Genomic characterization of six novel Bacillus pumilus bacteriophages

Virology

Volumn 444, Issue 1-2, 2013, Pages 374-383

  Lorenz, Laura ^a   Lins, Bridget ^b   Barrett, Jonathan ^a   Montgomery, Andrew ^a   Trapani, Stephanie ^a   Schindler, Anne ^a   Christie, Gail E ^c   Cresawn, Steven G ^a   Temple, Louise ^a  

^a JAMES MADISON UNIVERSITY   (United States)

^b UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Bacillus pumilus; Bacillus taxonomy; Bacteriophage; Genomics; Host range

Indexed keywords

ARTICLE; BACILLUS; BACILLUS ANTHRACIS; BACILLUS PHAGE; BACILLUS PUMILUS; BACILLUS SIMPLEX; BACILLUS THURINGIENSIS; BACTERIAL GENOME; BACTERIUM ISOLATION; CONTROLLED STUDY; GENE SEQUENCE; GENE TRANSFER; HOST RANGE; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN DETERMINATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY;

BACILLUS PUMILUS; BACILLUS SIMPLEX;

EID: 84882818351     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2013.07.004     Document Type: Article

References (54)

1. Abshire T.G., Brown J.E., Ezzell J.W. Production and validation of the use of gamma phage for identification of Bacillus anthracis. J. Clin. Microbiol. 2005, 43:4780-4788.
2. Alonso J.C., Lüder G., Stiege A.C., Chai S., Weise F., Trautner T.A. The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 1997, 204:201-212.
3. 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.
4. Becker B., de la Fuente N., Gassel M., Günther D., Tavares P., Lurz R., Trautner T.A., Alonso J.C. Head morphogenesis genes of the Bacillus subtilis bacteriophage SPP1. J. Mol. Biol. 1997, 268:822-839.
5. Bramucci M.G., Keggins K.M., Lovett P.S. Bacteriophage conversion of spore-negative mutants to spore-positive in Bacillus pumilus. J. Virol. 1977, 22:194-202.
6. Casjens S.R. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Microbiol. 2005, 8:451-458.
7. Christie G.E., Temple L.M., Bartlett B.A., Goodwin T.S. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. J. Bacteriol. 2002, 184:6522-6531.
8. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
9. Cresawn S.G., Bogel M., Day N., Jacobs-Sera D., Hendrix R.W., Hatfull G.F. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinform. 2011, 12:395-409.
10. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27:4636-4641.
11. Fierer, N., Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. In: Proceedings of the National Academy of Sciences of the United States of America. vol. 103, pp. 626-631.
12. 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.
13. From C., Hormazabal V., Granum P.E. Food poisoning associated with pumilacidin-producing Bacillus pumilus in rice. Int. J. Food Microbiol. 2007, 115:319-324.
14. Gioia J., Yerrapragada S., Qin X., Jiang H., Igboeli O.C., Muzny D., Dugan-Rocha S., Ding Y., Hawes A., Liu W., Perez L., Kovar C., Dinh H., Lee S., Nazareth L., Blyth P., Holder M., Buhay C., Tirumalai M.R., Liu Y., Dasgupta I., Bokhetache L., Fujita M., Karouia F., Eswara Moorthy P., Siefert J., Uzman A., Buzumbo P., Verma A., Zwiya H., McWilliams B.D., Olowu A., Clinkenbeard K.D., Newcombe D., Golebiewski L., Petrosino J.F., Nicholson W.L., Fox G.E., Venkateswaran K., Highlander S.K., Weinstock G.M. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS ONE 2007, 2:e928.
15. Gordon D., Abajian C., Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998, 8:195-202.
16. Haq I., Chaudhry W., Akhtar M., Andleeb S., Qadri I. Bacteriophages and their implications on future biotechnology: a review 2012, 9:9.
17. Hatfull G.F., Jacobs-Sera Deborah, Lawrence J.G., Pope W.H., Russell D.A., Ching-Chung Ko, Weber R.J., Patel M.C., Germane K.L., Edgar R.H., Hoyte N.N., Bowman C.A., Tantoco A.T., Paladin E.C., Myers M.S., Smith A.L., Grace M.S., Pham T.T., O'Brien Matthew B., Vogelsberger A.M., Hryckowian A.J., Wynalek J.L., Donis-Keller Helen, Bogel M.W., Peebles C.L., Cresawn S.G., Hendrix R.W. Comparative genomic analysis of 60 mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J. Mol. Biol. 2010, 397:119-143.
18. Katsura I., Hendrix R.W. Length determination in bacteriophage lambda tails. Cell 1984, 39:691-698.
19. Klumpp J., Lavigne R., Loessner M., Ackermann H. The SPO1-related bacteriophages. Arch. Virol. 2010, 155:1547-1561.
20. Kropinski A., Hayward M., Agnew M.D., Jarrell K. The genome of BCJA1c: a bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii. Extremophiles 2005, 9:99-109.
21. La Duc M.T., Kern R., Venkateswaran K. Microbial Monitoring of Spacecraft and Associated Environments. Microb. Ecol. 2004, 47:150-158.
22. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
23. Levin M., Hendrix R., Casjens S. A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein. J. Molec. Biol. 1993, 234:124-139.
24. Lewis S.E., Searle S.M.J., Harris N., Gibson M., Iyer V., Richter J., Wiel C., Bayraktaroglu L., Birney E., Crosby M.A., Kaminker J.S., Matthews B.B., Prochnik S.E., Smith C.D., Tupy J.L., Rubin G.M., Misra S., Mungall C.J., Clamp M.E. Apollo: a sequence annotation editor. Genome Biol. 2002, 3:1-14.
25. Logan N., Halket G. Developments in the Taxonomy of Aerobic, Endospore-Forming Bacteria 2011, 1-29. Springer, Berlin Heidelberg. N.A. Logan, P. Vos (Eds.).
26. Logan N.A. Bacillus and relatives in foodborne illness. J. Appl. Microbiol. 2012, 112:417-429.
27. Lukashin A.V., Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 1998, 26:1107-1115.
28. Marchler-Bauer A., Lu S., Anderson J.B., Chitsaz F., Derbyshire M.K., De Weese-Scott C., Fong J.H., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Lu F., Marchler G.H., Mullokandov M., Omelchenko M.V., Robertson C.L., Song J.S., Thanki N., Yamashita R.A., Zhang D., Zhang N., Zheng C., Bryant S.H. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39:D225-D229.
29. Maughan H., Van d.A. Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. Infect. Genet. Evol. 2011, 11:789-797.
30. McGuffin L.J., Bryson K., Jones D.T. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-405.
31. Meijer W.J.J., Horcajadas J.A., Salas M. Φ29 family of phages. Microbiol. Mol. Biol. Rev. 2001, 65:261-287.
32. 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.
33. Morais M.C., Kanamarul S., Badasso M.O., Koti J.S., Owen B.A.L., McMurray C.T., Anderson D.L., Rossmann M.G. Bacteriophage Φ29 scaffolding protein gp7 before and after prohead assembly. Nat. Struct. Biol. 2003, 10:572-576.
34. Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
35. Perrière G., Gouy M. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 1996, 364-369.
36. Pietila, M.K., Laurinmaki, P., Russell, D.A., Ko, C.C., Jacobs-Sera, D., Hendrix, R.W., Bamford, D.H., Butcher, S.J., 2013. Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story. Proc. Natl. Acad. Sci. U.S.A. 110, 10604-10609.
37. Promega, 2010. Wizard DNA Clean-Up System Technical Bulletin. 2008.
38. Reanney D.C., Teh C.K. Mapping pathways of possible phage-mediated genetic interchange among soil Bacilli. Soil Biol. Biochem. 1976, 8:305-311.
39. Roy A., Kucukural A., Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5:725-738.
40. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M., Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945.
41. Salkinoja-Salonen M.S., Vuorio R., Andersson M.A., Kampfer P., Andersson M.C., Honkanen-Buzalski T., Scoging A.C. Toxigenic strains of Bacillus licheniformis related to food poisoning. Appl. Environ. Microbiol. 1999, 65:4637-4645.
42. Schattner P., Brooks A.N., Lowe T.M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005, 33:W686-W689.
43. Schneider C.A., Rasband W.S., Eliceiri K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 2012, 9:671-675.
44. Shevchenko A., Tomas H., Havlis J., Olsen J.V., Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1:2856-2860.
45. Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Soding J., Thompson J.D., Higgins D.G. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7.
46. Söding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:W244-W248.
47. Stewart C.R., Casjens S.R., Cresawn S.G., Houtz J.M., Smith A.L., Ford M.E., Peebles C.L., Hatfull G.F., Hendrix R.W., Huang W.M., Pedulla M.L. The genome of Bacillus subtilis Bacteriophage SPO1. J. Mol. Biol. 2009, 388:48-70.
48. 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.
49. van Elsas J.D., Penido E.G.C. Isolation and characterization ofBacillus pumilus phages from Brazilian soil. Abl. Bakt. II. Abt. 1981, 136:581-589.
50. Xiang Y., Leiman P.G., Li L., Grimes S., Anderson D.L., Rossmann M.G. Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol. Cell 2009, 34:375-386.
51. Xu J., Hendrix R.W., Duda R.L. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell 2004, 16:11-21.
52. Young R. Bacteriophage lysis: mechanism and regulation. Microbiol. Rev. 1992, 56:430-481.
53. Young R., Bläsi U. Holins: form and function in bacteriophage lysis. FEMS Microbiol. Rev. 1995, 17:191-205.
54. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9. (40-2105-9-40).