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Journal of Nucleic Acids
Volume 2010, Article ID 179594, 32 pages
http://dx.doi.org/10.4061/2010/179594
Review Article

Molecular Mechanisms of the Whole DNA Repair System: A Comparison of Bacterial and Eukaryotic Systems

1Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
2RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
3Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan

Received 15 June 2010; Accepted 27 July 2010

Academic Editor: Shigenori Iwai

Copyright © 2010 Rihito Morita et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [41 citations]

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  • Tatsuya Yamamoto, Hitoshi Iino, Kwang Kim, Seiki Kuramitsu, and Kenji Fukui, “Evidence for ATP-dependent Structural Rearrangement of Nuclease Catalytic Site in DNA Mismatch Repair Endonuclease MutL,” Journal Of Biological Chemistry, vol. 286, no. 49, pp. 42337–42348, 2011. View at Publisher · View at Google Scholar
  • Shuhei Nakane, Taisuke Wakamatsu, Ryoji Masui, Seiki Kuramitsu, and Kenji Fukui, “In Vivo, in Vitro, and X-ray Crystallographic Analyses Suggest the Involvement of an Uncharacterized Triose-phosphate Isomerase (TIM) Barrel Protein in Protection against Oxidative Stress,” Journal Of Biological Chemistry, vol. 286, no. 48, pp. 41636–41646, 2011. View at Publisher · View at Google Scholar
  • Kenji Fukui, and Seiki Kuramitsu, “Structure and Function of the Small MutS-Related Domain.,” Molecular biology international, vol. 2011, pp. 691735, 2011. View at Publisher · View at Google Scholar
  • Alexandra Calle, Alberto Miranda, Raul Fernandez-Gonzalez, Eva Pericuesta, Ricardo Laguna, and Alfonso Gutierrez-Adan, “Male Mice Produced by In Vitro Culture Have Reduced Fertility and Transmit Organomegaly and Glucose Intolerance to Their Male Offspring,” Biology Of Reproduction, vol. 87, no. 2, 2012. View at Publisher · View at Google Scholar
  • Manoj K. Dhar, Shelly Sehgal, and Sanjana Kaul, “Structure, replication efficiency and fragility of yeast ARS elements,” Research in Microbiology, vol. 163, no. 4, pp. 243–253, 2012. View at Publisher · View at Google Scholar
  • Victor P. Shcherbakov, “Mismatch repair in recombination of bacteriophage T4,” Biomolecular Concepts, vol. 3, no. 6, pp. 523–534, 2012. View at Publisher · View at Google Scholar
  • Shuhei Nakane, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui, “The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair,” DNA Repair, vol. 11, no. 11, pp. 906–914, 2012. View at Publisher · View at Google Scholar
  • Leroy G. Henry, Wilson Aruni, Lawrence Sandberg, and Hansel M. Fletcher, “Protective Role of the PG1036-PG1037-PG1038 Operon in Oxidative Stress in Porphyromonas gingivalis W83,” Plos One, vol. 8, no. 8, 2013. View at Publisher · View at Google Scholar
  • Atsuhiro Shimada, Yoshitaka Kawasoe, Yoshito Hata, Tatsuro S. Takahashi, Ryoji Masui, Seiki Kuramitsu, and Kenji Fukui, “MutS stimulates the endonuclease activity of MutL in an ATP-hydrolysis-dependent manner,” FEBS Journal, 2013. View at Publisher · View at Google Scholar
  • Minal Patkari, and Sarika Mehra, “Transcriptomic study of ciprofloxacin resistance in Streptomyces coelicolor A3(2),” Molecular BioSystems, vol. 9, no. 12, pp. 3101, 2013. View at Publisher · View at Google Scholar
  • Moaz Ahmad, and Renu Tuteja, “Emerging importance of mismatch repair components including UvrD helicase and their cross-talk with the development of drug resistance in malaria parasite,” Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2014. View at Publisher · View at Google Scholar
  • Jiaxi Wu, and Shane Starr, “Low-fidelity compensatory backup alternative DNA repair pathways may unify current carcinogenesis theories,” Future Oncology, vol. 10, no. 7, pp. 1239–1253, 2014. View at Publisher · View at Google Scholar
  • Priscila Ramos-Ibeas, Alexandra Calle, Raul Fernandez-Gonzalez, Ricardo Laguna-Barraza, Eva Pericuesta, Antonia Calero, Miguel Angel Ramirez, and Alfonso Gutierrez-Adan, “Intracytoplasmic Sperm Injection Using DNA-Fragmented Sperm in Mice Negatively Affects Embryo-Derived Embryonic Stem Cells, Reduces the Fertility of Male Offspring and Induces Heritable Changes in Epialleles,” Plos One, vol. 9, no. 4, 2014. View at Publisher · View at Google Scholar
  • Dorothy A. Erie, and Keith R. Weninger, “Single molecule studies of DNA mismatch repair,” DNA Repair, 2014. View at Publisher · View at Google Scholar
  • Richa, Rajeshwar P Sinha, Donat-P H Ä Der, Richa, Rajeshwar P. Sinha, and Donat-P. Haeder, “Physiological aspects of UV-excitation of DNA,” Topics in Current Chemistry, vol. 356, pp. 203–248, 2014. View at Publisher · View at Google Scholar
  • Yu-Yuan Hsiao, Woei-Horng Fang, Chia-Chia Lee, Yi-Ping Chen, and Hanna S. Yuan, “Structural Insights Into DNA Repair by RNase T- An Exonuclease Processing 39 End of Structured DNA in Repair Pathways,” Plos Biology, vol. 12, no. 3, 2014. View at Publisher · View at Google Scholar
  • M. A. Lever, K. L. Rogers, K. G. Lloyd, J. Overmann, B. Schink, R. K. Thauer, T. M. Hoehler, and B. B. Jorgensen, “Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations,” FEMS Microbiology Reviews, 2015. View at Publisher · View at Google Scholar
  • Akio Ebihara, Miho Manzoku, Kenji Fukui, Atsuhiro Shimada, Rihito Morita, Ryoji Masui, and Seiki Kuramitsu, “Roles of Mn-catalase and a possible heme peroxidase homologue in protection from oxidative stress in Thermus thermophilus,” Extremophiles, 2015. View at Publisher · View at Google Scholar
  • Marcela Kokes, Joe Dan Dunn, Joshua A. Granek, Bidong D. Nguyen, Jeffrey R. Barker, Raphael H. Valdivia, and Robert J. Bastidas, “Integrating Chemical Mutagenesis and Whole-Genome Sequencing as a Platform for Forward and Reverse Genetic Analysis of Chlamydia,” Cell Host & Microbe, vol. 17, no. 5, pp. 716–725, 2015. View at Publisher · View at Google Scholar
  • Gisele D. Brisson, Liliane R. Alves, and Maria S. Pombo-De-Oliveira, “Genetic susceptibility in childhood acute leukaemias: A systematic review,” ecancermedicalscience, vol. 9, 2015. View at Publisher · View at Google Scholar
  • Hitoshi Iino, Takaaki Hikima, Yuya Nishida, Masaki Yamamoto, Seiki Kuramitsu, and Kenji Fukui, “Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein,” Extremophiles, 2015. View at Publisher · View at Google Scholar
  • Olga Novikova, Pradeepa Jayachandran, Danielle S. Kelley, Zachary Morton, Samantha Merwin, Natalya I. Topilina, and Marlene Belfort, “Intein Clustering Suggests Functional Importance in Different Domains of Life,” Molecular Biology and Evolution, pp. msv271, 2015. View at Publisher · View at Google Scholar
  • Elaine Ferreira, Rosa Giménez, María Alexandra Cañas, Laura Aguilera, Juan Aguilar, Josefa Badia, and Laura Baldomà, “Glyceraldehyde-3-phosphate dehydrogenase is required for efficient repair of cytotoxic DNA lesions in Escherichia coli,” The International Journal of Biochemistry & Cell Biology, 2015. View at Publisher · View at Google Scholar
  • Derek J. Richard, Emma Bolderson, Anne-Marie Baird, and Kenneth J. O’Byrne, “Epigenetics Underpinning DNA Damage Repair,” Epigenetic Cancer Therapy, pp. 595–612, 2015. View at Publisher · View at Google Scholar
  • Amjad Ali, Anam Naz, Siomar C Soares, Marriam Bakhtiar, Sandeep Tiwari, Syed S Hassan, Fazal Hanan, Rommel Ramos, Ulisses Pereira, Debmalya Barh, Henrique César Pereira Figueiredo, David W. Ussery, Anderson Miyoshi, Artur Silva, and Vasco Azevedo, “ Pan-Genome Analysis of Human Gastric Pathogen H. pylori : Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets ,” BioMed Research International, vol. 2015, pp. 1–17, 2015. View at Publisher · View at Google Scholar
  • Hiroki Okanishi, and Kwang Kim, “Functional discovery of functionally unknown proteins by mass spectrometry,” Seikagaku, vol. 87, no. 3, pp. 286–291, 2015. View at Publisher · View at Google Scholar
  • Oleg V. Belov, Denis L. Boyda, Ianik Plante, and Sergey Eh. Shirmovsky, “Simulation of the charge migration in DNA under irradiation with heavy ions,” Bio-Medical Materials And Engineering, vol. 26, pp. S1937–S1944, 2015. View at Publisher · View at Google Scholar
  • Kenji Fukui, Seiki Baba, Takato Yano, and Takashi Kumasaka, “Structural features and functional dependency on β-Clamp define distinct subfamilies of bacterial mismatch repair endonuclease MutL,” Journal of Biological Chemistry, vol. 291, no. 33, pp. 16990–17000, 2016. View at Publisher · View at Google Scholar
  • Cherie S. Tan, Jan Riedl, Aaron M. Fleming, Cynthia J. Burrows, and Henry S. White, “Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore,” ACS Nano, 2016. View at Publisher · View at Google Scholar
  • Clemens Glombitza, Rishi R. Adhikari, Natascha Riedinger, William P. Gilhooly, Kai-Uwe Hinrichs, and Fumio Inagaki, “Microbial Sulfate Reduction Potential in Coal-Bearing Sediments Down to ~2.5 km below the Seafloor off Shimokita Peninsula, Japan,” Frontiers in Microbiology, vol. 7, 2016. View at Publisher · View at Google Scholar
  • J.W. Gauer, S. LeBlanc, P. Hao, R. Qiu, B.C. Case, M. Sakato, M.M. Hingorani, D.A. Erie, and K.R. Weninger, “Single-Molecule FRET to Measure Conformational Dynamics of DNA Mismatch Repair Proteins,” 2016. View at Publisher · View at Google Scholar
  • Matthew S. Ackerman, Marcus M. Dillon, Clay Fuqua, Way Sung, Thomas G. Platt, Vaughn S. Cooper, and Michael Lynch, “Evolution of the insertion-deletion mutation rate across the tree of life,” G3: Genes, Genomes, Genetics, vol. 6, no. 8, pp. 2583–2591, 2016. View at Publisher · View at Google Scholar
  • Mohammed Tarique, Moaz Ahmad, Manish Chauhan, and Renu Tuteja, “Genome Wide In silico Analysis of the Mismatch Repair Components of Plasmodium falciparum and Their Comparison with Human Host,” Frontiers in Microbiology, vol. 08, 2017. View at Publisher · View at Google Scholar
  • Antonio Blanco, and Gustavo Blanco, “The Genetic Information (I),” Medical Biochemistry, pp. 465–492, 2017. View at Publisher · View at Google Scholar
  • Yuki Fujii, Masao Inoue, Kenji Fukui, Seiki Kuramitsu, and Ryoji Masui, “ Resistance to UV Irradiation Caused by Inactivation of nurA and herA Genes in Thermus thermophilus ,” Journal of Bacteriology, vol. 200, no. 16, 2018. View at Publisher · View at Google Scholar
  • Kuan-Wei Huang, Tung-Chang Liu, Ruei-Yue Liang, Lee-Ya Chu, Hiu-Lo Cheng, Jhih-Wei Chu, and Yu-Yuan Hsiao, “Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1,” PLOS Biology, vol. 16, no. 5, pp. e2005653, 2018. View at Publisher · View at Google Scholar
  • M Segovia, Mr Lorenzo, C Iñiguez, and C García-Gómez, “Physiological stress response associated with elevated CO2 and dissolved iron in a phytoplankton community dominated by the coccolithophore Emiliania huxleyi,” Marine Ecology Progress Series, vol. 586, pp. 73–89, 2018. View at Publisher · View at Google Scholar
  • Issay Narumi, and Shigenori Maruyama, “The Role of Natural Radiation in the Evolution of Ancient Microbes,” Journal of Geography (Chigaku Zasshi), vol. 128, no. 4, pp. 649–665, 2019. View at Publisher · View at Google Scholar
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  • Javiera Norambuena, Thomas E. Hanson, Tamar Barkay, and Jeffrey M. Boyd, “ Superoxide Dismutase and Pseudocatalase Increase Tolerance to Hg(II) in Thermus thermophilus HB27 by Maintaining the Reduced Bacillithiol Pool ,” mBio, vol. 10, no. 2, 2019. View at Publisher · View at Google Scholar