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1.
Cancer Genet ; 274-275: 54-58, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-37001204

RESUMEN

Lynch syndrome (LS) is an autosomal dominant inherited disorder, characterized by a predisposition to various cancers, mainly colorectal cancer (CRC). LS is caused by germline mutations in DNA mismatch repair genes i.e. mutL homolog 1 (MLH1), mutS homolog 2 (MSH2), mutS homolog 6 (MSH6), and post-meiotic segregation increased 2 (PMS2). In this study, we report a novel germline frameshift mutation in the MLH1 gene [NM_000249: exon1: c.99dup p.(Glu34ArgfsTer4)] in a 34-year-old male patient with LS. This MLH1 alteration has never been reported in any database or any publications. The frameshift mutation in MLH1 gene [NM_000249: exon1: c.99dup p.(Glu34ArgfsTer4)] was confirmed by Sanger sequencing conducted on peripheral blood of the proband. Meanwhile, Sanger sequencing results revealed the proband's uncle was the carrier. As multiple downstream germline frameshift mutations of this variation are pathogenic, such as MLH1 M35fs, N38fs, and S44fs, it is predicted that MLH1 p.(Glu34ArgfsTer4) might be also pathogenic. Meanwhile, this MLH1 mutation p.(Glu34ArgfsTer4) is predicted to be disease-causing by the MutationTaster software, as the duplication c.99dupA introduced a premature stop codon early in the translation, resulting in a non-functional protein. This study may contribute to the mutational spectrum of MLH1 leading to LS.


Asunto(s)
Neoplasias Colorrectales Hereditarias sin Poliposis , Masculino , Humanos , Adulto , Neoplasias Colorrectales Hereditarias sin Poliposis/genética , Neoplasias Colorrectales Hereditarias sin Poliposis/patología , Mutación del Sistema de Lectura , Predisposición Genética a la Enfermedad , Mutación de Línea Germinal , Homólogo 1 de la Proteína MutL/genética , Células Germinativas , Proteínas MutS/genética , Reparación de la Incompatibilidad de ADN
2.
J Biol Chem ; 298(11): 102505, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36126773

RESUMEN

MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.


Asunto(s)
Proteínas de Escherichia coli , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN , Humanos , Adenosina Trifosfato/metabolismo , Disparidad de Par Base , ADN/metabolismo , Reparación de la Incompatibilidad de ADN , Proteínas de Escherichia coli/metabolismo , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/genética , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/metabolismo , Proteína 2 Homóloga a MutS/genética , Proteína 2 Homóloga a MutS/metabolismo , Proteínas MutS/genética , Unión Proteica
3.
Genetics ; 221(4)2022 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-35686905

RESUMEN

Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.


Asunto(s)
Ribonucleótido Reductasas , Proteínas de Saccharomyces cerevisiae , Humanos , Desoxirribonucleósidos , Reparación de la Incompatibilidad de ADN , Reparación del ADN , Proteínas de Unión al ADN/metabolismo , Mutación , Proteína 2 Homóloga a MutS/genética , Proteína 2 Homóloga a MutS/metabolismo , Proteínas MutS/genética , Proteínas MutS/metabolismo , Ribonucleótido Reductasas/genética , Ribonucleótido Reductasas/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Especificidad por Sustrato
4.
J Biol Chem ; 298(7): 102102, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35667440

RESUMEN

Oxidative DNA damage contributes to aging and the pathogenesis of numerous human diseases including cancer. 8-hydroxyguanine (8-oxoG) is the major product of oxidative DNA lesions. Although OGG1-mediated base excision repair is the primary mechanism for 8-oxoG removal, DNA mismatch repair has also been implicated in processing oxidative DNA damage. However, the mechanism of the latter is not fully understood. Here, we treated human cells defective in various 8-oxoG repair factors with H2O2 and performed biochemical, live cell imaging, and chromatin immunoprecipitation sequencing analyses to determine their response to the treatment. We show that the mismatch repair processing of oxidative DNA damage involves cohesive interactions between mismatch recognition protein MutSα, histone mark H3K36me3, and H3K36 trimethyltransferase SETD2, which activates the ATM DNA damage signaling pathway. We found that cells depleted of MutSα or SETD2 accumulate 8-oxoG adducts and fail to trigger H2O2-induced ATM activation. Furthermore, we show that SETD2 physically interacts with both MutSα and ATM, which suggests a role for SETD2 in transducing DNA damage signals from lesion-bound MutSα to ATM. Consistently, MutSα and SETD2 are highly coenriched at oxidative damage sites. The data presented here support a model wherein MutSα, SETD2, ATM, and H3K36me3 constitute a positive feedback loop to help cells cope with oxidative DNA damage.


Asunto(s)
Reparación de la Incompatibilidad de ADN , N-Metiltransferasa de Histona-Lisina , Proteínas MutS , Estrés Oxidativo , Daño del ADN , Código de Histonas , N-Metiltransferasa de Histona-Lisina/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , Histonas/genética , Humanos , Peróxido de Hidrógeno/farmacología , Proteínas MutS/genética , Proteínas MutS/metabolismo
5.
Microb Genom ; 7(7)2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34292148

RESUMEN

Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, where they can establish chronic infections by adapting to the lower airway environment. To better understand the mechanisms contributing to a successful colonization by Achromobacter species, we sequenced the whole genome of 54 isolates from 26 patients with occasional and early/late chronic lung infection. We performed a phylogenetic analysis and compared virulence and resistance genes, genetic variants and mutations, and hypermutability mechanisms between chronic and occasional isolates. We identified five Achromobacter species as well as two non-affiliated genogroups (NGs). Among them were the frequently isolated Achromobacter xylosoxidans and four other species whose clinical importance is not yet clear: Achromobacter insuavis, Achromobacter dolens, Achromobacter insolitus and Achromobacter aegrifaciens. While A. insuavis and A. dolens were isolated only from chronically infected patients and A. aegrifaciens only from occasionally infected patients, the other species were found in both groups. Most of the occasional isolates lacked functional genes involved in invasiveness, chemotaxis, type 3 secretion system and anaerobic growth, whereas the great majority (>60%) of chronic isolates had these genomic features. Interestingly, almost all (n=22/23) late chronic isolates lacked functional genes involved in lipopolysaccharide production. Regarding antibiotic resistance, we observed a species-specific distribution of blaOXA genes, confirming what has been reported in the literature and additionally identifying blaOXA-2 in some A. insolitus isolates and observing no blaOXA genes in A. aegrifaciens or NGs. No significant difference in resistance genes was found between chronic and occasional isolates. The results of the mutator genes analysis showed that no occasional isolate had hypermutator characteristics, while 60% of early chronic (<1 year from first colonization) and 78% of late chronic (>1 year from first colonization) isolates were classified as hypermutators. Although all A. dolens, A. insuavis and NG isolates presented two different mutS genes, these seem to have a complementary rather than compensatory function. In conclusion, our results show that Achromobacter species can exhibit different adaptive mechanisms and some of these mechanisms might be more useful than others in establishing a chronic infection in CF patients, highlighting their importance for the clinical setting and the need for further studies on the less clinically characterized Achromobacter species.


Asunto(s)
Achromobacter/clasificación , Achromobacter/genética , Fibrosis Quística/microbiología , Genoma Bacteriano/genética , Infecciones por Bacterias Gramnegativas/microbiología , Infección Persistente/microbiología , Achromobacter/aislamiento & purificación , Farmacorresistencia Bacteriana/genética , Humanos , Pulmón/microbiología , Proteínas MutS/genética , Factores de Virulencia/genética , Secuenciación Completa del Genoma , beta-Lactamasas/genética
6.
Cells ; 10(5)2021 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-33925919

RESUMEN

Trinucleotide repeats are a peculiar class of microsatellites whose expansions are responsible for approximately 30 human neurological or developmental disorders. The molecular mechanisms responsible for these expansions in humans are not totally understood, but experiments in model systems such as yeast, transgenic mice, and human cells have brought evidence that the mismatch repair machinery is involved in generating these expansions. The present review summarizes, in the first part, the role of mismatch repair in detecting and fixing the DNA strand slippage occurring during microsatellite replication. In the second part, key molecular differences between normal microsatellites and those that show a bias toward expansions are extensively presented. The effect of mismatch repair mutants on microsatellite expansions is detailed in model systems, and in vitro experiments on mismatched DNA substrates are described. Finally, a model presenting the possible roles of the mismatch repair machinery in microsatellite expansions is proposed.


Asunto(s)
Reparación de la Incompatibilidad de ADN , Repeticiones de Microsatélite , Expansión de Repetición de Trinucleótido , Animales , ADN/metabolismo , Reparación del ADN , Genotipo , Humanos , Meiosis , Ratones , Ratones Transgénicos , Mitosis , Proteínas MutL/genética , Proteínas MutS/genética , Recombinación Genética , Saccharomyces cerevisiae , Schizosaccharomyces , Repeticiones de Trinucleótidos
7.
Microb Genom ; 7(2)2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33591248

RESUMEN

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.


Asunto(s)
Drosophila/microbiología , Proteínas MutL/genética , Proteínas MutS/genética , Spiroplasma/clasificación , Sustitución de Aminoácidos , Animales , Proteínas Bacterianas/genética , Evolución Molecular , Tasa de Mutación , Filogenia , Análisis de Secuencia de ADN , Spiroplasma/genética , Simbiosis
8.
Fungal Genet Biol ; 144: 103465, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32949723

RESUMEN

Wild-type filamentous fungus Neurospora crassa continues to grow its hyphae for a very lengthy period of time (>2 years), whereas mutations at the natural death (nd) locus shorten life span (approximately 20 days). By positional cloning based on heat augmented mutagen sensitivity of the nd strain, we identified a nonsense mutation in the msh1 gene, an eukaryotic homolog of bacterial MutS, and this mutation resulted in encoding non-functional polypeptide. By tagging with GFP, subcellular localization of the MSH1 protein in the mitochondria was observed, and knock out of the msh1 gene caused severe growth deficiency accompanying mitochondrial DNA (mtDNA) aberrations such as large-scale mtDNA deletions and rearrangements as seen in the nd strain. These results suggested that MSH1 may maintain mtDNA integrity. Thus, loss of function compromises mtDNA, leading to the acceleration of cellular aging.


Asunto(s)
ADN Mitocondrial/genética , Hifa/genética , Longevidad/genética , Proteínas MutS/genética , Secuencia de Aminoácidos/genética , Codón sin Sentido/genética , Proteínas de Unión al ADN/genética , Hifa/crecimiento & desarrollo , Mitocondrias/genética , Mitocondrias/metabolismo , Neurospora crassa/genética , Neurospora crassa/crecimiento & desarrollo , Recombinación Genética/genética , Saccharomyces cerevisiae/genética
9.
Isr Med Assoc J ; 22(1): 32-36, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31927803

RESUMEN

BACKGROUND: Evaluation of mismatch repair (MMR) deficiency is conducted via immunohistochemistry or by microsatellite instability (MSI) analysis. Heterogeneous immunohistochemistry staining for MMR proteins may show different patterns; however, according to current guidelines, all of those patterns should be interpreted as MMR proficient. This conclusion might lead to false negative results because although most cases of heterogeneity stem from technical factors and biological variability, other types of heterogeneity represent true MMR deficiency. OBJECTIVES: To identify a unique heterogeneity pattern that is associated with true MMR loss. METHODS: We analyzed 145 cases of colorectal carcinoma. Immunohistochemistry staining for MLH1, PMS2, MSH2, and MSH6 were performed. We defined geographic heterogeneity as areas of tumor nuclear staining adjacent to areas of loss of tumor nuclear staining with intact staining in the surrounding stroma. All cases were evaluated for the presence of geographic heterogeneity. In addition, 24 cases were also evaluated by MSI testing. RESULTS: Of the 145 cases, 24 (16.5%) were MMR deficient. Of the 24 cases for which MSI analysis was also available, 10 cases (41.7%) demonstrated biological heterogeneity, 5 (20.8%) demonstrated technical heterogeneity, and 2 (8.3%) demonstrated geographic heterogeneity. Only the two cases with geographic heterogeneity were MSI-high via MSI analysis. In addition, a germline mutation in MSH-6 was identified in one of these cases. CONCLUSIONS: Geographic heterogeneity may raise a suspicion for a MMR-deficient case, which should be further analyzed using additional methodologies such as MSI analysis.


Asunto(s)
Reparación de la Incompatibilidad de ADN/genética , Proteínas MutS/genética , Adenoma/genética , Adenoma/patología , Adulto , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Colorantes , Heterogeneidad Genética , Humanos , Masculino
10.
Eur J Hum Genet ; 28(5): 597-608, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-31822864

RESUMEN

Lynch syndrome (LS) is caused by germline defects in DNA mismatch repair (MMR) pathway, resulting in microsatellite instability (MSI-H) and loss of immunohistochemical staining (IHC) of the respective protein in tumor tissue. However, not in all clinically suspected LS patients with MSI-H tumors and IHC-loss, causative germline alterations in the MMR genes can be detected. Here, we investigated 128 of these patients to possibly define new pathomechanisms. A search for large genomic rearrangements and deep-intronic regulatory variants was performed via targeted next-generation sequencing (NGS) of exonic, intronic, and chromosomal regions upstream and downstream of MLH1, MSH2, MSH6, PMS2, MLH3, MSH3, PMS1, and EPCAM. Within this cohort, two different large rearrangements causative for LS were detected in three cases, belonging to two families (2.3%). The sensitivity to detect large rearrangements or copy number variations (CNV) was evaluated to be 50%. In 9 of the 128 patients (7%), previously overlooked pathogenic single-nucleotide variants (SNV) and two variants of uncertain significance (VUS) were identified in MLH1, MSH2, and MSH6. Pathogenic aberrations were not found in MLH3, MSH3, and PMS1. A potential effect on regulation was exerted for 19% of deep-intronic SNVs, predominantly located in chromosomal regions where the modification of histone proteins suggests an enhancer function. In conclusion, conventional variation analysis of coding regions is missing rare genomic rearrangements, nevertheless they should be analyzed. Assessment of deep-intronic SNVs is so far non-conclusive for medical questioning.


Asunto(s)
Neoplasias Colorrectales Hereditarias sin Poliposis/genética , Pruebas Genéticas/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Neoplasias Colorrectales Hereditarias sin Poliposis/diagnóstico , Molécula de Adhesión Celular Epitelial/genética , Pruebas Genéticas/normas , Secuenciación de Nucleótidos de Alto Rendimiento/normas , Humanos , Intrones , Proteínas MutL/genética , Proteínas MutS/genética , Polimorfismo Genético , Sensibilidad y Especificidad , Análisis de Secuencia de ADN/normas
11.
PLoS Genet ; 15(6): e1008201, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-31220082

RESUMEN

Accurate chromosome segregation during meiosis relies on the prior establishment of at least one crossover recombination event between homologous chromosomes. Most meiotic recombination intermediates that give rise to interhomolog crossovers are embedded within a hallmark chromosomal structure called the synaptonemal complex (SC), but the mechanisms that coordinate the processes of SC assembly (synapsis) and crossover recombination remain poorly understood. Among known structural components of the budding yeast SC, the Zip1 protein is unique for its independent role in promoting crossover recombination; Zip1 is specifically required for the large subset of crossovers that also rely on the meiosis-specific MutSγ complex. Here we report that adjacent regions within Zip1's N terminus encompass its crossover and synapsis functions. We previously showed that deletion of Zip1 residues 21-163 abolishes tripartite SC assembly and prevents robust SUMOylation of the SC central element component, Ecm11, but allows excess MutSγ crossover recombination. We find the reciprocal phenotype when Zip1 residues 2-9 or 10-14 are deleted; in these mutants SC assembles and Ecm11 is hyperSUMOylated, but MutSγ crossovers are strongly diminished. Interestingly, Zip1 residues 2-9 or 2-14 are required for the normal localization of Zip3, a putative E3 SUMO ligase and pro-MutSγ crossover factor, to Zip1 polycomplex structures and to recombination initiation sites. By contrast, deletion of Zip1 residues 15-20 does not detectably prevent Zip3's localization at Zip1 polycomplex and supports some MutSγ crossing over but prevents normal SC assembly and Ecm11 SUMOylation. Our results highlight distinct N terminal regions that are differentially critical for Zip1's roles in crossing over and SC assembly; we speculate that the adjacency of these regions enables Zip1 to serve as a liaison, facilitating crosstalk between the two processes by bringing crossover recombination and synapsis factors within close proximity of one another.


Asunto(s)
Proteínas de Ciclo Celular/genética , Intercambio Genético , Recombinación Homóloga/genética , Proteínas Nucleares/genética , Proteínas de Saccharomyces cerevisiae/genética , Complejo Sinaptonémico/genética , Centrómero/genética , Emparejamiento Cromosómico/genética , Segregación Cromosómica/genética , Meiosis/genética , Complejos Multiproteicos , Proteínas MutS/genética , Proteínas Recombinantes/genética , Saccharomyces cerevisiae/genética , Sumoilación/genética , Ubiquitina-Proteína Ligasas/genética
12.
PLoS Genet ; 15(6): e1008177, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-31170160

RESUMEN

During meiotic prophase I, double-strand breaks (DSBs) initiate homologous recombination leading to non-crossovers (NCOs) and crossovers (COs). In mouse, 10% of DSBs are designated to become COs, primarily through a pathway dependent on the MLH1-MLH3 heterodimer (MutLγ). Mlh3 contains an endonuclease domain that is critical for resolving COs in yeast. We generated a mouse (Mlh3DN/DN) harboring a mutation within this conserved domain that is predicted to generate a protein that is catalytically inert. Mlh3DN/DN males, like fully null Mlh3-/- males, have no spermatozoa and are infertile, yet spermatocytes have grossly normal DSBs and synapsis events in early prophase I. Unlike Mlh3-/- males, mutation of the endonuclease domain within MLH3 permits normal loading and frequency of MutLγ in pachynema. However, key DSB repair factors (RAD51) and mediators of CO pathway choice (BLM helicase) persist into pachynema in Mlh3DN/DN males, indicating a temporal delay in repair events and revealing a mechanism by which alternative DSB repair pathways may be selected. While Mlh3DN/DN spermatocytes retain only 22% of wildtype chiasmata counts, this frequency is greater than observed in Mlh3-/- males (10%), suggesting that the allele may permit partial endonuclease activity, or that other pathways can generate COs from these MutLγ-defined repair intermediates in Mlh3DN/DN males. Double mutant mice homozygous for the Mlh3DN/DN and Mus81-/- mutations show losses in chiasmata close to those observed in Mlh3-/- males, indicating that the MUS81-EME1-regulated crossover pathway can only partially account for the increased residual chiasmata in Mlh3DN/DN spermatocytes. Our data demonstrate that mouse spermatocytes bearing the MLH1-MLH3DN/DN complex display the proper loading of factors essential for CO resolution (MutSγ, CDK2, HEI10, MutLγ). Despite these functions, mice bearing the Mlh3DN/DN allele show defects in the repair of meiotic recombination intermediates and a loss of most chiasmata.


Asunto(s)
Proteínas de Unión al ADN/genética , Endonucleasas/genética , Profase Meiótica I/genética , Proteínas MutL/genética , Animales , Emparejamiento Cromosómico/genética , Intercambio Genético , Roturas del ADN de Doble Cadena , Reparación del ADN/genética , Recombinación Homóloga/genética , Masculino , Meiosis/genética , Ratones , Homólogo 1 de la Proteína MutL/genética , Proteínas MutS/genética , Recombinasa Rad51/genética , Espermatocitos/crecimiento & desarrollo , Espermatocitos/metabolismo
13.
Nat Commun ; 10(1): 2354, 2019 05 29.
Artículo en Inglés | MEDLINE | ID: mdl-31142748

RESUMEN

In allopolyploids, correct chromosome segregation requires suppression of non-homologous crossovers while levels of homologous crossovers are ensured. To date, no mechanism able to specifically inhibit non-homologous crossovers has been described in allopolyploids other than in bread wheat. Here, we show that reducing the number of functional copies of MSH4, an essential gene for the main crossover pathway, prevents non-homologous crossovers in allotetraploid Brassica napus. We show that non-homologous crossovers originate almost exclusively from the MSH4-dependent recombination pathway and that their numbers decrease when MSH4 returns to single copy in B. napus; by contrast, homologous crossovers remain unaffected by MSH4 duplicate loss. We also demonstrate that MSH4 systematically returns to single copy following numerous independent polyploidy events, a pattern that is probably not by chance. These results suggest that stabilization of allopolyploid meiosis can be enhanced by loss of a key meiotic recombination gene.


Asunto(s)
Brassica napus/genética , Segregación Cromosómica/genética , Intercambio Genético/genética , Meiosis/genética , Proteínas MutS/genética , Poliploidía , Cromosomas de las Plantas/metabolismo , Variaciones en el Número de Copia de ADN , Recombinación Homóloga
14.
Nat Commun ; 10(1): 836, 2019 02 19.
Artículo en Inglés | MEDLINE | ID: mdl-30783107

RESUMEN

Consensus ranking of protein affinity to identify point mutations has not been established. Therefore, analytical techniques that can detect subtle variations without interfering with native biomolecular interactions are required. Here we report a rapid method to identify point mutations by a single nanoparticle sensing system. DNA-directed gold crystallization forms rod-like nanoparticles with bridges based on structural design. The nanoparticles enhance Rayleigh light scattering, achieving high refractive-index sensitivity, and enable the system to monitor even a small number of protein-DNA binding events without interference. Analysis of the binding affinity can compile an atlas to distinguish the potential of various point mutations recognized by MutS protein. We use the atlas to analyze the presence and type of single point mutations in BRCA1 from samples of human breast and ovarian cancer cell lines. The strategy of synthesis-by-design of plasmonic nanoparticles for sensors enables direct identification of subtle biomolecular binding distortions and genetic alterations.


Asunto(s)
Análisis Mutacional de ADN/métodos , Nanopartículas del Metal/química , Mutación Puntual , Proteína BRCA1/genética , Línea Celular Tumoral , Cristalización , Análisis Mutacional de ADN/instrumentación , Femenino , Oro , Humanos , Límite de Detección , Células MCF-7 , Proteínas MutS/genética
15.
BMC Microbiol ; 18(1): 95, 2018 08 30.
Artículo en Inglés | MEDLINE | ID: mdl-30165819

RESUMEN

BACKGROUND: The functioning of DNA repair systems is based on correct interactions between proteins involved in DNA repair. Very Short Patch (VSP) repair is a DNA repair system that corrects mismatches resulting from the deamination of 5-methylcytosine. The key enzyme in the VSP system is Vsr endonuclease, which can cleave mismatched DNA independently of accessory proteins. Until now, in vivo activity has only been shown for V.EcoKDcm - the only Vsr endonuclease in Escherichia coli. Additionally, the VSP system of E. coli is the only one for which interactions between proteins of the system have been demonstrated. Neisseria gonorrhoeae FA1090 is the first bacterium that we previously demonstrated to encode two active in vitro Vsr endonucleases: V.NgoAXIII and V.NgoAXIV. RESULTS: We elucidate the mutator phenotype of N. gonorrhoeae mutants with disrupted genes encoding V.NgoAXIII or V.NgoAXIV endonuclease. Furthermore, we investigate the interactions between gonococcal Vsr endonucleases and MutL and MutS proteins. The Vsr endonucleases physically interact with gonococcal MutL protein but not with MutS protein. In the presence of the MutL protein, the efficiency of DNA cleavage by both V.NgoAXIII and V.NgoAXIV endonucleases increases, resulting in a decrease in the amount of Vsr enzyme required to complete digestion of mismatched DNA. Both Vsr endonucleases are also stimulated in vitro by the MutL protein of E. coli. In turn, the gonococcal MutS protein hinders DNA cleavage by the Vsr endonucleases. However, this effect is overridden in the presence of MutL, and furthermore, the simultaneous presence of MutL and MutS causes an increase in the efficiency of DNA cleavage by the Vsr endonucleases compared to the reaction catalyzed by V.NgoAXIII or V.NgoAXIV alone. CONCLUSIONS: For the first time, interactions between proteins of the DNA repair system encoded by N. gonorrhoeae that are responsible for the correction of mismatches resulting from the 5-methylcytosine deamination were identified. The increase in activity of Vsr endonucleases in the presence of MutL protein could allow for reduced synthesis of the Vsr endonucleases in cells, and the susceptibility of gonococcal Vsr endonucleases on MutL protein of E. coli implies a universal mechanism of Vsr stimulation by MutL protein.


Asunto(s)
Endodesoxirribonucleasas/metabolismo , Proteínas MutL/metabolismo , Proteínas MutS/metabolismo , Neisseria gonorrhoeae/enzimología , 5-Metilcitosina/metabolismo , Proteínas Bacterianas , División del ADN , Reparación del ADN , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , Proteínas de Unión al ADN , Endodesoxirribonucleasas/genética , Endonucleasas/genética , Endonucleasas/metabolismo , Activación Enzimática , Escherichia coli , Proteínas de Escherichia coli , Proteínas MutL/genética , Proteínas MutS/genética , Mutación , Neisseria gonorrhoeae/genética , Especificidad por Sustrato
16.
J Biol Chem ; 293(20): 7811-7823, 2018 05 18.
Artículo en Inglés | MEDLINE | ID: mdl-29610279

RESUMEN

Histone H3 trimethylation at lysine 36 (H3K36me3) is an important histone mark involved in both transcription elongation and DNA mismatch repair (MMR). It is known that H3K36me3 recruits the mismatch-recognition protein MutSα to replicating chromatin via its physical interaction with MutSα's PWWP domain, but the exact role of H3K36me3 in transcription is undefined. Using ChIP combined with whole-genome DNA sequencing analysis, we demonstrate here that H3K36me3, together with MutSα, is involved in protecting against mutation, preferentially in actively transcribed genomic regions. We found that H3K36me3 and MutSα are much more co-enriched in exons and actively transcribed regions than in introns and nontranscribed regions. The H3K36me3-MutSα co-enrichment correlated with a much lower mutation frequency in exons and actively transcribed regions than in introns and nontranscribed regions. Correspondingly, depleting H3K36me3 or disrupting the H3K36me3-MutSα interaction elevated the spontaneous mutation frequency in actively transcribed genes, but it had little influence on the mutation frequency in nontranscribed or transcriptionally inactive regions. Similarly, H2O2-induced mutations, which mainly cause base oxidations, preferentially occurred in actively transcribed genes in MMR-deficient cells. The data presented here suggest that H3K36me3-mediated MMR preferentially safeguards actively transcribed genes not only during replication by efficiently correcting mispairs in early replicating chromatin but also during transcription by directly or indirectly removing DNA lesions associated with a persistently open chromatin structure.


Asunto(s)
Reparación de la Incompatibilidad de ADN , Histonas/genética , Proteínas MutS/genética , Mutación , Transcripción Genética , Antígenos CD79/genética , Antígenos CD79/metabolismo , Sistemas CRISPR-Cas , Calreticulina/genética , Calreticulina/metabolismo , Proliferación Celular , Cromatina/química , Cromatina/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Puntos de Control de la Fase G1 del Ciclo Celular/genética , Factor de Transcripción GATA1/genética , Factor de Transcripción GATA1/metabolismo , Edición Génica , Regulación de la Expresión Génica , Células HeLa , N-Metiltransferasa de Histona-Lisina/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , Histonas/metabolismo , Humanos , Proteínas MutS/metabolismo , Proteínas Proto-Oncogénicas c-myc/genética , Proteínas Proto-Oncogénicas c-myc/metabolismo , Transducción de Señal , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo , Secuenciación Completa del Genoma
17.
Cell Res ; 26(7): 775-86, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-27255792

RESUMEN

Expansion of (CAG)•(CTG) repeats causes a number of familial neurodegenerative disorders. Although the underlying mechanism remains largely unknown, components involved in DNA mismatch repair, particularly mismatch recognition protein MutSß (a MSH2-MSH3 heterodimer), are implicated in (CAG)•(CTG) repeat expansion. In addition to recognizing small insertion-deletion loop-outs, MutSß also specifically binds DNA hairpin imperfect heteroduplexes formed within (CAG)n•(CTG)n sequences. However, whether or not and how MutSß binding triggers expansion of (CAG)•(CTG) repeats remain unknown. We show here that purified recombinant MutSß physically interacts with DNA polymerase ß (Polß) and stimulates Polß-catalyzed (CAG)n or (CTG)n hairpin retention. Consistent with these in vitro observations, MutSß and Polß interact with each other in vivo, and colocalize at (CAG)•(CTG) repeats during DNA replication. Our data support a model for error-prone processing of (CAG)n or (CTG)n hairpins by MutSß and Polß during DNA replication and/or repair: MutSß recognizes (CAG)n or (CTG)n hairpins formed in the nascent DNA strand, and recruits Polß to the complex, which then utilizes the hairpin as a primer for extension, leading to (CAG)•(CTG) repeat expansion. This study provides a novel mechanism for trinucleotide repeat expansion in both dividing and non-dividing cells.


Asunto(s)
ADN Polimerasa beta/metabolismo , ADN/biosíntesis , Proteínas MutS/metabolismo , Secuencia de Bases , Reparación de la Incompatibilidad de ADN , ADN Polimerasa III/genética , ADN Polimerasa III/metabolismo , ADN Polimerasa beta/genética , Replicación del ADN , Células HeLa , Humanos , Secuencias Invertidas Repetidas , Microscopía Confocal , Proteínas MutS/genética , Unión Proteica , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/aislamiento & purificación , Expansión de Repetición de Trinucleótido
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