Rethinking the evolution of single-stranded RNA (ssRNA) bacteriophages based on genomic sequences and characterizations of Two R-Plasmid-Dependent ssRNA Phages, C-1 and Hgal1

Journal of Bacteriology

Volumn 194, Issue 18, 2012, Pages 5073-5079

  Kannoly, Sherin ^a   Shao, Yongping ^a,b   Wang, Ing Nang ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED RNA;

ADSORPTION; ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIOPHAGE C 1; BACTERIOPHAGE HGAL1; BACTERIUM CONJUGATION; CELL ADHESION; COLIPHAGE; GENE SEQUENCE; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; R PLASMID;

BACTERIOPHAGES; BIOLOGICAL EVOLUTION; CLUSTER ANALYSIS; GENOME, VIRAL; LEVIVIRUS; MOLECULAR SEQUENCE DATA; PHYLOGENY; R FACTORS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

ALLOLEVIVIRUS; BACTERIA (MICROORGANISMS); LEVIVIRUS;

EID: 84866355634     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00929-12     Document Type: Article

References (63)

1. Adhin MR, Avots A, Berzin V, Overbeek GP, van Duin J. 1990. Complete nucleotide sequence of the group I RNA bacteriophage fr. Biochim. Biophys. Acta 1050:104-109.
2. Armougom F, et al. 2006. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34:W604-W608.
3. Atkins JF, Steitz JA, Anderson CW, Model P. 1979. Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Cell 18:247-256.
4. Beekwilder J, Nieuwenhuizen R, Poot R, van Duin J. 1996. Secondary structure model for the first three domains of Q.β RNA. Control of A-protein synthesis. J. Mol. Biol. 256:8-19.
5. Beekwilder MJ, Nieuwenhuizen R, van Duin J. 1995. Secondary structure model for the last two domains of single-stranded RNA phage Q.β. J. Mol. Biol. 247:903-917.
6. Beremand MN, Blumenthal T. 1979. Overlapping genes in RNA phage: a new protein implicated in lysis. Cell 18:257-266.
7. Bernhardt TG, Wang IN, Struck DK, Young R. 2002. Breaking free: "protein antibiotics" and phage lysis. Res. Microbiol. 153:493-501.
8. Bernhardt TG, Wang IN, Struck DK, Young R. 2001. A protein antibiotic in the phage Q.β virion: diversity in lysis targets. Science 292:2326-2329.
9. Bollback JP, Huelsenbeck JP. 2001. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). J. Mol. Evol. 52:117-128.
10. Bradley DE. 1966. The structure and infective process of a Pseudomonas aeruginosa bacteriophage containing ribonucleic acid. J. Gen. Microbiol. 45:83-96.
11. Bradley DE, Coetzee JN, Bothma T, Hedges RW. 1981. Phage t: a group T plasmid-dependent bacteriophage. J. Gen. Microbiol. 126:397-403.
12. Brion GM, Meschke JS, Sobsey MD. 2002. F-specific RNA coliphages: occurrence, types, and survival in natural waters. Water Res. 36:2419-2425.
13. - resistance factors. J. Bacteriol. 112:666-675.
14. Coetzee JN, et al. 1985. Phage pilHα: a phage which adsorbs to IncHI and IncHII plasmid-coded pili. J. Gen. Microbiol. 131:1115-1121.
15. 2-2: IncI plasmid-dependent bacteriophages. J. Gen. Microbiol. 128:2797-2804.
16. Coetzee JN, Bradley DE, Hedges RW, Fleming J, Lecatsas G. 1983. Bacteriophage M: an incompatibility group M plasmid-specific phage. J. Gen. Microbiol. 129:2271-2276.
17. 0lac h, SR, SF: phages which adsorb to pili encoded by plasmids of the S-complex. J. Gen. Microbiol. 132:2907-2917.
18. Coetzee JN, Bradley DE, Lecatsas G, du Toit L, Hedges RW. 1985. Bacteriophage D: an IncD group plasmid-specific phage. J. Gen. Microbiol. 131:3375-3383.
19. Couturier M, Bex F, Bergquist PL, Maas WK. 1988. Identification and classification of bacterial plasmids. Microbiol. Rev. 52:375-395.
20. -R factors. Nature 234:222-223.
21. Dereeper A, et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:W465-W469.
22. Di Tommaso P, et al. 2011. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39:W13-W17.
23. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
24. Fiers W, et al. 1976. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260:500-507.
25. Friedman SD, Genthner FJ, Gentry J, Sobsey MD, Vinje J. 2009. Gene mapping and phylogenetic analysis of the complete genome from 30 single-stranded RNA male-specific coliphages (family Leviviridae). J. Virol. 83:11233-11243.
26. Frost LS, Paranchych W. 1988. DNA sequence analysis of point mutations in traA, the F pilin gene, reveal two domains involved in F-specific bacteriophage attachment. Mol. Gen. Genet. 213:134-139.
27. Furuse K, Ando A, Osawa S, Watanabe I. 1981. Distribution of ribonucleic acid coliphages in raw sewage from treatment plants in Japan. Appl. Environ. Microbiol. 41:1139-1143.
28. Furuse K, et al. 1978. Distribution of ribonucleic acid coliphages in South and East Asia. Appl. Environ. Microbiol. 35:995-1002.
29. Furuse K, et al. 1983. Distribution of RNA coliphages in Senegal, Ghana, and Madagascar. Microbiol. Immunol. 27:347-358.
30. Goloboff PA. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15:415-428.
31. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
32. Haramoto E, Otagiri M, Morita H, Kitajima M. 2012. Genogroup distribution of F-specific coliphages in wastewater and river water in the Kofu basin in Japan. Lett. Appl. Microbiol. 54:367-373.
33. Hong Y, Cole TE, Brasier CM, Buck KW. 1998. Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch Elm Disease fungus, Ophiostoma novo-ulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome. Virology 246:158-169.
34. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
35. Inokuchi Y, et al. 1986. The complete nucleotide sequence of the group II RNA coliphage GA. J. Biochem. 99:1169-1180.
36. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
37. Kazaks A, Voronkova T, Rumnieks J, Dishlers A, Tars K. 2011. Genome structure of caulobacter phage phiCb5. J. Virol. 85:4628-4631.
38. Klovins J, Overbeek GP, van den Worm SH, Ackermann HW, van Duin J. 2002. Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages. J. Gen. Virol. 83:1523-1533.
39. Lutz R, Bujard H. 1997. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25:1203-1210.
40. Manchak J, Anthony KG, Frost LS. 2002. Mutational analysis of F-pilin reveals domains for pilus assembly, phage infection and DNA transfer. Mol. Microbiol. 43:195-205.
41. Murphy FA, et al. 1995. Virus taxonomy: the classification and nomenclature of viruses. The 6th report of the International Committee on Taxonomy of Viruses. Springer-Verlag, New York, NY.
42. Nixon KC. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15:407-414.
43. Nuttall D, Maker D, Colleran E. 1987. A method for the direct isolation of IncH plasmid-dependent bacteriophages. Lett. Appl. Microbiol. 5:37-40.
44. Olsen RH, Shipley P. 1973. Host range and properties of the Pseudomonas aeruginosa R factor R1822. J. Bacteriol. 113:772-780.
45. Olsen RH, Thomas DD. 1973. Characteristics and purification of PRR1, an RNA phage specific for the broad host range Pseudomonas R1822 drug resistance plasmid. J. Virol. 12:1560-1567.
46. Olsthoorn RC, Garde G, Dayhuff T, Atkins JF, Van Duin J. 1995. Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures. Virology 206:611-625.
47. Osawa S, et al. 1981. Distribution of ribonucleic acid coliphages in Korea. Appl. Environ. Microbiol. 41:909-911.
48. Osawa S, Furuse K, Watanabe I. 1981. Distribution of ribonucleic acid coliphages in animals. Appl. Environ. Microbiol. 41:164-168.
49. Rambaut A. 21 December 2009, posting date. FigTree v1.3.1: tree figure drawing tool. http://tree.bio.ed.ac.uk/software/figtree/.
50. Ronquist F, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61:1-4.
51. Ruokoranta TM, Grahn AM, Ravantti JJ, Poranen MM, Bamford DH. 2006. Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with Alloleviviruses. J. Virol. 80:9326-9330.
52. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
53. Sakurai T, Miyake T, Shiba T, Watanabe I. 1968. Isolation of a possible fourth group of RNA phage. Jpn. J. Microbiol. 12:544-546.
54. Schaper M, Jofre J, Uys M, Grabow WO. 2002. Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain. J. Appl. Microbiol. 92:657-667.
55. Sirgel FA, Coetzee JN, Hedges RW, Lecatsas G. 1981. Phage C-1: an IncC group; plasmid-specific phage. J. Gen. Microbiol. 122:155-160.
56. Sokal RR, Rohlf FJ. 2011. Biometry, 4th ed. W.H. Freeman, New York, NY.
57. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
58. van Duin J, Tsareva N. 2006. Single-stranded RNA phages, p 175-196. In Calendar R (ed), The bacteriophages. Oxford University Press, New York, NY.
59. Wallace IM, O'Sullivan O, Higgins DG, Notredame C. 2006. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34:1692-1699.
60. Watanabe I, Miyake T, Sakurai T, Shiba T, Ohno T. 1967. Isolation and grouping of RNA phages. Proc. Jpn. Acad. 43:204-209.
61. Watanabe T, Nishida H, Ogata C, Arai T, Sato S. 1964. Episomemediated transfer of drug resistance in Enterobacteriaceae. VII. Two types of naturally occurring R factors. J. Bacteriol. 88:716-726.
62. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximumlikelihood approach. Mol. Biol. Evol. 18:691-699.
63. Zinder ND (ed). 1975. RNA phages. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.