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Tesfahun AN, Alexeeva M, Tomkuvienė M, Arshad A, Guragain P, Klungland A, Klimašauskas S, Ruoff P, Bjelland S. Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein. Front Microbiol 2021; 12:608839. [PMID: 34276575 PMCID: PMC8278400 DOI: 10.3389/fmicb.2021.608839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/20/2021] [Indexed: 11/18/2022] Open
Abstract
DNA polymerase III mis-insertion may, where not corrected by its 3′→ 5′ exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in Escherichia coli, and its repair mechanism remains elusive. We present here in vitro evidence that C⋅C mismatch can be processed by base excision repair initiated by the E. coli formamidopyrimidine-DNA glycosylase (Fpg) protein. The kcat for C⋅C is, however, 2.5 to 10 times lower than for its primary substrate 8-oxoguanine (oxo8G)⋅C, but approaches those for 5,6-dihydrothymine (dHT)⋅C and thymine glycol (Tg)⋅C. The KM values are all in the same range, which indicates efficient recognition of C⋅C mismatches in DNA. Fpg activity was also exhibited for the thymine (T)⋅T mismatch and for N4- and/or 5-methylated C opposite C or T, Fpg activity being enabled on a broad spectrum of DNA lesions and mismatches by the flexibility of the active site loop. We hypothesize that Fpg plays a role in resolving C⋅C in particular, but also other pyrimidine⋅pyrimidine mismatches, which increases survival at the cost of some mutagenesis.
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Affiliation(s)
- Almaz Nigatu Tesfahun
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Aysha Arshad
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Prashanna Guragain
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Molecular Medicine, Life Sciences Center, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Peter Ruoff
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway.,Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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Warnecke T, Supek F, Lehner B. Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner. PLoS Comput Biol 2012; 8:e1002846. [PMID: 23284284 PMCID: PMC3527292 DOI: 10.1371/journal.pcbi.1002846] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/03/2012] [Indexed: 02/06/2023] Open
Abstract
The binding of proteins can shield DNA from mutagenic processes but also interfere with efficient repair. How the presence of DNA-binding proteins shapes intra-genomic differences in mutability and, ultimately, sequence variation in natural populations, however, remains poorly understood. In this study, we examine sequence evolution in Escherichia coli in relation to the binding of four abundant nucleoid-associated proteins: Fis, H-NS, IhfA, and IhfB. We find that, for a subset of mutations, protein occupancy is associated with both increased and decreased mutability in the underlying sequence depending on when the protein is bound during the bacterial growth cycle. On average, protein-bound DNA exhibits reduced mutability compared to protein-free DNA. However, this net protective effect is weak and can be abolished or even reversed during stages of colony growth where binding coincides – and hence likely interferes with – DNA repair activity. We suggest that the four nucleoid-associated proteins analyzed here have played a minor but significant role in patterning extant sequence variation in E. coli. Mutations can be more or less likely to occur depending on whether DNA is naked or bound by proteins. On the one hand, DNA-binding proteins can shield the DNA from certain mutagenic processes. On the other hand, the very same proteins can interfere with efficient DNA repair. In this study, we reconstruct the history of mutations across 54 E. coli genomes and ask whether mutation risk is higher or lower in regions occupied by proteins that help organize bacterial DNA into chromatin. Intriguingly, we find that the effect of binding depends on its timing. When we consider genomic regions bound during stationary phase, we observe that binding is associated with lower mutation risk for some mutation classes compared to naked DNA, albeit weakly. However, when binding occurs during exponential phase, bound regions actually experience more mutations on average. We argue that this is because, during exponential phase, the major effect of binding is that it interferes with efficient DNA repair, whereas in stationary phase – when many repair pathways are inactive – the protective effect of binding dominates. Our results suggest that the four DNA-binding proteins considered here have a small but significant growth phase-specific effect on mutation dynamics in E. coli.
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Affiliation(s)
- Tobias Warnecke
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain.
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Kamashev D, Oberto J, Serebryakova M, Gorbachev A, Zhukova Y, Levitskii S, Mazur AK, Govorun V. Mycoplasma gallisepticum Produces a Histone-like Protein That Recognizes Base Mismatches in DNA. Biochemistry 2011; 50:8692-702. [DOI: 10.1021/bi2009097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmitri Kamashev
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
| | - Jacques Oberto
- Institut
de Génétique et Microbiologie, CNRS UMR 8621, Université Paris XI, Paris, France
| | | | - Alexey Gorbachev
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
| | - Yulia Zhukova
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
| | - Sergei Levitskii
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
| | - Alexey K. Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut
de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris
75005, France
| | - Vadim Govorun
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
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Pitsikas P, Polosina YY, Cupples CG. Interaction between the mismatch repair and nucleotide excision repair pathways in the prevention of 5-azacytidine-induced CG-to-GC mutations in Escherichia coli. DNA Repair (Amst) 2009; 8:354-9. [DOI: 10.1016/j.dnarep.2008.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 11/14/2008] [Accepted: 11/20/2008] [Indexed: 01/07/2023]
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Huen MSY, Li XT, Lu LY, Watt RM, Liu DP, Huang JD. The involvement of replication in single stranded oligonucleotide-mediated gene repair. Nucleic Acids Res 2006; 34:6183-94. [PMID: 17088285 PMCID: PMC1693898 DOI: 10.1093/nar/gkl852] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Targeted gene repair mediated by single-stranded oligonucleotides (SSOs) has great potential for use in functional genomic studies and gene therapy. Genetic changes have been created using this approach in a number of prokaryotic and eukaryotic systems, including mouse embryonic stem cells. However, the underlying mechanisms remain to be fully established. In one of the current models, the ‘annealing-integration’ model, the SSO anneals to its target locus at the replication fork, serving as a primer for subsequent DNA synthesis mediated by the host replication machinery. Using a λ-Red recombination-based system in the bacterium Escherichia coli, we systematically examined several fundamental premises that form the mechanistic basis of this model. Our results provide direct evidence strongly suggesting that SSO-mediated gene repair is mechanistically linked to the process of DNA replication, and most likely involves a replication intermediate. These findings will help guide future experiments involving SSO-mediated gene repair in mammalian and prokaryotic cells, and suggest several mechanisms by which the efficiencies may be reliably and substantially increased.
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Affiliation(s)
- Michael S. Y. Huen
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Xin-tian Li
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)Beijing 100005, P.R. China
| | - Lin-Yu Lu
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Rory M. Watt
- Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong Pokfulam RoadHong Kong SAR, China
| | - De-Pei Liu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC)Beijing 100005, P.R. China
| | - Jian-Dong Huang
- Department of Biochemistry, The University of Hong Kong3/F Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
- To whom correspondence should be addressed. Tel: +852 2819 2810; Fax: +852 2855 1254;
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Doi T, Yonekura SI, Tano K, Yasuhira S, Yonei S, Zhang QM. The Shizosaccharomyces pombe homolog (SpMYH) of the Escherichia coli MutY is required for removal of guanine from 8-oxoguanine/guanine mispairs to prevent G:C to C:G transversions. JOURNAL OF RADIATION RESEARCH 2005; 46:205-14. [PMID: 15988139 DOI: 10.1269/jrr.46.205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The frequency of G:C-->C:G transversions significantly increases upon exposure of cells to ionizing radiation or reactive oxygen species. Transversions can be prevented by base excision repair, which removes the causative modified bases from DNA. Our previous studies revealed that MutY is responsible for removing guanine from 7,8-dihydro-8-oxoguanine/guanine mispairs (8-oxoG/G) and prevents the generation of G:C-->C:G transversions in E. coli. SpMYH, a homolog of E. coli MutY, had been identified and characterized in the fission yeast S. pombe. Purified SpMYH has adenine DNA glycosylase activity on A/8-oxoG and A/G mismatch-containing oligonucleotides. In this study, we examined whether SpMYH has a similar activity allowing it to remove G from 8-oxoG/G in DNA. The purified SpMYH tightly bound to duplex oligonucleotides containing 8-oxoG/G and removed the unmodified G from 8-oxoG/G as efficiently as A from 8-oxoG/A. The activity was absent in the cell extract prepared from an SpMYH-knockout strain of S. pombe. The expression of SpMYH markedly reduced the frequency of spontaneous G:C-->C:G transversions in the E. coli mutY mutant. These results demonstrate that SpMYH is involved in the repair of 8-oxoG/G, by which it prevents mutations induced by oxidative stress in S. pombe.
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Affiliation(s)
- Takashi Doi
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Japan
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Muheim-Lenz R, Buterin T, Marra G, Naegeli H. Short-patch correction of C/C mismatches in human cells. Nucleic Acids Res 2004; 32:6696-705. [PMID: 15613598 PMCID: PMC545458 DOI: 10.1093/nar/gkh990] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We examined whether the human nucleotide excision repair complex, which is specialized on the removal of bulky DNA adducts, also displays a correcting activity on base mismatches. The cytosine/cytosine (C/C) lesion was used as a model substrate to monitor the correction of base mismatches in human cells. Fibroblasts with different repair capabilities were transfected with shuttle vectors that contain a site-directed C/C mismatch in the replication origin, accompanied by an additional C/C mismatch in one of the flanking sequences that are not essential for replication. Analysis of the vector progeny obtained from these doubly modified substrates revealed that C/C mismatches were eliminated before DNA synthesis not only in the repair-proficient background, but also when the target cells carried a genetic defect in long-patch mismatch repair, in nucleotide excision repair, or when both pathways were deleted. Furthermore, cells deficient for long-patch mismatch repair as well as a cell line that combines mismatch and nucleotide excision repair defects were able to correct multiple C/C mispairs, placed at distances of 21-44 nt, in an independent manner, such that the removal of each lesion led to individual repair patches. These results support the existence of a concurrent short-patch mechanism that rectifies C/C mismatches.
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Affiliation(s)
- Regula Muheim-Lenz
- Institute of Pharmacology and Toxicology, University of Zürich-Vetsuisse, 8057 Zürich, Switzerland
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Dantzer F, Bjørås M, Luna L, Klungland A, Seeberg E. Comparative analysis of 8-oxoG:C, 8-oxoG:A, A:C and C:C DNA repair in extracts from wild type or 8-oxoG DNA glycosylase deficient mammalian and bacterial cells. DNA Repair (Amst) 2003; 2:707-18. [PMID: 12767349 DOI: 10.1016/s1568-7864(03)00041-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have investigated repair of DNA containing 8-oxoguanine and certain mismatches in cell-free extracts from mouse embryonic fibroblasts (MEFs) using a plasmid substrate with a single lesion at a defined position. Repair synthesis was monitored in a small restriction fragment with different size single strands in order to follow the fate of repair reactions in both strands at the same time. An important part of the study was to assess the role of OGG1 in various repair reactions and the experiments were carried out with extracts from mouse embryonic fibroblasts diploid for a mogg1 deletion (Ogg1(-/-)) as well as wild type. In wild type, DNA containing 8-oxoG:C was repaired in the expected fashion predominantly through short-patch repair. Overall repair was reduced to 20% in the Ogg1(-/-) extracts and to 40% if only long-patch repair was considered. The 8-oxoG:A pair was processed similarly in wild type and Ogg1(-/-) extracts and repair synthesis at A as well as at 8-oxoG could be demonstrated, however, to the same extent in Ogg1(-/-) and wild type for both strands. Extracts from Ogg1(-/-) behaved normally in the correction of A:C and C:C mismatches, with a strong bias for correction of A for A:C and no significant strand discrimination for C:C. Similar experiments with extracts from Escherichia coli showed a 50% reduction in the repair of 8-oxoG:C in fpg extracts and an increase to 50% above wild type in mutY. These results show that the mouse OGG1 is the major enzyme for 8-oxoG repair in the MEF cells and does not participate in mismatch repair of A:C or C:C. Furthermore, 8-oxoG opposite A appears to be repaired by a two-step repair pathway with sequential removal of A and 8-oxoG mediated by enzymes different from OGG1.
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Affiliation(s)
- Francoise Dantzer
- Centre for Molecular Biology and Neuroscience, and Institute of Medical Microbiology, University of Oslo, Rikshospitalet, 0027 Oslo, Norway
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Stanisławska-Sachadyn A, Sachadyn P, Jedrzejczak R, Kur J. Construction and purification of his6-Thermus thermophilus MutS protein. Protein Expr Purif 2003; 28:69-77. [PMID: 12651109 DOI: 10.1016/s1046-5928(02)00649-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mutS gene from the thermophilic bacterium Thermus thermophilus was PCR amplified, cloned, and expressed in Escherichia coli. The recombinant MutS protein containing an oligohistidine domain at the N-terminus was purified in a single step by Ni(2+) affinity chromatography to apparent homogeneity. The mismatch recognition properties of the his(6)-tagged MutS protein were confirmed by DNA protection against exonuclease digestion and retardation assays. The results of analytical gel filtration indicate that the predominant form of T. thermophilus MutS at micromolar concentrations is a tetramer.
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Affiliation(s)
- Anna Stanisławska-Sachadyn
- Technical University of Gdańsk, Department of Microbiology, ul. Narutowicza 11/12, Gdansk 80-952, Poland
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Olsen AK, Duale N, Bjørås M, Larsen CT, Wiger R, Holme JA, Seeberg EC, Brunborg G. Limited repair of 8-hydroxy-7,8-dihydroguanine residues in human testicular cells. Nucleic Acids Res 2003; 31:1351-63. [PMID: 12582255 PMCID: PMC150234 DOI: 10.1093/nar/gkg216] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Oxidative damage in testicular DNA is associated with poor semen quality, reduced fertility and increased risk of stillbirths and birth defects. These DNA lesions are predominantly removed by base excision repair. Cellular extracts from human and rat testicular cells and three enriched populations of rat male germ cells (primary spermatocytes, round spermatids and elongating/elongated spermatids) all showed proficient excision/incision of 5-hydroxycytosine, thymine glycol and 2,6-diamino-4-hydroxy-5-formamidopyrimidine. DNA containing 8-oxo-7,8-dihydroguanine was excised poorly by human testicular cell extracts, although 8-oxoguanine-DNA glycosylase-1 (hOGG1) was present in human testicular cells, at levels that varied markedly between 13 individuals. This excision was as low as with human mononuclear blood cell extracts. The level of endonuclease III homologue-1 (NTH1), which excises oxidised pyrimidines, was higher in testicular than in somatic cells of both species. Cellular repair studies of lesions recognised by formamidopyrimidine-DNA glycosylase (Fpg) or endonuclease III (Nth) were assayed with alkaline elution and the Comet assay. Consistent with the enzymatic activities, human testicular cells showed poor removal of Fpg-sensitive lesions but efficient repair of Nth-sensitive lesions. Rat testicular cells efficiently repaired both Fpg- and Nth-sensitive lesions. In conclusion, human testicular cells have limited capacity to repair important oxidative DNA lesions, which could lead to impaired reproduction and de novo mutations.
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Affiliation(s)
- Ann-Karin Olsen
- Department of Chemical Toxicology, Division of Environmental Medicine, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403 Oslo, Norway
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Abstract
Unpaired and mispaired bases in DNA can arise by replication errors, spontaneous or induced base modifications, and during recombination. The major pathway for correction of mismatches arising during replication is the MutHLS pathway of Escherichia coli and related pathways in other organisms. MutS initiates repair by binding to the mismatch, and activates together with MutL the MutH endonuclease, which incises at hemimethylated dam sites and thereby mediates strand discrimination. Multiple MutS and MutL homologues exist in eukaryotes, which play different roles in the mismatch repair (MMR) pathway or in recombination. No MutH homologues have been identified in eukaryotes, suggesting that strand discrimination is different to E. coli. Repair can be initiated by the heterodimers MSH2-MSH6 (MutSalpha) and MSH2-MSH3 (MutSbeta). Interestingly, MSH3 (and thus MutSbeta) is missing in some genomes, as for example in Drosophila, or is present as in Schizosaccharomyces pombe but appears to play no role in MMR. MLH1-PMS1 (MutLalpha) is the major MutL homologous heterodimer. Again some, but not all, eukaryotes have additional MutL homologues, which all form a heterodimer with MLH1 and which play a minor role in MMR. Additional factors with a possible function in eukaryotic MMR are PCNA, EXO1, and the DNA polymerases delta and epsilon. MMR-independent pathways or factors that can process some types of mismatches in DNA are nucleotide-excision repair (NER), some base excision repair (BER) glycosylases, and the flap endonuclease FEN-1. A pathway has been identified in Saccharomyces cerevisiae and human that corrects loops with about 16 to several hundreds of unpaired nucleotides. Such large loops cannot be processed by MMR.
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Affiliation(s)
- Thomas M Marti
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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