Chapter 31 : Double-Strand DNA Break Repair in Mycobacteria

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Double-Strand DNA Break Repair in Mycobacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818845/9781555818838_Chap31-1.gif /docserver/preview/fulltext/10.1128/9781555818845/9781555818838_Chap31-2.gif


Repair of double-strand DNA breaks (DSBs) is critical to all living organisms. Scission of the phosphodiester backbone of both DNA strands is lethal if not repaired because such loss of linear chromosome integrity compromises chromosome replication and thereby prevents genome duplication. In contrast to some other types of DNA lesions which can be bypassed by damage-tolerant DNA polymerases, there is no known mechanism for the replication or transcription machinery to bypass a DSB, mandating their repair before replication or transcription can proceed. As such, multiple systems have evolved to repair DSBs, from bacterial to human cells ( ). In the past decade, mycobacterial DNA repair systems in general, and mycobacterial DSB repair systems in particular, have received increasing attention. It has become clear that mycobacterial DSB repair differs substantially from the standard models of prokaryotic DSB repair derived from work in the system. Most prominent among these differences is the existence of two additional DSB repair pathways that are not present in and were previously thought not to exist in bacteria: nonhomologous end joining (NHEJ) and single-strand annealing (SSA). Multiple other novel features of mycobacterial DSB repair have also been elucidated, making mycobacteria a new model system for the study of prokaryotic DSB repair. As now conceptualized, mycobacterial DSB repair actually most resembles DSB repair in budding yeast rather than other prokaryotes ( Table 1 ). In addition to its emerging place as a model system, studies of mycobacterial DNA repair also are of great importance for understanding mechanisms of mutagenesis and genome diversification in , the ultimate cause of antimicrobial resistance in ( ). In addition to the information and references contained in this article, the reader is pointed to several excellent recently published reviews of mycobacterial DNA repair and mutagenesis ( ).

Citation: Glickman M. 2014. Double-Strand DNA Break Repair in Mycobacteria, p 657-666. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0024-2013
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Pathways of DSB repair in mycobacteria. Our present understanding of DSB repair in mycobacteria. The three pathways shown are HR, NHEJ, and SSA. For each pathway, the major DNA processing events are depicted with the factors required for each step, when known. A question mark indicates that no specific experimental genetic data is available about that step, despite the presence of predicted proteins in mycobacterial chromosomes that may mediate these steps, or even biochemical activities consistent with a role in these pathways. In the NHEJ column the three outcomes below the arrow indicate faithful repair, nucleotide addition, and nucleotide trimming, respectively. In the SSA column, the blue rectangles indicate repeat sequences that flank the DSB. Please see text for further details and references.

Citation: Glickman M. 2014. Double-Strand DNA Break Repair in Mycobacteria, p 657-666. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0024-2013
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Daley JM,, Palmbos PL,, Wu D,, Wilson TE . 2005. Nonhomologous end joining in yeast. Annu Rev Genet 39 : 431 451.[PubMed][CrossRef]
2. Dillingham MS,, Kowalczykowski SC . 2008. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev 72 : 642 671.[PubMed][CrossRef]
3. Lieber MR . 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79 : 181 211.[PubMed][CrossRef]
4. Shuman S,, Glickman MS . 2007. Bacterial DNA repair by nonhomologous end joining. Nat Rev Microbiol 5 : 852 861.[PubMed][CrossRef]
5. Symington LS,, Gautier J . 2011. Double-strand break end resection and repair pathway choice. Annu Rev Genet 45 : 247 271.[PubMed][CrossRef]
6. Yeeles JT,, Dillingham MS . 2010. The processing of double-stranded DNA breaks for recombinational repair by helicase-nuclease complexes. DNA Repair 9 : 276 285.[PubMed][CrossRef]
7. Ford CB,, Shah RR,, Maeda MK,, Gagneux S,, Murray MB,, Cohen T,, Johnston JC,, Gardy J,, Lipsitch M,, Fortune SM . 2013. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet 45 : 784 790.[PubMed][CrossRef]
8. Warner DF,, Tonjum T,, Mizrahi V . 2013. DNA metabolism in mycobacterial pathogenesis. Curr Top Microbiol Immunol 374 : 27 51.[PubMed][CrossRef]
9. Kurthkoti K,, Varshney U . 2012. Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth. Mech Ageing Dev 133 : 138 146.[PubMed][CrossRef]
10. Gorna AE,, Bowater RP,, Dziadek J . 2010. DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: varying activities at different stages of infection. Clin Sci 119 : 187 202.[PubMed][CrossRef]
11. Reijns MA,, Rabe B,, Rigby RE,, Mill P,, Astell KR,, Lettice LA,, Boyle S,, Leitch A,, Keighren M,, Kilanowski F,, Devenney PS,, Sexton D,, Grimes G,, Holt IJ,, Hill RE,, Taylor MS,, Lawson KA,, Dorin JR,, Jackson AP . 2012. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149 : 1008 1022.[PubMed][CrossRef]
12. Hiller B,, Achleitner M,, Glage S,, Naumann R,, Behrendt R,, Roers A . 2012. Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity. J Exp Med 209 : 1419 1426.[PubMed][CrossRef]
13. Wigley DB . 2013. Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 11 : 9 13.[PubMed][CrossRef]
14. Gupta R,, Barkan D,, Redelman-Sidi G,, Shuman S,, Glickman MS . 2011. Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways. Mol Microbiol 79 : 316 330.[PubMed][CrossRef]
15. Stephanou NC,, Gao F,, Bongiorno P,, Ehrt S,, Schnappinger D,, Shuman S,, Glickman MS . 2007. Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks. J Bacteriol 189 : 5237 5246.[PubMed][CrossRef]
16. Sinha KM,, Unciuleac MC,, Glickman MS,, Shuman S . 2009. AdnAB: a new DSB-resecting motor-nuclease from mycobacteria. Genes Dev 23 : 1423 1437.[PubMed][CrossRef]
17. Fernandez S,, Kobayashi Y,, Ogasawara N,, Alonso JC . 1999. Analysis of the Bacillus subtilis recO gene: RecO forms part of the RecFLOR function. Mol Gen Genet 261 : 567 573.[PubMed][CrossRef]
18. Gupta R,, Ryzhikov M,, Koroleva O,, Unciuleac M,, Shuman S,, Korolev S,, Glickman MS . 2013. A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing. Nucleic Acids Res 41 : 2284 2295.[PubMed][CrossRef]
19. Patil KN,, Singh P,, Muniyappa K . 2011. DNA binding, coprotease, and strand exchange activities of mycobacterial RecA proteins: implications for functional diversity among RecA nucleoprotein filaments. Biochemistry 50 : 300 311.[PubMed][CrossRef]
20. Ganesh N,, Muniyappa K . 2003. Characterization of DNA strand transfer promoted by Mycobacterium smegmatis RecA reveals functional diversity with Mycobacterium tuberculosis RecA. Biochemistry 42 : 7216 7225.[PubMed][CrossRef]
21. Datta S,, Krishna R,, Ganesh N,, Chandra NR,, Muniyappa K,, Vijayan M . 2003. Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes. J Bacteriol 185 : 4280 4284.[PubMed][CrossRef]
22. Reddy MS,, Guhan N,, Muniyappa K . 2001. Characterization of single-stranded DNA-binding proteins from mycobacteria. The carboxyl-terminal of domain of SSB is essential for stable association with its cognate RecA protein. J Biol Chem 276 : 45959 45968.[PubMed][CrossRef]
23. Dawson LF,, Dillury J,, Davis EO . 2010. RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. J Bacteriol 192 : 599 603.[PubMed][CrossRef]
24. Yang M,, Gao C,, Cui T,, An J,, He ZG . 2012. A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis. Nucleic Acids Res 40 : 1009 1020.[PubMed][CrossRef]
25. Davis EO,, Springer B,, Gopaul KK,, Papavinasasundaram KG,, Sander P,, Bottger EC . 2002. DNA damage induction of recA in Mycobacterium tuberculosis independently of RecA and LexA. Mol Microbiol 46 : 791 800.[PubMed][CrossRef]
26. Davis EO,, Dullaghan EM,, Rand L . 2002. Definition of the mycobacterial SOS box and use to identify LexA-regulated genes in Mycobacterium tuberculosis. J Bacteriol 184 : 3287 3295.[PubMed][CrossRef]
27. Brooks PC,, Movahedzadeh F,, Davis EO . 2001. Identification of some DNA damage-inducible genes of Mycobacterium tuberculosis: apparent lack of correlation with LexA binding. J Bacteriol 183 : 4459 4467.[PubMed][CrossRef]
28. Thakur RS,, 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.[PubMed][CrossRef]
29. Prabu JR,, Thamotharan S,, Khanduja JS,, Alipio EZ,, Kim CY,, Waldo GS,, Terwilliger TC,, Segelke B,, Lekin T,, Toppani D,, Hung LW,, Yu M,, Bursey E,, Muniyappa K,, Chandra NR,, Vijayan M . 2006. Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 : 731 734.[PubMed][CrossRef]
30. Khanduja JS,, Muniyappa K . 2012. Functional analysis of DNA replication fork reversal catalyzed by Mycobacterium tuberculosis RuvAB proteins. J Biol Chem 287 : 1345 1360.[PubMed][CrossRef]
31. Khanduja JS,, Tripathi P,, Muniyappa K . 2009. Mycobacterium tuberculosis RuvA induces two distinct types of structural distortions between the homologous and heterologous Holliday junctions. Biochemistry 48 : 27 40.[PubMed][CrossRef]
32. Aravind L,, Koonin EV . 2001. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res 11 : 1365 1374.[PubMed][CrossRef]
33. Nandakumar J,, Nair PA,, Shuman S . 2007. Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell 26 : 257 271.[PubMed][CrossRef]
34. Della M,, Palmbos PL,, Tseng HM,, Tonkin LM,, Daley JM,, Topper LM,, Pitcher RS,, Tomkinson AE,, Wilson TE,, Doherty AJ . 2004. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science 306 : 683 685.[PubMed][CrossRef]
35. Weller GR,, Kysela B,, Roy R,, Tonkin LM,, Scanlan E,, Della M,, Devine SK,, Day JP,, Wilkinson A,, d’Adda di Fagagna F,, Devine KM,, Bowater RP,, Jeggo PA,, Jackson SP,, Doherty AJ . 2002. Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297 : 1686 1689.[PubMed][CrossRef]
36. Aniukwu J,, Glickman MS,, Shuman S . 2008. The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends. Genes Dev 22 : 512 527.[PubMed][CrossRef]
37. Gong C,, Bongiorno P,, Martins A,, Stephanou NC,, Zhu H,, Shuman S,, Glickman MS . 2005. Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C. Nat Struct Mol Biol 12 : 304 312.[PubMed][CrossRef]
38. Gong C,, Martins A,, Bongiorno P,, Glickman M,, Shuman S . 2004. Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 279 : 20594 20606.[PubMed][CrossRef]
39. Wang ST,, Setlow B,, Conlon EM,, Lyon JL,, Imamura D,, Sato T,, Setlow P,, Losick R,, Eichenberger P . 2006. The forespore line of gene expression in Bacillus subtilis. J Mol Biol 358 : 16 37.[PubMed][CrossRef]
40. Pitcher RS,, Green AJ,, Brzostek A,, Korycka-Machala M,, Dziadek J,, Doherty AJ . 2007. NHEJ protects mycobacteria in stationary phase against the harmful effects of desiccation. DNA Repair 6 : 1271 1276.[PubMed][CrossRef]
41. Akey D,, Martins A,, Aniukwu J,, Glickman MS,, Shuman S,, Berger JM . 2006. Crystal structure and nonhomologous end-joining function of the ligase component of mycobacterium DNA ligase D. J Biol Chem 281 : 13412 13423.[PubMed][CrossRef]
42. Pitcher RS,, Brissett NC,, Picher AJ,, Andrade P,, Juarez R,, Thompson D,, Fox GC,, Blanco L,, Doherty AJ . 2007. Structure and function of a mycobacterial NHEJ DNA repair polymerase. J Mol Biol 366 : 391 405.[PubMed][CrossRef]
43. Zhu H,, Nandakumar J,, Aniukwu J,, Wang LK,, Glickman MS,, Lima CD,, Shuman S . 2006. Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D. Proc Natl Acad Sci USA 103 : 1711 1716.[PubMed][CrossRef]
44. Bebenek K,, Garcia-Diaz M,, Patishall SR,, Kunkel TA . 2005. Biochemical properties of Saccharomyces cerevisiae DNA polymerase IV. J Biol Chem 280 : 20051 20058.[PubMed][CrossRef]
45. Brissett NC,, Pitcher RS,, Juarez R,, Picher AJ,, Green AJ,, Dafforn TR,, Fox GC,, Blanco L,, Doherty AJ . 2007. Structure of a NHEJ polymerase-mediated DNA synaptic complex. Science 318 : 456 459.[PubMed][CrossRef]
46. Nair PA,, Smith P,, Shuman S . 2010. Structure of bacterial LigD 3′-phosphoesterase unveils a DNA repair superfamily. Proc Natl Acad Sci USA 107 : 12822 12827.[PubMed][CrossRef]
47. Zhu H,, Shuman S . 2006. Substrate specificity and structure-function analysis of the 3′-phosphoesterase component of the bacterial NHEJ protein, DNA ligase D. J Biol Chem 281 : 13873 13881.[PubMed][CrossRef]
48. Zhu H,, Wang LK,, Shuman S . 2005. Essential constituents of the 3′-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme. J Biol Chem 280 : 33707 33715.[PubMed][CrossRef]
49. Zhu H,, Shuman S . 2005. Novel 3′-ribonuclease and 3′-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D. J Biol Chem 280 : 25973 25981.[PubMed][CrossRef]
50. Zhu H,, Bhattarai H,, Yan HG,, Shuman S,, Glickman MS . 2012. Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D. Biochemistry 51 : 10147 10158.[PubMed][CrossRef]
51. Sinha KM,, Stephanou NC,, Gao F,, Glickman MS,, Shuman S . 2007. Mycobacterial UvrD1 is a Ku-dependent DNA helicase that plays a role in multiple DNA repair events, including double-strand break repair. J Biol Chem 282 : 15114 15125.[PubMed][CrossRef]
52. Li Z,, Wen J,, Lin Y,, Wang S,, Xue P,, Zhang Z,, Zhou Y,, Wang X,, Sui L,, Bi LJ,, Zhang XE . 2011. A Sir2-like protein participates in mycobacterial NHEJ. PloS One 6 : e20045. [PubMed][CrossRef]
53. Ivanov EL,, Sugawara N,, Fishman-Lobell J,, Haber JE . 1996. Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae. Genetics 142 : 693 704.[PubMed]
54. McEvoy CR,, Cloete R,, Muller B,, Schurch AC,, van Helden PD,, Gagneux S,, Warren RM,, Gey van Pittius NC . 2012. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PloS One 7 : e30593. [PubMed][CrossRef]
55. McEvoy CR,, van Helden PD,, Warren RM,, Gey van Pittius NC . 2009. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region. BMC Evol Biol 9 : 237. [PubMed][CrossRef]
56. Talarico S,, Cave MD,, Marrs CF,, Foxman B,, Zhang L,, Yang Z . 2005. Variation of the Mycobacterium tuberculosis PE_PGRS 33 gene among clinical isolates. J Clin Microbiol 43 : 4954 4960.[PubMed][CrossRef]
57. Talarico S,, Zhang L,, Marrs CF,, Foxman B,, Cave MD,, Brennan MJ,, Yang Z . 2008. Mycobacterium tuberculosis PE_PGRS16 and PE_PGRS26 genetic polymorphism among clinical isolates. Tuberculosis 88 : 283 294.[PubMed][CrossRef]
58. Wojcik EA,, Brzostek A,, Bacolla A,, Mackiewicz P,, Vasquez KM,, Korycka-Machala M,, Jaworski A,, Dziadek J . 2012. Direct and inverted repeats elicit genetic instability by both exploiting and eluding DNA double-strand break repair systems in mycobacteria. PloS One 7 : e51064. [PubMed][CrossRef]
59. Darwin KH,, Ehrt S,, Gutierrez-Ramos JC,, Weich N,, Nathan CF . 2003. The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide. Science 302 : 1963 1966.[PubMed][CrossRef]
60. Darwin KH,, Nathan CF . 2005. Role for nucleotide excision repair in virulence of Mycobacterium tuberculosis. Infect Immun 73 : 4581 4587.[PubMed][CrossRef]
61. Houghton J,, Townsend C,, Williams AR,, Rodgers A,, Rand L,, Walker KB,, Bottger EC,, Springer B,, Davis EO . 2012. Important role for Mycobacterium tuberculosis UvrD1 in pathogenesis and persistence apart from its function in nucleotide excision repair. J Bacteriol 194 : 2916 2923.[PubMed][CrossRef]
62. Sinha KM,, Stephanou NC,, Unciuleac MC,, Glickman MS,, Shuman S . 2008. Domain requirements for DNA unwinding by mycobacterial UvrD2, an essential DNA helicase. Biochemistry 47 : 9355 9364.[PubMed][CrossRef]
63. Williams A,, Guthlein C,, Beresford N,, Bottger EC,, Springer B,, Davis EO . 2011. UvrD2 is essential in Mycobacterium tuberculosis, but its helicase activity is not required. J Bacteriol 193 : 4487 4494.[PubMed][CrossRef]
64. Boshoff HI,, Reed MB,, Barry CE 3rd,, Mizrahi V . 2003. DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 113 : 183 193.[CrossRef]
65. Sander P,, Papavinasasundaram KG,, Dick T,, Stavropoulos E,, Ellrott K,, Springer B,, Colston MJ,, Bottger EC . 2001. Mycobacterium bovis BCG recA deletion mutant shows increased susceptibility to DNA-damaging agents but wild-type survival in a mouse infection model. Infect Immun 69 : 3562 3568.[PubMed][CrossRef]
66. Harper J,, Skerry C,, Davis SL,, Tasneen R,, Weir M,, Kramnik I,, Bishai WR,, Pomper MG,, Nuermberger EL,, Jain SK . 2012. Mouse model of necrotic tuberculosis granulomas develops hypoxic lesions. J Infect Dis 205 : 595 602.[PubMed][CrossRef]
67. Gill WP,, Harik NS,, Whiddon MR,, Liao RP,, Mittler JE,, Sherman DR . 2009. A replication clock for Mycobacterium tuberculosis. Nat Med 15 : 211 214.[PubMed][CrossRef]
68. Kana BD,, Abrahams GL,, Sung N,, Warner DF,, Gordhan BG,, Machowski EE,, Tsenova L,, Sacchettini JC,, Stoker NG,, Kaplan G,, Mizrahi V . 2010. Role of the DinB homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis. J Bacteriol 192 : 2220 2227.[PubMed][CrossRef]
69. Ford CB,, Lin PL,, Chase MR,, Shah RR,, Iartchouk O,, Galagan J,, Mohaideen N,, Ioerger TR,, Sacchettini JC,, Lipsitch M,, Flynn JL,, Fortune SM . 2011. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet 43 : 482 486.[PubMed][CrossRef]


Generic image for table
Table 1

Comparison of DSB repair systems in bacteria and yeast

Citation: Glickman M. 2014. Double-Strand DNA Break Repair in Mycobacteria, p 657-666. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0024-2013

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error