Comparative genomic analysis of twelve Streptococcus suis (pro)phages

Genomics

Volumn 101, Issue 6, 2013, Pages 336-344

  Tang, Fang ^a   Bossers, Alex ^b   Harders, Frank ^b   Lu, Chengping ^a   Smith, Hilde ^b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Genomics; Prophages; Streptococcus suis; Virulence

Indexed keywords

BACTERIAL PROTEIN; DNA METHYLTRANSFERASE; ENDOPEPTIDASE CLP; UNCLASSIFIED DRUG; VIRULENCE ASSOCIATED PROTEIN E;

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE CLUSTER; GENE STRUCTURE; GENOME ANALYSIS; LYSOGENIZATION; MORPHOGENESIS; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROPHAGE; PROPHAGE PHI20C; PROPHAGE PHI30C; PROPHAGE PHI5218; PROPHAGE PHI7917; PROPHAGE PHI891591; PROPHAGE PHID12; PROPHAGE PHINJ2; PROPHAGE PHIS10; PROPHAGE PHISS12; PROPHAGE PHISSUD 1; PROPHAGE PHIST1; PROPHAGE SMP; STREPTOCOCCUS SUIS;

AMINO ACID SEQUENCE; GENES, VIRAL; GENOME, VIRAL; GENOMICS; LYSOGENY; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPEN READING FRAMES; PHYLOGENY; PROPHAGES; STREPTOCOCCUS PHAGES; STREPTOCOCCUS SUIS; VIRAL PROTEINS; VIRULENCE FACTORS; VIRUS ASSEMBLY; VIRUS REPLICATION;

STREPTOCOCCUS SUIS;

EID: 84877927072     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.04.005     Document Type: Article

References (50)

1. Lun Z.R., Wang Q.P., Chen X.G., Li A.X., Zhu X.Q. Streptococcus suis: an emerging zoonotic pathogen. Lancet Infect. Dis. 2007, 7:201-209.
2. Tian Y., Aarestrup F.M., Lu C.P. Characterization of Streptococcus suis serotype 7 isolates from diseased pigs in Denmark. Vet. Microbiol. 2004, 103:55-62.
3. Buttner N., Beineke A., de Buhr N., Lilienthal S., Merkel J., Waldmann K.H., et al. Streptococcus suis serotype 9 bacterin immunogenicity and protective efficacy. Vet. Immunol. Immunopathol. 2012, 146:191-200.
4. Kerdsin A., Oishi K., Sripakdee S., Boonkerd N., Polwichai P., Nakamura S., et al. Clonal dissemination of human isolates of Streptococcus suis serotype 14 in Thailand. J. Med. Microbiol. 2009, 58:1508-1513.
5. Smith H.E., Rijnsburger M., Stockhofe-Zurwieden N., Wisselink H.J., Vecht U., Smits M.A. Virulent strains of Streptococcus suis serotype 2 and highly virulent strains of Streptococcus suis serotype 1 can be recognized by a unique ribotype profile. J. Clin. Microbiol. 1997, 35:1049-1053.
6. Ventura M., Canchaya C., Bernini V., Altermann E., Barrangou R., McGrath S., et al. Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei. Appl. Environ. Microbiol. 2006, 72:3130-3146.
7. Waldor M.K., Friedman D.I. Phage regulatory circuits and virulence gene expression. Curr. Opin. Microbiol. 2005, 8:459-465.
8. Fujisawa H., Minagawa T. DNA packaging by double stranded DNA phages. Uirusu 1986, 36:185-193.
9. Harel J., Martinez G., Nassar A., Dezfulian H., Labrie S.J., Brousseau R., et al. Identification of an inducible bacteriophage in a virulent strain of Streptococcus suis serotype 2. Infect. Immun. 2003, 71:6104-6108.
10. Hu P., Yang M., Zhang A., Wu J., Chen B., Hua Y., et al. Complete genome sequence of Streptococcus suis serotype 14 strain JS14. J. Bacteriol. 2011, 193:2375-2376.
11. Hu P., Yang M., Zhang A., Wu J., Chen B., Hua Y., et al. Complete genome sequence of Streptococcus suis serotype 3 strain ST3. J. Bacteriol. 2011, 193:3428-3429.
12. Ma Y.L., Lu C.P. Isolation and identification of a bacteriophage capable of infecting Streptococcus suis type 2 strains. Vet. Microbiol. 2008, 132:340-347.
13. Palmieri C., Princivalli M.S., Brenciani A., Varaldo P.E., Facinelli B. Different genetic elements carrying the tet(W) gene in two human clinical isolates of Streptococcus suis. Antimicrob. Agents Chemother. 2011, 55:631-636.
14. Pasharawipas T., Thaikua S., Sriurairatana S., Ruangpan L., Direkbusarakum S., Manopvisetcharean J., et al. Partial characterization of a novel bacteriophage of Vibrio harveyi isolated from shrimp culture ponds in Thailand. Virus Res. 2005, 114:63-69.
15. Bensing B.A., Siboo I.R., Sullam P.M. Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. Infect. Immun. 2001, 69:6186-6192.
16. Zhou Y., Liang Y., Lynch K.H., Dennis J.J., Wishart D.S. PHAST: a fast phage search tool. Nucleic Acids Res. 2011, 39:W347-W352.
17. Besemer J., Lomsadze A., Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001, 29:2607-2618.
18. Finn R.D., Mistry J., Tate J., Coggill P., Heger A., Pollington J.E., et al. The Pfam protein families database. Nucleic Acids Res. 2010, 38:D211-D222.
19. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, 37:D211-D215.
20. Hiller N.L., Janto B., Hogg J.S., Boissy R., Yu S., Powell E., et al. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J. Bacteriol. 2007, 189:8186-8195.
21. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001, 305:567-580.
22. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
23. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 1997, 14:685-695.
24. Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., et al. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5:R12.
25. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
26. Darling A.E., Mau B., Perna N.T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e11147.
27. Zhang A., Yang M., Hu P., Wu J., Chen B., Hua Y., et al. Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics 2011, 12:523.
28. Groth A.C., Olivares E.C., Thyagarajan B., Calos M.P. A phage integrase directs efficient site-specific integration in human cells. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:5995-6000.
29. Groth A.C., Calos M.P. Phage integrases: biology and applications. J. Mol. Biol. 2004, 335:667-678.
30. Zimmer M., Sattelberger E., Inman R.B., Calendar R., Loessner M.J. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed+1 translational frameshifting in structural protein synthesis. Mol. Microbiol. 2003, 50:303-317.
31. Thyagarajan B., Olivares E.C., Hollis R.P., Ginsburg D.S., Calos M.P. Site-specific genomic integration in mammalian cells mediated by phage phiC31 integrase. Mol. Cell. Biol. 2001, 21:3926-3934.
32. Mikkonen M., Alatossava T. Characterization of the genome region encoding structural proteins of Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H. Gene 1994, 151:53-59.
33. Wang I.N., Smith D.L., Young R. Holins: the protein clocks of bacteriophage infections. Annu. Rev. Microbiol. 2000, 54:799-825.
34. Schmelcher M., Donovan D.M., Loessner M.J. Bacteriophage endolysins as novel antimicrobials. Future Microbiol. 2012, 7:1147-1171.
35. Bloomfield G.A., Whittle G., McDonagh M.B., Katz M.E., Cheetham B.F. Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element. Microbiology 1997, 143(Pt. 2):553-562.
36. Romero P., Croucher N.J., Hiller N.L., Hu F.Z., Ehrlich G.D., Bentley S.D., et al. Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages. J. Bacteriol. 2009, 191:4854-4862.
37. Makarova K.S., Grishin N.V., Koonin E.V. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics 2006, 22:2581-2584.
38. Yamaguchi Y., Park J.H., Inouye M. Toxin-antitoxin systems in bacteria and archaea. Annu. Rev. Genet. 2011, 45:61-79.
39. Jermy A. Phage biology: T4 to TA, checkmate. Nat. Rev. Microbiol. 2012, 10:160.
40. Dziewit L., Jazurek M., Drewniak L., Baj J., Bartosik D. The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2. J. Bacteriol. 2007, 189:1983-1997.
41. Pruteanu M., Baker T.A. Controlled degradation by ClpXP protease tunes the levels of the excision repair protein UvrA to the extent of DNA damage. Mol. Microbiol. 2009, 71:912-924.
42. Gaillot O., Pellegrini E., Bregenholt S., Nair S., Berche P. The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes. Mol. Microbiol. 2000, 35:1286-1294.
43. Raju R.M., Unnikrishnan M., Rubin D.H., Krishnamoorthy V., Kandror O., Akopian T.N., et al. Mycobacterium tuberculosis ClpP1 and ClpP2 function together in protein degradation and are required for viability in vitro and during infection. PloS Pathog. 2012, 8:e1002511.
44. Wegrzyn A., Czyz A., Gabig M., Wegrzyn G. ClpP/ClpX-mediated degradation of the bacteriophage lambda O protein and regulation of lambda phage and lambda plasmid replication. Arch. Microbiol. 2000, 174:89-96.
45. Frees D., Andersen J.H., Hemmingsen L., Koskenniemi K., Baek K.T., Muhammed M.K., et al. New insights into Staphylococcus aureus stress tolerance and virulence regulation from an analysis of the role of the ClpP protease in the strains Newman, COL, and SA564. J. Proteome Res. 2012, 11:95-108.
46. Gunthert U., Reiners L., Lauster R. Cloning and expression of Bacillus subtilis phage DNA methyltransferase genes in Escherichia coli and B. subtilis. Gene 1986, 41:261-270.
47. Hoskisson P.A., Smith M.C. Hypervariation and phase variation in the bacteriophage 'resistome'. Curr. Opin. Microbiol. 2007, 10:396-400.
48. Bayliss C.D., Callaghan M.J., Moxon E.R. High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Nucleic Acids Res. 2006, 34:4046-4059.
49. Tang F., Zhang W., Lu C. Lysogenic Streptococcus suis isolate SS2-4 containing prophage SMP showed increased mortality in zebra fish compared to the wild-type isolate. PLoS One 2013, 8:e54227.
50. Brenciani A., Bacciaglia A., Vignaroli C., Pugnaloni A., Varaldo P.E., Giovanetti E. Phim46.1, the main Streptococcus pyogenes element carrying mef(A) and tet(O) genes. Antimicrob. Agents Chemother. 2010, 54:221-229.