Editor's Choice Effects of conserved residues and naturally occurring mutations on Mycobacterium tuberculosis RecG helicase activity

References

1. Arnold K., Bordoli L., Kopp J., Schwede T. ( 2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201 [View Article][PubMed]
   [Google Scholar]
2. Asai T., Kogoma T. ( 1994). Roles of ruvA, ruvC and recG gene functions in normal and DNA damage-inducible replication of the Escherichia coli chromosome. Genetics 137:895–902[PubMed]
   [Google Scholar]
3. Bifani P. J., Mathema B., Kurepina N. E., Kreiswirth B. N. ( 2002). Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol 10:45–52 [View Article][PubMed]
   [Google Scholar]
4. Briggs G. S., Mahdi A. A., Wen Q., Lloyd R. G. ( 2005). DNA binding by the substrate specificity (wedge) domain of RecG helicase suggests a role in processivity. J Biol Chem 280:13921–13927 [View Article][PubMed]
   [Google Scholar]
5. Brosh R. M. Jr, Opresko P. L., Bohr V. A. ( 2006). Enzymatic mechanism of the WRN helicase/nuclease. Methods Enzymol 409:52–85 [View Article][PubMed]
   [Google Scholar]
6. Cordin O., Tanner N. K., Doère M., Linder P., Banroques J. ( 2004). The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity. EMBO J 23:2478–2487 [View Article][PubMed]
   [Google Scholar]
7. Deyrup A. T., Krishnan S., Cockburn B. N., Schwartz N. B. ( 1998). Deletion and site-directed mutagenesis of the ATP-binding motif (P-loop) in the bifunctional murine ATP-sulfurylase/adenosine 5′-phosphosulfate kinase enzyme. J Biol Chem 273:9450–9456 [View Article][PubMed]
   [Google Scholar]
8. Dos Vultos T., Mestre O., Rauzier J., Golec M., Rastogi N., Rasolofo V., Tonjum T., Sola C., Matic I., Gicquel B. ( 2008). Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis.. PLoS ONE 3:e1538 [View Article][PubMed]
   [Google Scholar]
9. Dos Vultos T., Mestre O., Tønjum T., Gicquel B. ( 2009). DNA repair in Mycobacterium tuberculosis revisited. FEMS Microbiol Rev 33:471–487 [View Article][PubMed]
   [Google Scholar]
10. Ebrahimi-Rad M., Bifani P., Martin C., Kremer K., Samper S., Rauzier J., Kreiswirth B., Blazquez J., Jouan M. & other authors ( 2003). Mutations in putative mutator genes of Mycobacterium tuberculosis strains of the W-Beijing family. Emerg Infect Dis 9:838–845 [View Article][PubMed]
    [Google Scholar]
11. Edgar R. C. ( 2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
12. Ehrt S., Schnappinger D. ( 2009). Mycobacterial survival strategies in the phagosome: defence against host stresses. Cell Microbiol 11:1170–1178 [View Article][PubMed]
    [Google Scholar]
13. Elles L. M., Uhlenbeck O. C. ( 2008). Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype. Nucleic Acids Res 36:41–50 [View Article][PubMed]
    [Google Scholar]
14. European Concerted Action on New Generation Genetic Markers and Techniques for the Epidemiology and Control of Tuberculosis ( 2006). Beijing/W genotype Mycobacterium tuberculosis and drug resistance. Emerg Infect Dis 12:736–743 [View Article][PubMed]
    [Google Scholar]
15. Filliol I., Motiwala A. S., Cavatore M., Qi W., Hazbón M. H., Bobadilla del Valle M., Fyfe J., García-García L., Rastogi N. & other authors ( 2006). Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 188:759–772 [View Article][PubMed]
    [Google Scholar]
16. Gagneux S. ( 2009). Strain variation and evolution. Mycobacteria: Genomics and Molecular Biology1–18 Parish T., Brown A. Norwich: Caister Academic Press;
    [Google Scholar]
17. Gamulin V., Cetkovic H., Ahel I. ( 2004). Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis. FEMS Microbiol Lett 238:57–63[PubMed]
    [Google Scholar]
18. Gorbalenya A. E., Koonin E. V. ( 1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419–429 [View Article]
    [Google Scholar]
19. Gorna A. E., Bowater R. P., Dziadek J. ( 2010). DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection. Clin Sci (Lond) 119:187–202 [View Article][PubMed]
    [Google Scholar]
20. Hall M. C., Matson S. W. ( 1999). Helicase motifs: the engine that powers DNA unwinding. Mol Microbiol 34:867–877 [View Article][PubMed]
    [Google Scholar]
21. Kornberg A., Scott J. F., Bertsch L. L. ( 1978). ATP utilization by rep protein in the catalytic separation of DNA strands at a replicating fork. J Biol Chem 253:3298–3304[PubMed]
    [Google Scholar]
22. Lloyd R. G., Sharples G. J. ( 1993). Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J 12:17–22[PubMed]
    [Google Scholar]
23. Lohman T. M., Tomko E. J., Wu C. G. ( 2008). Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 9:391–401 [View Article][PubMed]
    [Google Scholar]
24. Mahdi A. A., Briggs G. S., Sharples G. J., Wen Q., Lloyd R. G. ( 2003). A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins. EMBO J 22:724–734 [View Article][PubMed]
    [Google Scholar]
25. Mahdi A. A., Briggs G. S., Lloyd R. G. ( 2012). Modulation of DNA damage tolerance in Escherichia coli recG and ruv strains by mutations affecting PriB, the ribosome and RNA polymerase. Mol Microbiol 86:675–691 [View Article][PubMed]
    [Google Scholar]
26. McGlynn P., Lloyd R. G. ( 2002). Genome stability and the processing of damaged replication forks by RecG. Trends Genet 18:413–419 [View Article][PubMed]
    [Google Scholar]
27. McGlynn P., Mahdi A. A., Lloyd R. G. ( 2000). Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res 28:2324–2332 [View Article][PubMed]
    [Google Scholar]
28. Mestre O., Luo T., Dos Vultos T., Kremer K., Murray A., Namouchi A., Jackson C., Rauzier J., Bifani P. & other authors ( 2011). Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair. PLoS ONE 6:e16020 [View Article][PubMed]
    [Google Scholar]
29. Myong S., Bruno M. M., Pyle A. M., Ha T. ( 2007). Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science 317:513–516 [View Article][PubMed]
    [Google Scholar]
30. O’Reilly E. K., Kreuzer K. N. ( 2004). Isolation of SOS constitutive mutants of Escherichia coli. J Bacteriol 186:7149–7160 [View Article][PubMed]
    [Google Scholar]
31. Pause A., Sonenberg N. ( 1992). Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A. EMBO J 11:2643–2654[PubMed]
    [Google Scholar]
32. Pyle A. M. ( 2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 37:317–336 [View Article][PubMed]
    [Google Scholar]
33. Rachman H., Strong M., Ulrichs T., Grode L., Schuchhardt J., Mollenkopf H., Kosmiadi G. A., Eisenberg D., Kaufmann S. H. ( 2006). Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect Immun 74:1233–1242 [View Article][PubMed]
    [Google Scholar]
34. Ramaswamy S. V., Reich R., Dou S. J., Jasperse L., Pan X., Wanger A., Quitugua T., Graviss E. A. ( 2003). Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 47:1241–1250 [View Article][PubMed]
    [Google Scholar]
35. Rudolph C. J., Upton A. L., Harris L., Lloyd R. G. ( 2009a). Pathological replication in cells lacking RecG DNA translocase. Mol Microbiol 73:352–366 [View Article][PubMed]
    [Google Scholar]
36. Rudolph C. J., Upton A. L., Lloyd R. G. ( 2009b). Replication fork collisions cause pathological chromosomal amplification in cells lacking RecG DNA translocase. Mol Microbiol 74:940–955 [View Article][PubMed]
    [Google Scholar]
37. Rudolph C. J., Upton A. L., Briggs G. S., Lloyd R. G. ( 2010). Is RecG a general guardian of the bacterial genome. DNA Repair (Amst) 9:210–223 [View Article][PubMed]
    [Google Scholar]
38. Sayers E. W., Barrett T., Benson D. A., Bolton E., Bryant S. H., Canese K., Chetvernin V., Church D. M., Dicuccio M. & other authors ( 2012). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40:Database issueD13–D25 [View Article][PubMed]
    [Google Scholar]
39. Schnappinger D., Ehrt S., Voskuil M. I., Liu Y., Mangan J. A., Monahan I. M., Dolganov G., Efron B., Butcher P. D. & other authors ( 2003). Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Exp Med 198:693–704 [View Article][PubMed]
    [Google Scholar]
40. Sharples G. J., Whitby M. C., Ryder L., Lloyd R. G. ( 1994). A mutation in helicase motif III of E. coli RecG protein abolishes branch migration of Holliday junctions. Nucleic Acids Res 22:308–313 [View Article][PubMed]
    [Google Scholar]
41. Sharples G. J., Ingleston S. M., Lloyd R. G. ( 1999). Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol 181:5543–5550[PubMed]
    [Google Scholar]
42. Singleton M. R., Scaife S., Wigley D. B. ( 2001). Structural analysis of DNA replication fork reversal by RecG. Cell 107:79–89 [View Article][PubMed]
    [Google Scholar]
43. Smollett K. L., Smith K. M., Kahramanoglou C., Arnvig K. B., Buxton R. S., Davis E. O. ( 2012). Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis. J Biol Chem 287:22004–22014 [View Article][PubMed]
    [Google Scholar]
44. Stallings C. L., Glickman M. S. ( 2010). Is Mycobacterium tuberculosis stressed out? A critical assessment of the genetic evidence. Microbes Infect 12:1091–1101 [View Article][PubMed]
    [Google Scholar]
45. Tanner N. K., Cordin O., Banroques J., Doère M., Linder P. ( 2003). The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol Cell 11:127–138 [View Article][PubMed]
    [Google Scholar]
46. Telenti A., Imboden P., Marchesi F., Matter L., Schopfer K., Bodmer T., Lowrie D., Colston M. J., Cole S. ( 1993). Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet 341:647–651 [View Article][PubMed]
    [Google Scholar]
47. Thakur R. S., Basavaraju S., Somyajit K., Jain A., Subramanya S., Muniyappa K., Nagaraju G. ( 2013). Evidence for the role of Mycobacterium tuberculosis RecG helicase in DNA repair and recombination. FEBS J 280:1841–1860 [View Article][PubMed]
    [Google Scholar]
48. Tuteja N., Tuteja R. ( 2004). Unraveling DNA helicases. Motif, structure, mechanism and function. Eur J Biochem 271:1849–1863 [View Article][PubMed]
    [Google Scholar]
49. Velankar S. S., Soultanas P., Dillingham M. S., Subramanya H. S., Wigley D. B. ( 1999). Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97:75–84 [View Article][PubMed]
    [Google Scholar]
50. Voskuil M. I., Bartek I. L., Visconti K., Schoolnik G. K. ( 2011). The response of Mycobacterium tuberculosis to reactive oxygen and nitrogen species. Front Microbiol 2:105 [View Article][PubMed]
    [Google Scholar]
51. Warner D. F., Tønjum T., Mizrahi V. ( 2013). DNA metabolism in mycobacterial pathogenesis. Curr Top Microbiol Immunol [View Article][PubMed]
    [Google Scholar]
52. Waterhouse A. M., Procter J. B., Martin D. M., Clamp M., Barton G. J. ( 2009). Jalview Version 2 – a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191 [View Article][PubMed]
    [Google Scholar]
53. Whitby M. C., Lloyd R. G. ( 1998). Targeting Holliday junctions by the RecG branch migration protein of Escherichia coli. J Biol Chem 273:19729–19739 [View Article][PubMed]
    [Google Scholar]
54. WHO ( 2011). Global Tuberculosis Control 2011 Geneva: World Health Organization;
    [Google Scholar]
55. WHO ( 2012). Global Tuberculosis Report 2012 Geneva: World Health Organization;
    [Google Scholar]
56. Wu Y., Sommers J. A., Loiland J. A., Kitao H., Kuper J., Kisker C., Brosh R. M. Jr ( 2012). The Q motif of Fanconi anemia group J protein (FANCJ) DNA helicase regulates its dimerization, DNA binding, and DNA repair function. J Biol Chem 287:21699–21716 [View Article][PubMed]
    [Google Scholar]
57. Zaczek A., Brzostek A., Augustynowicz-Kopec E., Zwolska Z., Dziadek J. ( 2009). Genetic evaluation of relationship between mutations in rpoB and resistance of Mycobacterium tuberculosis to rifampin. BMC Microbiol 9:10 [View Article][PubMed]
    [Google Scholar]
58. Zegeye E. D., Balasingham S. V., Laerdahl J. K., Homberset H., Tønjum T. ( 2012). Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions. Microbiology 158:1982–1993 [View Article][PubMed]
    [Google Scholar]