Characterization of a novel temperate phage originating from a cereulide-producing Bacillus cereus strain

Research in Microbiology

Volumn 162, Issue 4, 2011, Pages 446-459

  Smeesters, Pierre R ^a   Drèze, Pierre Alexandre ^a   Bousbata, Sabrina ^a   Parikka, Kaarle J ^a   Timmery, Sophie ^b   Hu, Xiaomin ^b   Perez Morga, David ^a   Deghorain, Marie ^a   Toussaint, Ariane ^a   Mahillon, Jacques ^b   Van Melderen, Laurence ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

ACLAME database; Bacteriophage; Circular prophage; Emetic Bacillus cereus strain

Indexed keywords

CEREULIDE;

ARTICLE; BACILLUS CEREUS; BACILLUS THURINGIENSIS; BACTERIAL STRAIN; BACTERIOPHAGE; GENE SEQUENCE; MOSAICISM; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEOMICS; UNINDEXED SEQUENCE;

BACILLUS CEREUS; BACILLUS PHAGES; DEPSIPEPTIDES; GENOME, VIRAL; OPEN READING FRAMES; PROPHAGES; SIPHOVIRIDAE;

BACILLUS CEREUS; BACILLUS THURINGIENSIS; SIPHOVIRIDAE;

EID: 79955166271     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2011.02.009     Document Type: Article

References (41)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic. Acids. Res. 1997, 25:3389-3402.
3. Andersson M.A., Jaaskelainen E.L., Shaheen R., Pirhonen T., Wijnands L.M., Salkinoja-Salonen M.S. Sperm bioassay for rapid detection of cereulide-producing Bacillus cereus in food and related environments. Int. J. Food. Microbiol. 2004, 94:175-183.
4. Besemer J., Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic. Acids. Res. 2005, 33:W451-W454.
5. Casjens S.R., Gilcrease E.B. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods. Mol. Biol. 2009, 502:91-111.
6. Casjens S.R., Gilcrease E.B., Winn-Stapley D.A., Schicklmaier P., Schmieger H., Pedulla M.L., Ford M.E., Houtz J.M., Hatfull G.F., Hendrix R.W. The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol. 2005, 187:1091-1104.
7. Challacombe J.F., Altherr M.R., Xie G., Bhotika S.S., Brown N., Bruce D., Campbell C.S., Campbell M.L., Chen J., Chertkov O., Cleland C., Dimitrijevic M., Doggett N.A., Fawcett J.J., Glavina T., Goodwin L.A., Green L.D., Han C.S., Hill K.K., Hitchcock P., Jackson P.J., Keim P., Kewalramani A.R., Longmire J., Lucas S., Malfatti S., Martinez D., McMurry K., Meincke L.J., Misra M., Moseman B.L., Mundt M., Munk A.C., Okinaka R.T., Parson-Quintana B., Reilly L.P., Richardson P., Robinson D.L., Saunders E., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Ticknor L.O., Wills P.L., Gilna P., Brettin T.S. The complete genome sequence of Bacillus thuringiensis Al Hakam. J. Bacteriol. 2007, 189:3680-3681.
8. Dierick K., Van Coillie E., Swiecicka I., Meyfroidt G., Devlieger H., Meulemans A., Hoedemaekers G., Fourie L., Heyndrickx M., Mahillon J. Fatal family outbreak of Bacillus cereus-associated food poisoning. J. Clin. Microbiol. 2005, 43:4277-4279.
9. Dorscht J., Klumpp J., Bielmann R., Schmelcher M., Born Y., Zimmer M., Calendar R., Loessner M.J. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J. Bacteriol. 2009, 191:7206-7215.
10. Fouts D.E., Rasko D.A., Cer R.Z., Jiang L., Fedorova N.B., Shvartsbeyn A., Vamathevan J.J., Tallon L., Althoff R., Arbogast T.S., Fadrosh D.W., Read T.D., Gill S.R. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J. Bacteriol. 2006, 188:3402-3408.
11. Gobom J., Nordhoff E., Mirgorodskaya E., Ekman R., Roepstorff P. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass. Spectrom. 1999, 34:105-116.
12. Hoton F., Fornelos N., N'Guessan E., Hu X., Swiecicka I., Dierick K., Jääskeläinen E., Salkinoja-Salonen M., Mahillon J. Family portrait of Bacillus cereus and Bacillus weihenstephanensis cereulide-producing strains. Environ. Microbiol. 2009, 177-183.
13. Huang J., Guo S., Mahillon J., Van der Auwera G.A., Wang L., Han D., Yu Z., Sun M. Molecular characterization of a DNA fragment harboring the replicon of pBMB165 from Bacillus thuringiensis subsp. tenebrionis. BMC. Genomics. 2006, 7:270.
14. Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V., Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M., Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G., Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 2003, 423:87-91.
15. Jensen O.N., Larsen M.R., Roepstorff P. Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: strategies and applications. Proteins 1998, Suppl. 2, 74-89.
16. Kolsto A.B., Tourasse N.J., Okstad O.A. What sets Bacillus anthracis apart from other Bacillus species?. Annu. Rev. Microbiol. 2009, 63:451-476.
17. Kropinski A.M., Prangishvili D., Lavigne R. Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Environ. Microbiol 2009.
18. Lapidus A., Goltsman E., Auger S., Galleron N., Segurens B., Dossat C., Land M.L., Broussolle V., Brillard J., Guinebretiere M.H., Sanchis V., Nguen-The C., Lereclus D., Richardson P., Wincker P., Weissenbach J., Ehrlich S.D., Sorokin A. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem. Biol. Interact. 2008, 171:236-249.
19. Leplae R., Hebrant A., Wodak S.J., Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic. Acids. Res. 2004, 32:D45-D49.
20. Lima-Mendez G., Van Helden J., Toussaint A., Leplae R. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 2008, 24:863-865.
21. Lima-Mendez G., Van Helden J., Toussaint A., Leplae R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 2008, 25:762-777.
22. Loessner M.J., Maier S.K., Daubek-Puza H., Wendlinger G., Scherer S. Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli. J. Bacteriol. 1997, 179:2845-2851.
23. Minakhin L., Semenova E., Liu J., Vasilov A., Severinova E., Gabisonia T., Inman R., Mushegian A., Severinov K. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J. Mol. Biol. 2005, 354:1-15.
24. Ravantti J.J., Gaidelyte A., Bamford D.H., Bamford J.K. Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage. Virology 2003, 313:401-414.
25. Read T.D., Peterson S.N., Tourasse N., Baillie L.W., Paulsen I.T., Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R., Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M., Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M., DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C., Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y., Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M., Watkins K.L., Nierman W.C., Hazen A., Cline R., Redmond C., Thwaite J.E., White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M., Hanna P.C., Kolsto A.B., Fraser C.M. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003, 423:81-86.
26. Rohwer F. Global phage diversity. Cell. 2003, 113:141.
27. Rombel I.T., Sykes K.F., Rayner S., Johnston S.A. ORF-FINDER: a vector for high-throughput gene identification. Gene 2002, 282:33-41.
28. Schobel S., Zellmeier S., Schumann W., Wiegert T. The Bacillus subtilis sigmaW anti-sigma factor RsiW is degraded by intramembrane proteolysis through YluC. Mol. Microbiol. 2004, 52:1091-1105.
29. Schuch R., Fischetti V.A. Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance. J. Bacteriol. 2006, 188:3037-3051.
30. Seedorf H., Fricke W.F., Veith B., Bruggemann H., Liesegang H., Strittmatter A., Miethke M., Buckel W., Hinderberger J., Li F., Hagemeier C., Thauer R.K., Gottschalk G. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. U S A 2008, 105:2128-2133.
31. Shevchenko A., Wilm M., Vorm O., Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 1996, 68:850-858.
32. Sozhamannan S., McKinstry M., Lentz S.M., Jalasvuori M., McAfee F., Smith A., Dabbs J., Ackermann H.W., Bamford J.K., Mateczun A., Read T.D. Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity. Appl. Environ. Microbiol. 2008, 74:6792-6796.
33. Stromsten N.J., Benson S.D., Burnett R.M., Bamford D.H., Bamford J.K. The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J. Bacteriol. 2003, 185:6985-6989.
34. Thomas J.A., Hardies S.C., Rolando M., Hayes S.J., Lieman K., Carroll C.A., Weintraub S.T., Serwer P. Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. Virology 2007, 368:405-421.
35. Timmery S., Modrie P., Minet O., Mahillon J. Plasmid capture by the Bacillus thuringiensis conjugative plasmid pXO16. J. Bacteriol. 2009, 191:2197-2205.
36. Tu K., Yu H., Zhu M. MEGO: gene functional module expression based on gene ontology. Biotechniques 2005, 38:277-283.
37. Verheust C., Fornelos N., Mahillon J. GIL16, a new gram-positive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 2005, 187:1966-1973.
38. Verheust C., Jensen G., Mahillon J. pGIL01, a linear tectiviral plasmid prophage originating from Bacillus thuringiensis serovar israelensis. Microbiology 2003, 149:2083-2092.
39. Wang J., Steggles J.R., Ellar D.J. Molecular characterization of virulence defects in Bacillus thuringiensis mutants. FEMS. Microbiol. Lett. 2008, 280:127-134.
40. Wu H., Sampson L., Parr R., Casjens S. The DNA site utilized by bacteriophage P22 for initiation of DNA packaging. Mol. Microbiol. 2002, 45:1631-1646.
41. Young R. Bacteriophage holins: deadly diversity. J. Mol. Microbiol. Biotechnol. 2002, 4:21-36.