Composite conserved promoter-terminator motifs (PeSLs) that mediate modular shuffling in the diverse T4-like myoviruses

Genome Biology and Evolution

Volumn 6, Issue 7, 2014, Pages 1611-1619

  Comeau, Andre M ^a,f   Arbiol, Christine ^b,c,d,e   Krisch, Henry M ^a,b  

^a Institut de Biologie Intégrative et des Systèmes UniversitéLaval ^*  (Switzerland)

^b CNRS   (France)

^c AIX MARSEILLE UNIVERSITY   (France)

^d INSTITUT PAOLI CALMETTES   (France)

^e AIX MARSEILLE UNIVERSITY   (France)

^f DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Genome evolution; Genome plasticity; PeSLs; T4 like phages; Vibrio; Yersinia

Indexed keywords

AMINO ACID SEQUENCE; ENTEROBACTERIA PHAGE T4; GENETICS; HUMAN; MOLECULAR GENETICS; MYOVIRIDAE; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN MOTIF; REGULATOR GENE; SEQUENCE ALIGNMENT;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIOPHAGE T4; CONSERVED SEQUENCE; HUMANS; MOLECULAR SEQUENCE DATA; MYOVIRIDAE; PROMOTER REGIONS, GENETIC; SEQUENCE ALIGNMENT; TERMINATOR REGIONS, GENETIC;

EID: 84926134063     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu129     Document Type: Article

References (27)

1. Ackermann H-W, Krisch H (1997) A catalogue of T4-type bacteriophages. Arch Virol. 142: 2329-2345.
2. Ackermann H-W, Krisch HM, Comeau AM (2011) Morphology and genome sequence of phage j1402) Bacteriophage 1: 138-142.
3. Albertini AM, Hofer M, Calos MP, Miller JH (1982) On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions. Cell 29: 319-328.
4. Arbiol C, Comeau AM, Kutateladze M, Adamia R, Krisch HM (2010) Mobile regulatory cassettes mediate modular shuffling in T4-type phage genomes. Genome Biol Evol. 2: 140-152.
5. Bair CL, Rifat D, Black LW (2007) Exclusion of glucosyl- hydroxymethylcytosine DNA containing bacteriophages is overcome by the injected protein inhibitor IPI. J Mol Biol. 366: 779-789.
6. Brok-Volchanskaya VS, et al (2008) Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage. Nucleic Acids Res. 36: 2094-2105.
7. Butina TV, Belykh OI, Maksimenko SY, Belikov SI (2010) Phylogenetic diversity of T4-like bacteriophages in Lake Baikal, East Siberia. FEMS Microbiol Lett. 309: 122-129.
8. Carlson K, Miller ES (1994) Experiments in T4 genetics. In: Karam JD, editor. Molecular biology of bacteriophage T4) Washington (DC): ASM Press. p. 421-483.
9. Casjens SR, Gilcrease EB (2009) Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. In: Clokie MRJ, Kropinski AM, editors. Bacteriophages: methods and protocols. New York: Humana Press. p. 91-111.
10. Comeau AM, Bertrand C, Letarov A, Tétart F, Krisch HM (2007) Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Virology 362: 384-396.
11. Comeau AM, Krisch HM (2005) War is peace-dispatches from the bacterial and phage killing fields. Curr Opin Microbiol. 8: 488-494.
12. Comeau AM, Krisch HM (2008) The capsid of the T4 phage superfamily: The evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Mol Biol Evol. 25: 1321-1332.
13. Filée J, Bapteste E, Susko E, Krisch HM (2006) A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.Mol Biol Evol. 23: 1688-1696.
14. Jia Z, Ishihara R, Nakajima Y, Asakawa S, Kimura M (2007) Molecular characterization of T4-type bacteriophages in a rice field. Environ Microbiol. 9: 1091-1096.
15. Kadyrov FA, Shlyapnikov MG, Kryukov VM (1997) A phage T4 sitespecific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages. FEBS Lett. 415: 75-80.
16. Knapp W, Zwillenberg LO (1964) Morphological differences between Pasteurella bacteriophages. Arch Ges Virusforsch. 14: 563-566.
17. Krisch HM, Comeau AM (2008) The immense journey of bacteriophage T4-from d'Hérelle to Delbrück and then to Darwin and beyond. Res Microbiol. 159: 314-324.
18. Lavigne R, et al (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 9: 224.
19. López-Bueno A, et al (2009) High diversity of the viral community from an Antarctic lake. Science 326: 858-861.
20. Matsuzaki S, Tanaka S, Koga T, Kawata T (1992) A broad-host-range vibriophage, KVP40, isolated from sea water. Microbiol Immunol. 36: 93-97.
21. Miller ES, et al (2003a. Complete genome sequence of the broad-hostrange vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol. 185: 5220-5233.
22. Miller ES, et al (2003b. Bacteriophage T4 genome. Microbiol Mol Biol Rev. 67: 86-156.
23. Petrov VM, Ratnayaka S, Nolan JM, Miller ES, Karam JD (2010) Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol J. 7: 292.
24. Repoila F, Tétart F, Bouet JY, Krisch HM (1994) Genomic polymorphism in the T-even bacteriophages. EMBO J (13: 4181-4192.
25. Tétart F, et al (2001) Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J Bacteriol. 183: 358-366.
26. Trojet SN, Caumont-Sarcos A, Perrody E, Comeau AM, Krisch HM (2011) The gp38 adhesins of the T4 superfamily: a complex modular determinant of the phage's host specificity. Genome Biol Evol. 3: 674-686.
27. Zachary A (1974) Isolation of bacteriophages of the marine bacterium Beneckea natriegens from coastal salt marshes. Appl Environ Microbiol. 31: 415-422.