The genome of BCJA1c: A bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii

Extremophiles

Volumn 9, Issue 2, 2005, Pages 99-109

  Kropinski, Andrew M ^a   Hayward, Melissa ^a   Agnew, M Dorothy ^a   Jarrell, Ken F ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

Alkaliphile; Bacillus clarkii; Bacteriophage; BCJA1; Frameshifting; Genomics; Integrase; Ribosomal slippage

Indexed keywords

COMPLEMENTARY DNA; INTEGRASE;

ARTICLE; BACILLUS; BACILLUS PHAGE; BACTERIOPHAGE; BIOLOGICAL MODEL; DNA REPLICATION; DNA SEQUENCE; FRAMESHIFT MUTATION; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENETICS; LYSOGENIZATION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PH; PROTEIN CONFORMATION; RIBOSOME; STREPTOCOCCUS; TEMPERATURE; VIROLOGY; VIRUS GENOME;

BACILLUS; BACILLUS PHAGES; BACTERIOPHAGES; BASE SEQUENCE; DNA REPLICATION; DNA, COMPLEMENTARY; FRAMESHIFT MUTATION; GENOME, VIRAL; HYDROGEN-ION CONCENTRATION; INTEGRASES; LYSOGENY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEIN CONFORMATION; RECOMBINATION, GENETIC; RIBOSOMES; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS; TEMPERATURE; TRANSCRIPTION, GENETIC;

BACILLUS CLARKII; BACTERIA (MICROORGANISMS); STREPTOCOCCUS;

EID: 18644362176     PISSN: 14310651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00792-004-0425-0     Document Type: Article

References (85)

1. Abeles AL, Snyder KM, Chattoraj DK (1984) P1 plasmid replication: replicon structure. J Mol Biol 173:307-324
2. Agnew MD, Koval SF, Jarrell KF (1995) Isolation and characterization of novel alkaliphiles from bauxite-processing waste and description of Bacillus vedderi sp. nov., a new obligate alkaliphile. Syst Appl Microbiol 18:221-230
3. Alam SL, Atkins JF, Gesteland RF (1999) Programmed ribosomal frameshifting: much ado about knotting! Proc Natl Acad Sci USA 96:14177-14179
4. Alonso JC, Luder G, Stiege AC, Chai S, Weise F, Trautner TA (1997) The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204:201-212
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
6. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-4022
7. Bankhead T, Segall AM (2000) Characterization of a mutation of bacteriophage λ integrase: putative role in core binding and strand exchange for a conserved residue. J Biol Sci 275:36949-36956
8. Banks DJ, Beres SB, Musser JM (2002) The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. Trends Microbiol 10:515-521
9. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276-280
10. Bensing BA, Rubens CE, Sullam PM (2001a) Genetic loci of Streptococcus mitis that mediate binding to human platelets. Infect Immun 69:1373-1380
11. Bensing BA, Siboo IR, Sullam PM (2001b) Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. Infect Immun 69:6186-6192
12. 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 (2002) Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci USA 99:10078-10083
13. Betermier M, Galas DJ, Chandler M (1994) Interaction of Fis protein with DNA: bending and specificity of binding. Biochimie 76:958-967
14. Brendel V, Trifonov EN (1984) A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Res 12:4411-4427
15. Brendel V, Hamm GH, Trifonov EN (1986) Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J Biomol Struct Dyn 3:705-723
16. Brüssow H, Bruttin A (1995) Characterization of a temperate Streptococcus thermophilus bacteriophage and its genetic relationship with lytic phages. Virology 212:632-640
17. Burr T, Mitchell J, Kolb A, Minchin S, Busby S (2000) DNA sequence elements located immediately upstream of the - 10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res 28:1864-1870
18. Campbell AM (1992) Chromosomal insertion sites for phages and plasmids. J Bacteriol 174:7495-7499
19. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6:417-424
20. Chattoraj DK, Snyder KM, Abeles AL (1985) P1 plasmid replication: multiple functions of RepA protein at the origin. Proc Natl Acad Sci USA 82:2588-2592
21. Craig NL, Roberts JW (1980) E. coli recA protein-directed cleavage of phage lambda repressor requires polynucleotide. Nature 283:26-30
22. Esposito D, Scocca JJ (1997) The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res 25:3605-3614
23. 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 (2001) Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci USA 98:4658-4663
24. Gertman E, White BN, Berry D, Kropinski AM (1986) IS222, a new insertion element associated with the genome of Pseudomonas aeruginosa. J Bacteriol 166:1134-1136
25. Goosen N, van de Putte P (1987) Regulation of transcription. In: Symonds N, Toussaint A, van de Putte P, Howe MM (eds) Phage Mu. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 41-52
26. Grigoriev A (1998) Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 26:2286-2290
27. Grove A, Galeone A, Mayol L, Geiduschek EP (1996) Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J Mol Biol 260:120-125
28. Grundling A, Bläsi U, Young R (2000) Biochemical and genetic evidence for three transmembrane domains in the class I holin, lambda S. J Biol Chem 275:769-776
29. Harger JW, Meskauskas A, Dinman JD (2002) An "integrated model" of programmed ribosomal frameshifting. Trends Biochem Sci 27:448-454
30. Hendrix RW (2002) Bacteriophages: evolution of the majority. Theor Popul Biol 61:471-480
31. Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 96:2192-2197
32. Hofmann K, Bucher P, Falquet L, Bairoch A (1999) The PROSITE database, its status in 1999. Nucleic Acids Res 27:215-219
33. Horikoshi K, Yonezawa Y (1978) A bacteriophage active on an alkalophilic Bacillus sp. J Gen Virol 39:183-185
34. 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 SD, Overbeek R, Kyrpides N (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423:87-91
35. Jarrell KF, Vydykhan T, Lee P, Agnew MD, Thomas NA (1997) Isolation and characterization of bacteriophage BCJA1, a novel temperate bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii. Extremophiles 1:199-206
36. Klein R, Baranyi U, Rossler N, Greineder B, Scholz H, Witte A (2002) Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol Microbiol 45:851-863
37. Kovalyova IV, Kropinski AM (2003) The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida - evidence for close relationship to the T7 group. Virology 311:305-315
38. Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S (2001) DNA asymmetry and the replicational mutational pressure. J Appl Genet 42:553-577
39. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtllis. Nature 390:249-256
40. Labrie S, Moineau S (2002) Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Virology 296:308-320
41. Lavigne R, Sun WD, Volckaert G (2004) PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20:629-6135
42. Lawrence JG, Hatfull GF, Hendrix RW (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 184:4891-4905
43. Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 30:242-244
44. Little JW (1991) Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease. Biochimie 73:411-421
45. Lobry JR (1999) Genomic landscapes. Microbiol Today 26:164-165
46. Mantri Y, Williams KP (2004a) Islander database. Available at http://129.79.232.60/cgi-bin/islander/islander.cgi
47. Mantri Y, Williams KP (2004b) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res 32 Database issue:D55-D58
48. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH (2003) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31:383-387
49. Mitchell JE, Zheng D, Busby SJ, Minchin SD (2003) Identification and analysis of 'extended - 10' promoters in Escherichia coli. Nucleic Acids Res 31:4689-4695
50. Nash HA (1990) Bending and supercoiling of DNA at the attachment site of bacteriophage λ. TIBS 15:222-227
51. Nielsen P, Fritze D, Priest FG (2004) Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745-1761
52. Nunes-Duby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26:391-406
53. Obregon V, Garcia JL, Garcia E, Lopez R, Garcia P (2003) Genome organization and molecular analysis of the temperate bacteriophage MM1 of Streptococcus pneumoniae. J Bacteriol 185:2362-2368
54. Ogawa T, Masukata H, Tomizawa J (1988) Transcriptional regulation of early functions of bacteriophage φ 80. J Mol Biol 202:551-563
55. Paces V, Vlcek C, Urbanek P, Hostomsky Z (1989) Nucleotide sequence of the right early region of Bacillus subtilis phage PZA completes the 19,366-bp sequence of PZA genome. Comparison with the homologous sequence of phage phi 29. Gene 44:115-120
56. Pande S, Vimaladithan A, Zhao H, Farabaugh PJ (1995) Pulling the ribosome out of frame by + 1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell Biol 15:298-304
57. Pecenkova T, Benes V, Paces J, Vlcek C, Paces V (1997) Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages. Gene 199:157-163
58. Prangishvili D (2003) Evolutionary insights from studies on viruses of hyperthermophilic archaea. Res Microbiol 154:289-294
59. Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brussow H (2002) The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J Bacteriol 184:6026-6036
60. Rachel R, Bettstetter M, Hedlund BP, Haring M, Kessler A, Stetter KO, Prangishvili D (2002) Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments. Arch Virol 147:2419-2429
61. Ravantti JJ, Duesterhoeft A, Soldo B, Hilbert H, Mauel C, Karamata D (2004) The complete nucleotide sequence of the Bacillus subtilis SPbetac2 prophage (GenBank accession number NC_001884).
62. Ravin NV, Kuprianov VV, Gilcrease EB, Casjens SR (2003) Bidirectional replication from an internal ori site of the linear N15 plasmid prophage. Nucleic Acids Res 31:6552-6560
63. Raymond-Denise A, Guillen N (1991) Identification of dinR, a DNA damage-inducible regulator gene of Bacillus subtilis. J Bacteriol 173:7084-7091
64. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86
65. Reeder J, Giegerich R (2004) Design implementation and evaluation of a practical pseudoknots folding algorithm based upon thermodynamics. BMC Bioinform 5:104-115
66. Roberts JW, Roberts CW, Mount DW (1977) Inactivation and proteolytic cleavage of phage lambda repressor in vitro in an ATP-dependent reaction. Proc Natl Acad Sci USA 74:2283-2287
67. Rohwer F (2003) Global phage diversity. Cell 113:141
68. Salas M (2004) Bacillus phage GA-1 virion, complete genome (GenBank accession number NC_002649)
69. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
70. Schultz J, Copley RR, Doerks T, Ponting CP, Bork P (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28:231-234
71. Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342-1346
72. Shine J, Dalgarno L (1975) Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the 3′-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome. Eur J Biochem 57:221-230
73. Slepecky RA, Hemphill RA (1992) The genus Bacillus - nonmedical. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer K-H (eds) The Prokaryotes. A handbook on the biology and bacteria: ecophysiology, isolation, identification, applications. Springer, Berlin Heidelberg New York, pp 1663-1696
74. Sonnhammer ELL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In: Glasgow J, Littlejohn T, Major F, Lathrop R, Sankoff D, Sensen C (eds) Proceedings of the 6th international conference on intelligent systems for molecular biology. AAAI, Menlo Park, pp 175-182
75. Stanley E, Fitzgerald GF, Le Marrec C, Fayard B, van Sinderen D (1997) Sequence analysis and characterization of phi O1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology 143:3417-3429
76. Studholme DJ, Dixon R (2003) Domain architectures of sigma54-dependent transcriptional activators. J Bacteriol 185:1757-1767
77. Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J 22:3749-3760
78. Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, Kuhara S, Horikoshi K (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res 28:4317-4331
79. Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30:3927-3935
80. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41
81. Unniraman S, Prakash R, Nagaraja V (2002) Conserved economics of transcription termination in eubacteria. Nucleic Acids Res 30:675-684
82. Ventura M, Canchaya C, Pridmore RD, Brüssow H (2004) The prophages of Lactobacillus johnsonii NCC 533: comparative genomics and transcription analysis. Virology 320:229-242
83. Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945-951
84. Young R (1992) Bacteriophage lysis: mechanism and regulation. Microbiol Rev 56:430-481
85. Young R, Bläsi U (1995) Holins: form and function in bacteriophage lysis. FEMS Microbiol Rev 17:191-205