Integration-Dependent Bacteriophage Immunity Provides Insights into the Evolution of Genetic Switches

Molecular Cell

Volumn 49, Issue 2, 2013, Pages 237-248

  Broussard, Gregory W ^a   Oldfield, Lauren M ^a   Villanueva, Valerie M ^a   Lunt, Bryce L ^a   Shine, Emilee E ^a   Hatfull, Graham F ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; GENE SWITCHING; GENETIC RECOMBINATION; IMMUNITY; LYSOGENIZATION; NONHUMAN; PROTEIN DEGRADATION; REPRESSOR GENE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, VIRAL; INTEGRASES; LYSOGENY; MICROBIAL VIABILITY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MYCOBACTERIOPHAGES; MYCOBACTERIUM SMEGMATIS; PROMOTER REGIONS, GENETIC; PROPHAGES; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, DNA; VIRAL PROTEINS;

EID: 84872783870     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2012.11.012     Document Type: Article

References (34)

1. Bonnet J., Subsoontorn P., Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl. Acad. Sci. USA 2012, 109:8884-8889.
2. Brown K.L., Sarkis G.J., Wadsworth C., Hatfull G.F. Transcriptional silencing by the mycobacteriophage L5 repressor. EMBO J. 1997, 16:5914-5921.
3. Chatterjee A., Kaznessis Y.N., Hu W.S. Tweaking biological switches through a better understanding of bistability behavior. Curr. Opin. Biotechnol. 2008, 19:475-481.
4. Cresawn S.G., Bogel M., Day N., Jacobs-Sera D., Hendrix R.W., Hatfull G.F. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 2011, 12:395.
5. Dodd I.B., Shearwin K.E., Egan J.B. Revisited gene regulation in bacteriophage lambda. Curr. Opin. Genet. Dev. 2005, 15:145-152.
6. Donnelly-Wu M.K., Jacobs W.R., Hatfull G.F. Superinfection immunity of mycobacteriophage L5: applications for genetic transformation of mycobacteria. Mol. Microbiol. 1993, 7:407-417.
7. Flynn J.M., Levchenko I., Seidel M., Wickner S.H., Sauer R.T., Baker T.A. Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc. Natl. Acad. Sci. USA 2001, 98:10584-10589.
8. Friedland A.E., Lu T.K., Wang X., Shi D., Church G., Collins J.J. Synthetic gene networks that count. Science 2009, 324:1199-1202.
9. Halder S., Datta A.B., Parrack P. Probing the antiprotease activity of lambdaCIII, an inhibitor of the Escherichia coli metalloprotease HflB (FtsH). J. Bacteriol. 2007, 189:8130-8138.
10. Hatfull G.F. Mycobacteriophages: genes and genomes. Annu. Rev. Microbiol. 2010, 64:331-356.
11. Hatfull G.F., Hendrix R.W. Bacteriophages and their genomes. Curr. Opin. Virol. 2011, 1:298-303.
12. Hatfull G.F., Pedulla M.L., Jacobs-Sera D., Cichon P.M., Foley A., Ford M.E., Gonda R.M., Houtz J.M., Hryckowian A.J., Kelchner V.A., et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2006, 2:e92. 10.1371/journal.pgen.0020092.
13. Hatfull G.F. Complete genome sequences of 138 mycobacteriophages. J. Virol. 2012, 86:2382-2384. Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program, KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course StudentsKwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students, Phage Hunters Integrating Research and Education ProgramPhage Hunters Integrating Research and Education Program.
14. Hochschild A., Douhan J., Ptashne M. How lambda repressor and lambda Cro distinguish between OR1 and OR3. Cell 1986, 47:807-816.
15. Jain S., Hatfull G.F. Transcriptional regulation and immunity in mycobacteriophage Bxb1. Mol. Microbiol. 2000, 38:971-985.
16. Kobiler O., Koby S., Teff D., Court D., Oppenheim A.B. The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis. Proc. Natl. Acad. Sci. USA 2002, 99:14964-14969.
17. Krinke L., Mahoney M., Wulff D.L. The role of the OOP antisense RNA in coliphage lambda development. Mol. Microbiol. 1991, 5:1265-1272.
18. Landy A. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 1989, 58:913-949.
19. Lee M.H., Hatfull G.F. Mycobacteriophage L5 integrase-mediated site-specific integration in vitro. J. Bacteriol. 1993, 175:6836-6841.
20. Lee M.H., Pascopella L., Jacobs W.R., Hatfull G.F. Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guérin. Proc. Natl. Acad. Sci. USA 1991, 88:3111-3115.
21. Lewis J.A., Hatfull G.F. Control of directionality in L5 integrase-mediated site-specific recombination. J. Mol. Biol. 2003, 326:805-821.
22. Lewis D., Le P., Zurla C., Finzi L., Adhya S. Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc. Natl. Acad. Sci. USA 2011, 108:14807-14812.
23. Little J.W. Evolution of complex gene regulatory circuits by addition of refinements. Curr. Biol. 2010, 20:R724-R734.
24. Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139-1150.
25. Oppenheim A.B., Kobiler O., Stavans J., Court D.L., Adhya S. Switches in bacteriophage lambda development. Annu. Rev. Genet. 2005, 39:409-429.
26. Pandey A.K., Raman S., Proff R., Joshi S., Kang C.M., Rubin E.J., Husson R.N., Sassetti C.M. Nitrile-inducible gene expression in mycobacteria. Tuberculosis (Edinb.) 2009, 89:12-16.
27. Peña C.E., Stoner J.E., Hatfull G.F. Positions of strand exchange in mycobacteriophage L5 integration and characterization of the attB site. J. Bacteriol. 1996, 178:5533-5536.
28. Peña C.E., Kahlenberg J.M., Hatfull G.F. Assembly and activation of site-specific recombination complexes. Proc. Natl. Acad. Sci. USA 2000, 97:7760-7765.
29. Pope W.H., Jacobs-Sera D., Russell D.A., Peebles C.L., Al-Atrache Z., Alcoser T.A., Alexander L.M., Alfano M.B., Alford S.T., Amy N.E., et al. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS ONE 2011, 6:e16329. 10.1371/journal.pone.0016329.
30. Raju R.M., Unnikrishnan M., Rubin D.H., Krishnamoorthy V., Kandror O., Akopian T.N., Goldberg A.L., Rubin E.J. 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. 10.1371/journal.ppat.1002511.
31. Sampson T., Broussard G.W., Marinelli L.J., Jacobs-Sera D., Ray M., Ko C.C., Russell D., Hendrix R.W., Hatfull G.F. Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. Microbiology 2009, 155:2962-2977.
32. Sarkis G.J., Hatfull G.F. Mycobacteriophages. Methods Mol. Biol. 1998, 101:145-173.
33. Sau S., Chattoraj P., Ganguly T., Lee C.Y., Mandal N.C. Cloning and sequencing analysis of the repressor gene of temperate mycobacteriophage L1. J. Biochem. Mol. Biol. 2004, 37:254-259.
34. Suttle C.A. Marine viruses-major players in the global ecosystem. Nat. Rev. Microbiol. 2007, 5:801-812.