Novel Podoviridae family bacteriophage infecting Weissella cibaria isolated from kimchi

Applied and Environmental Microbiology

Volumn 78, Issue 20, 2012, Pages 7299-7308

  Kleppen, Hans Petter ^a   Holo, Helge ^a   Jeon, Sang Rok ^b   Nes, Ingolf F ^a   Yoon, Sung Sik ^b  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b Yonsei University Wonju   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLETE GENOMES; DNA REPLICATIONS; ELECTRON MICROSCOPY ANALYSIS; FOOD FERMENTATION; GENOME SIZES; INDUSTRIAL FERMENTATION; OPEN READING FRAME; SEQUENCE ANALYSIS;

ELECTRON MICROSCOPY; FERMENTATION; GENES; PROTEINS;

BACTERIOPHAGES;

BACTERIAL DNA;

BACTERIOPHAGE; ELECTRON MICROSCOPY; FERMENTATION; GENOME; INFECTIOUS DISEASE; MORPHOLOGY; MORPHOTYPE; PROTEIN;

ARTICLE; BACTERIOPHAGE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA REPLICATION; DNA SEQUENCE; ELECTRON MICROSCOPY; FOOD CONTROL; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOUTH KOREA; ULTRASTRUCTURE; VIRION; VIROLOGY; VIRUS REPLICATION; WEISSELLA;

BACTERIOPHAGES; CLUSTER ANALYSIS; DNA REPLICATION; DNA, BACTERIAL; FOOD MICROBIOLOGY; MICROSCOPY, ELECTRON; MOLECULAR SEQUENCE DATA; PHYLOGENY; PODOVIRIDAE; REPUBLIC OF KOREA; SEQUENCE ANALYSIS, DNA; VIRION; VIRUS REPLICATION; WEISSELLA;

MIRIDAE; PODOVIRIDAE; WEISSELLA; WEISSELLA CIBARIA;

EID: 84868370149     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00031-12     Document Type: Article

References (63)

1. Ackermann HW. 1998. Tailed bacteriophages: the order Caudovirales. Adv. Virus Res. 51:135-201.
2. Ackermann HW. 2001. Frequency of morphological phage descriptions in the year 2000. Brief review. Arch. Virol. 146:843-857.
3. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Altschul SF, et al. 2005. Protein database searches using compositionally adjusted substitution matrices. FEBS J. 272:5101-5109.
5. Anderson D, Bodley JW. 1990. Role of RNA in bacteriophage phi 29DNA packaging. J. Struct. Biol. 104:70-74.
6. Bae JW, et al. 2005. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71:8825-8835.
7. Baranov PV, Gesteland RF, Atkins JF. 2004. P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA 10:221-230.
8. Barrangou R, Yoon SS, Breidt F, Jr, Fleming HP, Klaenhammer TR. 2002. Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation. Appl. Environ. Microbiol. 68:5452-5458.
9. Bjorkroth KJ, et al. 2002. Taxonomic study of Weissella confusa and description of Weissella cibaria sp. nov., detected in food and clinical samples. Int. J. Syst. Evol. Microbiol. 52:141-148.
10. Blanco L, Lazaro JM, de Vega M, Bonnin A, Salas M. 1994. Terminal protein-primed DNA amplification. Proc. Natl. Acad. Sci. U. S. A. 91: 12198-12202.
11. Bohannan BJM, Lenski RE. 2000. Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage. Ecol. Lett. 3:362-377.
12. Boulanger P. 2009. Purification of bacteriophages and SDS-PAGE analysis of phage structural proteins from ghost particles. Methods Mol. Biol. 502:227-238.
13. Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF. 2011. Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. J. Bacteriol. 193:2377-2378.
14. Brüssow H, Desiere F. 2001. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 39: 213-223.
15. Chang JY, Chang HC. 2011. Growth inhibition of foodborne pathogens by kimchi prepared with bacteriocin-producing starter culture. J. Food Sci. 76:M72-M78.
16. Chang JY, Chang HC. 2010. Improvements in the quality and shelf life of kimchi by fermentation with the induced bacteriocin-producing strain, Leuconostoc citreum GJ7 as a starter. J. Food Sci. 75:M103-M110.
17. Chevenet F, Brun C, Banuls A-L, Jacq B, Christen R. 2006. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7:439. doi:10.1186/1471-2105-7-439.
18. Cho J, et al. 2006. Microbial population dynamics of kimchi, a fermented cabbage product. FEMS Microbiol. Lett. 257:262-267.
19. Choi HJ, et al. 2002. Weissella kimchii sp. nov., a novel lactic acid bacterium from kimchi. Int. J. Syst. Evol. Microbiol. 52:507-511.
20. Choi IK, et al. 2003. Novel Leuconostoc citreum starter culture system for the fermentation of kimchi, a fermented cabbage product. Antonie Van Leeuwenhoek 84:247-253.
21. Dereeper A, et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:W465-W469.
22. Desiere F, McShan WM, van Sinderen D, Ferretti JJ, Brüssow H. 2001. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic streptococci: evolutionary implications for prophage-host interactions. Virology 288:325-341.
23. Ennahar S, Cai Y. 2002. 2004. Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Björkroth et al. Int. J. Syst. Evol. Microbiol. 54:463-465.
24. Eom HJ, Park JM, Seo MJ, Kim MD, Han NS. 2008. Monitoring of Leuconostoc mesenteroides DRC starter in fermented vegetable by random integration of chloramphenicol acetyltransferase gene. J. Ind. Microbiol. Biotechnol. 35:953-959.
25. Fraser JS, Maxwell KL, Davidson AR. 2007. Immunoglobulin-like domains on bacteriophage: weapons of modest damage? Curr. Opin. Microbiol. 10:382-387.
26. Fraser JS, Yu Z, Maxwell KL, Davidson AR. 2006. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J. Mol. Biol. 359:496-507.
27. Garcia JA, Carrascosa JL, Salas M. 1983. Assembly of the tail protein of the Bacillus subtilis phage phi 29. Virology 125:18-30.
28. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
29. Hagen EW, Reilly BE, Tosi ME, Anderson DL. 1976. Analysis of gene function of bacteriophageφ29 of Bacillus subtilis: identification of cistrons essential for viral assembly. J. Virol. 19:501-517.
30. Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi: 10.1186/1471-2105-11-119.
31. Hyman P, Abedon ST. 2009. Practical methods for determining phage growth parameters. Methods Mol. Biol. 501:175-202.
32. Jung JY, et al. 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77:2264-2274.
33. Kamtekar S, et al. 2006. The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition. EMBO J. 25:1335-1343.
34. Kawasaki T, et al. 2009. Genomic characterization of Ralstonia solanacearum phage φRSB1, a T7-like wide-host-range phage. J. Bacteriol. 191:422-427.
35. Kim J, Chun J, Han HU. 2000. Leuconostoc kimchii sp. nov., a new species from kimchi. Int. J. Syst. Evol. Microbiol. 50:1915-1919.
36. Kim M, Chun J. 2005. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103:91-96.
37. Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
38. Lee D, Kim S, Cho J, Kim J. 2008. Microbial population dynamics and temperature changes during fermentation of kimjang kimchi. J. Microbiol. 46:590-593.
39. Lee JS, et al. 1997. Classification of isolates originating from kimchi using carbon-source utilization patterns. J. Microbiol. Biotechnol. 7:68-74.
40. Lee JS, et al. 2005. Analysis of kimchi microflora using denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 102:143-150.
41. Lee JS, et al. 2002. Weissella koreensis sp. nov., isolated from kimchi. Int. J. Syst. Evol. Microbiol. 52:1257-1261.
42. Lu Z, Breidt F, Plengvidhya V, Fleming HP. 2003. Bacteriophage ecology in commercial sauerkraut fermentations. Appl. Environ. Microbiol. 69: 3192-3202.
43. Maniloff J, Ackermann HW. 1998. Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales. Arch. Virol. 143:2051-2063.
44. Marchler-Bauer A, et al. 2009. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 37:D205-D210.
45. Marchler-Bauer A, Bryant SH. 2004. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32:W327-W331.
46. Marchler-Bauer A, et al. 2011. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39:D225-D229.
47. Martin AC, Lopez R, Garcia P. 1996. Analysis of the complete nucleotide sequence and functional organization of the genome of Streptococcus pneumoniae bacteriophage Cp-1. J. Virol. 70:3678-3687.
48. Martin AC, Lopez R, Garcia P. 1995. Nucleotide sequence and transcription of the left early region of Streptococcus pneumoniae bacteriophage Cp-1 coding for the terminal protein and the DNA polymerase. Virology 211:21-32.
49. Meijer WJ, Horcajadas JA, Salas M. 2001. φ29 family of phages. Microbiol. Mol. Biol. Rev. 65:261-287.
50. Moineau S, Lévesque C. 2005. Control of bacteriophages in industrial fermentations, p 286-296. In Kutter E, Sulakvelidze A (ed), Bacteriophages: biology and applications. CRC Press, Boca Raton, FL.
51. Nam YD, Chang HW, Kim KH, Roh SW, Bae JW. 2009. Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays. Int. J. Food Microbiol. 130:140-146.
52. O'Connell-Motherway M, et al. 2000. Six putative two-component regulatory systems isolated from Lactococcus lactis subsp. cremoris MG1363. Microbiology 146:935-947.
53. Park JM, et al. 2010. Identification of the lactic acid bacteria in kimchi according to initial and over-ripened fermentation using PCR and 16S rRNA gene sequence analysis. Food Sci. Biotechnol. 19:541-546.
54. Pringsulaka O, Patarasinpaiboon N, Suwannasai N, Atthakor W, Rangsiruji A. 2011. Isolation and characterisation of a novel Podoviridae-phage infecting Weissella cibaria N 22 from Nham, a Thai fermented pork sausage. Food Microbiol. 28:518-525.
55. Rappsilber J, Ishihama Y, Mann M. 2003. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75:663-670.
56. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. 2006. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1:2856-2860.
57. Shin MS, Han SK, Ryu JS, Kim KS, Lee WK. 2008. Isolation and partial characterization of a bacteriocin produced by Pediococcus pentosaceus K23-2 isolated from kimchi. J. Appl. Microbiol. 105:331-339.
58. Simpson AA, et al. 2000. Structure of the bacteriophage phi29 DNA packaging motor. Nature 408:745-750.
59. Solheim M, Aakra A, Vebo H, Snipen L, Nes IF. 2007. Transcriptional responses of Enterococcus faecalis V583 to bovine bile and sodium dodecyl sulfate. Appl. Environ. Microbiol. 73:5767-5774.
60. Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27:1009-1010.
61. Xiang Y, et al. 2008. Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage φ29 tail. Proc. Natl. Acad. Sci. U. S. A. 105:9552-9557.
62. Yanisch-Perron C, Vieira J, Messing J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119.
63. Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP. 2007. Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J. Bacteriol. 189:1366-1381.