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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Prophages

  • As further evidence that the proteolytic activity of recA protein is responsible for its regulatory function, we show here that the ability of two mutationally altered recA proteins to cleave phage lambda repressor correlates with the ability of the mutant cells to induce prophage [1].
  • Thermoinduction of cells of E. coli carrying prophage lambdacI857 within the bfe gene brings about not only "escape synthesis" of core subunits of the DNA-dependent RNA polymerase (RNA nucleotidyltransferase, nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2-7-7-6), but also a striking stimulation of sigma factor synthesis [2].
  • The tum gene of coliphage 186, encoded on a LexA controlled operon, is essential for UV induction of a 186 prophage [3].
  • The product of the cloned recA+ gene of Proteus mirabilis substitutes for a defective recA protein in Escherichia coli recA- mutants and restores recombination, repair, and prophage induction functions to near normal levels (Eitner, G., Adler, B., Lanzov, V. A., and Hofemeister, J. (1982) Mol. Gen. Genet. 185, 481-486) [4].
  • With the exception of Mem and other minor ORFs, the striking similarity between the deduced proteomes of phiMFV1 and the recently described phiMAV1 of arthritogenic strains of Mycoplasma arthritidis, along with the prominent gene synteny between these elements, provides the taxonomic basis for a new family of prophage [5].

High impact information on Prophages

  • In lambda lysogens, cleavage of lambda Cl repressor in a similar but far slower reaction results in prophage induction [6].
  • Lambda cII expression from an induced prophage is increased twofold in the presence of a large excess of anti-OOP RNA [7].
  • Induction of a lambda E-W-S-cI857 prophage in which the pseT gene can be transcribed from the late lambda promoter, PR1, leads to greater than 100-fold amplification of pnk activity; pnk comprises approximately 7% of the total soluble cell protein [8].
  • Repression of cI by the lytic repressor was not required for prophage induction to occur [9].
  • Strain persistence or extinction between epidemics was strongly associated with presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A [10].

Chemical compound and disease context of Prophages

  • Plasmid R6-5 contains a locus whose product inhibits induction of sfiA and prophage lambda in a recA441 mutant at 42 degrees C and in a recA+ host after treatment with nalidixic acid [11].
  • Similar characteristics of induction were observed when the lactose genes were fused to a prophage lambda promoter by using Mud(ApR, lac) [12].
  • Of the dinucleotides tested, only d(A-G), d(G-G), and d(I-G) induced prophage [13].
  • Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant [14].
  • Since the Fels prophages are inducible by aflatoxin B1, by daunorubicin, and by other agents, it seems that mutagenesis and Fels prophage induction occur in separate subpopulations of cells; this situation had previously been reported to occur for mutagenesis and prophage lambda induction in Escherichia coli [15].

Biological context of Prophages


Anatomical context of Prophages

  • Both H2O2 and neutrophils were found to augment Stx2 production, raising the possibility that these agents may lead to prophage induction in vivo and thereby contribute to EHEC pathogenesis [21].

Gene context of Prophages

  • The addiction module of plasmid prophage P1 consists of a pair of genes called phd and doc [22].
  • We have purified the TraJ protein, using an Flac::lambda traJ lysogen that overproduces the protein after heat induction of the prophage [23].
  • Here, we show that thermal induction of the prophage accelerated araB-lacZ fusion formation, confirming that derepression is a rate-limiting step in the fusion process [24].
  • The upstream sequences include functional phd and doc genes, which encode an addiction system that stabilizes the P1 prophage state, and extend to and beyond pac, the site at which phage DNA packaging begins [25].
  • E. coli sbcA mutants and lambda reverse both express genes of the Rac prophage, and we have located the lar gene immediately downstream of recT in this element [26].

Analytical, diagnostic and therapeutic context of Prophages


  1. Two mutations that alter the regulatory activity of E. coli recA protein. Roberts, J.W., Roberts, C.W. Nature (1981) [Pubmed]
  2. Induction of sigma factor synthesis in Escherichia coli by the N gene product of bacteriophage lambda. Nakamura, Y., Yura, T. Proc. Natl. Acad. Sci. U.S.A. (1976) [Pubmed]
  3. The Tum protein of coliphage 186 is an antirepressor. Shearwin, K.E., Brumby, A.M., Egan, J.B. J. Biol. Chem. (1998) [Pubmed]
  4. Purification and properties of the recA protein of Proteus mirabilis. Comparison with Escherichia coli recA protein; specificity of interaction with single strand binding protein. West, S.C., Countryman, J.K., Howard-Flanders, P. J. Biol. Chem. (1983) [Pubmed]
  5. The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein. Röske, K., Calcutt, M.J., Wise, K.S. Mol. Microbiol. (2004) [Pubmed]
  6. LexA and lambda Cl repressors as enzymes: specific cleavage in an intermolecular reaction. Kim, B., Little, J.W. Cell (1993) [Pubmed]
  7. OOP RNA, produced from multicopy plasmids, inhibits lambda cII gene expression through an RNase III-dependent mechanism. Krinke, L., Wulff, D.L. Genes Dev. (1987) [Pubmed]
  8. T4 polynucleotide kinase; cloning of the gene (pseT) and amplification of its product. Midgley, C.A., Murray, N.E. EMBO J. (1985) [Pubmed]
  9. Role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach. Atsumi, S., Little, J.W. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  10. Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus. Beres, S.B., Richter, E.W., Nagiec, M.J., Sumby, P., Porcella, S.F., Deleo, F.R., Musser, J.M. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  11. An inhibitor of SOS induction, specified by a plasmid locus in Escherichia coli. Bagdasarian, M., Bailone, A., Bagdasarian, M.M., Manning, P.A., Lurz, R., Timmis, K.N., Devoret, R. Proc. Natl. Acad. Sci. U.S.A. (1986) [Pubmed]
  12. DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Kenyon, C.J., Walker, G.C. Proc. Natl. Acad. Sci. U.S.A. (1980) [Pubmed]
  13. Prophage (phi 80) induction in Escherichia coli K-12 by specific deoxyoligonucleotides. Irbe, R.M., Morin, L.M., Oishi, M. Proc. Natl. Acad. Sci. U.S.A. (1981) [Pubmed]
  14. The tripartite immunity system of phages P1 and P7. Heinrich, J., Velleman, M., Schuster, H. FEMS Microbiol. Rev. (1995) [Pubmed]
  15. Mutagenic response of Ames strains cured of their inducible Fels 1 and Fels 2 prophages. Affolter, M., Parent-Vaugeois, C., Anderson, A. Cancer Res. (1983) [Pubmed]
  16. Participation of Escherichia coli integration host factor in the P1 plasmid partition system. Funnell, B.E. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  17. Terminus region of the chromosome in Escherichia coli inhibits replication forks. Kuempel, P.L., Duerr, S.A., Seeley, N.R. Proc. Natl. Acad. Sci. U.S.A. (1977) [Pubmed]
  18. Escherichia coli single-strand DNA binding protein from wild type and lexC113 mutant affects in vitro proteolytic cleavage of phage lambda repressor. Resnick, J., Sussman, R. Proc. Natl. Acad. Sci. U.S.A. (1982) [Pubmed]
  19. Expression of a mammalian fatty acid-binding protein in Escherichia coli. Lowe, J.B., Strauss, A.W., Gordon, J.I. J. Biol. Chem. (1984) [Pubmed]
  20. Phage regulatory circuits and virulence gene expression. Waldor, M.K., Friedman, D.I. Curr. Opin. Microbiol. (2005) [Pubmed]
  21. Human neutrophils and their products induce Shiga toxin production by enterohemorrhagic Escherichia coli. Wagner, P.L., Acheson, D.W., Waldor, M.K. Infect. Immun. (2001) [Pubmed]
  22. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Lehnherr, H., Yarmolinsky, M.B. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  23. Overproduction in Escherichia coli K-12 and purification of the TraJ protein encoded by the conjugative plasmid F. Cuozzo, M., Silverman, P.M., Minkley, E.G. J. Biol. Chem. (1984) [Pubmed]
  24. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Lamrani, S., Ranquet, C., Gama, M.J., Nakai, H., Shapiro, J.A., Toussaint, A., Maenhaut-Michel, G. Mol. Microbiol. (1999) [Pubmed]
  25. The type IC hsd loci of the enterobacteria are flanked by DNA with high homology to the phage P1 genome: implications for the evolution and spread of DNA restriction systems. Tyndall, C., Lehnherr, H., Sandmeier, U., Kulik, E., Bickle, T.A. Mol. Microbiol. (1997) [Pubmed]
  26. Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12. King, G., Murray, N.E. Mol. Microbiol. (1995) [Pubmed]
  27. Vibrio cholerae O139 in Calcutta, 1992-1998: incidence, antibiograms, and genotypes. Basu, A., Garg, P., Datta, S., Chakraborty, S., Bhattacharya, T., Khan, A., Ramamurthy, S., Bhattacharya, S.K., Yamasaki, S., Takeda, Y., Nair, G.B. Emerging Infect. Dis. (2000) [Pubmed]
  28. Infectious CTXPhi and the vibrio pathogenicity island prophage in Vibrio mimicus: evidence for recent horizontal transfer between V. mimicus and V. cholerae. Boyd, E.F., Moyer, K.E., Shi, L., Waldor, M.K. Infect. Immun. (2000) [Pubmed]
  29. Isolation and characterization of plaque-forming lambdadnaZ+ transducing bacteriophages. Walker, J.R., Henson, J.M., Lee, C.S. J. Bacteriol. (1977) [Pubmed]
  30. Genotypic characterization of toxic shock syndrome toxin-1-producing strains of Staphylococcus aureus isolated in the Czech Republic. Hrstka, R., Růzicková, V., Petrás, P., Pantůcek, R., Rosypal, S., Doskar, J. Int. J. Med. Microbiol. (2006) [Pubmed]
  31. The Shiga-toxin VT2-encoding bacteriophage varphi297 integrates at a distinct position in the Escherichia coli genome. De Greve, H., Qizhi, C., Deboeck, F., Hernalsteens, J.P. Biochim. Biophys. Acta (2002) [Pubmed]
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