Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Okamoto, Akira ^a   Yamada, Keiko ^a  

^a NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HYPOTHETICAL PROTEIN; MESSENGER RNA; PROTEIN; PROTEOME; UNCLASSIFIED DRUG; VIRULENCE FACTOR; BACTERIAL DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM CULTURE; CELL FRACTIONATION; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC DATABASE; MASS FRAGMENTOGRAPHY; NONHUMAN; OPEN READING FRAME; PROTEIN EXPRESSION; PROTEIN SECRETION; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STREPTOCOCCUS PYOGENES; STREPTOCOCCUS PYOGENES SF370; BIOLOGY; GENETICS; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE;

STREPTOCOCCUS PYOGENES;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DNA, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; PROTEOME; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; STREPTOCOCCUS PYOGENES;

EID: 80755189686     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-249     Document Type: Article

References (51)

1. Functional annotation of hypothetical proteins-A review. Sivashankari S, Shanmughavel P, Bioinformation 2006 1 8 335 338 17597916
2. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P, Nucleic acids research 2000 28 17 3278 3288 10.1093/nar/28.17.3278 10954595 (Pubitemid 30662292)
3. Genome reannotation of Escherichia coli CFT073 with new insights into virulence. Luo C, Hu GQ, Zhu H, BMC genomics 2009 10 552 10.1186/1471-2164-10- 552 19930606
4. A proteogenomic update to Yersinia: enhancing genome annotation. Payne SH, Huang ST, Pieper R, BMC genomics 11 460
5. Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes. Bocs S, Danchin A, Medigue C, BMC bioinformatics 2002 3 5 10.1186/1471-2105-3-5 11879526 (Pubitemid 38751199)
6. Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. Guo FB, Wang J, Zhang CT, DNA Res 2004 11 6 361 370 10.1093/dnares/11.6.361 15871459 (Pubitemid 40873611)
7. Identify protein-coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS. Guo FB, Lin Y, Journal of biomolecular structure & dynamics 2009 26 4 413 420 22074399
8. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. Kim W, Silby MW, Purvine SO, Nicoll JS, Hixson KK, Monroe M, Nicora CD, Lipton MS, Levy SB, PloS one 2009 4 12 8455 10.1371/journal.pone. 0008455 20041161
9. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS Jr, Kolesov G, Frishman D, Galperin MY, Nucleic acids research 2004 32 8 2353 2361 10.1093/nar/gkh555 15121896 (Pubitemid 38854789)
10. LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris. Zhang W, Culley DE, Gritsenko MA, Moore RJ, Nie L, Scholten JC, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ, Biochemical and biophysical research communications 2006 349 4 1412 1419 10.1016/j.bbrc.2006.09.019 16982031 (Pubitemid 44416414)
11. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM, Proceedings of the National Academy of Sciences of the United States of America 2005 102 6 2099 2104 10.1073/pnas.0409111102 15684069 (Pubitemid 40262018)
12. Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. Jiang SY, Christoffels A, Ramamoorthy R, Ramachandran S, Plant physiology 2009 150 4 1997 2008 10.1104/pp.109.139402 19535473
13. Proteome analysis of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1. Yamazaki S, Yamazaki J, Nishijima K, Otsuka R, Mise M, Ishikawa H, Sasaki K, Tago S, Isono K, Mol Cell Proteomics 2006 5 5 811 823 10.1074/mcp.M500312-MCP200 16455681 (Pubitemid 43792791)
14. Proteomic analysis of proteins secreted by Streptococcus pyogenes. Chaussee MA, McDowell EJ, Chaussee MS, Methods in molecular biology (Clifton, NJ 2008 431 15 24 10.1007/978-1-60327-032-8-2
15. Proteomic analysis and identification of Streptococcus pyogenes surface-associated proteins. Severin A, Nickbarg E, Wooters J, Quazi SA, Matsuka YV, Murphy E, Moutsatsos IK, Zagursky RJ, Olmsted SB, Journal of bacteriology 2007 189 5 1514 1522 10.1128/JB.01132-06 17142387 (Pubitemid 46446112)
16. Growth phase-associated changes in the transcriptome and proteome of Streptococcus pyogenes. Chaussee MA, Dmitriev AV, Callegari EA, Chaussee MS, Archives of microbiology 2008 189 1 27 41 17665172 (Pubitemid 350159673)
17. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, Lai HS, Lin SP, Qian Y, Jia HG, Najar FZ, Ren Q, Zhu H, Song L, White J, Yuan X, Clifton SW, Roe BA, McLaughlin R, Proceedings of the National Academy of Sciences of the United States of America 2001 98 8 4658 4663 10.1073/pnas.071559398 11296296 (Pubitemid 32295032)
18. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Smoot JC, Barbian KD, Van Gompel JJ, Smoot LM, Chaussee MS, Sylva GL, Sturdevant DE, Ricklefs SM, Porcella SF, Parkins LD, Beres SB, Campbell DS, Smith TM, Zhang Q, Kapur V, Daly JA, Veasy LG, Musser JM, Proceedings of the National Academy of Sciences of the United States of America 2002 99 7 4668 4673 10.1073/pnas.062526099 11917108 (Pubitemid 34286042)
19. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Beres SB, Sylva GL, Barbian KD, Lei B, Hoff JS, Mammarella ND, Liu MY, Smoot JC, Porcella SF, Parkins LD, Campbell DS, Smith TM, McCormick JK, Leung DY, Schlievert PM, Musser JM, Proceedings of the National Academy of Sciences of the United States of America 2002 99 15 10078 10083 10.1073/pnas.152298499 12122206 (Pubitemid 34831175)
20. Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Nakagawa I, Kurokawa K, Yamashita A, Nakata M, Tomiyasu Y, Okahashi N, Kawabata S, Yamazaki K, Shiba T, Yasunaga T, Hayashi H, Hattori M, Hamada S, Genome research 2003 13 6A 1042 1055 12799345 (Pubitemid 36764186)
21. Genome sequence of a serotype M28 strain of group A Streptococcus: potential new insights into puerperal sepsis and bacterial disease specificity. Green NM, Zhang S, Porcella SF, Nagiec MJ, Barbian KD, Beres SB, LeFebvre RB, Musser JM, The Journal of infectious diseases 2005 192 5 760 770 10.1086/430618 16088825 (Pubitemid 41193073)
22. Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus. Beres SB, Richter EW, Nagiec MJ, Sumby P, Porcella SF, DeLeo FR, Musser JM, Proceedings of the National Academy of Sciences of the United States of America 2006 103 18 7059 7064 10.1073/pnas.0510279103 16636287
23. Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. Banks DJ, Porcella SF, Barbian KD, Beres SB, Philips LE, Voyich JM, DeLeo FR, Martin JM, Somerville GA, Musser JM, The Journal of infectious diseases 2004 190 4 727 738 10.1086/422697 15272401 (Pubitemid 39050003)
24. Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo. Holden MT, Scott A, Cherevach I, Chillingworth T, Churcher C, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S, Jagels K, Moule S, Mungall K, Quail MA, Price C, Rabbinowitsch E, Sharp S, Skelton J, Whitehead S, Barrell BG, Kehoe M, Parkhill J, Journal of bacteriology 2007 189 4 1473 1477 10.1128/JB.01227-06 17012393 (Pubitemid 46239771)
25. Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. McShan WM, Ferretti JJ, Karasawa T, Suvorov AN, Lin S, Qin B, Jia H, Kenton S, Najar F, Wu H, Scott J, Roe BA, Savic DJ, Journal of bacteriology 2008 190 23 7773 7785 10.1128/JB.00672-08 18820018
26. Evolutionary origin and emergence of a highly successful clone of serotype M1 group A Streptococcus involved multiple horizontal gene transfer events. Sumby P, Porcella SF, Madrigal AG, Barbian KD, Virtaneva K, Ricklefs SM, Sturdevant DE, Graham MR, Vuopio-Varkila J, Hoe NP, Musser JM, The Journal of infectious diseases 2005 192 5 771 782 10.1086/432514 16088826 (Pubitemid 41193074)
27. Application of both high-performance liquid chromatography combined with tandem mass spectrometry shotgun and 2-D polyacrylamide gel electrophoresis for streptococcal exoproteins gave reliable proteomic data. Okamoto A, Hasegawa T, Yamada K, Ohta M, Microbiology and immunology 2011 55 2 84 94 10.1111/j.1348-0421.2010.00302.x 21204954
28. Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. Mitaku S, Hirokawa T, Tsuji T, Bioinformatics (Oxford, England) 2002 18 4 608 616 10.1093/bioinformatics/18.4.608 (Pubitemid 34521049)
29. Improved prediction of signal peptides: SignalP 3.0. Bendtsen JD, Nielsen H, von Heijne G, Brunak S, Journal of molecular biology 2004 340 4 783 795 10.1016/j.jmb.2004.05.028 15223320 (Pubitemid 38829638)
30. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Nielsen H, Engelbrecht J, Brunak S, von Heijne G, Protein engineering 1997 10 1 1 6 10.1093/protein/10.1.1 9239223
31. Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Canchaya C, Desiere F, McShan WM, Ferretti JJ, Parkhill J, Brussow H, Virology 2002 302 2 245 258 10.1006/viro.2002.1570 12441069 (Pubitemid 35373853)
32. The ERGO genome analysis and discovery system. Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N, Nucleic acids research 2003 31 1 164 171 10.1093/nar/gkg148 12519973 (Pubitemid 36150356)
33. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Frishman D, Mironov A, Mewes HW, Gelfand M, Nucleic acids research 1998 26 12 2941 2947 10.1093/nar/26.12.2941 9611239 (Pubitemid 28297528)
34. Microbial gene identification using interpolated Markov models. Salzberg SL, Delcher AL, Kasif S, White O, Nucleic acids research 1998 26 2 544 548 10.1093/nar/26.2.544 9421513 (Pubitemid 28291582)
35. BASys: a web server for automated bacterial genome annotation. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS, Nucleic acids research 2005 33 Web Server 455 459
36. Effects of oligopeptide permease in group A Streptococcal infection. Wang CH, Lin CY, Luo YH, Tsai PJ, Lin YS, Lin MT, Chuang WJ, Liu CC, Wu JJ, Infection and immunity 2005 73 5 2881 2890 10.1128/IAI.73.5.2881-2890.2005 15845494 (Pubitemid 40570357)
37. Molecular characterization of group A streptococcal (GAS) oligopeptide permease (opp) and its effect on cysteine protease production. Podbielski A, Pohl B, Woischnik M, Korner C, Schmidt KH, Rozdzinski E, Leonard BA, Molecular microbiology 1996 21 5 1087 1099 10.1046/j.1365-2958.1996.661421.x 8885277 (Pubitemid 26297773)
38. CovS inactivates CovR and is required for growth under conditions of general stress in Streptococcus pyogenes. Dalton TL, Scott JR, Journal of bacteriology 2004 186 12 3928 3937 10.1128/JB.186.12.3928-3937.2004 15175307 (Pubitemid 38746069)
39. Growth phase-dependent effect of clindamycin on production of exoproteins by Streptococcus pyogenes. Sawai J, Hasegawa T, Kamimura T, Okamoto A, Ohmori D, Nosaka N, Yamada K, Torii K, Ohta M, Antimicrobial agents and chemotherapy 2007 51 2 461 467 10.1128/AAC.00539-06 17101685 (Pubitemid 46185261)
40. Streptococcus pyogenes CovRS mediates growth in iron starvation and in the presence of the human cationic antimicrobial peptide LL-37. Froehlich BJ, Bates C, Scott JR, Journal of bacteriology 2009 191 2 673 677 10.1128/JB.01256-08 18996992
41. A two-component regulatory system, CsrR-CsrS, represses expression of three Streptococcus pyogenes virulence factors, hyaluronic acid capsule, streptolysin S, and pyrogenic exotoxin B. Heath A, DiRita VJ, Barg NL, Engleberg NC, Infection and immunity 1999 67 10 5298 5305 10496909 (Pubitemid 29455305)
42. emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Shinoda K, Tomita M, Ishihama Y, Bioinformatics (Oxford, England) 2010 26 4 576 577 10.1093/bioinformatics/btp700
43. Protein abundance profiling of the Escherichia coli cytosol. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D, BMC genomics 2008 9 102 10.1186/1471-2164-9-102 18304323 (Pubitemid 351517450)
44. Effect of antibiotics on group A Streptococcus exoprotein production analyzed by two-dimensional gel electrophoresis. Tanaka M, Hasegawa T, Okamoto A, Torii K, Ohta M, Antimicrobial agents and chemotherapy 2005 49 1 88 96 10.1128/AAC.49.1.88-96.2005 15616280 (Pubitemid 40065777)
45. Molecular basis of group A streptococcal virulence. Bisno AL, Brito MO, Collins CM, The Lancet infectious diseases 2003 3 4 191 200 10.1016/S1473- 3099(03)00576-0 12679262 (Pubitemid 36389182)
46. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Masuda T, Saito N, Tomita M, Ishihama Y, Mol Cell Proteomics 2009 8 12 2770 2777 10.1074/mcp.M900240-MCP200 19767571
47. PRIDE Converter: making proteomics data-sharing easy. Barsnes H, Vizcaino JA, Eidhammer I, Martens L, Nature biotechnology 2009 27 7 598 599 10.1038/nbt0709-598 19587657
48. Artemis: sequence visualization and annotation. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B, Bioinformatics (Oxford, England) 2000 16 10 944 945 10.1093/bioinformatics/16.10.944
49. Clustal W and Clustal X version 2.0. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Bioinformatics (Oxford, England) 2007 23 21 2947 2948 10.1093/bioinformatics/btm404 (Pubitemid 350162903)
50. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Nature genetics 2000 25 1 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
51. High-throughput functional annotation and data mining with the Blast2GO suite. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A, Nucleic acids research 2008 36 10 3420 3435 10.1093/nar/gkn176 18445632 (Pubitemid 351859009)