Bacterial DNA repair: Recent insights into the mechanism of RecBCD, AddAB and AdnAB

Nature Reviews Microbiology

Volumn 11, Issue 1, 2013, Pages 9-13

  Wigley, Dale B ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADDAB; ADENOSINE TRIPHOSPHATE; ADNAB; BACTERIAL DNA; CALCIUM; DOUBLE STRANDED DNA; ENZYME; EXODEOXYRIBONUCLEASE V; MAGNESIUM; RECOMBINASE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL TRANSLOCATION; CELL DIVISION; CRYSTAL STRUCTURE; DNA CLEAVAGE; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA STRAND; DNA TEMPLATE; ENZYME ACTIVITY; ESCHERICHIA COLI; MYCOBACTERIUM; NONHUMAN; PRIORITY JOURNAL;

BACTERIA; DNA BREAKS, DOUBLE-STRANDED; DNA REPAIR; DNA REPAIR ENZYMES; DNA, BACTERIAL; EVOLUTION, MOLECULAR; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; HOMOLOGOUS RECOMBINATION; MODELS, BIOLOGICAL; MODELS, MOLECULAR; REC A RECOMBINASES;

BACTERIA (MICROORGANISMS);

EID: 84871340015     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro2917     Document Type: Article

References (38)

1. Chapman, J. R., Taylor, M. R. & Boulton, S. J. Playing the end game: DNA double-strand break repair pathway choice. Mol. Cell 47, 497-510 (2012).
2. Lieber, M. R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79, 181-211 (2010).
3. Shuman, S. & Glickman, M. S. Bacterial DNA repair by non-homologous end joining. Nature Rev. Microbiol. 5, 852-861 (2007).
4. Chayot, R., Montagne, B., Mazel, D. & Ricchetti, M. An end-joining repair mechanism in Escherichia coli. Proc. Natl Acad. Sci. USA 107, 2141-2146 (2010).
5. Ayora, S. et al. Double-strand break repair in bacteria: A view from Bacillus subtilis. FEMS Microbiol. Rev. 35, 1055-1081 (2011).
6. Singleton, M. R., Dillingham, M. S., Gaudier, M., Kowalczykowski, S. C. & Wigley, D. B. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432, 187-193 (2004).
7. Singleton, M. R., Dillingham, M. S. & Wigley, D. B. Structure and mechanism of helicases and nucleic acid translocases. Ann. Rev. Biochem. 76, 23-50 (2007).
8. Spies, M. & Kowalczykowski, S. C. The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins. Mol. Cell 21, 573-580 (2006).
9. Taylor, A. F. & Smith, G. R. RecBC enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature 423, 869-893 (2003).
10. Dillingham, M. S., Spies, M. & Kowalczykowski, S. C. RecBCD enzyme is a bipolar DNA helicase. Nature 423, 893-897 (2003).
11. Dixon, D. A. & Kowalczykowski, S. C. The recombination hotspot chi is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell 73, 87-96 (1993).
12. Bianco, P. R. & Kowalczykowski, S. C. The recombination hot spot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5-GCTGGTGG3. Proc. Natl Acad. Sci. USA 94, 6706-6711 (1997).
13. Anderson, D. G. & Kowalczykowski, S. C. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a χregulated manner. Cell 90, 77-86 (1997).
14. Saikrishnan, K., Griffiths, S. P., Cook, N., Court, R. & Wigley, D. B. DNA binding to RecD: Role of the 1B domain in SF1B helicase activity. EMBO J. 27, 2222-2229 (2008).
15. Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramanya, H. S. & Wigley, D. B. Crystal structures of complexes of PcrA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84 (1999).
16. Saikrishnan, K., Powell, B., Cook, N. J., Webb, M. R. & Wigley, D. B. Mechanistic basis of 53 translocation in SF1B helicases. Cell 137, 849-859 (2009).
17. Smith, G. R. How RecBCD enzyme and Chi promote DNA break repair and recombination: A molecular biologist's view. Microbiol. Mol. Biol. Rev. 76, 217-228 (2012).
18. Farah, J. A. & Smith, G. R. The RecBCD enzyme initiation complex for DNA unwinding: Enzyme positioning and DNA opening. J. Mol. Biol. 272, 699-715 (1997).
19. Wu, C. G., Bradford, C. & Lohman, T. M. Escherichia coli RecBC helicase has two translocase activities controlled by a single ATPase motor. Nature Struct. Mol. Biol. 17, 1210-1217 (2010).
20. Wu, C. G., Xie, F. & Lohman, T. M. The primary and secondary translocase activities within E. coli RecBC helicase are tightly coupled to ATP hydrolysis by the RecB motor. J. Mol. Biol. 423, 303-314 (2012).
21. Spies, M. et al. A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114, 647-654 (2003).
22. Spies, M., Amitani, I., Baskin, R. J. & Kowalczykowski, S. C. RecBCD enzyme switches lead motor subunits in response to χ recognition. Cell 131, 694-705 (2007).
23. Handa, N., Bianco, P. R., Baskin, R. J. & Kowalczykowski, S. C. Direct visualization of RecBCD movement reveals cotranslocation of the RecD motor after chi recognition. Mol. Cell 17, 745-750 (2005).
24. Handa, N. et al. Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme. Proc. Natl Acad. Sci. USA 109, 8901-8906 (2012).
25. Yang, L. et al. Alteration of χ recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control. Proc. Natl Acad. Sci. USA 109, 8907-8912 (2012).
26. Chiota;din, F., Noirot, P., Biaudet, V. & Ehrlich, S. D. A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis. Mol. Microbiol. 29, 1369-1377 (1998).
27. Chiota;din, F., Handa, N., Dillingham, M. S. & Kowalczykowski, S. C. The AddAB helicase/nuclease forms a stable complex with its cognate χ sequence during translocation. J. Biol. Chem. 281, 18610-18617 (2006).
28. Saikrishnan, K. et al. Insights into Chi recognition from the structure of an AddAB-type helicaseYnuclease complex. EMBO J. 31, 1568-1578 (2012).
29. Yeeles, J. T., Gwynn, E. J., Webb, M. R. & Dillingham, M. S. The AddAB helicase-nuclease catalyses rapid and processive DNA unwinding using a single Superfamily 1A motor domain. Nucleic Acids Res. 39, 2271-2285 (2011).
30. Yeeles, J. T. & Dillingham, M. S. A dual-nuclease mechanism for DNA break processing by AddAB-type helicase-nucleases. J. Mol. Biol. 371, 66-78 (2007).
31. Yeeles, J. T., van Aelst, K., Dillingham, M. S. & Moreno-Herrero, F. Recombination hotspots and single-stranded DNA binding proteins couple DNA translocation to DNA unwinding by the AddAB helicase-nuclease. Mol. Cell 42, 806-816 (2011).
32. Sinha, K. M., Unciuleac, M. C., Glickman, M. S. & Shuman, S. AdnAB: A new DSB-resecting motorY nuclease from mycobacteria. Genes Dev. 23, 1423-1437 (2009).
33. Unciuleac, M. C. & Shuman, S. Characterization of the mycobacterial AdnAB DNA motor provides insights into the evolution of bacterial motor-nuclease machines. J. Biol. Chem. 285, 2632-2641 (2010).
34. Unciuleac, M. C. & Shuman, S. Double strand break unwinding and resection by the mycobacterial helicase-nuclease AdnAB in the presence of single strand DNA-binding protein (SSB). J. Biol. Chem. 285, 34319-34329 (2010).
35. Lam, S. T., Stahl, M. M., McMilin, K. D. & Stahl, F. W. Rec-mediated recombinational hot spot activity in bacteriophage lambda. II. A mutation which causes hot spot activity. Genetics 77, 425-433 (1974).
36. Halpern, D. et al. Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling. PLoS Genet. 3, 1614-1621 (2007).
37. Dixon, D. A., Churchill, J. J. & Kowalczykowski, S. C. Reversible inactivation of the Escherichia coli RecBCD enzyme by the recombination hotspot χ in vitro: Evidence for functional inactivation or loss of the RecD subunit. Proc. Natl Acad. Sci. USA 91, 2980-2984 (1994).
38. Korolev, S., Hsieh, J., Gauss, G. H., Lohman, T. M. & Waksman, G. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635-647 (1997).