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A.M. Turgimbayeva

National Center for Biotechnology, Korgalzhyn hwy, 13/5, Astana, 010000, Kazakhstan
L.N. Gumilyov Eurasian National University, Satpayev Street, 2, Astana, 010000, Kazakhstan

S.K. Abeldenov

National Center for Biotechnology, Korgalzhyn hwy, 13/5, Astana, 010000, Kazakhstan

D.G. Akhmetova

Republican Diagnostic Center, Syganak Street, 2, Astana, 010000, Kazakhstan

M.K. Saparbayev

Institute of Gustav Roussy, CNRS UMR 8200, 114 Rue Edouard Vaillant, Villejuif, 94805, France

Y.M. Ramankulov

National Center for Biotechnology, Korgalzhyn hwy, 13/5, Astana, 010000, Kazakhstan

B.B. Khassenov

National Center for Biotechnology, Korgalzhyn hwy, 13/5, Astana, 010000, Kazakhstan


Studies on bacterial DNA repair mechanisms have historically been carried out in Escherichia coli as the model system. However, evidence is accumulating that DNA repair mechanisms in other bacterial species may differ fundamentally from those of E. coli. Pathogens such as Mycobacterium tuberculosis, Helicobacter pylori, and Staphylococcus aureus have evolved various DNA repair mechanisms that help them to persist. When bacterial pathogens enter the human body they are exposed to a range of host defense mechanisms, such as the formation of reactive oxygen species and reactive nitrogen intermediates that can induce mutations in their genomes. Bacterial infections can induce a range of pathogenic diseases, and each of the causative bacterial species has characteristic DNA repair mechanisms. The study of the functions and biological roles of DNA repair enzymes is very important for understanding bacterial persistence in the human body. Moreover, repair enzymes might be potentially new targets for therapeutic agents. In this study, the DNA repair mechanisms of various human pathogens are described.


DNA repair, Mycobacterium tuberculosis, Helicobacter pylori, Staphylococcus aureus

Article Details


Seeberg E., Eide L., Bjoras M. The base excision repair pathway. Trends Biochem Sci., 1995, vol. 20, no. 1, pp. 391-397.

Lindahl T. New class of enzymes acting on damaged DNA. Nature, 1976, vol. 259, no. 5538, pp. 64-66.

Abeldenov S., Talhaoui I., Zharkov D. O., Ishchenko A.A., Ramanculov E., Saparbaev M., Khassenov B. Characterization of DNA substrate specificities of apurinic/apyrimidinic endonucleases from Mycobacterium tuberculosis. DNA Repair (Amst), 2015, vol. 33, pp. 1-16.

Puri R.V., Singh N., Gupta R.K., Tyagi A.K. Endonuclease IV Is the major apurinic/apyrimidinic endonuclease in Mycobacterium tuberculosis and is important for protection against oxidative damage. PLoS One, 2013, vol. 8, no. 8, pp. e71535.

Arif S.M., Geethanandan K., Mishra P., Surolia A., Varshney U., Vijayan M. Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications. Acta Crystallogr D Biol Crystallogr, 2015, vol. 71, Pt. 7, pp. 1514-1527.

Srinath T., Bharti S.K., Varshney U. Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis. DNA Repair (Amst), 2007, vol. 6, no. 10, pp. 1517-1528.

Guo Y., Bandaru V., Jaruga P., Zhao X., Burrows C.J., Iwai S., Dizdaroglu M., Bond J.P., Wallace S.S. The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts. DNA Repair (Amst), 2010, vol. 9, no. 2, pp. 177-190.

Sidorenko V.S., Rot M.A., Filipenko M.L., Nevinsky G.A., Zharkov D.O. Novel DNA glycosylases from Mycobacterium tuberculosis. Biochemistry (Mosc), 2008, vol. 73, no. 4, pp. 442-450.

Kurthkoti K., Srinath T., Kumar P., Malshetty V.S., Sang P.B., Jain R., Manjunath R., Varshney U. A distinct physiological role of MutY in mutation prevention in mycobacteria. Microbiology, 2010, vol. 156, Pt 1, pp. 88-93.

Yang M., Aamodt R.M., Dalhus B., Balasingham S., Helle I., Andersen P., Tonjum T., Alseth I., Rognes T., Bjoras M. The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage. DNA Repair (Amst), 2011, vol. 10, no. 6, pp. 595-602.

Yang Q., Huang F., Hu L., He Z.G. Physical and functional interactions between 3-methyladenine DNA glycosylase and topoisomerase I in mycobacteria. Biochemistry (Mosc), 2012, vol. 77, no. 4, pp. 378-387.

Rossi F., Khanduja J.S., Bortoluzzi A., Houghton J., Sander P., Guthlein C., Davis E.O., Springer B., Bottger E.C., Relini A., Penco A., Muniyappa K., Rizzi M. The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action. Nucleic Acids Res., 2011, vol. 39, no. 16, pp. 7316-7328.

Thakur M., Kumar M.B., Muniyappa K. Mycobacterium tuberculosis UvrB Is a Robust DNA-Stimulated ATPase That Also Possesses Structure-Specific ATP-Dependent DNA Helicase Activity. Biochemistry, 2016, vol. 55, no. 41, pp. 5865-5883.

Parulekar R.S., Barage S.H., Jalkute C.B., Dhanavade M.J., Fandilolu P.M., Sonawane K.D. Homology modeling, molecular docking and DNA binding studies of nucleotide excision repair UvrC protein from M. tuberculosis. Protein J., 2013, vol. 32, no. 6, pp. 467-476.

Houghton J., Townsend C., Williams A. R., Rodgers A., Rand L., Walker K.B., Bottger E.C., Springer B., Davis E.O. Important role for Mycobacterium tuberculosis UvrD1 in pathogenesis and persistence apart from its function in nucleotide excision repair. J Bacteriol., 2012, vol. 194, no. 11, pp. 2916-2923.

Kazarian K., Cassani C., Rizzi M. Expression, purification and characterization of UvrD2 helicase from Mycobacterium tuberculosis. Protein Expr Purif., 2010, vol. 69, no. 2, pp. 215-218.

Balasingham S.V., Zegeye E.D., Homberset H., Rossi M.L., Laerdahl J.K., Bohr V.A., Tonjum T. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB. PLoS One, 2012, vol. 7, no. 5, pp. e36960.

Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S., Glickman M.S. Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C. Nat Struct Mol Biol., 2005, vol. 12, no. 4, pp. 304-312.

Castaneda-Garcia A., Prieto A.I., Rodriguez-Beltran J. et al. A non-canonical mismatch repair pathway in prokaryotes. Nat Commun., 2017, vol. 8, pp. 14246.

Peek R.M., Jr., Crabtree J.E. Helicobacter infection and gastric neoplasia. J Pathol., 2006, vol. 208, no. 2, pp. 233-248.

Parkin D.M., Bray F., Ferlay J., Pisani P. Global cancer statistics, 2002. CA Cancer J Clin., 2005, vol. 55, no. 2, pp. 74-108.

Tomb J.F., White O., Kerlavage A.R., Clayton R.A. et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature, 1997, vol. 388, no. 6642, pp. 539-547.

Wroblewski L.E., Peek R.M., Jr., Wilson K.T. Helicobacter pylori and gastric cancer: factors that modulate disease risk. Clin Microbiol Rev., 2010, vol. 23, no. 4, pp. 713-739.

Wang G., Alamuri P., Humayun M.Z., Taylor D.E., Maier R.J. The Helicobacter pylori MutS protein confers protection from oxidative DNA damage. Mol Microbiol., 2005, vol. 58, no. 1, pp. 166-176.

O'Rourke E.J., Chevalier C., Pinto A.V., Thiberge J.M., Ielpi L., Labigne A., Radicella J.P. Pathogen DNA as target for host-generated oxidative stress: role for repair of bacterial DNA damage in Helicobacter pylori colonization. Proc Natl Acad Sci USA, 2003, vol. 100, no. 5, pp. 2789-2794.

Baldwin D.N., Shepherd B., Kraemer P., Hall M.K., Sycuro L.K., Pinto-Santini D.M., Salama N.R. Identification of Helicobacter pylori genes that contribute to stomach colonization. Infect Immun., 2007, vol. 75, no. 2, pp. 1005-1016.

Huang S., Kang J., Blaser M.J. Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori. J Bacteriol., 2006, vol. 188, no. 17, pp. 6224-6234.

Thompson S.A., Latch R.L., Blaser J.M. Molecular characterization of the Helicobacter pylori uvr B gene. Gene., 1998, vol. 209, no. 1-2, pp. 113-122.

Lee G.H., Jeong J.Y., Chung J.W. et al. The Helicobacter pylori Mfd protein is important for antibiotic resistance and DNA repair. Diagn Microbiol Infect Dis. 2009, vol. 65, no. 4, pp. 454-456.

Pinto A.V., Mathieu A., Marsin S., Veaute X., Ielpi L., Labigne A., Radicella J.P. Suppression of homologous and homeologous recombination by the bacterial MutS2 protein. Mol Cell., 2005, vol. 17, no. 1, pp. 113-120.

Marsin S., Lopes A., Mathieu A., Dizet E., Orillard E., Guerois R., Radicella J.P. Genetic dissection of Helicobacter pylori AddAB role in homologous recombination. FEMS Microbiol Lett., 2010, vol. 311, no. 1, pp. 44-50.

Amundsen S.K., Fero J., Hansen L.M., Cromie G.A., Solnick J.V., Smith G.R., Salama N.R. Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization. Mol Microbiol., 2008, vol. 69, no. 4, pp. 994-1007.

Kang J., Tavakoli D., Tschumi A., Aras R.A., Blaser M.J. Effect of host species on recG phenotypes in Helicobacter pylori and Escherichia coli. J Bacteriol., 2004, vol. 186, no. 22, pp. 7704-7713.

Bjorkholm B., Sjolund M., Falk P.G., Berg O.G., Engstrand L., Andersson D.I. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc Natl Acad Sci USA, 2001, vol. 98, no. 25, pp. 14607-14612.

Suerbaum S., Josenhans C. Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat Rev Microbiol., 2007, vol. 5, no. 6, pp. 441-452.

McCaig L.F., McDonald L.C., Mandal S., Jernigan D.B. Staphylococcus aureus-associated skin and soft tissue infections in ambulatory care. Emerg Infect Dis., 2006, vol. 12, no. 11, pp. 1715-1723.

Lowy F.D. Staphylococcus aureus infections. N Engl J Med., 1998, vol. 339, no. 8, pp. 520-532.

Wertheim H.F., Melles D.C., Vos M.C., van Leeuwen W. et al. The role of nasal carriage in Staphylococcus aureus infections. Lancet Infect Dis., 2005, vol. 5, no. 12, pp. 751-762.

Foster T.J. Colonization and infection of the human host by staphylococci: adhesion, survival and immune evasion. Vet Dermatol., 2009, vol. 20, no. 5-6, pp. 456-470.

Boucher H.W., Corey G.R. Epidemiology of methicillin-resistant Staphylococcus aureus. Clin Infect Dis., 2008, vol. 46, Suppl 5, pp. S344-349.

Moran G.J., Krishnadasan A., Gorwitz R.J., Fosheim G.E., McDougal L.K., Carey R.B., Talan D.A. Methicillin-resistant S. aureus infections among patients in the emergency department. N Engl J Med., 2006, vol. 355, no. 7, pp. 666-674.

Liu G.Y., Essex A., Buchanan J.T., Datta V., Hoffman H.M., Bastian J.F., Fierer J., Nizet V. Staphylococcus aureus golden pigment impairs neutrophil killing and promotes virulence through its antioxidant activity. J Exp Med., 2005, vol. 202, no. 2, pp. 209-215.

Liu C.I., Liu G.Y., Song Y., Yin F., Hensler M.E., Jeng W.Y., Nizet V., Wang A.H., Oldfield E. A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Science, 2008, vol. 319, no. 5868, pp. 1391-1394.

Mishra N.N., Liu G.Y., Yeaman M.R., Nast C.C., Proctor R.A., McKinnell J., Bayer A.S. Carotenoid-related alteration of cell membrane fluidity impacts Staphylococcus aureus susceptibility to host defense peptides. Antimicrob Agents Chemother., 2011, vol. 55, no. 2, pp. 526-531.

Ambur O.H., Davidsen T., Frye S.A., Balasingham S.V., Lagesen K., Rognes T., Tønjum T. Genome dynamics in major bacterial pathogens. FEMS Microbiology Reviews., 2009, vol. 33, no. 3, pp. 453-470.

Mol C.D., Hosfield D.J., Tainer J.A. Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means. Mutat Res., 2000, vol. 460, no. 3-4, pp. 211-229.

Michaels M.L., Miller J.H. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol., 1992, vol. 174, no. 20, pp. 6321-6325.

Prunier A.L., Leclercq R. Role of mutS and mutL genes in hypermutability and recombination in Staphylococcus aureus. J Bacteriol., 2005, vol. 187, no. 10, pp. 3455-3464.

Ambur O.H., Davidsen T., Frye S.A., Balasingham S.V., Lagesen K., Rognes T., Tonjum T. Genome dynamics in major bacterial pathogens. FEMS Microbiol Rev., 2009, vol. 33, no. 3, pp. 453-470.

Wolf C., Hochgrafe F., Kusch H., Albrecht D., Hecker M., Engelmann S. Proteomic analysis of antioxidant strategies of Staphylococcus aureus: diverse responses to different oxidants. Proteomics, 2008, vol. 8, no. 15, pp. 3139-3153.