Identification of lytic bacteriophage MmP1, assigned to a new member of T7-like phages infecting Morganella morganii

Genomics

Volumn 96, Issue 3, 2010, Pages 167-172

  Zhu, Junmin ^a   Rao, Xiancai ^a   Tan, Yinling ^a   Xiong, Kun ^a   Hu, Zhen ^a   Chen, Zhijin ^a   Jin, Xiaolin ^a   Li, Shu ^a   Chen, Yao ^a   Hu, Fuquan ^a  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Bacteriophage; Genome annotation; Genome sequence; Podoviridae; RNA polymerase; Structural proteins; T7 group; T7 like phages

Indexed keywords

BACTERIAL DNA; CYTOSINE; DOUBLE STRANDED DNA; GUANINE; RNA POLYMERASE; STRUCTURAL PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIOPHAGE MMP1; BIODIVERSITY; CONTROLLED STUDY; DNA SEQUENCE; ENTEROBACTERIACEAE INFECTION; EVOLUTIONARY ADAPTATION; MORGANELLA MORGANII; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITISM; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); MORGANELLA MORGANII; PODOVIRIDAE;

EID: 77955661456     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.06.001     Document Type: Article

References (42)

1. Huff W.E., Huff G.R., Rath N.C., Donoghue A.M. Evaluation of the influence of bacteriophage titer on the treatment of colibacillosis in broiler chickens. Poult. Sci. 2006, 85:1373-1377.
2. Atterbury R.J., et al. Bacteriophage therapy to reduce salmonella colonization of broiler chickens. Appl. Environ. Microbiol. 2007, 73:4543-4549.
3. Tan Y., et al. Whole genome sequencing of a novel temperate bacteriophage of P. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome. Cell Microbiol. 2007, 9:479-491.
4. Wang Pauline W., Chu Linda, Guttman David S. Complete sequence and evolutionary genomic analysis of the pseudomonas aeruginosa transposable bacteriophage D3112. J. Bacteriol. 2004, 186:400-410.
5. Hausmann R. The T7 group. The Bacteriophages 1988, vol. 1:259-289. Plenum Press, New York. R. Calendar (Ed.).
6. Chen Zehua, Schneider Thomas D. Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res. 2005, 33:6172-6187.
7. Lavigne R., Seto D., Mahadevan P., Ackermann H.W., Kropinski A.M. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol. 2008, 159:406-414.
8. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 1983, 166:477-535.
9. Pajunen M.I., Kiljunen S.J., Söderholm M.E.-L., Skurnik M. Complete genomic sequence of the lytic bacteriophage phiYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 2001, 183:1928-1937.
10. Pajunen M.I., Elizondo M.R., Skurnik M., Kieleczawa J., Molineux I.J. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol. 2002, 319:1115-1132.
11. Kovalayova I.V., Kropinski A.M. The complete genomic sequence of lytic bacteriophage gh-1 infecting pseudomanas putida-evidence for close relationship to the T7 group. Virology 2003, 311:305-315.
12. Garcia E., et al. The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes. J. Bacteriol. 2003, 185:5248-5262.
13. Scholl D., Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J. Bacteriol. 2005, 187:8499-8503.
14. Kwon H.J., et al. Characterization of a T7-like lytic bacteriophage (phiSG-JL2) of Salmonella enterica serovar gallinarum biovar gallinarum. Appl. Environ. Microbiol. 2008, 74:6970-6979.
15. Michalewicz J., Hsu E., Larson J.J., Nicholson A.W. Physical map and genetic early region of the T7-related coliphage, BA14. Gene 1991, 98:89-93.
16. Han K.G., Kim D.H., Junn E., Lee S.S., Kang C. Identification of bacteriophage K11 genomic promoters for K11 RNA polymerase. J. Biochem. Mol. Biol. 2002, 35:637-641.
17. Lingohr E.J., Villegas A., She Y.M., Ceyssens P.J., Kropinski A.M. The genome and proteome of the Kluyvera bacteriophage Kvp1-another member of the T7-like Autographivirinae. Virol. J. 2008, 5:122.
18. Lee I.K., Liu J.W. Clinical characteristics and risk factors for mortality in Morganella morganii bacteremia. J. Microbiol. Immunol. Infect. 2006, 39:328-334.
19. Rohwer F., Edwards R. The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol. 2002, 184:4529-4535.
20. Ackermann H.W. 5500 Phages examined in the electron microscope. Arch. Virol. 2007, 152:227-243.
21. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 2nd ed.
22. Sambrook J., Russel D.W. Molecular Cloning 2001, Cold Spring Harbor Laboratory Press. 3th ed.
23. Imberechts H., Wild P., Charlier G., De Greve H., Lintermans P., Pohl P. Characterization of F18 fimbrial genes fedE and fedF involved in adhesion and length of enterotoxemic Escherichia coli strain 107/86. Microb. Pathog. 1996, 21:183-192.
24. Dong H., et al. Genomic sequence and expression analyses of human chromatin assembly factor 1 p150 gene. Gene. 2001, 264:187-196.
25. de la Bastide M., McCombie W.R. Assembling genomic DNA sequences with PHRAP (Chapter 11) 2007, Unit 11.4. Curr. Protoc. Bioinform., Wiley John Wiley & Sons.
26. Laslett D., Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004, 32:11-16.
27. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 1997, 25:955-964.
28. Besemer J., Borodovsky M. Heuristic approach to deriving models for gene finding. NAR 1999, 27:3911-3920.
29. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-4022.
30. Chenna R., et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003, 31:3497-3500.
31. Page R.D. Visualizing phylogenetic trees using TreeView (Chapter 6) 2002, Unit 6.2.. Curr. Protoc. Bioinform., Wiley John Wiley & Sons.
32. Reese M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 2001, 26:51-56.
33. Lavigne R., Sun W.D., Volckaert G. PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 2004, 20:629-635.
34. Carver T., et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24:2672-2676.
35. Darling A.C., Mau B., Blattner F.R., Perna N.T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome 2004, 14:1394-1403.
36. Zafar N., Mazumder R., Seto D. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics 2002, 3:12.
37. Matthews R.E.F. The classification and nomenclature of viruses. Intervirology 1981, 16:53-60.
38. Studier F.W. Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction system of its host. J. Mol. Biol. 1975, 94:283-295.
39. Garcia L.R., Molineux I.J. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli. J. Bacteriol. 1995, 177:4066-4076.
40. Zhang X., Studier F.W. Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection. J. Mol. Biol. 2004, 340:707-730.
41. Molineux I.J. The T7 Family of Bacteriophages. Encyclopedia of molecular biology 1999, 2495-2507. John Wiley and Co., New York. T.E. Creighton (Ed.).
42. Imburgio D., Rong M., Ma K., McAllister W.T. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Biochemistry 2000, 39:10419-10430.