Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Jian, Huahua ^a,b   Xu, Jun ^b   Xiao, Xiang ^b   Wang, Fengping ^b,c  

^a XIAMEN UNIVERSITY   (China)

^b Shanghai Jiao Tong University   (China)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; COLD SHOCK RESPONSE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA REPLICATION; ENVIRONMENTAL CHANGE; FPSA GENE; FPSR GENE; GENE ACTIVITY; GENETIC TRANSCRIPTION; GROWTH CURVE; HIGH TEMPERATURE; LOW TEMPERATURE; MONITORING; NONHUMAN; REGULATORY MECHANISM; SHEWANELLA PIEZOTOLERANS WP3; SW1 GENE;

BACTERIOPHAGES; COLD-SHOCK RESPONSE; DNA REPLICATION; DNA, VIRAL; ECOSYSTEM; EVOLUTION, MOLECULAR; GENES, VIRAL; OCEANS AND SEAS; SHEWANELLA; TRANSCRIPTION, GENETIC; VIRAL PROTEINS; VIRUS REPLICATION;

BACTERIA (MICROORGANISMS); SHEWANELLA;

EID: 84864758161     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041578     Document Type: Article

References (42)

1. Danovaro R, Dell'Anno A, Corinaldesi C, Magagnini M, Noble R, et al. (2008) Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454: 1084-1087.
2. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ, (2011) Microbial Ecology of the Dark Ocean above, at, and below the Seafloor. Microbiol Mol Biol Rev 75: 361-422.
3. Wells LE, Deming JW, (2006) Characterization of a cold-active bacteriophage on two psychrophilic marine hosts. Aquat Microb Ecol 45: 15-29.
4. Johnson RM, (1968) Characteristics of a marine Vibrio-bacteriophage system. J Arizona Acad Sci 5: 28-33.
5. Wiebe W, Liston J, (1968) Isolation and characterization of a marine bacteriophage. Mar Biol 1: 244-249.
6. Wang F, Wang P, Chen M, Xiao X, (2004) Isolation of extremophiles with the detection and retrieval of Shewanella strains in deep-sea sediments from the west Pacific. Extremophiles 8: 165-168.
7. Xiao X, Wang P, Zeng X, Bartlett DH, Wang F, (2007) Shewanella psychrophila sp. nov. and Shewanella piezotolerans sp. nov., isolated from west Pacific deep-sea sediment. Int J Syst Evol Microbiol 57: 60.
8. Wang F, Li Q, Xiao X, (2007) A novel filamentous phage from a deep-sea bacterium Shewanella piezotolerans WP3 is induced at low temperature. J Bacteriol 189: 7151-7153.
9. Rakonjac J, Bennett NJ, Spagnuolo J, Gagic D, Russel M, (2011) Filamentous Bacteriophage: Biology, Phage Display and Nanotechnology Applications. Curr Issues Mol Biol 13: 51-76.
10. Marvin D, (1998) Filamentous phage structure, infection and assembly. Curr Opin Struct Biol 8: 150-158.
11. Davis BM, Waldor MK, (2003) Filamentous phages linked to virulence of Vibrio cholerae. Curr opin Microbiol 6: 35-42.
12. Higashitani N, Higashitani A, Guan ZW, Horiuchi K, (1996) Recognition mechanisms of the minus-strand origin of phage f1 by Escherichia coli RNA polymerase. Genes Cells 1: 829-841.
13. Higashitani A, Higashitani N, Horiuchi K, (1997) Minus-strand origin of filamentous phage versus transcriptional promoters in recognition of RNA polymerase. Proc Natl Acad Sci USA 94: 2909.
14. Horiuchi K, (1997) Initiation mechanisms in replication of filamentous phage DNA. Genes Cells 2: 425-432.
15. Wang F, Wang J, Jian H, Zhang B, Li S, et al. (2008) Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS One 3: e1937.
16. Yamanaka K, Fang L, Inouye M, (1998) The CspA family in Escherichia coli: multiple gene duplication for stress adaptation. Mol Microbiol 27: 247-255.
17. Hebraud M, Potier P, (1999) Cold shock response and low temperature adaptation in psychrotrophic bacteria. J Mol Microbiol Biotechnol 1: 211-219.
18. Gualerzi CO, Maria Giuliodori A, Pon CL, (2003) Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 331: 527-539.
19. Phadtare S, (2004) Recent developments in bacterial cold-shock response. Curr Issues Mol Biol 6: 125-136.
20. Giladi H, Goldenberg D, Koby S, Oppenheim AB, (1995) Enhanced activity of the bacteriophage lambda PL promoter at low temperature. Proc Natl Acad Sci USA 92: 2184.
21. Obuchowski M, Shotland Y, Koby S, Giladi H, Gabig M, et al. (1997) Stability of CII is a key element in the cold stress response of bacteriophage lambda infection. J Bacteriol 179: 5987-5991.
22. Gabig M, Obuchowski M, Srutkowska S, Wegrzyn G, (1998) Regulation of replication of λ phage and λ plasmid DNAs at low temperature. Mol Gen Genet 258: 494-502.
23. Chen Y, Wang F, Xu J, Mehmood MA, Xiao X, (2010) Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J 5: 843-855.
24. Li S, Xiao X, Li J, Luo J, Wang F, (2006) Identification of genes regulated by changing salinity in the deep-sea bacterium Shewanella sp. WP3 using RNA arbitrarily primed PCR. Extremophiles 10: 97-104.
25. Li S, Xiao X, Sun P, Wang F, (2008) Screening of genes regulated by cold shock in Shewanella piezotolerans WP3 and time course expression of cold-regulated genes. Arch Microbiol 189: 549-556.
26. Wang F, Xiao X, Ou HY, Gai Y, (2009) Role and regulation of fatty acid biosynthesis in the response of Shewanella piezotolerans WP3 to different temperatures and pressures. J Bacteriol 191: 2574-2584.
27. Wegrzyn G, Wegrzyn A, (2002) Stress responses and replication of plasmids in bacterial cells. Microbial cell factories 1: 1-12.
28. Wegrzyn G, Wegrzyn A, Barauska S, Czyz A, (2001) Regulation of bacteriophage lambda development. Recent Res Dev Virol 3: 375-386.
29. Wegrzyn A, Wegrzyn G, (2001) Inheritance of the replication complex: a unique or common phenomenon in the control of DNA replication? Arch Microbiol 175: 86-93.
30. Taylor K, (1995) Replication of coliphage lambda DNA. FEMS Microbiol Rev 17: 109-119.
31. Wegrzyn G, (1995) Amplification of λ plasmids in Escherichia coli relA mutants. J Biotechnol 43: 139-143.
32. Fukasawa T, Hirai K, Segawa T, Obonai K, (1978) Regional replication of the bacterial chromosome induced by derepression of prophage lambda. Molecular and General Genetics MGG 167: 83-93.
33. Willard M, Echols H, (1968) Role of bacteriophage DNA replication in λ dg escape synthesis. J Mol Biol 32: 37-46.
34. Frye JG, Porwollik S, Blackmer F, Cheng P, McClelland M, (2005) Host gene expression changes and DNA amplification during temperate phage induction. J Bacteriol 187: 1485-1492.
35. Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, et al. (2010) The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA. Mol Cell 37: 21-33.
36. Fang L, Xia B, Inouye M, (1999) Transcription of cspA, the gene for the major cold-shock protein of Escherichia coli, is negatively regulated at 37°C by the 5′ untranslated region of its mRNA. FEMS Microbiol Lett 176: 39-43.
37. Fang L, Jiang W, Bae W, Inouye M, (1997) Promoter-independent cold-shock induction of cspA and its derepression at 37°C by mRNA stabilization. Mol Microbiol 23: 355-364.
38. Gao H, Yang ZK, Wu L, Thompson DK, Zhou J, (2006) Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J Bacteriol 188: 4560-4569.
39. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold spring harbor laboratory press.
40. Skulj M, Okrslar V, Jalen S, Jevsevar S, Slanc P, et al. (2008) Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb Cell Fact 7: 6.
41. Lee C, Kim J, Shin SG, Hwang S, (2006) Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. J Biotechnol 123: 273-280.
42. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25: 402-408.