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Putnam CD, Kolodner RD. Insights into DNA cleavage by MutL homologs from analysis of conserved motifs in eukaryotic Mlh1. Bioessays 2023; 45:e2300031. [PMID: 37424007 PMCID: PMC10530380 DOI: 10.1002/bies.202300031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
MutL family proteins contain an N-terminal ATPase domain (NTD), an unstructured interdomain linker, and a C-terminal domain (CTD), which mediates constitutive dimerization between subunits and often contains an endonuclease active site. Most MutL homologs direct strand-specific DNA mismatch repair by cleaving the error-containing daughter DNA strand. The strand cleavage reaction is poorly understood; however, the structure of the endonuclease active site is consistent with a two- or three-metal ion cleavage mechanism. A motif required for this endonuclease activity is present in the unstructured linker of Mlh1 and is conserved in all eukaryotic Mlh1 proteins, except those from metamonads, which also lack the almost absolutely conserved Mlh1 C-terminal phenylalanine-glutamate-arginine-cysteine (FERC) sequence. We hypothesize that the cysteine in the FERC sequence is autoinhibitory, as it sequesters the active site. We further hypothesize that the evolutionary co-occurrence of the conserved linker motif with the FERC sequence indicates a functional interaction, possibly by linker motif-mediated displacement of the inhibitory cysteine. This role is consistent with available data for interactions between the linker motif with DNA and the CTDs in the vicinity of the active site.
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Affiliation(s)
- Christopher D. Putnam
- Ludwig Institute for Cancer Research San Diego Branch, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Departments of Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Moores Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
| | - Richard D. Kolodner
- Ludwig Institute for Cancer Research San Diego Branch, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Cellular and Molecular Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Moores Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
- Institute of Genomic Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0660
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2
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Micol-Ponce R, García-Alcázar M, Lebrón R, Capel C, Pineda B, García-Sogo B, Alché JDD, Ortiz-Atienza A, Bretones S, Yuste-Lisbona FJ, Moreno V, Capel J, Lozano R. Tomato POLLEN DEFICIENT 2 encodes a G-type lectin receptor kinase required for viable pollen grain formation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:178-193. [PMID: 36260406 PMCID: PMC9786849 DOI: 10.1093/jxb/erac419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/18/2022] [Indexed: 05/16/2023]
Abstract
Pollen development is a crucial biological process indispensable for seed set in flowering plants and for successful crop breeding. However, little is known about the molecular mechanisms regulating pollen development in crop species. This study reports a novel male-sterile tomato mutant, pollen deficient 2 (pod2), characterized by the production of non-viable pollen grains and resulting in the development of small parthenocarpic fruits. A combined strategy of mapping-by-sequencing and RNA interference-mediated gene silencing was used to prove that the pod2 phenotype is caused by the loss of Solanum lycopersicum G-type lectin receptor kinase II.9 (SlG-LecRK-II.9) activity. In situ hybridization of floral buds showed that POD2/SlG-LecRK-II.9 is specifically expressed in tapetal cells and microspores at the late tetrad stage. Accordingly, abnormalities in meiosis and tapetum programmed cell death in pod2 occurred during microsporogenesis, resulting in the formation of four dysfunctional microspores leading to an aberrant microgametogenesis process. RNA-seq analyses supported the existence of alterations at the final stage of microsporogenesis, since we found tomato deregulated genes whose counterparts in Arabidopsis are essential for the normal progression of male meiosis and cytokinesis. Collectively, our results revealed the essential role of POD2/SlG-LecRK-II.9 in regulating tomato pollen development.
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Affiliation(s)
| | | | - Ricardo Lebrón
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46011 Valencia, Spain
| | - Begoña García-Sogo
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46011 Valencia, Spain
| | - Juan de Dios Alché
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, Estación Experimental del Zaidín-CSIC, 18008 Granada, Spain
| | - Ana Ortiz-Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Sandra Bretones
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Fernando Juan Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46011 Valencia, Spain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
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3
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Shodhan A, Xaver M, Wheeler D, Lichten M. Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae. Genetics 2022; 222:iyac106. [PMID: 35876814 PMCID: PMC9434160 DOI: 10.1093/genetics/iyac106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
The DNA double-strand breaks that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for double-strand break formation; double-strand break levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with double-strand break levels. How axis protein levels influence double-strand break formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased double-strand breaks and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in double-strand breaks did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote double-strand break formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local double-strand break levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
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Affiliation(s)
- Anura Shodhan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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4
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Vimal D, Saini S, Kristipati RR, Chowdhuri DK. Atrazine or bisphenol A mediated negative modulation of mismatch repair gene, mlh1 leads to defective oogenesis and reduced female fertility in Drosophila melanogaster. CHEMOSPHERE 2019; 225:247-258. [PMID: 30877919 DOI: 10.1016/j.chemosphere.2019.02.134] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/15/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
The study reports the effects of an herbicide (atrazine) and a plasticizer (Bisphenol A, BPA) on the transcriptional modulation of a mismatch repair gene (mlh1) and its adverse consequences on female fertility using Drosophila as a model. Through a chemical screen, we show that exposure to atrazine or BPA significantly downregulates mlh1 and the exposed flies had reduced fertility with smaller ovaries having reduced number of mature oocytes and abnormal distribution of ovarian follicles with increased apoptosis in them. These females had increased double-strand breaks as well as reduced synaptonemal complex formation in their ovaries suggesting altered meiotic crossing over. The eggs of these females were defective in their maternal transcripts as well as proteins and consequently, after fertilization, these eggs exhibited abnormal embryonic development. Interestingly, these phenotypes parallel that of mlh1 mutants. Further, exposure of females having reduced Mlh1 levels (mlh1e00130/CyO) to atrazine or BPA caused severe defective phenotypes at a higher proportion than normal flies. Our findings reveal the critical role of mlh1 in atrazine and BPA mediated female reproductive toxicity, and opens up a possibility of toxicants affecting female fertility by modulating the MMR genes.
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Affiliation(s)
- Divya Vimal
- Embryotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Lucknow, India
| | - Sanjay Saini
- Embryotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Ravi Ram Kristipati
- Embryotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Lucknow, India.
| | - Debapratim Kar Chowdhuri
- Embryotoxicology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Lucknow, India.
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5
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Noncanonical Contributions of MutLγ to VDE-Initiated Crossovers During Saccharomyces cerevisiae Meiosis. G3-GENES GENOMES GENETICS 2019; 9:1647-1654. [PMID: 30902890 PMCID: PMC6505156 DOI: 10.1534/g3.119.400150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In Saccharomyces cerevisiae, the meiosis-specific axis proteins Hop1 and Red1 are present nonuniformly across the genome. In a previous study, the meiosis-specific VMA1-derived endonuclease (VDE) was used to examine Spo11-independent recombination in a recombination reporter inserted in a Hop1/Red1-enriched region (HIS4) and in a Hop1/Red1-poor region (URA3). VDE-initiated crossovers at HIS4 were mostly dependent on Mlh3, a component of the MutLγ meiotic recombination intermediate resolvase, while VDE-initiated crossovers at URA3 were mostly Mlh3-independent. These differences were abolished in the absence of the chromosome axis remodeler Pch2, and crossovers at both loci became partly Mlh3-dependent. To test the generality of these observations, we examined inserts at six additional loci that differed in terms of Hop1/Red1 enrichment, chromosome size, and distance from centromeres and telomeres. All six loci behaved similarly to URA3: the vast majority of VDE-initiated crossovers were Mlh3-independent. This indicates that, counter to previous suggestions, levels of meiotic chromosome axis protein enrichment alone do not determine which recombination pathway gives rise to crossovers during VDE-initiated meiotic recombination. In pch2∆ mutants, the fraction of VDE-induced crossovers that were Mlh3-dependent increased to levels previously observed for Spo11-initiated crossovers in pch2∆, indicating that Pch2-dependent processes play an important role in controlling the balance between MutLγ-dependent and MutLγ-independent crossovers.
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6
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Manhart CM, Alani E. Roles for mismatch repair family proteins in promoting meiotic crossing over. DNA Repair (Amst) 2016; 38:84-93. [PMID: 26686657 PMCID: PMC4740264 DOI: 10.1016/j.dnarep.2015.11.024] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/14/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
The mismatch repair (MMR) family complexes Msh4-Msh5 and Mlh1-Mlh3 act with Exo1 and Sgs1-Top3-Rmi1 in a meiotic double strand break repair pathway that results in the asymmetric cleavage of double Holliday junctions (dHJ) to form crossovers. This review discusses how meiotic roles for Msh4-Msh5 and Mlh1-Mlh3 do not fit paradigms established for post-replicative MMR. We also outline models used to explain how these factors promote the formation of meiotic crossovers required for the accurate segregation of chromosome homologs during the Meiosis I division.
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Affiliation(s)
- Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA.
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7
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A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2016; 6:669-82. [PMID: 26747203 PMCID: PMC4777129 DOI: 10.1534/g3.115.024380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions.
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8
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Verma A, Rajput S, Kumar S, De S, Chakravarty AK, Kumar R, Datta TK. Differential histone modification status of spermatozoa in relation to fertility of buffalo bulls. J Cell Biochem 2015; 116:743-53. [PMID: 25501625 DOI: 10.1002/jcb.25029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/04/2014] [Indexed: 01/21/2023]
Abstract
In this study genome-wide di-methylated H3K4 (H3K4me2) and tri-methylated H3K27 (H3K27me3) modification profiles were analyzed in spermatozoa of buffalo bulls having wide fertility differences. The custom designed 4 × 180 K buffalo (Bubalus bubalis) ChIP-on-chip array was fabricated by employing array-based sequential hybridization using bovine and buffalo genomic DNA for comparative hybridization. The buffalo specific array developed had 177,440 features assembled from Coding sequences, Promoter and CpG regions comprising 2967 unique genes. A total of 84 genes for H3K4me2 and 80 genes for H3K27me3 were found differentially enriched in mature sperm of high and sub-fertile buffalo bulls. Gene Ontology analysis of these genes revealed their association with different cellular functions and biological processes. Genes identified as differentially enriched between high and sub-fertile bulls were found to be involved in the processes of germ cell development, spermatogenesis and embryonic development. This study presents the first genome-wide H3K4me2 and H3K27me3 profiling of buffalo bull sperm. Results provide a list of specific genes which could be made responsible for differential bull fertility.
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Affiliation(s)
- Arpana Verma
- Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132001, Haryana, India
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9
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Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
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10
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Genetic analysis of mlh3 mutations reveals interactions between crossover promoting factors during meiosis in baker's yeast. G3-GENES GENOMES GENETICS 2013; 3:9-22. [PMID: 23316435 PMCID: PMC3538346 DOI: 10.1534/g3.112.004622] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 10/30/2012] [Indexed: 12/01/2022]
Abstract
Crossing over between homologous chromosomes occurs during the prophase of meiosis I and is critical for chromosome segregation. In baker’s yeast, two heterodimeric complexes, Msh4-Msh5 and Mlh1-Mlh3, act in meiosis to promote interference-dependent crossing over. Mlh1-Mlh3 also plays a role in DNA mismatch repair (MMR) by interacting with Msh2-Msh3 to repair insertion and deletion mutations. Mlh3 contains an ATP-binding domain that is highly conserved among MLH proteins. To explore roles for Mlh3 in meiosis and MMR, we performed a structure−function analysis of eight mlh3 ATPase mutants. In contrast to previous work, our data suggest that ATP hydrolysis by both Mlh1 and Mlh3 is important for both meiotic and MMR functions. In meiotic assays, these mutants showed a roughly linear relationship between spore viability and genetic map distance. To further understand the relationship between crossing over and meiotic viability, we analyzed crossing over on four chromosomes of varying lengths in mlh3Δ mms4Δ strains and observed strong decreases (6- to 17-fold) in crossing over in all intervals. Curiously, mlh3Δ mms4Δ double mutants displayed spore viability levels that were greater than observed in mms4Δ strains that show modest defects in crossing over. The viability in double mutants also appeared greater than would be expected for strains that show such severe defects in crossing over. Together, these observations provide insights for how Mlh1-Mlh3 acts in crossover resolution and MMR and for how chromosome segregation in Meiosis I can occur in the absence of crossing over.
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11
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Zakharyevich K, Tang S, Ma Y, Hunter N. Delineation of joint molecule resolution pathways in meiosis identifies a crossover-specific resolvase. Cell 2012; 149:334-47. [PMID: 22500800 DOI: 10.1016/j.cell.2012.03.023] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/31/2012] [Accepted: 03/27/2012] [Indexed: 11/18/2022]
Abstract
At the final step of homologous recombination, Holliday junction-containing joint molecules (JMs) are resolved to form crossover or noncrossover products. The enzymes responsible for JM resolution in vivo remain uncertain, but three distinct endonucleases capable of resolving JMs in vitro have been identified: Mus81-Mms4(EME1), Slx1-Slx4(BTBD12), and Yen1(GEN1). Using physical monitoring of recombination during budding yeast meiosis, we show that all three endonucleases are capable of promoting JM resolution in vivo. However, in mms4 slx4 yen1 triple mutants, JM resolution and crossing over occur efficiently. Paradoxically, crossing over in this background is strongly dependent on the Blooms helicase ortholog Sgs1, a component of a well-characterized anticrossover activity. Sgs1-dependent crossing over, but not JM resolution per se, also requires XPG family nuclease Exo1 and the MutLγ complex Mlh1-Mlh3. Thus, Sgs1, Exo1, and MutLγ together define a previously undescribed meiotic JM resolution pathway that produces the majority of crossovers in budding yeast and, by inference, in mammals.
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Affiliation(s)
- Kseniya Zakharyevich
- Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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12
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Zakharyevich K, Ma Y, Tang S, Hwang PYH, Boiteux S, Hunter N. Temporally and biochemically distinct activities of Exo1 during meiosis: double-strand break resection and resolution of double Holliday junctions. Mol Cell 2010; 40:1001-15. [PMID: 21172664 PMCID: PMC3061447 DOI: 10.1016/j.molcel.2010.11.032] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 09/21/2010] [Accepted: 10/21/2010] [Indexed: 01/09/2023]
Abstract
The Rad2/XPG family nuclease, Exo1, functions in a variety of DNA repair pathways. During meiosis, Exo1 promotes crossover recombination and thereby facilitates chromosome segregation at the first division. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs). Nucleolytic resection of DSBs generates long 3' single-strand tails that undergo strand exchange with a homologous chromosome to form joint molecule (JM) intermediates. We show that meiotic DSB resection is dramatically reduced in exo1Δ mutants and test the idea that Exo1-catalyzed resection promotes crossing over by facilitating formation of crossover-specific JMs called double Holliday junctions (dHJs). Contrary to this idea, dHJs form at wild-type levels in exo1Δ mutants, implying that Exo1 has a second function that promotes resolution of dHJs into crossovers. Surprisingly, the dHJ resolution function of Exo1 is independent of its nuclease activities but requires interaction with the putative endonuclease complex, Mlh1-Mlh3. Thus, the DSB resection and procrossover functions of Exo1 during meiosis involve temporally and biochemically distinct activities.
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Affiliation(s)
- Kseniya Zakharyevich
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Yunmei Ma
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Shangming Tang
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Patty Yi-Hwa Hwang
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Serge Boiteux
- CEA SDV/IRCM UMR217 CNRS Radiobiologie Moléculaire et Cellulaire, CEA Fontenay aux Roses, France
| | - Neil Hunter
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
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13
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Cotton VE, Hoffmann ER, Borts RH. Distinct regulation of Mlh1p heterodimers in meiosis and mitosis in Saccharomyces cerevisiae. Genetics 2010; 185:459-67. [PMID: 20382827 PMCID: PMC2881129 DOI: 10.1534/genetics.110.116806] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 04/07/2010] [Indexed: 11/18/2022] Open
Abstract
Mlh1p forms three heterodimers that are important for mismatch repair (Mlh1p/Pms1p), crossing over during meiosis (Mlh1p/Mlh3p), and channeling crossover events into a specific pathway (Mlh1p/Mlh2p). All four proteins contain highly conserved ATPase domains and Pms1p has endonuclease activity. Studies of the functional requirements for Mlh1p/Pms1p in Saccharomyces cerevisae revealed an asymmetric contribution of the ATPase domains to repairing mismatches. Here we investigate the functional requirements of the Mlh1p and Mlh3p ATPase domains in meiosis by constructing separation of function mutations in Mlh3p. These mutations are analogous to mutations of Mlh1p that have been shown to lead to loss of ATP binding and/or ATP hydrolysis. Our data suggest that ATP binding by Mlh3p is required for meiotic crossing over while ATP hydrolysis is dispensable. This has been seen previously for Mlh1p. However, when mutations that affect ATP hydrolysis by both Mlh3p and Mlh1p are combined within a single cell, meiotic crossover frequencies are reduced. These observations suggest that the function of the Mlh1p/Mlh3p heterodimer requires both subunits to bind ATP but only one to efficiently hydrolyze it. Additionally, two different amino acid substitutions to the same residue (G97) in Mlh3p affect the minor mismatch repair function of Mlh3p while only one of them compromises its ability to promote crossing over. These studies thus reveal different functional requirements among the heterodimers formed by Mlh1p.
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Affiliation(s)
- Victoria E. Cotton
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom and Medical Research Council Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, United Kingdom
| | - Eva R. Hoffmann
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom and Medical Research Council Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, United Kingdom
| | - Rhona H. Borts
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom and Medical Research Council Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, United Kingdom
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14
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Arana ME, Holmes SF, Fortune JM, Moon AF, Pedersen LC, Kunkel TA. Functional residues on the surface of the N-terminal domain of yeast Pms1. DNA Repair (Amst) 2010; 9:448-57. [PMID: 20138591 PMCID: PMC2856611 DOI: 10.1016/j.dnarep.2010.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Revised: 01/07/2010] [Accepted: 01/07/2010] [Indexed: 01/21/2023]
Abstract
Saccharomyces cerevisiae MutLalpha is a heterodimer of Mlh1 and Pms1 that participates in DNA mismatch repair (MMR). Both proteins have weakly conserved C-terminal regions (CTDs), with the CTD of Pms1 harboring an essential endonuclease activity. These proteins also have conserved N-terminal domains (NTDs) that bind and hydrolyze ATP and bind to DNA. To better understand Pms1 functions and potential interactions with DNA and/or other proteins, we solved the 2.5A crystal structure of yeast Pms1 (yPms1) NTD. The structure is similar to the homologous NTDs of Escherichia coli MutL and human PMS2, including the site involved in ATP binding and hydrolysis. The structure reveals a number of conserved, positively charged surface residues that do not interact with other residues in the NTD and are therefore candidates for interactions with DNA, with the CTD and/or with other proteins. When these were replaced with glutamate, several replacements resulted in yeast strains with elevated mutation rates. Two replacements also resulted in NTDs with decreased DNA binding affinity in vitro, suggesting that these residues contribute to DNA binding that is important for mismatch repair. Elevated mutation rates also resulted from surface residue replacements that did not affect DNA binding, suggesting that these conserved residues serve other functions, possibly involving interactions with other MMR proteins.
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Affiliation(s)
- Mercedes E. Arana
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Shannon F. Holmes
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - John M. Fortune
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Andrea F. Moon
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, 27709
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15
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Zanders S, Alani E. The pch2Delta mutation in baker's yeast alters meiotic crossover levels and confers a defect in crossover interference. PLoS Genet 2009; 5:e1000571. [PMID: 19629178 PMCID: PMC2709914 DOI: 10.1371/journal.pgen.1000571] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 06/23/2009] [Indexed: 12/24/2022] Open
Abstract
Pch2 is a widely conserved protein that is required in baker's yeast for the organization of meiotic chromosome axes into specific domains. We provide four lines of evidence suggesting that it regulates the formation and distribution of crossover events required to promote chromosome segregation at Meiosis I. First, pch2Δ mutants display wild-type crossover levels on a small (III) chromosome, but increased levels on larger (VII, VIII, XV) chromosomes. Second, pch2Δ mutants show defects in crossover interference. Third, crossovers observed in pch2Δ require both Msh4-Msh5 and Mms4-Mus81 functions. Lastly, the pch2Δ mutation decreases spore viability and disrupts crossover interference in spo11 hypomorph strains that have reduced levels of meiosis-induced double-strand breaks. Based on these and previous observations, we propose a model in which Pch2 functions at an early step in crossover control to ensure that every homolog pair receives an obligate crossover. During meiosis, cells that ultimately become gametes (such as eggs or sperm) undergo a single round of DNA replication followed by two consecutive divisions. In most organisms, the segregation of chromosomes at the first meiotic division is dependent upon genetic exchange, or crossing over, at homologous sites along chromosomes. Crossing over must therefore be regulated to ensure that every pair of matched chromosomes receives at least one crossover. Matched chromosomes that do not receive a crossover frequently undergo missegregation at the first meiotic division, yielding gametes that do not contain the normal chromosome number. Such missegregation events have been linked to human infertility syndromes. We used a genetic approach to study meiotic crossover control in baker's yeast. Our work suggests that Pch2 is required in crossover control during meiosis; mutants lacking Pch2 display altered crossover levels and distribution. Furthermore, pch2 mutations cause enhanced gamete inviability in strains that are mildly defective in initiating recombination. Based on these observations, we hypothesize that Pch2 acts early in crossover control, in steps that occur prior to those proposed for previously characterized crossover-promoting factors.
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Affiliation(s)
- Sarah Zanders
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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16
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Clyne M, Offman J, Shanley S, Virgo JD, Radulovic M, Wang Y, Ardern-Jones A, Eeles R, Hoffmann E, Yu VPCC. The G67E mutation in hMLH1 is associated with an unusual presentation of Lynch syndrome. Br J Cancer 2009; 100:376-80. [PMID: 19142183 PMCID: PMC2634701 DOI: 10.1038/sj.bjc.6604860] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 12/02/2008] [Accepted: 12/03/2008] [Indexed: 12/20/2022] Open
Abstract
Germline mutations in the mismatch repair (MMR) genes are associated with Lynch syndrome, also known as hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Here, we characterise a variant of hMLH1 that confers a loss-of-function MMR phenotype. The mutation changes the highly conserved Gly67 residue to a glutamate (G67E) and is reminiscent of the hMLH1-p.Gly67Arg mutation, which is present in several Lynch syndrome cohorts. hMLH1-Gly67Arg has previously been shown to confer loss-of-function (Shimodaira et al, 1998), and two functional assays suggest that the hMLH1-Gly67Glu protein fails to sustain normal MMR functions. In the first assay, hMLH1-Gly67Glu abolishes the protein's ability to interfere with MMR in yeast. In the second assay, mutation of the analogous residue in yMLH1 (yMLH1-Gly64Glu) causes a loss-of-function mutator phenotype similar to yMLH1-Gly64Arg. Despite these molecular similarities, an unusual spectrum of tumours is associated with hMLH1-Gly67Glu, which is not typical of those associated with Lynch syndrome and differs from those found in families carrying the hMLH1-Gly67Arg allele. This suggests that hMLH1 may have different functions in certain tissues and/or that additional factors may modify the influence of hMLH1 mutations in causing Lynch syndrome.
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Affiliation(s)
- M Clyne
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - J Offman
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - S Shanley
- Cancer Genetics Unit, Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | - J D Virgo
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - M Radulovic
- Eukaryotic Chromatin Dynamics Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Y Wang
- Eukaryotic Chromatin Dynamics Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - A Ardern-Jones
- Cancer Genetics Unit, Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | - R Eeles
- Cancer Genetics Unit, Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- Translational Cancer Genetics Team, The Institute of Cancer Research, 15 Cotswold Road, Sutton SM25NG, UK
| | - E Hoffmann
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - V P C C Yu
- Cancer Genetics Unit, Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- Eukaryotic Chromatin Dynamics Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
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17
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Cotton VE, Hoffmann ER, Abdullah MFF, Borts RH. Interaction of genetic and environmental factors in Saccharomyces cerevisiae meiosis: the devil is in the details. Methods Mol Biol 2009; 557:3-20. [PMID: 19799172 DOI: 10.1007/978-1-59745-527-5_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
One of the most important principles of scientific endeavour is that the results be reproducible from lab to lab. Although research groups rarely redo the published experiments of their colleagues, research plans almost always rely on the work of someone else. The assumption is that if the same experiment were repeated in another lab, results would be so similar that the same interpretation would be favoured. This notion allows one researcher to compare his/her own results to earlier work from other labs. An essential prerequisite for this is that the experiments are done in identical conditions and therefore the methodology must be clearly stated. While this may be scientific common sense, adherence is difficult because "standard" methods vary from one laboratory to another in subtle ways that are often not reported. More importantly, for many years the field ofyeast meiotic recombination considered typical differences to be innocuous. This chapter will highlight the documented environmental and genetic variables that are known to influence meiotic recombination in Saccharomyces cerevisiae. Other potential methodological sources of variation in meiotic experiments are also discussed. A careful assessment of the effects of these variables, has led to insights into our understanding of the control of recombination and meiosis.
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Affiliation(s)
- Victoria E Cotton
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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18
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Wanat JJ, Kim KP, Koszul R, Zanders S, Weiner B, Kleckner N, Alani E. Csm4, in collaboration with Ndj1, mediates telomere-led chromosome dynamics and recombination during yeast meiosis. PLoS Genet 2008; 4:e1000188. [PMID: 18818741 PMCID: PMC2533701 DOI: 10.1371/journal.pgen.1000188] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 08/04/2008] [Indexed: 11/18/2022] Open
Abstract
Chromosome movements are a general feature of mid-prophase of meiosis. In budding yeast, meiotic chromosomes exhibit dynamic movements, led by nuclear envelope (NE)-associated telomeres, throughout the zygotene and pachytene stages. Zygotene motion underlies the global tendency for colocalization of NE-associated chromosome ends in a "bouquet." In this study, we identify Csm4 as a new molecular participant in these processes and show that, unlike the two previously identified components, Ndj1 and Mps3, Csm4 is not required for meiosis-specific telomere/NE association. Instead, it acts to couple telomere/NE ensembles to a force generation mechanism. Mutants lacking Csm4 and/or Ndj1 display the following closely related phenotypes: (i) elevated crossover (CO) frequencies and decreased CO interference without abrogation of normal pathways; (ii) delayed progression of recombination, and recombination-coupled chromosome morphogenesis, with resulting delays in the MI division; and (iii) nondisjunction of homologs at the MI division for some reason other than absence of (the obligatory) CO(s). The recombination effects are discussed in the context of a model where the underlying defect is chromosome movement, the absence of which results in persistence of inappropriate chromosome relationships that, in turn, results in the observed mutant phenotypes.
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Affiliation(s)
- Jennifer J. Wanat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Keun P. Kim
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Romain Koszul
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sarah Zanders
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Beth Weiner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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19
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Abstract
The four mammalian MutL homologs (MLH1, MLH3, PMS1, and PMS2) participate in a variety of events, including postreplicative DNA repair, prevention of homeologous recombination, and crossover formation during meiosis. In this latter role, MLH1-MLH3 heterodimers predominate and are essential for prophase I progression. Previous studies demonstrated that mice lacking Mlh1 exhibit a 90% reduction in crossing over at the Psmb9 hot spot while noncrossovers, which do not result in exchange of flanking markers but arise from the same double-strand break event, are unaffected. Using a PCR-based strategy that allows for detailed analysis of crossovers and noncrossovers, we show here that Mlh3(-/-) exhibit a 85-94% reduction in the number of crossovers at the Psmb9 hot spot. Most of the remaining crossovers in Mlh3(-/-) meiocytes represent simple exchanges similar to those seen in wild-type mice, with a small fraction (6%) representing complex events that can extend far from the initiation zone. Interestingly, we detect an increase of noncrossovers in Mlh3(-/-) spermatocytes. These results suggest that MLH3 functions predominantly with MLH1 to promote crossovers, while noncrossover events do not require these activities. Furthermore, these results indicate that approximately 10% of crossovers in the mouse are independent of MLH3, suggesting the existence of alternative crossover pathways in mammals.
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20
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Distinct effects of the recurrent Mlh1G67R mutation on MMR functions, cancer, and meiosis. Proc Natl Acad Sci U S A 2008; 105:4247-52. [PMID: 18337503 DOI: 10.1073/pnas.0800276105] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mutations in the human DNA mismatch repair (MMR) gene MLH1 are associated with hereditary nonpolyposis colorectal cancer (Lynch syndrome, HNPCC) and a significant proportion of sporadic colorectal cancer. The inactivation of MLH1 results in the accumulation of somatic mutations in the genome of tumor cells and resistance to the genotoxic effects of a variety of DNA damaging agents. To study the effect of MLH1 missense mutations on cancer susceptibility, we generated a mouse line carrying the recurrent Mlh1(G67R) mutation that is located in one of the ATP-binding domains of Mlh1. Although the Mlh1(G67R) mutation resulted in DNA repair deficiency in homozygous mutant mice, it did not affect the MMR-mediated cellular response to DNA damage, including the apoptotic response of epithelial cells in the intestinal mucosa to cisplatin, which was defective in Mlh1(-/-) mice but remained normal in Mlh1(G67R/G67R) mice. Similar to Mlh1(-/-) mice, Mlh1(G67R/G67R) mutant mice displayed a strong cancer predisposition phenotype. However, in contrast to Mlh1(-/-) mice, Mlh1(G67R/G67R) mutant mice developed significantly fewer intestinal tumors, indicating that Mlh1 missense mutations can affect MMR tumor suppressor functions in a tissue-specific manner. In addition, Mlh1(G67R/G67R) mice were sterile because of the inability of the mutant Mlh1(G67R) protein to interact with meiotic chromosomes at pachynema, demonstrating that the ATPase activity of Mlh1 is essential for fertility in mammals.
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21
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Gammie AE, Erdeniz N, Beaver J, Devlin B, Nanji A, Rose MD. Functional characterization of pathogenic human MSH2 missense mutations in Saccharomyces cerevisiae. Genetics 2007; 177:707-21. [PMID: 17720936 PMCID: PMC2034637 DOI: 10.1534/genetics.107.071084] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Hereditary nonpolyposis colorectal cancer (HNPCC) is associated with defects in DNA mismatch repair. Mutations in either hMSH2 or hMLH1 underlie the majority of HNPCC cases. Approximately 25% of annotated hMSH2 disease alleles are missense mutations, resulting in a single change out of 934 amino acids. We engineered 54 missense mutations in the cognate positions in yeast MSH2 and tested for function. Of the human alleles, 55% conferred strong defects, 8% displayed intermediate defects, and 38% showed no defects in mismatch repair assays. Fifty percent of the defective alleles resulted in decreased steady-state levels of the variant Msh2 protein, and 49% of the Msh2 variants lost crucial protein-protein interactions. Finally, nine positions are predicted to influence the mismatch recognition complex ATPase activity. In summary, the missense mutations leading to loss of mismatch repair defined important structure-function relationships and the molecular analysis revealed the nature of the deficiency for Msh2 variants expressed in the tumors. Of medical relevance are 15 human alleles annotated as pathogenic in public databases that conferred no obvious defects in mismatch repair assays. This analysis underscores the importance of functional characterization of missense alleles to ensure that they are the causative factor for disease.
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Affiliation(s)
- Alison E Gammie
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1014, USA.
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22
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Dion E, Li L, Jean M, Belzile F. An Arabidopsis MLH1 mutant exhibits reproductive defects and reveals a dual role for this gene in mitotic recombination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:431-40. [PMID: 17559505 DOI: 10.1111/j.1365-313x.2007.03145.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The eukaryotic DNA mismatch repair (MMR) system contributes to maintaining genome integrity and DNA sequence fidelity in at least two important ways: by correcting errors arising during DNA replication, and also by preventing recombination events between divergent sequences. This study aimed to investigate the role of one key MMR gene in recombination. We obtained a mutant line in which the AtMLH1 gene has been disrupted by the insertion of a T-DNA within the coding region. Transcript analysis indicated that no full-length transcript was produced in mutant plants. The loss of a functional AtMLH1 gene led to a significant reduction in fertility in both homozygotes and heterozygotes, and we observed a strong bias against transmission of the mutant allele. To investigate the role of AtMLH1 in mitotic recombination, the mutant was crossed to a series of recombination reporter lines. A strong decrease (72%) in the frequency of homologous recombination was observed in the mutant. However, the decline in recombination due to homeology was less severe in the Atmlh1 mutant than in a wild-type control. These data demonstrate a dual role for AtMLH1 in recombination: it is both required for recombination and acts to limit recombination between diverged sequences.
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Affiliation(s)
- Eric Dion
- Département de phytologie, 1243 Pavillon C.-E. Marchand, Université Laval, Québec, QC, G1K 7P4, Canada
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23
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Oh SD, Lao JP, Hwang PYH, Taylor AF, Smith GR, Hunter N. BLM ortholog, Sgs1, prevents aberrant crossing-over by suppressing formation of multichromatid joint molecules. Cell 2007; 130:259-72. [PMID: 17662941 PMCID: PMC2034285 DOI: 10.1016/j.cell.2007.05.035] [Citation(s) in RCA: 227] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 04/18/2007] [Accepted: 05/15/2007] [Indexed: 11/19/2022]
Abstract
Bloom's helicase (BLM) is thought to prevent crossing-over during DNA double-strand-break repair (DSBR) by disassembling double-Holliday junctions (dHJs) or by preventing their formation. We show that the Saccharomyces cerevisiae BLM ortholog, Sgs1, prevents aberrant crossing-over during meiosis by suppressing formation of joint molecules (JMs) comprising three and four interconnected duplexes. Sgs1 and procrossover factors, Msh5 and Mlh3, are antagonistic since Sgs1 prevents dHJ formation in msh5 cells and sgs1 mutation alleviates crossover defects of both msh5 and mlh3 mutants. We propose that differential activity of Sgs1 and procrossover factors at the two DSB ends effects productive formation of dHJs and crossovers and prevents multichromatid JMs and counterproductive crossing-over. Strand invasion of different templates by both DSB ends may be a common feature of DSBR that increases repair efficiency but also the likelihood of associated crossing-over. Thus, by disrupting aberrant JMs, BLM-related helicases maximize repair efficiency while minimizing the risk of deleterious crossing-over.
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Affiliation(s)
- Steve D. Oh
- Sections of Microbiology and Molecular & Cellular Biology, University of California Davis One Shields Ave., Davis, CA 95616, USA
| | - Jessica P. Lao
- Sections of Microbiology and Molecular & Cellular Biology, University of California Davis One Shields Ave., Davis, CA 95616, USA
| | - Patty Yi-Hwa Hwang
- Sections of Microbiology and Molecular & Cellular Biology, University of California Davis One Shields Ave., Davis, CA 95616, USA
| | - Andrew F. Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, P.O. Box 19024, Seattle, WA 98109, USA
| | - Gerald R. Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, P.O. Box 19024, Seattle, WA 98109, USA
| | - Neil Hunter
- Sections of Microbiology and Molecular & Cellular Biology, University of California Davis One Shields Ave., Davis, CA 95616, USA
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24
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Hooker GW, Roeder GS. A Role for SUMO in meiotic chromosome synapsis. Curr Biol 2006; 16:1238-43. [PMID: 16782016 DOI: 10.1016/j.cub.2006.04.045] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 04/25/2006] [Accepted: 04/28/2006] [Indexed: 11/29/2022]
Abstract
During meiotic prophase, homologous chromosomes engage in a complex series of interactions that ensure their proper segregation at meiosis I. A central player in these interactions is the synaptonemal complex (SC), a proteinaceous structure elaborated along the lengths of paired homologs. In mutants that fail to make SC, crossing over is decreased, and chromosomes frequently fail to recombine; consequently, many meiotic products are inviable because of aneuploidy. Here, we have investigated the role of the small ubiquitin-like protein modifier (SUMO) in SC formation during meiosis in budding yeast. We show that SUMO localizes specifically to synapsed regions of meiotic chromosomes and that this localization depends on Zip1, a major building block of the SC. A non-null allele of the UBC9 gene, which encodes the SUMO-conjugating enzyme, impairs Zip1 polymerization along chromosomes. The Ubc9 protein localizes to meiotic chromosomes, coincident with SUMO staining. In the zip1 mutant, SUMO localizes to discrete foci on chromosomes. These foci coincide with axial associations, where proteins involved in synapsis initiation are located. Our data suggest a model in which SUMO modification of chromosomal proteins promotes polymerization of Zip1 along chromosomes. The ubc9 mutant phenotype provides the first evidence for a cause-and-effect relationship between sumoylation and synapsis.
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Affiliation(s)
- Gillian W Hooker
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, USA
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25
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Martini E, Diaz RL, Hunter N, Keeney S. Crossover homeostasis in yeast meiosis. Cell 2006; 126:285-95. [PMID: 16873061 PMCID: PMC1949389 DOI: 10.1016/j.cell.2006.05.044] [Citation(s) in RCA: 277] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 03/22/2006] [Accepted: 05/02/2006] [Indexed: 01/17/2023]
Abstract
Crossovers produced by homologous recombination promote accurate chromosome segregation in meiosis and are controlled such that at least one forms per chromosome pair and multiple crossovers are widely spaced. Recombination initiates with an excess number of double-strand breaks made by Spo11 protein. Thus, crossover control involves a decision by which some breaks give crossovers while others follow a predominantly noncrossover pathway(s). To understand this decision, we examined recombination when breaks are reduced in yeast spo11 hypomorphs. We find that crossover levels tend to be maintained at the expense of noncrossovers and that genomic loci differ in expression of this "crossover homeostasis." These findings define a previously unsuspected manifestation of crossover control, i.e., that the crossover/noncrossover ratio can change to maintain crossovers. Our results distinguish between existing models of crossover control and support the hypothesis that an obligate crossover is a genetically programmed event tied to crossover interference.
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Affiliation(s)
- Emmanuelle Martini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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26
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Yang D, Goldsmith EB, Lin Y, Waldman BC, Kaza V, Waldman AS. Genetic exchange between homeologous sequences in mammalian chromosomes is averted by local homology requirements for initiation and resolution of recombination. Genetics 2006; 174:135-44. [PMID: 16816418 PMCID: PMC1569803 DOI: 10.1534/genetics.106.060590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examined the mechanism by which recombination between imperfectly matched sequences (homeologous recombination) is suppressed in mammalian chromosomes. DNA substrates were constructed, each containing a thymidine kinase (tk) gene disrupted by insertion of an XhoI linker and referred to as a "recipient" gene. Each substrate also contained one of several "donor" tk sequences that could potentially correct the recipient gene via recombination. Each donor sequence either was perfectly homologous to the recipient gene or contained homeologous sequence sharing only 80% identity with the recipient gene. Mouse Ltk(-) fibroblasts were stably transfected with the various substrates and tk(+) segregants produced via intrachromosomal recombination were recovered. We observed exclusion of homeologous sequence from gene conversion tracts when homeologous sequence was positioned adjacent to homologous sequence in the donor but not when homeologous sequence was surrounded by homology in the donor. Our results support a model in which homeologous recombination in mammalian chromosomes is suppressed by a nondestructive dismantling of mismatched heteroduplex DNA (hDNA) intermediates. We suggest that mammalian cells do not dismantle mismatched hDNA by responding to mismatches in hDNA per se but rather rejection of mismatched hDNA appears to be driven by a requirement for localized homology for resolution of recombination.
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Affiliation(s)
- Derek Yang
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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27
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Guillon H, Baudat F, Grey C, Liskay RM, de Massy B. Crossover and noncrossover pathways in mouse meiosis. Mol Cell 2006; 20:563-73. [PMID: 16307920 DOI: 10.1016/j.molcel.2005.09.021] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 08/26/2005] [Accepted: 09/27/2005] [Indexed: 11/29/2022]
Abstract
During meiosis, recombination between homologous chromosomes generates crossover (CR) and noncrossover (NCR) products. CRs establish connections between homologs, whereas intermediates leading to NCRs have been proposed to participate in homologous pairing. How these events are differentiated and regulated remains to be determined. We have developed a strategy to detect, quantify, and map NCRs in parallel to CRs, at the Psmb9 meiotic recombination hot spot, in male and female mouse germ lines. Our results report direct molecular evidence for distinct CR and NCR pathways of DNA double-strand break (DSB) repair in mouse meiosis based on three observations: both CRs and NCRs require Spo11, NCR products have shorter conversion tracts than CRs, and only CRs require the MutL homolog Mlh1. We show that both products are formed from middle to late pachytene of meiotic prophase and provide evidence for an Mlh1-independent CR pathway, where mismatch repair does not require Mlh1.
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Affiliation(s)
- Hélène Guillon
- Institute of Human Genetics, Centre National de la Recherche Scientifique, UPR1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Abstract
DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication and escape proofreading. MMR proteins also participate in many other DNA transactions, such that inactivation of MMR can have wide-ranging biological consequences, which can be either beneficial or detrimental. We begin this review by briefly considering the multiple functions of MMR proteins and the consequences of impaired function. We then focus on the biochemical mechanism of MMR replication errors. Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error.
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Affiliation(s)
- Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
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Abdullah MFF, Hoffmann ER, Cotton VE, Borts RH. A role for the MutL homologue MLH2 in controlling heteroduplex formation and in regulating between two different crossover pathways in budding yeast. Cytogenet Genome Res 2005; 107:180-90. [PMID: 15467363 DOI: 10.1159/000080596] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Accepted: 02/23/2004] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND AIMS Mismatch repair proteins play important roles during meiotic recombination in the budding yeast Saccharomyces cerevisiae and most eukaryotic organisms studied to date. To study the functions of the mismatch repair protein Mlh2p in meiosis, we constructed mlh2Delta strains and measured rates of crossing over, gene conversion, post-meiotic segregation and spore viability. We also analysed mlh1Delta, mlh3Delta, msh4Delta, msh5Delta, exo1Delta and mus81Delta mutant strains singularly and in various combinations. RESULTS Loss of MLH2 resulted in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies but had no apparent effect on crossing over. Deletion of MLH2 in mlh3Delta, msh4Delta or msh5Delta strains resulted in significant proportion of the "lost" crossovers found in single deletion strains being regained in some genetic intervals. We and others propose that there are at least two pathways to generate crossovers in yeast (Ross-Macdonald and Roeder, 1994; Zalevsky et al., 1999; Khazanehdari and Borts, 2000; Novak et al., 2001; de los Santos et al., 2003). Most recombination intermediates are processed by the "major", Msh4-dependent pathway, which requires the activity of Mlh1p/Mlh3p/Msh4p/Msh5p as well as a number of other proteins. The minor pathway(s) utilizes Mms4p/Mus81p. We suggest that the absence of Mlh2p allows some crossovers from the MSH4 pathway to traverse the MUS81-dependent pathway.
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Affiliation(s)
- M F F Abdullah
- Department of Genetics, University of Leicester, Leicester, UK
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Hoffmann ER, Borts RH. Meiotic recombination intermediates and mismatch repair proteins. Cytogenet Genome Res 2005; 107:232-48. [PMID: 15467368 DOI: 10.1159/000080601] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 03/21/2004] [Indexed: 11/19/2022] Open
Abstract
Mismatch repair proteins are a highly diverse group of proteins that interact with numerous DNA structures during DNA repair and replication. Here we review data for the role of Msh4, Msh5, Mlh1, Mlh3 and Exo1 in crossing over. Based on the paradigm of interactions developed from studies of mismatch repair, we propose models for the mechanism of crossover implementation by Msh4/Msh5 and Mlh1/Mlh3.
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Affiliation(s)
- E R Hoffmann
- Department of Genetics, University of Leicester, Leicester, UK
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Hoffmann ER, Eriksson E, Herbert BJ, Borts RH. MLH1 and MSH2 promote the symmetry of double-strand break repair events at the HIS4 hotspot in Saccharomyces cerevisiae. Genetics 2005; 169:1291-303. [PMID: 15654114 PMCID: PMC1449535 DOI: 10.1534/genetics.104.033399] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Double-strand breaks (DSBs) initiate meiotic recombination. The DSB repair model predicts that both genetic markers spanning the DSB should be included in heteroduplex DNA and be detectable as non-Mendelian segregations (NMS). In experiments testing this, a significant fraction of events do not conform to this prediction, as only one of the markers displays NMS (one-sided events). Two explanations have been proposed to account for the discrepancies between the predictions and experimental observations. One suggests that two-sided events are the norm but are "hidden" as heteroduplex repair frequently restores the parental configuration of one of the markers. Another explanation posits that one-sided events reflect events in which heteroduplex is formed predominantly on only one side of the DSB. In the absence of heteroduplex repair, the first model predicts that two-sided events would be revealed at the expense of one-sided events, while the second predicts no effect on the distribution of events when heteroduplex repair is lost. We tested these predictions by deleting the DNA mismatch repair genes MSH2 or MLH1 and analyzing the proportion of two-sided events. Unexpectedly, the results do not match the predictions of either model. In both mlh1Delta and msh2Delta, the proportion of two-sided events is significantly decreased relative to wild type. These observations can be explained in one of two ways. Either Msh2p/Mlh1p-independent mispair removal leads to restoration of one of the markers flanking the DSB site or Msh2p/Mlh1p actively promote two-sided events.
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Hoffmann ER, Borts RH. Trans events associated with crossovers are revealed in the absence of mismatch repair genes in Saccharomyces cerevisiae. Genetics 2005; 169:1305-10. [PMID: 15654113 PMCID: PMC1449536 DOI: 10.1534/genetics.104.033407] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic analysis of recombination in Saccharomyces cerevisiae has revealed products with structures not predicted by the double-strand break repair model of meiotic recombination. A particular type of recombinant containing trans heteroduplex DNA has been observed at two loci. Trans events were originally identified only in tetrads in which the non-Mendelian segregations were not associated with a crossover. Because of this, these events were proposed to have arisen from the unwinding of double Holliday junctions. Previous studies used palindromes, refractory to mismatch repair, as genetic markers whereas we have used a complementary approach of deleting mismatch repair proteins to identify heteroduplex DNA. We found that the markers occurred in trans and were associated with crossovers. In both mlh1Delta and msh2Delta strains, the frequency of trans events associated with a crossover exceeded that predicted from the random association of crossovers with noncrossover trans events. We propose two different models to account for trans events associated with crossovers and discuss the relevance to wild-type DSB repair.
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Lenzi ML, Smith J, Snowden T, Kim M, Fishel R, Poulos BK, Cohen PE. Extreme heterogeneity in the molecular events leading to the establishment of chiasmata during meiosis i in human oocytes. Am J Hum Genet 2005; 76:112-27. [PMID: 15558497 PMCID: PMC1196414 DOI: 10.1086/427268] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 11/08/2004] [Indexed: 01/08/2023] Open
Abstract
In humans, ~50% of conceptuses are chromosomally aneuploid as a consequence of errors in meiosis, and most of these aneuploid conceptuses result in spontaneous miscarriage. Of these aneuploidy events, 70% originate during maternal meiosis, with the majority proposed to arise as a direct result of defective crossing over during meiotic recombination in prophase I. By contrast, <1%-2% of mouse germ cells exhibit prophase I-related nondisjunction events. This disparity among mammalian species is surprising, given the conservation of genes and events that regulate meiotic progression. To understand the mechanisms that might be responsible for the high error rates seen in human females, we sought to further elucidate the regulation of meiotic prophase I at the molecular cytogenetic level. Given that these events occur during embryonic development in females, samples were obtained during a defined period of gestation (17-24 weeks). Here, we demonstrate that human oocytes enter meiotic prophase I and progress through early recombination events in a similar temporal framework to mice. However, at pachynema, when chromosomes are fully paired, we find significant heterogeneity in the localization of the MutL homologs, MLH1 and MLH3, among human oocyte populations. MLH1 and MLH3 have been shown to mark late-meiotic nodules that correlate well with--and are thought to give rise to--the sites of reciprocal recombination between homologous chromosomes, which suggests a possible 10-fold variation in the processing of nascent recombination events. If such variability persists through development and into adulthood, these data would suggest that as many as 30% of human oocytes are predisposed to aneuploidy as a result of prophase I defects in MutL homolog-related events.
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Affiliation(s)
- Michelle L. Lenzi
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Jenetta Smith
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Timothy Snowden
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Mimi Kim
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Richard Fishel
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Bradford K. Poulos
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
| | - Paula E. Cohen
- Departments of Molecular Genetics, Epidemiology and Population Health, and Pathology, Albert Einstein College of Medicine, Bronx, NY; and Kimmel Cancer Center, Philadelphia
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Abstract
DNA mismatch repair (MMR) guards the integrity of the genome in virtually all cells. It contributes about 1000-fold to the overall fidelity of replication and targets mispaired bases that arise through replication errors, during homologous recombination, and as a result of DNA damage. Cells deficient in MMR have a mutator phenotype in which the rate of spontaneous mutation is greatly elevated, and they frequently exhibit microsatellite instability at mono- and dinucleotide repeats. The importance of MMR in mutation avoidance is highlighted by the finding that defects in MMR predispose individuals to hereditary nonpolyposis colorectal cancer. In addition to its role in postreplication repair, the MMR machinery serves to police homologous recombination events and acts as a barrier to genetic exchange between species.
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Affiliation(s)
- Mark J Schofield
- Genetics and Biochemistry Branch, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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35
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John Wiley & Sons, Ltd.. Current awareness on yeast. Yeast 2003. [DOI: 10.1002/yea.947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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