A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria

Nucleic Acids Research

Volumn 41, Issue 15, 2013, Pages 7260-7275

  Quiles Puchalt, Nuria ^a,b   Tormo Más, María Ángeles ^b,c   Campoy, Susana ^d   Toledo Arana, Alejandro ^e   Monedero, Vicente ^f   Lasa, Íñigo ^e   Novick, Richard P ^g   Christie, Gail E ^h   Penadés, José R ^a,c,i  

^a INSTITUTO DE BIOMEDICINA DE VALENCIA   (Spain)

^b INSTITUTO VALENCIANO DE INVESTIGACIONES AGRARIAS IVIA   (Spain)

^c UNIVERSIDAD CEU CARDENAL HERRERA   (Spain)

^d UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^e PUBLIC UNIVERSITY OF NAVARRE   (Spain)

^f INSTITUTO DE AGROQUÍMICA Y TECNOLOGÍA DE ALIMENTOS CSIC   (Spain)

^g NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h VIRGINIA COMMONWEALTH UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; LATE TRANSCRIPTIONAL REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIOLYSIS; BACTERIOPHAGE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; FIRMICUTES; GENE CLUSTER; GENE DELETION; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE TRANSFER; GENETIC CODE; MORPHOGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; TERS GENE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; UPREGULATION;

BASE SEQUENCE; ENTEROCOCCUS FAECALIS; GENE DELETION; GENE EXPRESSION REGULATION, VIRAL; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTATION; OPERON; PROMOTER REGIONS, GENETIC; PROPHAGES; REPETITIVE SEQUENCES, NUCLEIC ACID; SIPHOVIRIDAE; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION; VIRUS ASSEMBLY; VIRUS RELEASE;

EID: 84883478089     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt508     Document Type: Article

References (39)

1. Bru ssow,H., Canchaya,C. and Hardt,W.-D. (2004) Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev., 68, 560-602
2. Tormo-Mas,M.A., Donderis,J., Garc a-Caballer,M., Alt,A., Mir-Sanchis,I., Marina,A. and Penades,J.R. (2013) Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. Mol. Cell, 49, 947-958
3. Tormo-Mas,M.A., Mir,I., Shrestha,A., Tallent,S.M., Campoy,S., Lasa,I., Barbe,J., Novick,R.P., Christie,G.E. and Penades,J.R. (2010) Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands. Nature, 465, 779-782
4. Novick,R.P., Christie,G.E. and Penades,J.R. (2010) The phagerelated chromosomal islands of Gram-positive bacteria. Nat. Rev. Microbiol., 8, 541-551
5. Banks,D.J., Porcella,S.F., Barbian,K.D., Beres,S.B., Philips,L.E., Voyich,J.M., DeLeo,F.R., Martin,J.M., Somerville,G.A. and Musser,J.M. (2004) Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. J. Infect. Dis., 190, 727-738
6. Schuch,R. and Fischetti,V.A. (2009) The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations. PLoS One, 4, e6532
7. Court,D.L., Oppenheim,A.B. and Adhya,S.L. (2006) A new look at bacteriophage genetic networks. J. Bacteriol., 189, 298-304
8. Campbell,A. (1994) Comparative molecular biology of lambdoid phages. Annu. Rev. Microbiol., 48, 193-222
9. Ferrer,M.D., Quiles-Puchalt,N., Harwich,M.D., Tormo-Mas,M.A., Campoy,S., Barbe,J., Lasa,I., Novick,R.P., Christie,G.E. and Penades,J.R. (2011) RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria. Nucleic Acids Res., 39, 5866-5878
10. Ubeda,C., Maiques,E., Knecht,E., Lasa,I., Novick,R.P. and Penades,J.R. (2005) Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Mol. Microbiol., 56, 836-844
11. Ubeda,C., Maiques,E., Barry,P., Matthews,A., Tormo,M.A., Lasa,I., Novick,R.P. and Penades,J.R. (2008) SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage. Mol. Microbiol., 67, 493-503
12. Simossis,V.A. and Heringa,J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res., 33, W289-W294
13. Tamura,K., Peterson,D., Peterson,N., Stecher,G., Nei,M. and Kumar,S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28, 2731-2739
14. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856
15. Perocchi,F., Xu,Z., Clauder-Mu nster,S. and Steinmetz,L.M. (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res., 35, e128
16. Nicol,J.W., Helt,G.A., Blanchard,S.G., Raja,A. and Loraine,A.E. (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics, 25, 2730-2731
17. Ubeda,C., Maiques,E., Tormo,M., Campoy,S., Lasa,I., Barbe,J., Novick,R.P. and Penades,J.R. (2007) SaPI operon I is required for SaPI packaging and is controlled by LexA. Mol. Microbiol., 65, 41-50
18. Lleo ,M.M., Fontana,R. and Solioz,M. (1995) Identification of a gene (arpU) controlling muramidase-2 export in Enterococcus hirae. J. Bacteriol., 177, 5912-5917
19. Dombroski,A.J., Walter,W.A., Record,M.T., Siegele,D.A. and Gross,C.A. (1992) Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell, 70, 501-512
20. Christie,G.E., Matthews,A.M., King,D.G., Lane,K.D., Olivarez,N.P., Tallent,S.M., Gill,S.R. and Novick,R.P. (2010) The complete genomes of Staphylococcus aureus bacteriophages 80 and 80a-Implications for the specificity of SaPI mobilization. Virology, 407, 381-390
21. Lasa,I., Toledo-Arana,A., Dobin,A., Villanueva,M., de Los Mozos,I.R., Vergara-Irigaray,M., Segura,V., Fagegaltier,D., Penades,J.R., Valle,J. et al. (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proc. Natl Acad. Sci. USA, 108, 20172-20177
22. Tormo,M.A., Ferrer,M.D., Maiques,E., Ubeda,C., Selva,L., Lasa,I., Calvete,J.J., Novick,R.P. and Penades,J.R. (2008) Staphylococcus aureus pathogenicity island DNA is packaged in particles composed of phage proteins. J. Bacteriol., 190, 2434-2440
23. Tallent,S.M., Langston,T.B., Moran,R.G. and Christie,G.E. (2007) Transducing particles of Staphylococcus aureus pathogenicity island SaPI1 are comprised of helper phage-encoded proteins. J. Bacteriol., 189, 7520-7524
24. Dhaese,P., Seurinck,J., De Smet,B. and Van Montagu,M. (1985) Nucleotide sequence and mutational analysis of an immunity repressor gene from Bacillus subtilis temperate phage phi 105. Nucleic Acids Res., 13, 5441-5455
25. Das,M., Ganguly,T., Chattoraj,P., Chanda,P.K., Bandhu,A., Lee,C.Y. and Sau,S. (2007) Purification and characterization of repressor of temperate S. aureus phage phi11. J. Biochem. Mol. Biol., 40, 740-748
26. Pedersen,M., Ligowska,M. and Hammer,K. (2010) Characterization of the CI repressor protein encoded by the temperate lactococcal phage TP901-1. J. Bacteriol., 192, 2102-2110
27. Lucchini,S., Desiere,F. and Bru ssow,H. (1999) Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria. Virology, 263, 427-435
28. Walker,S.A. and Klaenhammer,T.R. (1998) Molecular characterization of a phage-inducible middle promoter and its transcriptional activator from the lactococcal bacteriophage phi31. J. Bacteriol., 180, 921-931
29. Walker,S.A., Dombroski,C.S. and Klaenhammer,T.R. (1998) Common elements regulating gene expression in temperate and lytic bacteriophages of Lactococcus species. Appl. Environ. Microbiol., 64, 1147-1152
30. Brøndsted,L., Pedersen,M. and Hammer,K. (2001) An activator of transcription regulates phage TP901-1 late gene expression. Appl. Environ. Microbiol., 67, 5626-5633
31. Pedersen,M., Kilstrup,M. and Hammer,K. (2006) Identification of DNA-binding sites for the activator involved in late transcription of the temperate lactococcal phage TP901-1. Virology, 345, 446-456
32. Ventura,M., Bruttin,A., Canchaya,C. and Bru ssow,H. (2002) Transcription analysis of Streptococcus thermophilus phages in the lysogenic state. Virology, 302, 21-32
33. Rohwer,F. and Thurber,R.V. (2009) Viruses manipulate the marine environment. Nature, 459, 207-212
34. Kreiswirth,B.N., Lo fdahl,S., Betley,M.J., O'Reilly,M., Schlievert,P.M., Bergdoll,M.S. and Novick,R.P. (1983) The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature, 305, 709-712
35. Yasmin,A., Kenny,J.G., Shankar,J., Darby,A.C., Hall,N., Edwards,C. and Horsburgh,M.J. (2010) Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages. J. Bacteriol., 192, 1122-1130
36. Ubeda,C., Barry,P., Penades,J.R. and Novick,R.P. (2007) A pathogenicity island replicon in Staphylococcus aureus replicates as an unstable plasmid. Proc. Natl Acad. Sci. USA, 104, 14182-14188
37. Arnaud,M., Chastanet,A. and Debarbouille,M. (2004) New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria. Appl. Environ. Microbiol., 70, 6887-6891
38. Charpentier,E., Anton,A.I., Barry,P., Alfonso,B., Fang,Y. and Novick,R.P. (2004) Novel cassette-based shuttle vector system for gram-positive bacteria. Appl. Environ. Microbiol., 70, 6076-6085
39. So ding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.