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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Crickard JB, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. Genetics 2024; 227:iyae066. [PMID: 38657110 PMCID: PMC11228845 DOI: 10.1093/genetics/iyae066] [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: 11/12/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80% of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates to perform its role in crossover resolution. We performed a gene dosage screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3. Specifically, we looked for genes whose lowered dosage reduced meiotic crossing over using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. To our surprise we identified genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and in vivo. Partial complementation of Mlh3 crossover functions was observed when MLH3 was expressed under the control of the CLB1 promoter (NDT80 regulon), suggesting that Mlh3 function can be provided late in meiotic prophase at some functional cost. A model for how Dmc1 could facilitate Mlh1-Mlh3's role in crossover resolution is presented.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Piscitelli JM, Witte SJ, Sakinejad YS, Manhart CM. The Mlh1-Pms1 endonuclease uses ATP to preserve DNA discontinuities as strand discrimination signals to facilitate mismatch repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598860. [PMID: 38915520 PMCID: PMC11195183 DOI: 10.1101/2024.06.13.598860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
In eukaryotic post-replicative mismatch repair, MutS homologs (MSH) detect mismatches and recruit MLH complexes to nick the newly replicated DNA strand upon activation by the replication processivity clamp, PCNA. This incision enables mismatch removal and DNA repair. Biasing MLH endonuclease activity to the newly replicated DNA strand is crucial for repair. In reconstituted in vitro assays, PCNA is loaded at pre-existing discontinuities and orients the major MLH endonuclease Mlh1-Pms1/MLH1-PMS2 (yeast/human) to nick the discontinuous strand. In vivo, newly replicated DNA transiently contains discontinuities which are critical for efficient mismatch repair. How these discontinuities are preserved as strand discrimination signals during the window of time where mismatch repair occurs is unknown. Here, we demonstrate that yeast Mlh1-Pms1 uses ATP binding to recognize DNA discontinuities. This complex does not efficiently interact with PCNA, which partially suppresses ATPase activity, and prevents dissociation from the discontinuity. These data suggest that in addition to initiating mismatch repair by nicking newly replicated DNA, Mlh1-Pms1 protects strand discrimination signals, aiding in maintaining its own strand discrimination signposts. Our findings also highlight the significance of Mlh1-Pms1's ATPase activity for inducing DNA dissociation, as mutant proteins deficient in this function become immobilized on DNA post-incision, explaining in vivo phenotypes.
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Affiliation(s)
| | - Scott J. Witte
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Yasmine S. Sakinejad
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Carol M. Manhart
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
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3
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Brooks Crickard J, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566911. [PMID: 38014100 PMCID: PMC10680668 DOI: 10.1101/2023.11.13.566911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restricting MLH3 expression to roughly the time of crossover resolution resulted in a mlh3 null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
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4
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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5
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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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6
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Firnau MB, Plotz G, Zeuzem S, Brieger A. Key role of phosphorylation sites in ATPase domain and Linker region of MLH1 for DNA binding and functionality of MutLα. Sci Rep 2023; 13:12503. [PMID: 37532794 PMCID: PMC10397344 DOI: 10.1038/s41598-023-39750-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023] Open
Abstract
MutLα is essential for human DNA mismatch repair (MMR). It harbors a latent endonuclease, is responsible for recruitment of process associated proteins and is relevant for strand discrimination. Recently, we demonstrated that the MMR function of MutLα is regulated by phosphorylation of MLH1 at serine (S) 477. In the current study, we focused on S87 located in the ATPase domain of MLH1 and on S446, S456 and S477 located in its linker region. We analysed the phosphorylation-dependent impact of these amino acids on DNA binding, MMR ability and thermal stability of MutLα. We were able to demonstrate that phosphorylation at S87 of MLH1 inhibits DNA binding of MutLα. In addition, we detected that its MMR function seems to be regulated predominantly via phosphorylation of serines in the linker domain, which are also partially involved in the regulation of DNA binding. Furthermore, we found that the thermal stability of MutLα decreased in relation to its phosphorylation status implying that complete phosphorylation might lead to instability and degradation of MLH1. In summary, we showed here, for the first time, a phosphorylation-dependent regulation of DNA binding of MutLα and hypothesized that this might significantly impact its functional regulation during MMR in vivo.
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Affiliation(s)
- May-Britt Firnau
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Guido Plotz
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Stefan Zeuzem
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Angela Brieger
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Biomedical Research Laboratory, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
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7
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Wolf K, Kosinski J, Gibson TJ, Wesch N, Dötsch V, Genuardi M, Cordisco EL, Zeuzem S, Brieger A, Plotz G. A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation. Nucleic Acids Res 2023; 51:6307-6320. [PMID: 37224528 PMCID: PMC10325900 DOI: 10.1093/nar/gkad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.
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Affiliation(s)
- Karla Wolf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Centre for Structural Systems Biology (CSSB), Hamburg, 22607, Germany
| | - Toby J Gibson
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Maurizio Genuardi
- UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome00168, Italy
| | - Emanuela Lucci Cordisco
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome00168, Italy
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Angela Brieger
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Guido Plotz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
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8
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Investigation of the mechanisms leading to human sperm DNA damage based on transcriptome analysis by RNA-seq techniques. Reprod Biomed Online 2023; 46:11-19. [PMID: 36272896 DOI: 10.1016/j.rbmo.2022.08.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
RESEARCH QUESTION What are the molecular mechanisms leading to human sperm DNA damage? DESIGN Semen samples were collected and the sperm DNA fragmentation index (DFI) was assessed. Differentially expressed RNA in spermatozoa with a high (DFI ≥30%, experimental group) or normal (DFI <30%, control group) DFI were identified by RNA-sequencing (RNA-seq) technology, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed. Three differentially expressed RNA related to sperm DNA damage and repair, namely PMS1, TP53BP1 and TLK2, were validated using real-time quantitative (RT-qPCR). RESULTS A total of 19,970 expressed RNA were detected in the two groups. Compared with the control group, the expression levels of 189 RNA in the experimental group were significantly increased and those of 163 genes decreased. Gene Ontology enrichment analysis showed that these RNA were mainly concentrated in the ATPase-dependent transmembrane transport complex, extracellular exosome, somatic cell DNA recombination, protein binding, cytoplasm and regulation of localization. KEGG pathway analysis showed that these RNA were mainly related to the PI3K-Akt signalling pathway, endocytosis, p53 signalling pathway and cGMP-PKG signalling pathway. The RT-qPCR results showed that the expression levels of PMS1, TP53BP1 and TLK2 in the experimental group were significantly lower than in the control group (P = 0.01, 0.015 and 0.004, respectively), which was identical to the results of RNA sequencing. CONCLUSIONS Differentially expressed RNA related to sperm DNA damage and repair may be identified by RNA-seq technology, which provides new insights into the understanding of sperm DNA damage and repair, and will help to discover new biomarkers related to sperm DNA damage.
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9
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The unstructured linker of Mlh1 contains a motif required for endonuclease function which is mutated in cancers. Proc Natl Acad Sci U S A 2022; 119:e2212870119. [PMID: 36215471 PMCID: PMC9586283 DOI: 10.1073/pnas.2212870119] [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] [Indexed: 11/18/2022] Open
Abstract
DNA mismatch repair (MMR) prevents mutations caused by DNA-replication errors and suppresses multiple types of cancers. During MMR, the Mlh1-Pms1 complex is recruited to mispair-containing DNA and nicks the newly replicated DNA strand, targeting it for degradation and resynthesis. Here, we identified an amino acid sequence within the unstructured linker of Mlh1 required for endonuclease activity. This sequence functioned when moved within the Mlh1 linker or when moved to the Pms1 linker. These results reveal a functional role for the intrinsically disordered region, which is conserved from yeast to humans and is mutated in cancer, suggesting that it organizes the catalytically active complex even though the required sequence can be distant from the active site. Eukaryotic DNA mismatch repair (MMR) depends on recruitment of the Mlh1-Pms1 endonuclease (human MLH1-PMS2) to mispaired DNA. Both Mlh1 and Pms1 contain a long unstructured linker that connects the N- and carboxyl-terminal domains. Here, we demonstrated the Mlh1 linker contains a conserved motif (Saccharomyces cerevisiae residues 391–415) required for MMR. The Mlh1-R401A,D403A-Pms1 linker motif mutant protein was defective for MMR and endonuclease activity in vitro, even though the conserved motif could be >750 Å from the carboxyl-terminal endonuclease active site or the N-terminal adenosine triphosphate (ATP)-binding site. Peptides encoding this motif inhibited wild-type Mlh1-Pms1 endonuclease activity. The motif functioned in vivo at different sites within the Mlh1 linker and within the Pms1 linker. Motif mutations in human cancers caused a loss-of-function phenotype when modeled in S. cerevisiae. These results suggest that the Mlh1 motif promotes the PCNA-activated endonuclease activity of Mlh1-Pms1 via interactions with DNA, PCNA, RFC, or other domains of the Mlh1-Pms1 complex.
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10
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Furman CM, Wang TY, Zhao Q, Yugandhar K, Yu H, Alani E. Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair. Nucleic Acids Res 2021; 49:9327-9341. [PMID: 34390347 PMCID: PMC8450099 DOI: 10.1093/nar/gkab694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
The DNA mismatch repair (MMR) factor Mlh1–Pms1 contains long intrinsically disordered regions (IDRs) whose exact functions remain elusive. We performed cross-linking mass spectrometry to identify interactions within Mlh1–Pms1 and used this information to insert FRB and FKBP dimerization domains into their IDRs. Baker's yeast strains bearing these constructs were grown with rapamycin to induce dimerization. A strain containing FRB and FKBP domains in the Mlh1 IDR displayed a complete defect in MMR when grown with rapamycin. but removing rapamycin restored MMR functions. Strains in which FRB was inserted into the IDR of one MLH subunit and FKBP into the other subunit were also MMR defective. The MLH complex containing FRB and FKBP domains in the Mlh1 IDR displayed a rapamycin-dependent defect in Mlh1–Pms1 endonuclease activity. In contrast, linking the Mlh1 and Pms1 IDRs through FRB-FKBP dimerization inappropriately activated Mlh1–Pms1 endonuclease activity. We conclude that dynamic and coordinated rearrangements of the MLH IDRs both positively and negatively regulate how the MLH complex acts in MMR. The application of the FRB-FKBP dimerization system to interrogate in vivo functions of a critical repair complex will be useful for probing IDRs in diverse enzymes and to probe transient loss of MMR on demand.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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11
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Furman CM, Elbashir R, Alani E. Expanded roles for the MutL family of DNA mismatch repair proteins. Yeast 2020; 38:39-53. [PMID: 32652606 DOI: 10.1002/yea.3512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
The MutL family of DNA mismatch repair proteins plays a critical role in excising and repairing misincorporation errors during DNA replication. In many eukaryotes, members of this family have evolved to modulate and resolve recombination intermediates into crossovers during meiosis. In these organisms, such functions promote the accurate segregation of chromosomes during the meiosis I division. What alterations occurred in MutL homolog (MLH) family members that enabled them to acquire these new roles? In this review, we present evidence that the yeast Mlh1-Mlh3 and Mlh1-Mlh2 complexes have evolved novel enzymatic and nonenzymatic activities and protein-protein interactions that are critical for their meiotic functions. Curiously, even with these changes, these complexes retain backup and accessory roles in DNA mismatch repair during vegetative growth.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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12
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Mardenborough YSN, Nitsenko K, Laffeber C, Duboc C, Sahin E, Quessada-Vial A, Winterwerp HHK, Sixma TK, Kanaar R, Friedhoff P, Strick TR, Lebbink JHG. The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair. Nucleic Acids Res 2020; 47:11667-11680. [PMID: 31598722 PMCID: PMC6902014 DOI: 10.1093/nar/gkz834] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
DNA mismatch repair (MMR) maintains genome stability through repair of DNA replication errors. In Escherichia coli, initiation of MMR involves recognition of the mismatch by MutS, recruitment of MutL, activation of endonuclease MutH and DNA strand incision at a hemimethylated GATC site. Here, we studied the mechanism of communication that couples mismatch recognition to daughter strand incision. We investigated the effect of catalytically-deficient Cas9 as well as stalled RNA polymerase as roadblocks placed on DNA in between the mismatch and GATC site in ensemble and single molecule nanomanipulation incision assays. The MMR proteins were observed to incise GATC sites beyond a roadblock, albeit with reduced efficiency. This residual incision is completely abolished upon shortening the disordered linker regions of MutL. These results indicate that roadblock bypass can be fully attributed to the long, disordered linker regions in MutL and establish that communication during MMR initiation occurs along the DNA backbone.
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Affiliation(s)
| | - Katerina Nitsenko
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Charlie Laffeber
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Camille Duboc
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Enes Sahin
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Audrey Quessada-Vial
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | | | - Titia K Sixma
- Oncode Institute, the Netherlands.,Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Terence R Strick
- Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.,Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Superieure, CNRS, INSERM, PSL Research University, 75005 Paris, France.,Programme "Equipe Labellisée", Ligue Nationale contre le Cancer
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, the Netherlands
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13
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Kim Y, Furman CM, Manhart CM, Alani E, Finkelstein I. Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex. Nucleic Acids Res 2019; 47:1823-1835. [PMID: 30541127 PMCID: PMC6393296 DOI: 10.1093/nar/gky1244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins. Using a combination of genetics, biochemistry and single-molecule biophysics, we characterize how IDRs regulate the functions of the yeast MutLα (Mlh1-Pms1) mismatch repair (MMR) complex. Shortening or scrambling the IDRs in both subunits ablates MMR in vivo. Mlh1-Pms1 complexes with shorter IDRs that disrupt MMR retain wild-type DNA binding affinity but are impaired for diffusion on both naked and nucleosome-coated DNA. Moreover, the IDRs also regulate the adenosine triphosphate hydrolysis and nuclease activities that are encoded in the structured N- and C-terminal domains of the complex. This combination of phenotypes underlies the catastrophic MMR defect seen with the mutant MutLα in vivo. More broadly, this work highlights an unanticipated multi-functional role for IDRs in regulating both facilitated diffusion on chromatin and nucleolytic processing of a DNA substrate.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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14
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Al-Sweel N, Raghavan V, Dutta A, Ajith VP, Di Vietro L, Khondakar N, Manhart CM, Surtees JA, Nishant KT, Alani E. mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide. PLoS Genet 2017; 13:e1006974. [PMID: 28827832 PMCID: PMC5578695 DOI: 10.1371/journal.pgen.1006974] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/31/2017] [Accepted: 08/12/2017] [Indexed: 12/11/2022] Open
Abstract
Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker’s yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination maps were constructed for wild-type and MMR+ crossover-, MMR- crossover+, endonuclease defective and null mlh3 mutants in an S288c/YJM789 hybrid background. Compared to wild-type, all of the mlh3 mutants showed increases in the number of noncrossover events, consistent with recombination intermediates being resolved through alternative recombination pathways. Our observations provide a structure-function map for Mlh3 that reveals the importance of protein-protein interactions in regulating Mlh1-Mlh3’s enzymatic activity. They also illustrate how defective meiotic components can alter the fate of meiotic recombination intermediates, providing new insights for how meiotic recombination pathways are regulated. During meiosis, diploid germ cells that become eggs or sperm undergo a single round of DNA replication followed by two consecutive chromosomal divisions. The segregation of chromosomes at the first meiotic division is dependent in most organisms on at least one genetic exchange, or crossover event, between chromosome homologs. Homologs that do not receive a crossover frequently undergo nondisjunction at the first meiotic division, yielding gametes that lack chromosomes or contain additional copies. Such events have been linked to human disease and infertility. Recent studies suggest that the Mlh1-Mlh3 complex is an endonuclease that resolves recombination intermediates into crossovers. Interestingly, this complex also acts as a matchmaker in DNA mismatch repair (MMR) to remove DNA replication errors. How does one complex act in two different processes? We investigated this question by performing a mutational analysis of the baker’s yeast Mlh3 protein. Five mutations were identified that disrupted MMR but not crossing over, and one mutation disrupted crossing over while maintaining MMR. Using a combination of biochemical and genetic analyses to further characterize these mutants we illustrate the importance of protein-protein interactions for Mlh1-Mlh3’s activity. Importantly, our data illustrate how defective meiotic components can alter the outcome of meiotic recombination events. They also provide new insights for the basis of infertility syndromes.
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Affiliation(s)
- Najla Al-Sweel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Vandana Raghavan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Abhishek Dutta
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - V. P. Ajith
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Luigi Di Vietro
- Department of Life Sciences and Systems Biology, University of Turin, Via Verdi, Turin, Italy
| | - Nabila Khondakar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Carol M. Manhart
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jennifer A. Surtees
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - K. T. Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
- Center for Computation Modelling and Simulation, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
- * E-mail: (EA); (KTN)
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (EA); (KTN)
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15
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Claeys Bouuaert C, Keeney S. Distinct DNA-binding surfaces in the ATPase and linker domains of MutLγ determine its substrate specificities and exert separable functions in meiotic recombination and mismatch repair. PLoS Genet 2017; 13:e1006722. [PMID: 28505149 PMCID: PMC5448812 DOI: 10.1371/journal.pgen.1006722] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/30/2017] [Accepted: 03/29/2017] [Indexed: 11/18/2022] Open
Abstract
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA-binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes. In vitro, MutLγ displayed separable DNA-binding activities toward Holliday junctions (HJ) and, surprisingly, single-stranded DNA (ssDNA), which was not predicted from current models. MutLγ bound DNA cooperatively, could bind multiple substrates simultaneously, and formed higher-order complexes. FeBABE hydroxyl radical footprinting indicated that the DNA-binding interfaces of MutLγ for ssDNA and HJ substrates only partially overlap. Most contacts with HJ substrates were located in the linker regions of MutLγ, whereas ssDNA contacts mapped within linker regions as well as the N-terminal ATPase domains. Using yeast genetic assays for mismatch repair and meiotic recombination, we found that mutations within different DNA-binding surfaces exert separable effects in vivo. For example, mutations within the Mlh1 linker conferred little or no meiotic phenotype but led to mismatch repair deficiency. Interestingly, mutations in the N-terminal domain of Mlh1 caused a stronger meiotic defect than mlh1Δ, suggesting that the mutant proteins retain an activity that interferes with alternative recombination pathways. Furthermore, mlh3Δ caused more chromosome missegregation than mlh1Δ, whereas mlh1Δ but not mlh3Δ partially alleviated meiotic defects of msh5Δ mutants. These findings illustrate functional differences between Mlh1 and Mlh3 during meiosis and suggest that their absence impinges on chromosome segregation not only via reduced formation of crossovers. Taken together, our results offer insights into the structure-function relationships of the MutLγ complex and reveal unanticipated genetic relationships between components of the meiotic recombination machinery.
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Affiliation(s)
- Corentin Claeys Bouuaert
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center and Howard Hughes Medical Institute, New York, New York, United States of America
- * E-mail: (C.C.B.); (S.K.)
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center and Howard Hughes Medical Institute, New York, New York, United States of America
- * E-mail: (C.C.B.); (S.K.)
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16
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Arora S, Huwe PJ, Sikder R, Shah M, Browne AJ, Lesh R, Nicolas E, Deshpande S, Hall MJ, Dunbrack RL, Golemis EA. Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods. Cancer Biol Ther 2017; 18:519-533. [PMID: 28494185 DOI: 10.1080/15384047.2017.1326439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS.
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Affiliation(s)
- Sanjeevani Arora
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Peter J Huwe
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Rahmat Sikder
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Manali Shah
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Amanda J Browne
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Randy Lesh
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Emmanuelle Nicolas
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Sanat Deshpande
- b Immersion Science Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Michael J Hall
- c Department of Clinical Genetics , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Roland L Dunbrack
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
| | - Erica A Golemis
- a Molecular Therapeutics Program , Fox Chase Cancer Center , Philadelphia , PA , USA
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17
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Hingorani MM. Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair. DNA Repair (Amst) 2016; 38:24-31. [PMID: 26704427 PMCID: PMC4740199 DOI: 10.1016/j.dnarep.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS-our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation.
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18
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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: 9.4] [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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19
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Evolution of the methyl directed mismatch repair system in Escherichia coli. DNA Repair (Amst) 2015; 38:32-41. [PMID: 26698649 DOI: 10.1016/j.dnarep.2015.11.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/26/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022]
Abstract
DNA mismatch repair (MMR) repairs mispaired bases in DNA generated by replication errors. MutS or MutS homologs recognize mispairs and coordinate with MutL or MutL homologs to direct excision of the newly synthesized DNA strand. In most organisms, the signal that discriminates between the newly synthesized and template DNA strands has not been definitively identified. In contrast, Escherichia coli and some related gammaproteobacteria use a highly elaborated methyl-directed MMR system that recognizes Dam methyltransferase modification sites that are transiently unmethylated on the newly synthesized strand after DNA replication. Evolution of methyl-directed MMR is characterized by the acquisition of Dam and the MutH nuclease and by the loss of the MutL endonuclease activity. Methyl-directed MMR is present in a subset of Gammaproteobacteria belonging to the orders Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales, and a subset of the Alteromonadales (the EPVAA group) as well as in gammaproteobacteria that have obtained these genes by horizontal gene transfer, including the medically relevant bacteria Fluoribacter, Legionella, and Tatlockia and the marine bacteria Methylophaga and Nitrosococcus.
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20
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Groothuizen FS, Sixma TK. The conserved molecular machinery in DNA mismatch repair enzyme structures. DNA Repair (Amst) 2015; 38:14-23. [PMID: 26796427 DOI: 10.1016/j.dnarep.2015.11.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/05/2015] [Accepted: 11/30/2015] [Indexed: 12/25/2022]
Abstract
The machinery of DNA mismatch repair enzymes is highly conserved in evolution. The process is initiated by recognition of a DNA mismatch, and validated by ATP and the presence of a processivity clamp or a methylation mark. Several events in MMR promote conformational changes that lead to progression of the repair process. Here we discuss functional conformational changes in the MMR proteins and we compare the enzymes to paralogs in other systems.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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21
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Gallardo IF, Pasupathy P, Brown M, Manhart CM, Neikirk DP, Alani E, Finkelstein IJ. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10310-7. [PMID: 26325477 PMCID: PMC4624423 DOI: 10.1021/acs.langmuir.5b02416] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Single-molecule studies of protein-DNA interactions have shed critical insights into the molecular mechanisms of nearly every aspect of DNA metabolism. The development of DNA curtains-a method for organizing arrays of DNA molecules on a fluid lipid bilayer-has greatly facilitated these studies by increasing the number of reactions that can be observed in a single experiment. However, the utility of DNA curtains is limited by the challenges associated with depositing nanometer-scale lipid diffusion barriers onto quartz microscope slides. Here, we describe a UV lithography-based method for large-scale fabrication of chromium (Cr) features and organization of DNA molecules at these features for high-throughput single-molecule studies. We demonstrate this approach by assembling 792 independent DNA arrays (containing >900,000 DNA molecules) within a single microfluidic flowcell. As a first proof of principle, we track the diffusion of Mlh1-Mlh3-a heterodimeric complex that participates in DNA mismatch repair and meiotic recombination. To further highlight the utility of this approach, we demonstrate a two-lane flowcell that facilitates concurrent experiments on different DNA substrates. Our technique greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large statistical data sets from individual single-molecule experiments.
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Affiliation(s)
| | | | | | - Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
| | | | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
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22
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Smith CE, Bowen N, Graham WJ, Goellner EM, Srivatsan A, Kolodner RD. Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System. J Biol Chem 2015; 290:21580-90. [PMID: 26170454 PMCID: PMC4571882 DOI: 10.1074/jbc.m115.662189] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 11/07/2022] Open
Abstract
Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5′ nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3′ nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg2+ and Mn2+ for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR.
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Affiliation(s)
| | - Nikki Bowen
- From the Ludwig Institute for Cancer Research
| | | | | | | | - Richard D Kolodner
- From the Ludwig Institute for Cancer Research, the Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center, and the Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093
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23
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Guarné A, Charbonnier JB. Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:149-156. [PMID: 25701376 DOI: 10.1016/j.pbiomolbio.2015.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 01/31/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
DNA mismatch repair (MMR) is a conserved pathway that safeguards genome integrity by correcting replication errors. The coordinated actions of two proteins (MutS and MutL) initiate the mismatch repair response and defects in the genes encoding for these proteins have been linked to sporadic and hereditary cancers. The basic steps to repair a mismatch include recognizing the mismatch, discriminating the newly synthesized from the parental strand, removing and re-synthesizing the erroneous strand. Although the DNA mismatch repair pathway has been extensively studied over the last four decades, the strand discrimination mechanism has remained elusive in most organisms. Work over the last decade has brought significant progress onto this step of the pathway, in turn ascribing new and critical roles to the MutL protein. In this review, we describe biochemical, biophysical and structural analyses that have clarified how MutL aids at discriminating the newly synthesized strand from its template and marking it for removal.
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Affiliation(s)
- Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
| | - Jean-Baptiste Charbonnier
- CEA, IBITECS, Laboratoire de Biologie Structurale et Radiobiologie, CE-Saclay, F-91191 Gif sur Yvette, France; CNRS, URA 2096, F-91191 Gif sur Yvette, France.
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24
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Velho S, Fernandes MS, Leite M, Figueiredo C, Seruca R. Causes and consequences of microsatellite instability in gastric carcinogenesis. World J Gastroenterol 2014; 20:16433-16442. [PMID: 25469011 PMCID: PMC4248186 DOI: 10.3748/wjg.v20.i44.16433] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/24/2014] [Accepted: 09/05/2014] [Indexed: 02/06/2023] Open
Abstract
Loss of DNA mismatch repair (MMR) function, due to somatic or germline epi/genetic alterations of MMR genes leads to the accumulation of numerous mutations across the genome, creating a molecular phenotype known as microsatellite instability (MSI). In gastric cancer (GC), MSI occurs in about 15% to 30% of the cases. This review summarizes the current knowledge on the molecular mechanisms underlying the acquisition of MSI in GC as well as on the clinic, pathologic and molecular consequences of the MSI phenotype. Additionally, current therapeutic strategies for GC and their applicability in the MSI subset are also discussed.
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25
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Ranjha L, Anand R, Cejka P. The Saccharomyces cerevisiae Mlh1-Mlh3 heterodimer is an endonuclease that preferentially binds to Holliday junctions. J Biol Chem 2014; 289:5674-86. [PMID: 24443562 DOI: 10.1074/jbc.m113.533810] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MutLγ, a heterodimer of the MutL homologues Mlh1 and Mlh3, plays a critical role during meiotic homologous recombination. The meiotic function of Mlh3 is fully dependent on the integrity of a putative nuclease motif DQHAX2EX4E, inferring that the anticipated nuclease activity of Mlh1-Mlh3 is involved in the processing of joint molecules to generate crossover recombination products. Although a vast body of genetic and cell biological data regarding Mlh1-Mlh3 is available, mechanistic insights into its function have been lacking due to the unavailability of the recombinant protein complex. Here we expressed the yeast Mlh1-Mlh3 heterodimer and purified it into near homogeneity. We show that recombinant MutLγ is a nuclease that nicks double-stranded DNA. We demonstrate that MutLγ binds DNA with a high affinity and shows a marked preference for Holliday junctions. We also expressed the human MLH1-MLH3 complex and show that preferential binding to Holliday junctions is a conserved capacity of eukaryotic MutLγ complexes. Specific DNA recognition has never been observed with any other eukaryotic MutL homologue. MutLγ thus represents a new paradigm for the function of the eukaryotic MutL protein family. We provide insights into the mode of Holliday junction recognition and show that Mlh1-Mlh3 prefers to bind the open unstacked Holliday junction form. This further supports the model where MutLγ is part of a complex acting on joint molecules to generate crossovers in meiosis.
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Affiliation(s)
- Lepakshi Ranjha
- From the Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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26
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Rogacheva MV, Manhart CM, Chen C, Guarne A, Surtees J, Alani E. Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease. J Biol Chem 2014; 289:5664-73. [PMID: 24403070 DOI: 10.1074/jbc.m113.534644] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair.
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Affiliation(s)
- Maria V Rogacheva
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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