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Genes Jan 2020The fission yeast--has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have... (Review)
Review
The fission yeast--has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
Topics: Cell Division; DNA Breaks, Double-Stranded; DNA Helicases; DNA Repair; DNA Replication; DNA-Binding Proteins; Mitosis; Recombination, Genetic; Schizosaccharomyces; Schizosaccharomyces pombe Proteins
PubMed: 31936815
DOI: 10.3390/genes11010079 -
Genes Feb 2022Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy... (Review)
Review
Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy of PARP inhibitors in treating BRCA2 cancers and RECQ inhibitors in treating cancers with microsatellite instabilities. Thus, understanding the cellular role of recombination mediators is critically important, both to improve current therapies and develop new ones that target these pathways. Our mechanistic understanding of BRCA2 and RECQ began in . Here, we review the cellular roles of RecF and RecQ, often considered functional homologs of these proteins in bacteria. Although these proteins were originally isolated as genes that were required during replication in sexual cell cycles that produce recombinant products, we now know that their function is similarly required during replication in asexual or mitotic-like cell cycles, where recombination is detrimental and generally not observed. Cells mutated in these gene products are unable to protect and process replication forks blocked at DNA damage, resulting in high rates of cell lethality and recombination events that compromise genome integrity during replication.
Topics: Bacterial Proteins; DNA-Binding Proteins; Escherichia coli; Escherichia coli Proteins; Genomic Instability; Humans; Neoplasms; Recombination, Genetic
PubMed: 35327990
DOI: 10.3390/genes13030437 -
DNA Repair Apr 2019There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly... (Review)
Review
There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly implicated in genetic diseases including cancer, rapid aging, and infertility. MCM8/9 are recent additions to the catalog of helicases involved in recombination, and so far, the evidence is sparse, making assignment of function difficult. Mutations in MCM8/9 correlate principally with primary ovarian failure/insufficiency (POF/POI) and infertility indicating a meiotic defect. However, they also act when replication forks collapse/break shuttling products into mitotic recombination and several mutations are found in various somatic cancers. This review puts MCM8/9 in context with other replication and recombination helicases to narrow down its genomic maintenance role. We discuss the known structure/function relationship, the mutational spectrum, and dissect the available cellular and organismal data to better define its role in recombination.
Topics: Animals; DNA Replication; Genome; Humans; Infertility; Meiosis; Minichromosome Maintenance Proteins; Recombination, Genetic
PubMed: 30743181
DOI: 10.1016/j.dnarep.2019.02.003 -
MBio Mar 2019Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic...
Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR. Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.
Topics: Europe; Evolution, Molecular; Forests; Genetic Variation; Genotype; Mitosis; North America; Phytophthora; Plant Diseases; Recombination, Genetic; Sequence Analysis, DNA
PubMed: 30862749
DOI: 10.1128/mBio.02452-18 -
Methods in Molecular Biology (Clifton,... 2021DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides...
DNA break lesions pose a serious threat to the integrity of the genome. Eukaryotic cells can repair these lesions using the homologous recombination pathway that guides the repair reaction by using a homologous DNA template. The budding yeast Saccharomyces cerevisiae is an excellent model system with which to study this repair mechanism and the resulting patterns of genomic change resulting from it. In this chapter, we describe an approach that utilizes whole-genome sequencing data to support the analysis of tracts of loss-of-heterozygosity (LOH) that can arise from mitotic recombination in the context of the entire diploid yeast genome. The workflow and the discussion in this chapter are intended to enable classically trained molecular biologists and geneticists with limited experience in computational methods to conceptually understand and execute the steps of genome-wide LOH analysis as well as to adapt and apply them to their own specific studies and experimental models.
Topics: Chromosomes, Fungal; Computational Biology; Loss of Heterozygosity; Mitosis; Recombination, Genetic; Saccharomyces cerevisiae; Whole Genome Sequencing; Workflow
PubMed: 32840782
DOI: 10.1007/978-1-0716-0644-5_15 -
Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated Gene Cluster in the Yeast .Genetics Jun 2017In the yeast , the genes encoding the metallothionein protein Cup1 are located in a tandem array on chromosome VIII. Using a diploid strain that is heterozygous for an...
In the yeast , the genes encoding the metallothionein protein Cup1 are located in a tandem array on chromosome VIII. Using a diploid strain that is heterozygous for an insertion of a selectable marker () within this tandem array, and heterozygous for markers flanking the array, we measured interhomolog recombination and intra/sister chromatid exchange in the locus. The rate of intra/sister chromatid recombination exceeded the rate of interhomolog recombination by >10-fold. Loss of the Rad51 and Rad52 proteins, required for most interhomolog recombination, led to a relatively small reduction of recombination in the array. Although interhomolog mitotic recombination in the locus is elevated relative to the average genomic region, we found that interhomolog meiotic recombination in the array is reduced compared to most regions. Lastly, we showed that high levels of copper (previously shown to elevate transcription) lead to a substantial elevation in rate of both interhomolog and intra/sister chromatid recombination in the array; recombination events that delete the insertion from the array occur at a rate of >10/division in unselected cells. This rate is almost three orders of magnitude higher than observed for mitotic recombination events involving single-copy genes. In summary, our study shows that some of the basic properties of recombination differ considerably between single-copy and tandemly-repeated genes.
Topics: Homologous Recombination; Meiosis; Metallothionein; Mitosis; Multigene Family; Rad51 Recombinase; Rad52 DNA Repair and Recombination Protein; Recombination, Genetic; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sister Chromatid Exchange; Tandem Repeat Sequences
PubMed: 28381587
DOI: 10.1534/genetics.117.201285 -
Cell Reports Dec 2023During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs...
During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs in normal human tissues and is prevalent in pathological genetic conditions and cancers. While studies in yeast have defined DNA repair mechanisms that can promote LOH, the predominant pathways and environmental triggers in somatic tissues of multicellular organisms are not well understood. Here, we investigate mechanisms underlying LOH in intestinal stem cells in Drosophila. Infection with the pathogenic bacteria, Erwinia carotovora carotovora 15, but not Pseudomonas entomophila, increases LOH frequency. Using whole genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features and genetic evidence argue against a break-induced replication mechanism and instead support cross-over via double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination, an important mediator of LOH, and its effects on stem cells in vivo.
Topics: Animals; Humans; Drosophila; Recombination, Genetic; DNA Repair; Loss of Heterozygosity; Saccharomyces cerevisiae; Stem Cells
PubMed: 38032794
DOI: 10.1016/j.celrep.2023.113485 -
BioEssays : News and Reviews in... Sep 2017The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic... (Review)
Review
The functions of the Bloom syndrome helicase (BLM) and its orthologs are well characterized in mitotic DNA damage repair, but their roles within the context of meiotic recombination are less clear. In meiotic recombination, multiple repair pathways are used to repair meiotic DSBs, and current studies suggest that BLM may regulate the use of these pathways. Based on literature from Saccharomyces cerevisiae, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans, we present a unified model for a critical meiotic role of BLM and its orthologs. In this model, BLM and its orthologs utilize helicase activity to regulate the use of various pathways in meiotic recombination by continuously disassembling recombination intermediates. This unwinding activity provides the meiotic program with a steady pool of early recombination substrates, increasing the probability for a DSB to be processed by the appropriate pathway. As a result of BLM activity, crossovers are properly placed throughout the genome, promoting proper chromosomal disjunction at the end of meiosis. This unified model can be used to further refine the complex role of BLM and its orthologs in meiotic recombination.
Topics: Animals; Bloom Syndrome; Chromosomes; DNA Helicases; DNA Repair; Humans; Meiosis; RecQ Helicases; Recombination, Genetic
PubMed: 28792069
DOI: 10.1002/bies.201700073 -
Scientific Reports Jun 2021mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces...
mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes.
Topics: DNA, Fungal; DNA, Mitochondrial; Genes, Fungal; Genetic Introgression; Genome, Mitochondrial; Hybridization, Genetic; Introns; Open Reading Frames; Recombination, Genetic; Saccharomyces; Saccharomyces cerevisiae
PubMed: 34135414
DOI: 10.1038/s41598-021-92125-y -
PLoS Genetics Mar 2009
Review
Topics: DNA Breaks, Double-Stranded; DNA Repair; Genomic Instability; Mitosis; Recombination, Genetic; Saccharomyces cerevisiae
PubMed: 19282976
DOI: 10.1371/journal.pgen.1000411