e   Salazar, Luz M ^a   Soto, Carlos Y ^a   Vizcaíno, Carolina ^b,c   Patarroyo, Manuel E ^b,c   Patarroyo, Manuel A ^b,c   Gámez, Arley ^c  

^a UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^b FUNDACIÓN INSTITUTO DE INMUNOLOGÍA DE COLOMBIA FIDIC   (Colombia)

^c UNIVERSIDAD DEL ROSARIO   (Colombia)

^d UNIVERSIDAD DEL QUINDÍO   (Colombia)

^e NONE   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HEMOLYSIN; PROTEIN TLYA; RIBOSOME PROTEIN; RNA METHYLTRANSFERASE; UNCLASSIFIED DRUG; VIRULENCE FACTOR; RECN PROTEIN, BACTERIA; RESTRICTION ENDONUCLEASE; TLYA PROTEIN, MYCOBACTERIUM TUBERCULOSIS;

ARTICLE; BETA SHEET; BIOINFORMATICS; CELLULAR DISTRIBUTION; HYDROPHOBICITY; MOLECULAR MODEL; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CYTOLOGY; GENETIC TRANSCRIPTION; GENETICS; HUMAN; INTRACELLULAR SPACE; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOUSE; OPERON; PATHOGENICITY; PROTEIN CONFORMATION; PROTEIN TRANSPORT; REPRODUCIBILITY;

BACILLI (CLASS); BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DNA RESTRICTION ENZYMES; EVOLUTION, MOLECULAR; HEMOLYSIN PROTEINS; HUMANS; INTRACELLULAR SPACE; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; OPERON; PROTEIN CONFORMATION; PROTEIN TRANSPORT; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; TRANSCRIPTION, GENETIC; VIRULENCE FACTORS;

EID: 79953091378     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-11-16     Document Type: Article

References (56)

1. From magic bullets back to the magic mountain: the rise of extensively drug-resistant tuberculosis. SE Dorman RE Chaisson, Nat Med 2007 13 295 298 10.1038/nm0307-295 17342143 (Pubitemid 46376673)
2. Prospects for development of new antimycobacterial drugs. H Tomioka, J Infect Chemother 2000 6 8 20 10.1007/s101560050043 11810525 (Pubitemid 30241860)
3. Tuberculosis chemotherapy: the influence of bacillary stress and damage response pathways on drug efficacy. DF Warner V Mizrahi, Clin Microbiol Rev 2006 19 558 570 10.1128/CMR.00060-05 16847086 (Pubitemid 44134310)
4. Identification of the biosynthetic gene cluster and an additional gene for resistance to the antituberculosis drug capreomycin. EA Felnagle MR Rondon AD Berti HA Crosby MG Thomas, Appl Environ Microbiol 2007 73 4162 4170 10.1128/AEM.00485-07 17496129 (Pubitemid 47068153)
5. Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs. SK Johansen CE Maus BB Plikaytis S Douthwaite, Mol Cell 2006 23 173 182 10.1016/j.molcel.2006.05.044 16857584 (Pubitemid 44081881)
6. Characterization of a haemolysin from Mycobacterium tuberculosis with homology to a virulence factor of Serpulina hyodysenteriae. BW Wren RA Stabler SS Das PD Butcher JA Mangan JD Clarke N Casali T Parish NG Stoker, Microbiology 1998 144 (Pt 5) 1205 1211 10.1099/00221287-144-5-1205 9611795 (Pubitemid 28233824)
7. Cloning of a beta-hemolysin gene of Brachyspira (Serpulina) hyodysenteriae and its expression in Escherichia coli. T Hsu DL Hutto FC Minion RL Zuerner MJ Wannemuehler, Infect Immun 2001 69 706 711 10.1128/IAI.69.2.706- 711.2001 11159958 (Pubitemid 32109529)
8. Molecular characterization of tlyA gene product, Rv1694 of Mycobacterium tuberculosis: a non-conventional hemolysin and a ribosomal RNA methyl transferase. A Rahman SS Srivastava A Sneh N Ahmed MV Krishnasastry, BMC Biochem 2010 11 35 10.1186/1471-2091-11-35 20854656
9. The antibiotic viomycin traps the ribosome in an intermediate state of translocation. DN Ermolenko PC Spiegel ZK Majumdar RP Hickerson RM Clegg HF Noller, Nat Struct Mol Biol 2007 14 493 497 10.1038/nsmb1243 17515906 (Pubitemid 46871807)
10. Mutation of tlyA confers capreomycin resistance in Mycobacterium tuberculosis. CE Maus BB Plikaytis TM Shinnick, Antimicrob Agents Chemother 2005 49 571 577 10.1128/AAC.49.2.571-577.2005 15673735 (Pubitemid 40175664)
11. Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis. JM Johnston VL Arcus CJ Morton MW Parker EN Baker, J Bacteriol 2003 185 4057 4065 10.1128/JB.185.14.4057-4065.2003 12837779 (Pubitemid 36835244)
12. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. AG Tsolaki S Gagneux AS Pym YO Goguet de la Salmoniere BN Kreiswirth D Van Soolingen PM Small, J Clin Microbiol 2005 43 3185 3191 10.1128/JCM.43.7.3185-3191.2005 16000433 (Pubitemid 40981321)
13. Bioinformatics-Guided Identification and Experimental Characterization of Novel RNA Methyltransferases. JM Bujnicki L Droogmans H Grosjean SK Purushothaman B Lapeyre, Practical Bioinformatics Berlin: Springer-Verlag, Bujnicki JM, 2004 15 139 168 full-text
14. Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. M Feder J Pas LS Wyrwicz JM Bujnicki, Gene 2003 302 129 138 10.1016/S0378-1119(02)01097-1 12527203 (Pubitemid 36078404)
15. Novel predicted RNA-binding domains associated with the translation machinery. L Aravind EV Koonin, J Mol Evol 1999 48 291 302 10.1007/PL00006472 10093218 (Pubitemid 29116074)
16. RNA base-amino acid interaction strengths derived from structures and sequences. B Lustig S Arora RL Jernigan, Nucleic Acids Res 1997 25 2562 2565 10.1093/nar/25.13.2562 9185564 (Pubitemid 27298149)
17. RNA methylation under heat shock control. H Bugl EB Fauman BL Staker F Zheng SR Kushner MA Saper JC Bardwell U Jakob, Mol Cell 2000 6 349 360 10.1016/S1097-2765(00)00035-6 10983982
18. Flavivirus methyltransferase: a novel antiviral target. H Dong B Zhang PY Shi, Antiviral Res 2008 80 1 10 10.1016/j.antiviral.2008.05.003 18571739
19. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. SC Lovell IW Davis WB Arendall PI de Bakker JM Word MG Prisant JS Richardson DC Richardson, Proteins 2003 50 437 450 10.1002/prot.10286 12557186 (Pubitemid 36158457)
20. Validating subcellular localization prediction tools with mycobacterial proteins. D Restrepo-Montoya C Vizcaino LF Nino M Ocampo ME Patarroyo MA Patarroyo, BMC Bioinformatics 2009 10 134 10.1186/1471-2105-10-134 19422713
21. Support vector machine approach for protein subcellular localization prediction. S Hua Z Sun, Bioinformatics 2001 17 721 728 10.1093/bioinformatics/ 17.8.721 11524373 (Pubitemid 32851380)
22. Prediction of lipoprotein signal peptides in Gram-negative bacteria. AS Juncker H Willenbrock G Von Heijne S Brunak H Nielsen A Krogh, Protein Sci 2003 12 1652 1662 10.1110/ps.0303703 12876315 (Pubitemid 36910046)
23. The capsule of Mycobacterium tuberculosis and its implications for pathogenicity. M Daffe G Etienne, Tuber Lung Dis 1999 79 153 169 10.1054/tuld.1998.0200 10656114 (Pubitemid 29348506)
24. LsaA, an antigen involved in cell attachment and invasion, is expressed by Lawsonia intracellularis during infection in vitro and in vivo. J McCluskey J Hannigan JD Harris B Wren DG Smith, Infect Immun 2002 70 2899 2907 10.1128/IAI.70.6.2899-2907.2002 12010978 (Pubitemid 34564147)
25. Evolution of protein function, from a structural perspective. AE Todd CA Orengo JM Thornton, Curr Opin Chem Biol 1999 3 548 556 10.1016/S1367-5931(99) 00007-1 10508675 (Pubitemid 29447489)
26. Cholesterol-dependent cytolysins, a family of versatile pore-forming toxins. RK Tweten, Infect Immun 2005 73 6199 6209 10.1128/IAI.73.10.6199-6209. 2005 16177291 (Pubitemid 41368781)
27. The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis. GL Card NA Peterson CA Smith B Rupp BM Schick EN Baker, J Biol Chem 2005 280 13978 13986 10.1074/jbc.M413904200 15695811 (Pubitemid 40517299)
28. Structural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase. HA Watkins EN Baker, J Bacteriol 2006 188 3589 3599 10.1128/JB.188.10.3589-3599.2006 16672613 (Pubitemid 43726223)
29. Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. M Rashid S Saha GP Raghava, BMC Bioinformatics 2007 8 337 10.1186/1471-2105-8-337 17854501
30. Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. HB Shen KC Chou, Protein Eng Des Sel 2007 20 39 46 10.1093/protein/gzl053 17244638
31. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. AM Schnoes SD Brown I Dodevski PC Babbitt, PLoS Comput Biol 2009 5 1000605 10.1371/journal.pcbi.1000605 20011109
32. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
33. Multiple sequence alignment with the Clustal series of programs. R Chenna H Sugawara T Koike R Lopez TJ Gibson DG Higgins JD Thompson, Nucleic Acids Res 2003 31 3497 3500 10.1093/nar/gkg500 12824352 (Pubitemid 37442184)
34. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucl Acids Symp Ser 1999 41 95 98
35. SMART, a simple modular architecture research tool: identification of signaling domains. J Schultz F Milpetz P Bork CP Ponting, Proc Natl Acad Sci USA 1998 95 5857 5864 10.1073/pnas.95.11.5857 9600884 (Pubitemid 28248931)
36. Pfam: clans, web tools and services. RD Finn J Mistry B Schuster-Bockler S Griffiths-Jones V Hollich T Lassmann S Moxon M Marshall A Khanna R Durbin,, et al. Nucleic Acids Res 2006 34 247 251 10.1093/nar/gkj149 16381856
37. Predicting protein structure using only sequence information. K Karplus C Barrett M Cline M Diekhans L Grate R Hughey, Proteins 1999 Suppl 3 121 125 10.1002/(SICI)1097-0134(1999)37:3+<121::AID-PROT16>3.0.CO;2-Q 10526360 (Pubitemid 29463523)
38. The PSIPRED protein structure prediction server. LJ McGuffin K Bryson DT Jones, Bioinformatics 2000 16 404 405 10.1093/bioinformatics/16.4.404 10869041 (Pubitemid 30417087)
39. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. JA Cuff GJ Barton, Proteins 2000 40 502 511 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q 10861942 (Pubitemid 30624459)
40. The SWISS-MODEL Repository and associated resources. F Kiefer K Arnold M Kunzli L Bordoli T Schwede, Nucleic Acids Res 2009 37 387 392 10.1093/nar/gkn750 18931379
41. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. RM Bennett-Lovsey AD Herbert MJ Sternberg LA Kelley, Proteins 2008 70 611 625 10.1002/prot.21688 17876813 (Pubitemid 351161924)
42. UCSF Chimera - a visualization system for exploratory research and analysis. EF Pettersen TD Goddard CC Huang GS Couch DM Greenblatt EC Meng TE Ferrin, J Comput Chem 2004 25 1605 1612 10.1002/jcc.20084 15264254
43. Protein function prediction using local 3D templates. RA Laskowski JD Watson JM Thornton, J Mol Biol 2005 351 614 626 10.1016/j.jmb.2005.05.067 16019027 (Pubitemid 41021944)
44. A combined transmembrane topology and signal peptide prediction method. L Kall A Krogh EL Sonnhammer, J Mol Biol 2004 338 1027 1036 10.1016/j.jmb.2004. 03.016 15111065 (Pubitemid 38542831)
45. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. JL Gardy MR Laird F Chen S Rey CJ Walsh M Ester FS Brinkman, Bioinformatics 2005 21 617 623 10.1093/bioinformatics/bti057 15501914 (Pubitemid 40424787)
46. Predicting subcellular localization of proteins using machine-learned classifiers. Z Lu D Szafron R Greiner P Lu DS Wishart B Poulin J Anvik C Macdonell R Eisner, Bioinformatics 2004 20 547 556 10.1093/bioinformatics/btg447 14990451 (Pubitemid 38344335)
47. Prediction of protein subcellular localization. CS Yu YC Chen CH Lu JK Hwang, Proteins 2006 64 643 651 10.1002/prot.21018 16752418
48. Mimicking cellular sorting improves prediction of subcellular localization. R Nair B Rost, J Mol Biol 2005 348 85 100 10.1016/j.jmb.2005.02. 025 15808855 (Pubitemid 40461842)
49. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. KC Chou HB Shen, Biochem Biophys Res Commun 2007 360 339 345 10.1016/j.bbrc.2007.06.027 17586467
50. Discrimination of outer membrane proteins using support vector machines. KJ Park MM Gromiha P Horton M Suwa, Bioinformatics 2005 21 4223 4229 10.1093/bioinformatics/bti697 16204348 (Pubitemid 41724301)
51. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. M Terribilini JD Sander JH Lee P Zaback RL Jernigan V Honavar D Dobbs, Nucleic Acids Res 2007 35 578 584 10.1093/nar/gkm294 17483510
52. A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. PG Bagos TD Liakopoulos IC Spyropoulos SJ Hamodrakas, BMC Bioinformatics 2004 5 29 10.1186/1471-2105-5-29 15070403
53. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
54. Evolutionary trace report-maker: a new type of service for comparative analysis of proteins. I Mihalek I Res O Lichtarge, Bioinformatics 2006 22 1656 1657 10.1093/bioinformatics/btl157 16644792
55. Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis. CA Innis J Shi TL Blundell, Protein Eng 2000 13 839 847 10.1093/protein/13.12.839 11239083 (Pubitemid 32233943)
56. DnaSP, DNA polymorphism analyses by the coalescent and other methods. J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas, Bioinformatics 2003 19 2496 2497 10.1093/bioinformatics/btg359 14668244 (Pubitemid 38016658)