Different expression patterns of genes from the Exo-Xis region of bacteriophage λ and Shiga toxin-converting bacteriophage Φ24Bfollowing infection or prophage induction in Escherichia coli

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Bloch, Sylwia ^a   Nejman Faleńczyk, Bozena ^a   Dydecka, Aleksandra ^a   Łos̈, Joanna M ^a   Felczykowska, Agnieszka ^a   We¸grzyn, Alicja ^b   We¸grzyn, Grzegorz ^a  

^a UNIVERSITY OF GDA SK   (Poland)

^b UNIVERSITY OF SZCZECIN   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN PEROXIDE; MITOMYCIN; SHIGA TOXIN;

ARTICLE; BACTERIAL CELL; BACTERIAL VIABILITY; BACTERIOPHAGE; BACTERIOPHAGE LAMBDA; BACTERIOPHAGE PHI 24B; BACTERIOPHAGE SHIGA; CONTROLLED STUDY; DNA CONTENT; ESCHERICHIA COLI; EXO XIS REGION; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENE STRUCTURE; GENOME ANALYSIS; GROWTH REGULATION; HOST CELL; LIFE CYCLE STAGE; NONHUMAN; OPEN READING FRAME; PROMOTER REGION; PROPHAGE; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UPREGULATION; ENTEROBACTERIA PHAGE LAMBDA; ENTEROHEMORRHAGIC ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; VIRUS ACTIVATION;

ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI;

BACTERIOPHAGE LAMBDA; BACTERIOPHAGES; ENTEROHEMORRHAGIC ESCHERICHIA COLI; GENE EXPRESSION REGULATION, VIRAL; PROPHAGES; SHIGA TOXIN; VIRUS ACTIVATION;

EID: 84907895541     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108233     Document Type: Article

References (48)

1. We¸grzyn G, Licznerska K, We¸grzyn A (2012) Phage λ - new insights into regulatory circuits. Adv Virus Res 82: 155-178.
2. Ptashne M (2004) A genetic switch: phage lambda revisited. 3rd edn. Cold Spring Harbor Laboratory Press.
3. We¸grzyn G, We¸grzyn A (2005) Genetic switches during bacteriophage lambda development. Prog Nucleic Acid Res Mol Biol 79: 1-48.
4. Gyles CL (2007) Shiga toxin-producing Escherichia coli: an overview. J Anim Sci 85: E45-62.
5. Hunt JM (2010) Shiga toxin-producing Escherichia coli (STEC). Clin Lab Med 30: 21-45.
6. Mauro SA, Koudelka GB (2011) Shiga toxin: expression, distribution, and its role in the environment. Toxins 3: 608-625.
7. Allison HE (2007) Stx-phages: drivers and mediators of the evolution of STEC and STEC-like pathogens. Future Microbiol 2: 165-174.
8. Łos̈ JM, Łos̈ M, We¸grzyn G (2011) Bacteriophages carrying Shiga toxin genes: genomic variations, detection and potential treatment of pathogenic bacteria. Future Microbiol 6: 909-924.
9. Łos̈ JM, Łos̈ M, We¸grzyn A, We¸grzyn G (2012) Altruism of Shiga toxin-producing Escherichia coli: recent hypothesis versus experimental results. Front Cell Infect Microbiol 2: 166.
10. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6: e22751.
11. Beutin L, Martin A (2012) Outbreak of Shiga toxin-producing Escherichia coli (STEC) O104:H4 infection in Germany causes a paradigm shift with regard to human pathogenicity of STEC strains. J Food Prot 75: 408-418.
12. Bloch S, Felczykowska A, Nejman-Faleńczyk B (2012) Escherichia coli O104:H4 outbreak - have we learnt a lesson from it? Acta Biochim Pol 59: 483-488.
13. Karch H, Denamur E, Dobrindt U, Finlay BB, Hengge R, et al. (2012) The enemy within us: lessons from the 2011 European Escherichia coli O104:H4 outbreak. EMBO Mol Med 4: 841-848.
14. Werber D, Krause G, Frank C, Fruth A, Flieger A, et al. (2012) Outbreaks of virulent diarrheagenic Escherichia coli - are we in control? BMC Med 10: 11.
15. Herold S, Karch H, Schmidt H (2004) Shiga toxin-encoding bacteriophages - genomes in motion. Int J Med Microbiol 294: 115-121.
16. Waldor MK, Friedman DI (2005) Phage regulatory circuits and virulence gene expression. Curr Opin Microbiol 8: 459-465.
17. Nowicki D, Kobiela W, We¸grzyn A, Wegrzyn G, Szalewska-Pałasz A (2013) ppGpp-dependent negative control of DNA replication of Shiga toxin-converting bacteriophages in Escherichia coli. J Bacteriol 195: 5007-5015.
18. Nowicki D, Macia¸g-Dorszyńska M, Kobiela W, Herman-Antosiewicz A, We¸grzyn A, et al. (2014) Phenethyl isothiocyanate inhibits Shiga toxin production in enterohemorrhagic Escherichia coli by stringent response induction. Antimicrob Agents Chemother 58: 2304-2315.
19. Riley LM, Veses-Garcia M, Hillman JD, Handfield M, McCarthy AJ, et al. (2012) Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B. BMC Microbiol 12: 42.
20. Łos̈ JM, Łos̈ M, We¸grzyn G, We¸grzyn A (2009) Differential efficiency of induction of various lambdoid prophages responsible for production of Shiga toxin in response to different induction agents. Microb Pathog 47: 289-298.
21. Łos̈ JM, Łos̈ M, We¸grzyn A, We¸grzyn G (2010) Hydrogen peroxide-mediated induction of the Shiga toxin-converting lambdoid prophages ST2-8624 in Escherichia coli O157:H7. FEMS Immunol Med Microbiol 58: 322-329.
22. Łos̈ JM, Łos̈ M, Wegrzyn A, Wegrzyn G (2008) Role of the bacteriophage λ exo-xis region in the virus development. Folia Microbiol 53: 443-450.
23. Bloch S, Nejman-Faleńczyk B, Łos̈ JM, Barańska S, Łepek K, et al. (2013) Genes from the exo-xis region of λ and Shiga toxin-converting bacteriophages influence lysogenization and prophage induction. Arch Microbiol 195: 693-703.
24. Kwan JJ, Smirnova E, Khazai S, Evanics F, Maxwell KL, et al. (2013) The solution structures of two prophage homologues of the bacteriophage λ Ea8.5 protein reveal a newly discovered hybrid homeodomain/zinc-finger fold. Biochemistry 52: 3612-3614.
25. Allison HE, Sergeant MJ, James CE, Saunders JR, Smith DL, et al. (2003) Immunity profiles of wild-type and recombinant shiga-like toxin-encoding bacteriophages and characterization of novel double lysogens. Infect Immun 71: 3409-3418.
26. Jensen KF (1993) The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol 175: 3401-3407.
27. Łos̈ JM, Golec P, We¸grzyn G, We¸grzyn A, Łos̈ M (2008b) Simple method for plating Escherichia coli bacteriophages forming very small plaques or no plaques under standard conditions. Appl Environ Microbiol 74: 5113-5120.
28. Hoerr V, Ziebuhr W, Kozitskaya S, Katzowitsch E, Holzgrabe U (2007) Laser-induced fluorescence-capillary electrophoresis and fluorescence microplate reader measurement: two methods to quantify the effect of antibiotics. Anal Chem 79: 7510-7518.
29. Maruyama A, Oda M, Higashihara T (1993) Abundance of virus-sized non-DNase-digestible DNA (coated DNA) in eutrophic seawater. Appl Environ Microbiol 59: 712-717.
30. Strauch E, Hammerl JA, Konietzny A, Schneiker-Bekel S, Arnold W, et al. (2008) Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. Infect Immun 76: 5466-5477.
31. Roche (2009) LightCycler Real-Time PCR Systems - Application Manual. Germany: Roche Diagnostics GmbH. 140 p.
32. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2007) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339: 62-66.
33. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, et al. (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37: e45.
34. Cikos S, Bukovská A, Koppel J (2007) Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis. BMC Mol Biol 8: 113.
35. Feng J, Zeng R, Chen J (2008) Accurate and efficient data processing for quantitative real-time PCR using a tripartite plant virus as a model. Biotechniques 44: 901-912.
36. Regier N, Frey B (2010) Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar. BMC Mol Biol 11: 57.
37. Aglawe SB, Fakrudin B, Patole CB, Bhairappanavar SB, Koti RV, et al. (2012) Quantitative RT-PCR analysis of 20 transcription factor genes of MADS, ARF, HAP2, MBF and HB families in moisture stressed shoot and root tissues of sorghum. Physiol Mol Biol Plants 18: 287-300.
38. Borges A, Tsai SM, Caldas DG (2012) Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses. Plant Cell Rep 31: 827-838.
39. Solovyev V, Salamov A (2011) Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In: Li RW, editor. Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies. p 61-78.
40. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, et al. (1994) Fast folding and comparison of RNA secondary structures. Monastch Chem 125: 167-188.
41. Gautheret D, Lambert A (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 313: 1003-1011.
42. Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, et al. (2001) Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res 29: 3583-3594.
43. Macke T, Ecker D, Gutell R, Gautheret D, Case DA, et al. (2001) RNAMotif - a new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res 29: 4724-4735.
44. Liu X, Jiang H, Gu Z, Roberts JW (2013) High-resolution view of bacteriophage lambda gene expression by ribosome profiling. Proc Natl Acad Sci USA 110: 11928-11933.
45. Ibrahim M, Nicolas P, Bessieres P, Bolotin A, Monnet V, et al. (2007) A genome-wide survey of short coding sequences in Streptococci . Microbiology 153: 3631-3644.
46. Hemm MR, Paul BJ, Schneider TD, Storz G, Rudd KE (2008) Small membrane proteins found by comparative genomics and ribosome binding site models. Mol Microbiol 70: 1487-1501.
47. Hobbs EC, Fontaine F, Yin X, Storz G (2011) An expanding universe of small proteins. Curr Opin Microbiol 14: 167-173.
48. Sergueev K, Court D, Reaves L, Austin S (2002) E. coli cell-cycle regulation by bacteriophage lambda. J Mol Biol 324: 297-307.