Editing Mycobacterium smegmatis (section)

==DNA repair==
''Mycobacterium smegmatis'' relies on [[DNA repair]] pathways to resist DNA damage. Double-strand breaks are especially threatening to bacterial viability.  ''M. smegmatis'' has three options for repairing double-strand breaks; [[homologous recombination]] (HR), [[non-homologous end joining]] (NHEJ), and [[Homologous recombination#SSA pathway|single-strand annealing (SSA)]].<ref name=Gupta>{{cite journal | vauthors = Gupta R, Barkan D, Redelman-Sidi G, Shuman S, Glickman MS | title = Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways | journal = Molecular Microbiology | volume = 79 | issue = 2 | pages = 316–30 | date = January 2011 | pmid = 21219454 | pmc = 3812669 | doi = 10.1111/j.1365-2958.2010.07463.x }}</ref>  The HR pathway of ''M. smegmatis'' is the major determinant of resistance to ionizing radiation and oxidative DNA damage.  This pathway involves exchange of information between a damaged chromosome and another homologous chromosome in the same cell.  It depends on the RecA protein that catalyzes strand exchange and the ADN protein that acts as a presynaptic nuclease.<ref name=Gupta />  HR is an accurate repair process and is the preferred pathway during logarithmic growth.<ref name=Pitcher>{{cite journal | vauthors = Pitcher RS, Green AJ, Brzostek A, Korycka-Machala M, Dziadek J, Doherty AJ | title = NHEJ protects mycobacteria in stationary phase against the harmful effects of desiccation | journal = DNA Repair | volume = 6 | issue = 9 | pages = 1271–6 | date = September 2007 | pmid = 17360246 | doi = 10.1016/j.dnarep.2007.02.009 | url = http://sro.sussex.ac.uk/id/eprint/1122/1/DNA_Doherty.pdf }}</ref>

The NHEJ pathway for repairing double-strand breaks involves the rejoining of the broken ends. It does not depend on a second homologous chromosome.  This pathway requires the [[Ku (protein)|Ku protein]] and a specialized poly-functional ATP-dependent DNA ligase (ligase D).<ref name=Gong>{{cite journal | vauthors = Gong C, Bongiorno P, Martins A, Stephanou NC, Zhu H, Shuman S, Glickman MS | title = Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C | journal = Nature Structural & Molecular Biology | volume = 12 | issue = 4 | pages = 304–12 | date = April 2005 | pmid = 15778718 | doi = 10.1038/nsmb915 | s2cid = 6879518 }}</ref>  NHEJ is efficient but inaccurate.  Sealing of blunt DNA ends within a functional gene sequence occurs with a mutation frequency of about 50%.<ref name=Gong />  NHEJ is the preferred pathway during stationary phase, and it protects ''M. smegmatis'' against the harmful effects of desiccation.<ref name=Pitcher />

SSA is employed as a repair pathway when a double-strand break arises between direct repeat sequences in DNA.  SSA involves single-strand resection, annealing of the repeats, flap removal, gap filling and ligation.  In ''M. smegmatis'' the SSA pathway depends on the RecBCD helicase-nuclease.<ref name=Gupta />