Identification and initial characterization of prophages in Vibrio campbellii

PLoS ONE

Volumn 11, Issue 5, 2016, Pages

  Lorenz, Nicola ^a   Reiger, Matthias ^a,d   Toro Nahuelpan, Mauricio ^b,c   Brachmann, Andreas ^a   Poettinger, Lisa ^a   Plener, Laure ^a,e   Lassak, Jürgen ^a   Jung, Kirsten ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF BAYREUTH   (Germany)

^c MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^d TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^e AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; MITOMYCIN;

ARTICLE; BACTERIAL GENOME; BACTERIUM CULTURE; CHROMOSOME 1; CHROMOSOME 2; CONTROLLED STUDY; HEAT STRESS; MYOVIRIDAE; NONHUMAN; PROMOTER REGION; PROPHAGE; SEQUENCE ANALYSIS; TEMPERATURE; VIBRIO HARVEYI; BACTERIAL CHROMOSOME; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENETICS; HEAT; ISOLATION AND PURIFICATION; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; VIBRIO; VIROLOGY; VIRUS RELEASE;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; GENOME, BACTERIAL; HOT TEMPERATURE; MYOVIRIDAE; PROPHAGES; SEQUENCE ANALYSIS, DNA; VIBRIO; VIRUS RELEASE;

EID: 84971268740     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0156010     Document Type: Article

References (43)

1. Lin B, Wang Z, Malanoski AP, O'Grady EA, Wimpee CF, Vuddhakul V, et al. Comparative genomic analyses identify the Vibrio harveyi genome sequenced strains BAA-1116 and HY01 as Vibrio campbellii. Environ Microbiol Rep. 2010; 2(1):81-89. doi: 10.1111/j.1758-2229.2009.00100.x PMID: 20686623
2. Jiravanichpaisal P, Miyazaki T, Limsuwan C. Histopathology, biochemistry, and pathogenicity of Vibrio harveyi infecting black tiger prawn Penaeus monodon. J Aquat Anim Health. 1994; 6(1):27-35. doi: 10.1577/1548-8667(1994)006〈0027:HBAPOV〉2.3.CO;2
3. Catap ES, Lavilla-Pitogo CR, Maeno Y, Travina RD. Occurrence, histopathology and experimental transmission of hepatopancreatic parvovirus infection in Penaeus monodon postlarvae. Dis Aquat Organ. 2003; 57(1-2):11-17. doi: 10.3354/dao057011 PMID: 14735916
4. Widder EA. Bioluminescence in the ocean: origins of biological, chemical, and ecological diversity. Science. 2010; 328(5979):704-708. doi: 10.1126/science.1174269 PMID: 20448176
5. Lapota D, Galt C, Losee JR, Huddell HD, Orzech JK, Nealson KH. Observations and measurements of planktonic bioluminescence in and around a milky sea. J Exp Mar Biol Ecol. 1988; 119(1):55-81. doi: 10.1016/0022-0981(88)90152-9
6. Miller SD, Haddock SH, Elvidge CD, Lee TF. Detection of a bioluminescent milky sea from space. Proc Natl Acad Sci USA. 2005; 102(40):14181-14184. doi: 10.1073/pnas.0507253102 PMID: 16186481
7. Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H. Prophage genomics. Microbiol Mol Biol Rev. 2003; 67(2):238-276. PMID: 12794192
8. Ackermann HW. 5500 Phages examined in the electron microscope. Arch Virol. 2007; 152(2):227-243. doi: 10.1007/s00705-006-0849-1 PMID: 17051420
9. Ackermann HW, DuBow MS. Viruses of Prokaryotes: General properties of bacteriophages. Boca Raton, FL: CRC Press; 1987.
10. Campbell NA, Reece JB. Biology. Boston, MA: Pearson, Benjamin Cummings; 2005.
11. Roberts JW, Devoret R. Lysogenic induction. Cold Spring Harbor, NY Cold Spring Harbor Laboratory Press; 1983. 123-144 p.
12. Hershey AD, Dove W. Introduction to Lambda. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1983.
13. Miller HI. Multilevel regulation of bacteriophage λ lysogeny by the E. coli himA gene. Cell. 1981; 25(1):269-276. doi: 10.1016/0092-8674(81)90252-X PMID: 6456071
14. Bergh O, Borsheim KY, Bratbak G, Heldal M. High abundance of viruses found in aquatic environments. Nature. 1989; 340(6233):467-468. doi: 10.1038/340467a0 PMID: 2755508
15. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: A fast phage search tool. Nucleic Acids Res. 2011; 39:W347-W352. doi: 10.1093/nar/gkr485 PMID: 21672955
16. Mobberley JM, Authement RN, Segall AM, Paul JH. The temperate marine phage φHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome. J Virol. 2008; 82(13):6618-6630. doi: 10.1128/JVI.00140-08 PMID: 18448537
17. Guidolin A, Manning PA. Genetics of Vibrio cholerae and its bacteriophages. Microbiol Rev. 1987; 51(2):285-298. PMID: 3299030
18. Chang B, Miyamoto H, Taniguchi H, Yoshida S. Isolation and genetic characterization of a novel filamentous bacteriophage, a deleted form of phage f237, from a pandemic Vibrio parahaemolyticus O4: K68 strain. Microbiol Immunol. 2002; 46(8):565-569. doi: 10.1111/j.1348-0421.2002.tb02734.x PMID: 12363020
19. Nasu H, Iida T, Sugahara T, Yamaichi Y, Park KS, Yokoyama K, et al. A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains. J Clin Microbiol. 2000; 38(6):2156-2161. PMID: 10834969
20. Jiang SC, Paul JH. Significance of lysogeny in the marine environment: studies with isolates and a model of lysogenic phage production. Microb Ecol. 1998; 35(3):235-243. doi: 10.1007/s002489900079 PMID: 9569281
21. Gödeke J, Paul K, Lassak J, Thormann KM. Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1. ISME J. 2011; 5(4):613-626. doi: 10.1038/ismej.2010.153 PMID: 20962878
22. Nanda AM, Heyer A, Kramer C, Grünberger A, Kohlheyer D, Frunzke J. Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level. J Bacteriol. 2014; 196(1):180-188. doi: 10.1128/jb.01018-13 PMID: 24163339
23. Cui J, Schlub TE, Holmes EC. An allometric relationship between the genome length and virion volume of viruses. J Virol. 2014; 88(11):6403-6410. doi: 10.1128/jvi.00362-14 PMID: 24672040
24. Bondy-Denomy J, Davidson AR. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol. 2014; 52(3):235-242. doi: 10.1007/s12275-014-4083-3 PMID: 24585054
25. Nanda AM, Thormann K, Frunzke J. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions. J Bacteriol. 2015; 197(3):410-419. doi: 10.1128/jb.02230-14 PMID: 25404701
26. Veening JW, Smits WK, Kuipers OP. Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol. 2008; 62:193-210. doi: 10.1146/annurev.micro.62.081307.163002 PMID: 18537474
27. Crothers-Stomps C, Hoj L, Bourne DG, Hall MR, Owens L. Isolation of lytic bacteriophage against Vibrio harveyi. J Appl Microbiol. 2010; 108(5):1744-1750. doi: 10.1111/j.1365-2672.2009.04578.x PMID: 19886890
28. Gerdes JC, Romig WR. Complete and defective bacteriophages of classical Vibrio cholerae: relationship to the kappa type bacteriophage. J Virol. 1975; 15(5):1231-1238. PMID: 16789156
29. Faruque SM, Bin Naser I, Fujihara K, Diraphat P, Chowdhury N, Kamruzzaman M, et al. Genomic sequence and receptor for the Vibrio cholerae phage KSF-1phi: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer. J Bacteriol. 2005; 187(12):4095-4103. doi: 10.1128/jb.187.12.4095-4103.2005 PMID: 15937172
30. Defoirdt T, Sorgeloos P. Monitoring of Vibrio harveyi quorum sensing activity in real time during infection of brine shrimp larvae. ISME J. 2012; 6(12):2314-2319. doi: 10.1038/ismej.2012.58 PMID: 22673627
31. Rossmann FS, Racek T, Wobser D, Puchalka J, Rabener EM, Reiger M, et al. Phage-mediated dispersal of biofilm and distribution of bacterial virulence genes is induced by quorum sensing. PLoS Pathog. 2015; 11(2):e1004653. doi: 10.1371/journal.ppat.1004653 PMID: 25706310
32. Anetzberger C, Reiger M, Fekete A, Schell U, Stambrau N, Plener L, et al. Autoinducers act as biological timers in Vibrio harveyi. PloS One. 2012; 7(10):e48310. doi: 10.1371/journal.pone.0048310 PMID: 23110227
33. Greenberg EP, Hastings JW, Ulitzur S. Induction of luciferase synthesis in Beneckea harveyi by other marine bacteria. Arch Microbiol. 1979; 120(2):87-91. doi: 10.1007/BF00409093
34. Sambrook J. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1989.
35. Inoue H, Nojima H, Okayama H. High efficiency transformation of Escherichia coli with plasmids. Gene. 1990; 96(1):23-28. PMID: 2265755
36. Fried L, Lassak J, Jung K. A comprehensive toolbox for the rapid construction of lacZ fusion reporters. J Microbiol Methods. 2012; 91(3):537-543. doi: 10.1016/j.mimet.2012.09.023 PMID: 23022912
37. Plener L, Lorenz N, Reiger M, Ramalho T, Gerland U, Jung K. The phosphorylation flow of the Vibrio harveyi quorum sensing cascade determines levels of phenotypic heterogeneity in the population. J Bacteriol. 2015. doi: 10.1128/jb.02544-14
38. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet. 1995; 11(6):217-218. PMID: 7638902
39. Fritz G, Koller C, Burdack K, Tetsch L, Haneburger I, Jung K, et al. Induction kinetics of a conditional pH stress response system in Escherichia coli. J Mol Biol. 2009; 393(2):272-286. doi: 10.1016/j.jmb.2009.08.037 PMID: 19703467
40. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protocols. 2008; 3(6):1101-1108. doi: 10.1038/nprot.2008.73 PMID: 18546601
41. Miller VL, Mekalanos JJ. A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J Bacteriol. 1988; 170(6):2575-2583. PMID: 2836362
42. Bassler BL, Greenberg EP, Stevens AM. Cross-species induction of luminescence in the quorum-sensing bacterium Vibrio harveyi. J Bacteriol. 1997; 179(12):4043-4045. PMID: 9190823
43. Lassak J, Henche AL, Binnenkade L, Thormann KM. ArcS, the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. Appl Environ Microbiol. 2010; 76(10):3263-3274. doi: 10.1128/AEM.00512-10 PMID: 20348304