151
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Kobayashi W, Takaku M, Machida S, Tachiwana H, Maehara K, Ohkawa Y, Kurumizaka H. Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing. Sci Rep 2016; 6:24228. [PMID: 27052786 PMCID: PMC4823753 DOI: 10.1038/srep24228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/22/2016] [Indexed: 01/17/2023] Open
Abstract
In eukaryotes, genomic DNA is compacted as chromatin, in which histones and DNA form the nucleosome as the basic unit. DMC1 and RAD51 are essential eukaryotic recombinases that mediate homologous chromosome pairing during homologous recombination. However, the means by which these two recombinases distinctly function in chromatin have remained elusive. Here we found that, in chromatin, the human DMC1-single-stranded DNA complex bypasses binding to the nucleosome, and preferentially promotes homologous pairing at the nucleosome-depleted regions. Consistently, DMC1 forms ternary complex recombination intermediates with the nucleosome-free DNA or the nucleosome-depleted DNA region. Surprisingly, removal of the histone tails improperly enhances the nucleosome binding by DMC1. In contrast, RAD51 does not specifically target the nucleosome-depleted region in chromatin. These are the first demonstrations that the chromatin architecture specifies the sites to promote the homologous recombination reaction by DMC1, but not by RAD51.
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Affiliation(s)
- Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Motoki Takaku
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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152
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Scott DE, Marsh M, Blundell TL, Abell C, Hyvönen M. Structure-activity relationship of the peptide binding-motif mediating the BRCA2:RAD51 protein-protein interaction. FEBS Lett 2016; 590:1094-102. [PMID: 26992456 PMCID: PMC4855620 DOI: 10.1002/1873-3468.12139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/25/2016] [Accepted: 03/14/2016] [Indexed: 12/18/2022]
Abstract
RAD51 is a recombinase involved in the homologous recombination of double‐strand breaks in DNA. RAD51 forms oligomers by binding to another molecule of RAD51 via an ‘FxxA’ motif, and the same recognition sequence is similarly utilised to bind BRCA2. We have tabulated the effects of mutation of this sequence, across a variety of experimental methods and from relevant mutations observed in the clinic. We use mutants of a tetrapeptide sequence to probe the binding interaction, using both isothermal titration calorimetry and X‐ray crystallography. Where possible, comparison between our tetrapeptide mutational study and the previously reported mutations is made, discrepancies are discussed and the importance of secondary structure in interpreting alanine scanning and mutational data of this nature is considered.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - May Marsh
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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153
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Marsh ME, Scott DE, Ehebauer MT, Abell C, Blundell TL, Hyvönen M. ATP half-sites in RadA and RAD51 recombinases bind nucleotides. FEBS Open Bio 2016; 6:372-85. [PMID: 27419043 PMCID: PMC4856416 DOI: 10.1002/2211-5463.12052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination is essential for repair of DNA double-strand breaks. Central to this process is a family of recombinases, including archeal RadA and human RAD51, which form nucleoprotein filaments on damaged single-stranded DNA ends and facilitate their ATP-dependent repair. ATP binding and hydrolysis are dependent on the formation of a nucleoprotein filament comprising RadA/RAD51 and single-stranded DNA, with ATP bound between adjacent protomers. We demonstrate that truncated, monomeric Pyrococcus furiosus RadA and monomerised human RAD51 retain the ability to bind ATP and other nucleotides with high affinity. We present crystal structures of both apo and nucleotide-bound forms of monomeric RadA. These structures reveal that while phosphate groups are tightly bound, RadA presents a shallow, poorly defined binding surface for the nitrogenous bases of nucleotides. We suggest that RadA monomers would be constitutively bound to nucleotides in the cell and that the bound nucleotide might play a structural role in filament assembly.
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Affiliation(s)
- May E Marsh
- Department of Biochemistry University of Cambridge UK; Present address: Paul Scherrer Institut Villingen Switzerland
| | | | - Matthias T Ehebauer
- Department of Biochemistry University of Cambridge UK; Present address: Target Discovery Institute Nuffield Department of Medicine University of Oxford UK
| | - Chris Abell
- Department of Chemistry University of Cambridge UK
| | | | - Marko Hyvönen
- Department of Biochemistry University of Cambridge UK
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154
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Lee HB, Sundberg BN, Sigafoos AN, Clark KJ. Genome Engineering with TALE and CRISPR Systems in Neuroscience. Front Genet 2016; 7:47. [PMID: 27092173 PMCID: PMC4821859 DOI: 10.3389/fgene.2016.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.
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Affiliation(s)
- Han B Lee
- Neurobiology of Disease Graduate Program, Mayo Graduate School Rochester, MN, USA
| | - Brynn N Sundberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Ashley N Sigafoos
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Karl J Clark
- Neurobiology of Disease Graduate Program, Mayo Graduate SchoolRochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo ClinicRochester, MN, USA
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155
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Hunter CM, Huang W, Mackay TFC, Singh ND. The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster. PLoS Genet 2016; 12:e1005951. [PMID: 27035832 PMCID: PMC4817973 DOI: 10.1371/journal.pgen.1005951] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/01/2016] [Indexed: 01/01/2023] Open
Abstract
Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. During meiosis, homologous chromosomes exchange genetic material through recombination. In most sexually reproducing species, recombination is necessary for chromosomes to properly segregate. Recombination defects can generate gametes with an incorrect number of chromosomes, which is devastating for organismal fitness. Despite the central role of recombination for chromosome segregation, recombination is highly variable process both within and between species. Though it is clear that this variation is due at least in part to genetics, the specific genes contributing to variation in recombination within and between species remain largely unknown. This is particularly true in the model organism, Drosophila melanogaster. Here, we use the D. melanogaster Genetic Reference Panel to determine the scale of population-level variation in recombination rate and to identify genes significantly associated with this variation. We estimated rates of recombination on two different chromosomes in 205 strains of D. melanogaster. We also used genome-wide association mapping to identify genetic factors associated with recombination rate variation. We find that recombination rate on the two chromosomes are independent traits. We further find that population-level variation in recombination is mediated by many loci of small effect, and that the genes contributing to variation in recombination rate are outside of the well-characterized meiotic recombination pathway.
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Affiliation(s)
- Chad M. Hunter
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Wen Huang
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Nadia D. Singh
- Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
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156
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Identification of potential biomarkers for xylene exposure by microarray analyses of gene expression and methylation. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-016-0003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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157
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Ahlawat S, Chopra M, Jaiswal L, Sharma R, Arora R, Brahma B, Lal SV, De S. Exon skipping creates novel splice variants of DMC1 gene in ruminants. Mol Cell Probes 2016; 30:66-73. [PMID: 26945774 DOI: 10.1016/j.mcp.2016.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 11/26/2022]
Abstract
Disrupted meiotic cDNA1 (DMC1) recombinase plays a pivotal role in homology search and strand exchange reactions during meiotic homologous recombination. In the present study, full length coding sequence of DMC1 gene was sequence characterized for the first time from four ruminant species (cattle, buffalo, sheep and goat) and phylogenetic relationship of ruminant DMC1 with other eukaryotes was analyzed. DMC1 gene encodes a putative protein of 340 amino acids in cattle, sheep and buffalo and 341 amino acids in goat. A high degree of evolutionary conservation at both nucleotide and amino acid level was observed for the four ruminant orthologs. In cattle and sheep, novel alternatively spliced mRNAs with skipping of exons 7 and 8 (Transcript variant 1, TV1) were isolated in addition to the full length (FL) transcript. Novel transcript variants with partial skipping of exon 7 and complete skipping of exon 8 (Transcript variant 2, TV2) were found in sheep and goat. The presence of these variants was validated by amplifying cDNA isolated from testis tissue of ruminants using two oligonucleotides flanking the deleted region. To accurately estimate their relative proportions, real-time PCR was performed using primers specific for each variant. Expression level of DMC1-FL was significantly higher than that of TV1 in cattle and TV2 in goat (P < 0.05). Relative ratio for expression of DMC1-FL: TV1: TV2 in sheep was 6.78: 1.43: 1. In-silico analysis revealed presence of splice variants of DMC1 gene across other mammalian species underpinning the role of alternative splicing in functional innovation.
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Affiliation(s)
- S Ahlawat
- National Bureau of Animal Genetic Resources, Karnal, 132001, India.
| | - M Chopra
- National Dairy Research Institute, Karnal, 132001, India
| | - L Jaiswal
- National Dairy Research Institute, Karnal, 132001, India
| | - R Sharma
- National Bureau of Animal Genetic Resources, Karnal, 132001, India
| | - R Arora
- National Bureau of Animal Genetic Resources, Karnal, 132001, India
| | - B Brahma
- Krishi Vigyan Kendra, Bhaderwah, SKUAST, Jammu, 180016, India
| | - S V Lal
- National Dairy Research Institute, Karnal, 132001, India
| | - S De
- National Dairy Research Institute, Karnal, 132001, India
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158
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Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Semin Cell Dev Biol 2016; 59:118-125. [PMID: 26957474 DOI: 10.1016/j.semcdb.2016.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 02/07/2023]
Abstract
Retrotransposons play an important role in genome evolution but pose acute challenges to host genome integrity, particularly in early stage germ cells where epigenetic control is relaxed to permit genome-wide reprogramming. In most species, the inability to silence retrotransposons in the germline is usually associated with sterility. LINE1 is the most abundant retrotransposon type in the mammalian genome. Mammalian germ cells employ multiple mechanisms to suppress retrotransposon activity, including small non-coding piRNAs, DNA methylation, and repressive histone modifications. Novel factors contributing to the epigenetic silencing of retrotransposons in the germline continue to be identified. Recent studies have provided insight into how epigenetic changes associated with retrotransposon activation impact on fertility.
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Affiliation(s)
- Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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159
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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160
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Challa K, Lee MS, Shinohara M, Kim KP, Shinohara A. Rad61/Wpl1 (Wapl), a cohesin regulator, controls chromosome compaction during meiosis. Nucleic Acids Res 2016; 44:3190-203. [PMID: 26825462 PMCID: PMC4838362 DOI: 10.1093/nar/gkw034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/12/2016] [Indexed: 11/12/2022] Open
Abstract
Meiosis-specific cohesin, required for the linking of the sister chromatids, plays a critical role in various chromosomal events during meiotic prophase I, such as chromosome morphogenesis and dynamics, as well as recombination. Rad61/Wpl1 (Wapl in other organisms) negatively regulates cohesin functions. In this study, we show that meiotic chromosome axes are shortened in the budding yeast rad61/wpl1 mutant, suggesting that Rad61/Wpl1 negatively regulates chromosome axis compaction. Rad61/Wpl1 is required for efficient resolution of telomere clustering during meiosis I, indicating a positive effect of Rad61/Wpl1 on the cohesin function required for telomere dynamics. Additionally, we demonstrate distinct activities of Rad61/Wpl1 during the meiotic recombination, including its effects on the efficient processing of intermediates. Thus, Rad61/Wpl1 both positively and negatively regulates various cohesin-mediated chromosomal processes during meiosis.
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Affiliation(s)
- Kiran Challa
- Institute for Protein Research, Graduate School of Science, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Min-Su Lee
- Department of Life Sciences, Chung-Ang University, Seoul 156-756, Korea
| | - Miki Shinohara
- Institute for Protein Research, Graduate School of Science, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul 156-756, Korea
| | - Akira Shinohara
- Institute for Protein Research, Graduate School of Science, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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161
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Shao J, Xu Z, Peng X, Chen M, Zhu Y, Xu L, Zhu H, Yang B, Luo P, He Q. Gefitinib Synergizes with Irinotecan to Suppress Hepatocellular Carcinoma via Antagonizing Rad51-Mediated DNA-Repair. PLoS One 2016; 11:e0146968. [PMID: 26752698 PMCID: PMC4709237 DOI: 10.1371/journal.pone.0146968] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/23/2015] [Indexed: 11/24/2022] Open
Abstract
Chemotherapy is the only choice for most of the advanced hepatocellular carcinoma (HCC) patients, while few agents were available, making it an urgent need to develop new chemotherapy strategies. A phase II clinical trial suggested that the efficacy of irinotecan in HCC was limited due to dose-dependent toxicities. Here, we found that gefitinib exhibited synergistic activity in combination with SN-38, an active metabolite of irinotecan, in HCC cell lines. And the enhanced apoptosis induced by gefitinib plus SN-38 was a result from caspase pathway activation. Mechanistically, gefitinib dramatically promoted the ubiquitin–proteasome-dependent degradation of Rad51 protein, suppressed the DNA repair, gave rise to more DNA damages, and ultimately resulted in the synergism of these two agents. In addition, the increased antitumor efficacy of gefitinib combined with irinotecan was further validated in a HepG2 xenograft mice model. Taken together, our data demonstrated for the first time that the combination of irinotecan and gefitinib showed potential benefit in HCC, which suggests that Rad51 is a promising target and provides a rationale for clinical trials investigating the efficacy of the combination of topoisomerase I inhibitors and gefitinib in HCC.
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Affiliation(s)
- Jinjin Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhifei Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xueming Peng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Min Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuanrun Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peihua Luo
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- * E-mail: (PL); (QH)
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- * E-mail: (PL); (QH)
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162
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Catching a (Double-Strand) Break: The Rad51 and Dmc1 Strand Exchange Proteins Can Co-occupy Both Ends of a Meiotic DNA Double-Strand Break. PLoS Genet 2016; 11:e1005741. [PMID: 26720282 PMCID: PMC4699915 DOI: 10.1371/journal.pgen.1005741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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163
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Non-coding RNA in Spermatogenesis and Epididymal Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:95-120. [PMID: 26659489 DOI: 10.1007/978-94-017-7417-8_6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Testicular germ and somatic cells express many classes of small ncRNAs, including Dicer-independent PIWI-interacting RNAs, Dicer-dependent miRNAs, and endogenous small interfering RNA. Several studies have identified ncRNAs that are highly, exclusively, or preferentially expressed in the testis and epididymis in specific germ and somatic cell types. Temporal and spatial expression of proteins is a key requirement of successful spermatogenesis and large-scale gene transcription occurs in two key stages, just prior to transcriptional quiescence in meiosis and then during spermiogenesis just prior to nuclear silencing in elongating spermatids. More than 60 % of these transcripts are then stockpiled for subsequent translation. In this capacity ncRNAs may act to interpret and transduce cellular signals to either maintain the undifferentiated stem cell population and/or drive cell differentiation during spermatogenesis and epididymal maturation. The assignation of specific roles to the majority of ncRNA species implicated as having a role in spermatogenesis and epididymal function will underpin fundamental understanding of normal and disease states in humans such as infertility and the development of germ cell tumours.
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164
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Brown MS, Grubb J, Zhang A, Rust MJ, Bishop DK. Small Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand Break. PLoS Genet 2015; 11:e1005653. [PMID: 26719980 PMCID: PMC4697796 DOI: 10.1371/journal.pgen.1005653] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/15/2015] [Indexed: 11/19/2022] Open
Abstract
The Eukaryotic RecA-like proteins Rad51 and Dmc1 cooperate during meiosis to promote recombination between homologous chromosomes by repairing programmed DNA double strand breaks (DSBs). Previous studies showed that Rad51 and Dmc1 form partially overlapping co-foci. Here we show these Rad51-Dmc1 co-foci are often arranged in pairs separated by distances of up to 400 nm. Paired co-foci remain prevalent when DSBs are dramatically reduced or when strand exchange or synapsis is blocked. Super-resolution dSTORM microscopy reveals that individual foci observed by conventional light microscopy are often composed of two or more substructures. The data support a model in which the two tracts of ssDNA formed by a single DSB separate from one another by distances of up to 400 nm, with both tracts often bound by one or more short (about 100 nt) Rad51 filaments and also by one or more short Dmc1 filaments.
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Affiliation(s)
- M. Scott Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Jennifer Grubb
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Annie Zhang
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Michael J. Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Douglas K. Bishop
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- * E-mail:
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165
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Abstract
The genome of spinach single chromosome complement is about 1000 Mbp, which is the model material to study the molecular mechanisms of plant sex differentiation. The cytological study showed that the biggest spinach chromosome (chromosome 1) was taken as spinach sex chromosome. It had three alleles of sex-related X,X(m) and Y. Many researchers have been trying to clone the sex-determining genes and investigated the molecular mechanism of spinach sex differentiation. However,there are no successful cloned reports about these genes. A new technology combining chromosome microdissection with hybridization-specific amplification (HSA) was adopted. The spinach Y chromosome degenerate oligonucleotide primed-PCR (DOP-PCR) products were hybridized with cDNA of the male spinach flowers in florescence. The female spinach genome was taken as blocker and cDNA library specifically expressed in Y chromosome was constructed. Moreover, expressed sequence tag (EST) sequences in cDNA library were cloned, sequenced and bioinformatics was analysed. There were 63 valid EST sequences obtained in this study. The fragment size was between 53 and 486 bp. BLASTn homologous alignment indicated that 12 EST sequences had homologous sequences of nucleic acids, the rest were new sequences. BLASTx homologous alignment indicated that 16 EST sequences had homologous protein-encoding nucleic acid sequence. The spinach Y chromosome-specific EST sequences laid the foundation for cloning the functional genes, specifically expressed in spinach Y chromosome. Meanwhile, the establishment of the technology system in the research provided a reference for rapid cloning of other biological sex chromosome-specific EST sequences.
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166
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The Double-Strand Break Landscape of Meiotic Chromosomes Is Shaped by the Paf1 Transcription Elongation Complex in Saccharomyces cerevisiae. Genetics 2015; 202:497-512. [PMID: 26627841 DOI: 10.1534/genetics.115.177287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023] Open
Abstract
Histone modification is a critical determinant of the frequency and location of meiotic double-strand breaks (DSBs), and thus recombination. Set1-dependent histone H3K4 methylation and Dot1-dependent H3K79 methylation play important roles in this process in budding yeast. Given that the RNA polymerase II associated factor 1 complex, Paf1C, promotes both types of methylation, we addressed the role of the Paf1C component, Rtf1, in the regulation of meiotic DSB formation. Similar to a set1 mutation, disruption of RTF1 decreased the occurrence of DSBs in the genome. However, the rtf1 set1 double mutant exhibited a larger reduction in the levels of DSBs than either of the single mutants, indicating independent contributions of Rtf1 and Set1 to DSB formation. Importantly, the distribution of DSBs along chromosomes in the rtf1 mutant changed in a manner that was different from the distributions observed in both set1 and set1 dot1 mutants, including enhanced DSB formation at some DSB-cold regions that are occupied by nucleosomes in wild-type cells. These observations suggest that Rtf1, and by extension the Paf1C, modulate the genomic DSB landscape independently of H3K4 methylation.
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167
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Saha S, Mandal P, Ganguly S, Jana D, Ayaz A, Banerjee A, Chouhan R, Sarkar DK. Decreased Expression of BRCA2 Accelerates Sporadic Breast Cancer Progression. Indian J Surg Oncol 2015; 6:378-383. [PMID: 27065665 PMCID: PMC4809839 DOI: 10.1007/s13193-015-0449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022] Open
Abstract
Human tumor suppressor BRCA2 has been known to function in the repair of DNA double strand break. Germ line mutation in BRCA genes predisposes individuals to familial breast and ovarian cancer. The aim of present study was to characterize the implication of BRCA2 expression in cases of non - hereditary (sporadic) breast cancer. Female breast cancer patients aged between 20 and 75 years who underwent surgery were randomly selected. Patients with Stage IV disease at time of primary diagnosis or previous history of any other malignancy other than breast carcinoma or undergoing neoadjuvant chemotherapy were excluded from the study. Total 48 patients full filled these criteria. Patients were treated with either modified radical mastectomy or breast conservation therapy. Concentration of BRCA2 was measured by Sandwiched method of ELISA. Immunohistochemistry was used to determine the hormonal receptor status. Stage of the disease was not found to have any significant correlation on the BRCA2 expression. In patients with higher grade of tumors the level of BRCA2 expression was found to be low. Decreased expression of BRCA2 was found to be triple negative, had aggressive features and associated with higher chances of axillary metastasis. Genetic instability caused by decreased expression of BRCA2 could trigger mutations in sporadic breast cancer cases and mutations in turn leads to uncontrolled proliferation and invasive growth.
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Affiliation(s)
- Soumi Saha
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Pranab Mandal
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Suvro Ganguly
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Debarshi Jana
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Asif Ayaz
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Abhirup Banerjee
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Rahul Chouhan
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
| | - Diptendra Kumar Sarkar
- Departement of General Surgery, IPGME&R/SSKMH, 244, A.J.C Bose Road, 700020 Kolkata, India
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168
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Therapeutic Implications for Overcoming Radiation Resistance in Cancer Therapy. Int J Mol Sci 2015; 16:26880-913. [PMID: 26569225 PMCID: PMC4661850 DOI: 10.3390/ijms161125991] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/29/2015] [Accepted: 10/29/2015] [Indexed: 12/17/2022] Open
Abstract
Ionizing radiation (IR), such as X-rays and gamma (γ)-rays, mediates various forms of cancer cell death such as apoptosis, necrosis, autophagy, mitotic catastrophe, and senescence. Among them, apoptosis and mitotic catastrophe are the main mechanisms of IR action. DNA damage and genomic instability contribute to IR-induced cancer cell death. Although IR therapy may be curative in a number of cancer types, the resistance of cancer cells to radiation remains a major therapeutic problem. In this review, we describe the morphological and molecular aspects of various IR-induced types of cell death. We also discuss cytogenetic variations representative of IR-induced DNA damage and genomic instability. Most importantly, we focus on several pathways and their associated marker proteins responsible for cancer resistance and its therapeutic implications in terms of cancer cell death of various types and characteristics. Finally, we propose radiation-sensitization strategies, such as the modification of fractionation, inflammation, and hypoxia and the combined treatment, that can counteract the resistance of tumors to IR.
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169
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Chung D, Dellaire G. The Role of the COP9 Signalosome and Neddylation in DNA Damage Signaling and Repair. Biomolecules 2015; 5:2388-416. [PMID: 26437438 PMCID: PMC4693240 DOI: 10.3390/biom5042388] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/28/2023] Open
Abstract
The maintenance of genomic integrity is an important process in organisms as failure to sense and repair damaged DNA can result in a variety of diseases. Eukaryotic cells have developed complex DNA repair response (DDR) mechanisms to accurately sense and repair damaged DNA. Post-translational modifications by ubiquitin and ubiquitin-like proteins, such as SUMO and NEDD8, have roles in coordinating the progression of DDR. Proteins in the neddylation pathway have also been linked to regulating DDR. Of interest is the COP9 signalosome (CSN), a multi-subunit metalloprotease present in eukaryotes that removes NEDD8 from cullins and regulates the activity of cullin-RING ubiquitin ligases (CRLs). This in turn regulates the stability and turnover of a host of CRL-targeted proteins, some of which have established roles in DDR. This review will summarize the current knowledge on the role of the CSN and neddylation in DNA repair.
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Affiliation(s)
- Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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170
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Kelso AA, Say AF, Sharma D, Ledford LL, Turchick A, Saski CA, King AV, Attaway CC, Temesvari LA, Sehorn MG. Entamoeba histolytica Dmc1 Catalyzes Homologous DNA Pairing and Strand Exchange That Is Stimulated by Calcium and Hop2-Mnd1. PLoS One 2015; 10:e0139399. [PMID: 26422142 PMCID: PMC4589404 DOI: 10.1371/journal.pone.0139399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/12/2015] [Indexed: 01/03/2023] Open
Abstract
Meiosis depends on homologous recombination (HR) in most sexually reproducing organisms. Efficient meiotic HR requires the activity of the meiosis-specific recombinase, Dmc1. Previous work shows Dmc1 is expressed in Entamoeba histolytica, a eukaryotic parasite responsible for amoebiasis throughout the world, suggesting this organism undergoes meiosis. Here, we demonstrate Dmc1 protein is expressed in E. histolytica. We show that purified ehDmc1 forms presynaptic filaments and catalyzes ATP-dependent homologous DNA pairing and DNA strand exchange over at least several thousand base pairs. The DNA pairing and strand exchange activities are enhanced by the presence of calcium and the meiosis-specific recombination accessory factor, Hop2-Mnd1. In combination, calcium and Hop2-Mnd1 dramatically increase the rate of DNA strand exchange activity of ehDmc1. The biochemical system described herein provides a basis on which to better understand the role of ehDmc1 and other HR proteins in E. histolytica.
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Affiliation(s)
- Andrew A. Kelso
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Amanda F. Say
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Deepti Sharma
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - LeAnna L. Ledford
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Audrey Turchick
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher A. Saski
- Clemson University Genomics and Computational Biology Laboratory, Institute for Translational Genomics, Clemson, South Carolina, United States of America
| | - Ada V. King
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher C. Attaway
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Clemson University School of Health Research, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Michael G. Sehorn
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Clemson University School of Health Research, Clemson, South Carolina, United States of America
- Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, South Carolina, United States of America
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171
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Sebestova H, Vozdova M, Kubickova S, Cernohorska H, Kotrba R, Rubes J. Effect of species-specific differences in chromosome morphology on chromatin compaction and the frequency and distribution of RAD51 and MLH1 foci in two bovid species: cattle (Bos taurus) and the common eland (Taurotragus oryx). Chromosoma 2015; 125:137-49. [PMID: 26194101 DOI: 10.1007/s00412-015-0533-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Meiotic recombination between homologous chromosomes is crucial for their correct segregation into gametes and for generating diversity. We compared the frequency and distribution of MLH1 foci and RAD51 foci, synaptonemal complex (SC) length and DNA loop size in two related Bovidae species that share chromosome arm homology but show an extreme difference in their diploid chromosome number: cattle (Bos taurus, 2n = 60) and the common eland (Taurotragus oryx, 2nmale = 31). Compared to cattle, significantly fewer MLH1 foci per cell were observed in the common eland, which can be attributed to the lower number of initial double-strand breaks (DSBs) detected as RAD51 foci in leptonema. Despite the significantly shorter total autosomal SC length and longer DNA loop size of the common eland bi-armed chromosomes compared to those of bovine acrocentrics, the overall crossover density in the common eland was still lower than in cattle, probably due to the reduction in the number of MLH1 foci in the proximal regions of the bi-armed chromosomes. The formation of centric fusions during karyotype evolution of the common eland accompanied by meiotic chromatin compaction has greater implications in the reduction in the number of DSBs in leptonema than in the decrease of MLH1 foci number in pachynema.
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Affiliation(s)
- Hana Sebestova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Radim Kotrba
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
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172
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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173
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Choi K, Henderson IR. Meiotic recombination hotspots - a comparative view. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:52-61. [PMID: 25925869 DOI: 10.1111/tpj.12870] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 05/18/2023]
Abstract
During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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174
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McNair K, Edwards RA. GenomePeek-an online tool for prokaryotic genome and metagenome analysis. PeerJ 2015; 3:e1025. [PMID: 26157610 PMCID: PMC4476108 DOI: 10.7717/peerj.1025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 05/25/2015] [Indexed: 12/23/2022] Open
Abstract
As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
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Affiliation(s)
- Katelyn McNair
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA
| | - Robert A Edwards
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA ; Computational Sciences Research Center, San Diego State University , San Diego, CA , USA ; Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL , USA
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175
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Tsabar M, Mason JM, Chan YL, Bishop DK, Haber JE. Caffeine inhibits gene conversion by displacing Rad51 from ssDNA. Nucleic Acids Res 2015; 43:6902-18. [PMID: 26019181 PMCID: PMC4538809 DOI: 10.1093/nar/gkv525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/07/2015] [Indexed: 01/08/2023] Open
Abstract
Efficient repair of chromosomal double-strand breaks (DSBs) by homologous recombination relies on the formation of a Rad51 recombinase filament that forms on single-stranded DNA (ssDNA) created at DSB ends. This filament facilitates the search for a homologous donor sequence and promotes strand invasion. Recently caffeine treatment has been shown to prevent gene targeting in mammalian cells by increasing non-productive Rad51 interactions between the DSB and random regions of the genome. Here we show that caffeine treatment prevents gene conversion in yeast, independently of its inhibition of the Mec1ATR/Tel1ATM-dependent DNA damage response or caffeine's inhibition of 5′ to 3′ resection of DSB ends. Caffeine treatment results in a dosage-dependent eviction of Rad51 from ssDNA. Gene conversion is impaired even at low concentrations of caffeine, where there is no discernible dismantling of the Rad51 filament. Loss of the Rad51 filament integrity is independent of Srs2's Rad51 filament dismantling activity or Rad51's ATPase activity and does not depend on non-specific Rad51 binding to undamaged double-stranded DNA. Caffeine treatment had similar effects on irradiated HeLa cells, promoting loss of previously assembled Rad51 foci. We conclude that caffeine treatment can disrupt gene conversion by disrupting Rad51 filaments.
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Affiliation(s)
- Michael Tsabar
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Jennifer M Mason
- Department of Radiation and Cellular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yuen-Ling Chan
- Department of Radiation and Cellular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Douglas K Bishop
- Department of Radiation and Cellular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
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176
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Sansam CL, Pezza RJ. Connecting by breaking and repairing: mechanisms of DNA strand exchange in meiotic recombination. FEBS J 2015; 282:2444-57. [PMID: 25953379 PMCID: PMC4573575 DOI: 10.1111/febs.13317] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/26/2015] [Accepted: 05/06/2015] [Indexed: 01/03/2023]
Abstract
During prophase of meiosis I, homologous chromosomes interact and undergo recombination. Successful completion of these processes is required in order for the homologous chromosomes to mount the meiotic spindle as a pair. The organization of the chromosomes into pairs ensures orderly segregation to opposite poles of the dividing cell, such that each gamete receives one copy of each chromosome. Chiasmata, the cytological manifestation of crossover products of recombination, physically connect the homologs in pairs, providing a linkage that facilitates their segregation. Consequently, mutations that reduce the level of recombination are invariably associated with increased errors in meiotic chromosome segregation. In this review, we focus on recent biochemical and genetic advances in elucidating the mechanisms of meiotic DNA strand exchange catalyzed by the Dmc1 protein. We also discuss the mode by which two recombination mediators, Hop2 and Mnd1, facilitate rate-limiting steps of DNA strand exchange catalyzed by Dmc1.
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Affiliation(s)
- Christopher L Sansam
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation and the Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Roberto J Pezza
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation and the Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
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177
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Ziolkowski PA, Berchowitz LE, Lambing C, Yelina NE, Zhao X, Kelly KA, Choi K, Ziolkowska L, June V, Sanchez-Moran E, Franklin C, Copenhaver GP, Henderson IR. Juxtaposition of heterozygous and homozygous regions causes reciprocal crossover remodelling via interference during Arabidopsis meiosis. eLife 2015; 4:e03708. [PMID: 25815584 PMCID: PMC4407271 DOI: 10.7554/elife.03708] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
During meiosis homologous chromosomes undergo crossover recombination. Sequence differences between homologs can locally inhibit crossovers. Despite this, nucleotide diversity and population-scaled recombination are positively correlated in eukaryote genomes. To investigate interactions between heterozygosity and recombination we crossed Arabidopsis lines carrying fluorescent crossover reporters to 32 diverse accessions and observed hybrids with significantly higher and lower crossovers than homozygotes. Using recombinant populations derived from these crosses we observed that heterozygous regions increase crossovers when juxtaposed with homozygous regions, which reciprocally decrease. Total crossovers measured by chiasmata were unchanged when heterozygosity was varied, consistent with homeostatic control. We tested the effects of heterozygosity in mutants where the balance of interfering and non-interfering crossover repair is altered. Crossover remodeling at homozygosity-heterozygosity junctions requires interference, and non-interfering repair is inefficient in heterozygous regions. As a consequence, heterozygous regions show stronger crossover interference. Our findings reveal how varying homolog polymorphism patterns can shape meiotic recombination.
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Affiliation(s)
- Piotr A Ziolkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Luke E Berchowitz
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Krystyna A Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Liliana Ziolkowska
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Viviana June
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Chris Franklin
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gregory P Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, United States
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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178
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Epigenetic control of meiotic recombination in plants. SCIENCE CHINA-LIFE SCIENCES 2015; 58:223-31. [PMID: 25651968 DOI: 10.1007/s11427-015-4811-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
Meiotic recombination is a deeply conserved process within eukaryotes that has a profound effect on patterns of natural genetic variation. During meiosis homologous chromosomes pair and undergo DNA double strand breaks generated by the Spo11 endonuclease. These breaks can be repaired as crossovers that result in reciprocal exchange between chromosomes. The frequency of recombination along chromosomes is highly variable, for example, crossovers are rarely observed in heterochromatin and the centromeric regions. Recent work in plants has shown that crossover hotspots occur in gene promoters and are associated with specific chromatin modifications, including H2A.Z. Meiotic chromosomes are also organized in loop-base arrays connected to an underlying chromosome axis, which likely interacts with chromatin to organize patterns of recombination. Therefore, epigenetic information exerts a major influence on patterns of meiotic recombination along chromosomes, genetic variation within populations and evolution of plant genomes.
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179
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An Introspective Update on the Influence of miRNAs in Breast Carcinoma and Neuroblastoma Chemoresistance. GENETICS RESEARCH INTERNATIONAL 2014; 2014:743050. [PMID: 25548681 PMCID: PMC4273469 DOI: 10.1155/2014/743050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/23/2014] [Accepted: 11/04/2014] [Indexed: 02/08/2023]
Abstract
Chemoresistance to conventional cytotoxic drugs may occur in any type of cancer and this can either be inherent or develop through time. Studies have linked this acquired resistance to the abnormal expression of microRNAs (miRNAs) that normally silence genes. At abnormal levels, miRNAs can either gain ability to silence tumour suppressor genes or else lose ability to silence oncogenes. miRNAs can also affect pathways that are involved in drug metabolism, such as drug efflux pumps, resulting in a resistant phenotype. The scope of this review is to provide an introspective analysis on the specific niches of breast carcinoma and neuroblastoma research.
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180
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Abstract
Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.
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Affiliation(s)
- M Scott Brown
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
| | - Douglas K Bishop
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
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181
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RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination. Proc Natl Acad Sci U S A 2014; 111:E5133-42. [PMID: 25411316 DOI: 10.1073/pnas.1420009111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinational DNA repair by the RecF pathway of Escherichia coli requires the coordinated activities of RecA, RecFOR, RecQ, RecJ, and single-strand DNA binding (SSB) proteins. These proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsDNA) and supercoiled DNA. Repair starts with resection of the broken dsDNA by RecQ, a 3'→5' helicase, RecJ, a 5'→3' exonuclease, and SSB protein. The ends of a dsDNA break can be blunt-ended, or they may possess either 5'- or 3'-single-stranded DNA (ssDNA) overhangs of undefined length. Here we show that RecJ nuclease alone can initiate nucleolytic resection of DNA with 5'-ssDNA overhangs, and that RecQ helicase can initiate resection of DNA with blunt-ends or 3'-ssDNA overhangs by DNA unwinding. We establish that in addition to its well-known ssDNA exonuclease activity, RecJ can display dsDNA exonuclease activity, degrading 100-200 nucleotides of the strand terminating with a 5'-ssDNA overhang. The dsDNA product, with a 3'-ssDNA overhang, is an optimal substrate for RecQ, which unwinds this intermediate to reveal the complementary DNA strand with a 5'-end that is degraded iteratively by RecJ. On the other hand, RecJ cannot resect duplex DNA that is either blunt-ended or terminated with 3'-ssDNA; however, such DNA is unwound by RecQ to create ssDNA for RecJ exonuclease. RecJ requires interaction with SSB for exonucleolytic degradation of ssDNA but not dsDNA. Thus, complementary action by RecJ and RecQ permits initiation of recombinational repair from all dsDNA ends: 5'-overhangs, blunt, or 3'-overhangs. Such helicase-nuclease coordination is a common mechanism underlying resection in all organisms.
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182
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Uringa EJ, Baldeyron C, Odijk H, Wassenaar E, van Cappellen WA, Maas A, Hoeijmakers JHJ, Baarends WM, Kanaar R, Essers J. A mRad51-GFP antimorphic allele affects homologous recombination and DNA damage sensitivity. DNA Repair (Amst) 2014; 25:27-40. [PMID: 25463395 DOI: 10.1016/j.dnarep.2014.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
Accurate DNA double-strand break repair through homologous recombination is essential for preserving genome integrity. Disruption of the gene encoding RAD51, the protein that catalyzes DNA strand exchange during homologous recombination, results in lethality of mammalian cells. Proteins required for homologous recombination, also play an important role during DNA replication. To explore the role of RAD51 in DNA replication and DSB repair, we used a knock-in strategy to express a carboxy-terminal fusion of green fluorescent protein to mouse RAD51 (mRAD51-GFP) in mouse embryonic stem cells. Compared to wild-type cells, heterozygous mRad51(+/wt-GFP) embryonic stem cells showed increased sensitivity to DNA damage induced by ionizing radiation and mitomycin C. Moreover, gene targeting was found to be severely impaired in mRad51(+/wt-GFP) embryonic stem cells. Furthermore, we found that mRAD51-GFP foci were not stably associated with chromatin. From these experiments we conclude that this mRad51-GFP allele is an antimorphic allele. When this allele is present in a heterozygous condition over wild-type mRad51, embryonic stem cells are proficient in DNA replication but display defects in homologous recombination and DNA damage repair.
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Affiliation(s)
- Evert-Jan Uringa
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Céline Baldeyron
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Hanny Odijk
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Evelyne Wassenaar
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Alex Maas
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Reproduction and Development, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Surgical Oncology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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183
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Terasawa M, Shinohara A, Shinohara M. Double-strand break repair-adox: Restoration of suppressed double-strand break repair during mitosis induces genomic instability. Cancer Sci 2014; 105:1519-25. [PMID: 25287622 PMCID: PMC4317954 DOI: 10.1111/cas.12551] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 12/18/2022] Open
Abstract
Double-strand breaks (DSBs) are one of the severest types of DNA damage. Unrepaired DSBs easily induce cell death and chromosome aberrations. To maintain genomic stability, cells have checkpoint and DSB repair systems to respond to DNA damage throughout most of the cell cycle. The failure of this process often results in apoptosis or genomic instability, such as aneuploidy, deletion, or translocation. Therefore, DSB repair is essential for maintenance of genomic stability. During mitosis, however, cells seem to suppress the DNA damage response and proceed to the next G1 phase, even if there are unrepaired DSBs. The biological significance of this suppression is not known. In this review, we summarize recent studies of mitotic DSB repair and discuss the mechanisms of suppression of DSB repair during mitosis. DSB repair, which maintains genomic integrity in other phases of the cell cycle, is rather toxic to cells during mitosis, often resulting in chromosome missegregation and aberration. Cells have multiple safeguards to prevent genomic instability during mitosis: inhibition of 53BP1 or BRCA1 localization to DSB sites, which is important to promote non-homologous end joining or homologous recombination, respectively, and also modulation of the non-homologous end joining core complex to inhibit DSB repair. We discuss how DSBs during mitosis are toxic and the multiple safeguard systems that suppress genomic instability.
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184
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Liu T, Huang J. Quality control of homologous recombination. Cell Mol Life Sci 2014; 71:3779-97. [PMID: 24858417 PMCID: PMC11114062 DOI: 10.1007/s00018-014-1649-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022]
Abstract
Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR.
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Affiliation(s)
- Ting Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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185
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Canonical non-homologous end joining in mitosis induces genome instability and is suppressed by M-phase-specific phosphorylation of XRCC4. PLoS Genet 2014; 10:e1004563. [PMID: 25166505 PMCID: PMC4148217 DOI: 10.1371/journal.pgen.1004563] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by one of two major pathways-non-homologous end-joining (NHEJ) and homologous recombination (HR)-depending on whether cells are in G1 or S/G2 phase, respectively. However, the mechanisms of DSB repair during M phase remain largely unclear. In this study, we demonstrate that transient treatment of M-phase cells with the chemotherapeutic topoisomerase inhibitor etoposide induced DSBs that were often associated with anaphase bridge formation and genome instability such as dicentric chromosomes. Although most of the DSBs were carried over into the next G1 phase, some were repaired during M phase. Both NHEJ and HR, in particular NHEJ, promoted anaphase-bridge formation, suggesting that these repair pathways can induce genome instability during M phase. On the other hand, C-terminal-binding protein interacting protein (CtIP) suppressed anaphase bridge formation, implying that CtIP function prevents genome instability during mitosis. We also observed M-phase-specific phosphorylation of XRCC4, a regulatory subunit of the ligase IV complex specialized for NHEJ. This phosphorylation required cyclin-dependent kinase (CDK) activity as well as polo-like kinase 1 (Plk1). A phosphorylation-defective XRCC4 mutant showed more efficient M-phase DSB repair accompanied with an increase in anaphase bridge formation. These results suggest that phosphorylation of XRCC4 suppresses DSB repair by modulating ligase IV function to prevent genome instability during M phase. Taken together, our results indicate that XRCC4 is required not only for the promotion of NHEJ during interphase but also for its M-phase-specific suppression of DSB repair.
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186
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Normand A, Rivière E, Renodon-Cornière A. Identification and characterization of human Rad51 inhibitors by screening of an existing drug library. Biochem Pharmacol 2014; 91:293-300. [PMID: 25124703 DOI: 10.1016/j.bcp.2014.07.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022]
Abstract
Homologous Recombination (HR) plays an essential role in cellular proliferation and in maintaining genomic stability by repairing DNA double-stranded breaks that appear during replication. Rad51, a key protein of HR in eukaryotes, can have an elevated expression level in tumor cells, which correlates with their resistance to anticancer therapies. Therefore, targeted inhibition of Rad51 through inhibitor may improve the tumor response to these therapies. In order to identify small molecules that inhibit Rad51 activity, we screened the Prestwick Library (1120 molecules) for their effect on the strand exchange reaction catalyzed by Rad51. We found that Chicago Sky Blue (CSB) is a potent inhibitor of Rad51, showing IC₅₀ values in the low nanomolar range (400 nM). Biochemical analysis demonstrated that the inhibitory mechanism probably occurs by disrupting the Rad51 association with the single-stranded DNA, which prevents the nucleoprotein filament formation, the first step of the protein activity. Structure Activity Relationship analysis with a number of compounds that shared structure homology with CSB was also performed. The sensitivity of Rad51 inhibition to CSB modifications suggests specific interactions between the molecule and Rad51 nucleofilament. CSB and some of its analogs open up new perspectives in the search for agents capable of potentiating chemo- and radio-therapy treatments for cancer. Moreover, these compounds may be excellent tools to analyze Rad51 cellular functions. Our study also highlights how CSB and its analogs, which are frequently used in colorants, stains and markers, could be responsible of unwanted side effects by perturbing the DNA repair process.
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Affiliation(s)
- Anaïs Normand
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Emmanuelle Rivière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France
| | - Axelle Renodon-Cornière
- Research Unit UFIP UMR 6286, Centre National de la Recherche Scientifique & University of Nantes, F-44322 Nantes cedex 3, France.
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187
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Lee Y, Kim K, Kang KT, Lee JS, Yang SS, Chung WH. Atmospheric-pressure plasma jet induces DNA double-strand breaks that require a Rad51-mediated homologous recombination for repair in Saccharomyces cerevisiae. Arch Biochem Biophys 2014; 560:1-9. [PMID: 25086216 DOI: 10.1016/j.abb.2014.07.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 01/15/2023]
Abstract
Non-thermal plasma generated under atmospheric pressure produces a mixture of chemically reactive molecules and has been developed for a number of biomedical applications. Recently, plasma jet has been proposed as novel cancer therapies based on the observation that free radicals generated by plasma jet induce mitochondria-mediated apoptotic cell death. We show here that air plasma jet induces DNA double-strand breaks (DSBs) in yeast chromosomes leading to genomic instability and loss of viability, which are alleviated by Rad51, the yeast homolog of Escherichiacoli RecA recombinase, through DNA damage repair by a homologous recombination (HR) process. Hypersensitivity of rad51 mutant to air plasma was not restored by antioxidant treatment unlike sod1 mutant that was highly sensitive to reactive oxygen species (ROS) challenge, suggesting that plasma jet induces DSB-mediated cell death independent of ROS generation. These results may provide a new insight into the mechanism of air plasma jet-induced cell death.
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Affiliation(s)
- Yoonna Lee
- College of Pharmacy, Duksung Women's University, Seoul 132-714, Republic of Korea
| | - Kangil Kim
- Department of Electrical and Computer Engineering, Ajou University, Suwon 443-749, Republic of Korea
| | - Kyu-Tae Kang
- College of Pharmacy, Duksung Women's University, Seoul 132-714, Republic of Korea
| | - Jong-Soo Lee
- Department of Life Sciences, Ajou University, Suwon 443-749, Republic of Korea
| | - Sang Sik Yang
- Department of Electrical and Computer Engineering, Ajou University, Suwon 443-749, Republic of Korea.
| | - Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul 132-714, Republic of Korea.
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188
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The proteasome factor Bag101 binds to Rad22 and suppresses homologous recombination. Sci Rep 2014; 3:2022. [PMID: 23779158 PMCID: PMC3685826 DOI: 10.1038/srep02022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/31/2013] [Indexed: 11/08/2022] Open
Abstract
Although RAD52 plays a critical role in the initiation of homologous recombination (HR) by facilitating the replacement of RPA with RAD51, the mechanism controlling RAD52 remains elusive. Here, we show that Bag101, a factor implicated in proteasome functioning, regulates RAD52 protein levels and subsequent HR. LC-MS/MS analysis identified Bag101 which binds to Rad22, the fission yeast homologue of RAD52. Bag101 reduced HR frequency through its overexpression and conversely, HR frequencies were enhanced when it was deleted. Consistent with this observation, Rad22 protein levels was reduced in cells where bag101 was overexpressed even when Rad22 transcription was up-regulated, suggesting the operation of proteasome-mediated Rad22 degradation. Indeed, Rad22 protein levels were stabilized in proteasome mutants. Rad22 physically interacted with the BAG domain of Bag101, and a lack of this domain enhanced HR frequency. Similarly, radiation exposure triggered the dissociation of these proteins so that Rad22 was stabilized and able to enhance HR.
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189
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Lozano JC, Schatt P, Botebol H, Vergé V, Lesuisse E, Blain S, Carré IA, Bouget FY. Efficient gene targeting and removal of foreign DNA by homologous recombination in the picoeukaryote Ostreococcus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1073-83. [PMID: 24698018 DOI: 10.1111/tpj.12530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 02/14/2014] [Accepted: 03/31/2014] [Indexed: 05/03/2023]
Abstract
With fewer than 8000 genes and a minimalist cellular organization, the green picoalga Ostreococcus tauri is one of the simplest photosynthetic eukaryotes. Ostreococcus tauri contains many plant-specific genes but exhibits a very low gene redundancy. The haploid genome is extremely dense with few repeated sequences and rare transposons. Thanks to the implementation of genetic transformation and vectors for inducible overexpression/knockdown this picoeukaryotic alga has emerged in recent years as a model organism for functional genomics analyses and systems biology. Here we report the development of an efficient gene targeting technique which we use to knock out the nitrate reductase and ferritin genes and to knock in a luciferase reporter in frame to the ferritin native protein. Furthermore, we show that the frequency of insertion by homologous recombination is greatly enhanced when the transgene is designed to replace an existing genomic insertion. We propose that a natural mechanism based on homologous recombination may operate to remove inserted DNA sequences from the genome.
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Affiliation(s)
- Jean-Claude Lozano
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France; CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France
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190
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Dot1-dependent histone H3K79 methylation promotes the formation of meiotic double-strand breaks in the absence of histone H3K4 methylation in budding yeast. PLoS One 2014; 9:e96648. [PMID: 24797370 PMCID: PMC4010517 DOI: 10.1371/journal.pone.0096648] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/09/2014] [Indexed: 11/19/2022] Open
Abstract
Epigenetic marks such as histone modifications play roles in various chromosome dynamics in mitosis and meiosis. Methylation of histones H3 at positions K4 and K79 is involved in the initiation of recombination and the recombination checkpoint, respectively, during meiosis in the budding yeast. Set1 promotes H3K4 methylation while Dot1 promotes H3K79 methylation. In this study, we carried out detailed analyses of meiosis in mutants of the SET1 and DOT1 genes as well as methylation-defective mutants of histone H3. We confirmed the role of Set1-dependent H3K4 methylation in the formation of double-strand breaks (DSBs) in meiosis for the initiation of meiotic recombination, and we showed the involvement of Dot1 (H3K79 methylation) in DSB formation in the absence of Set1-dependent H3K4 methylation. In addition, we showed that the histone H3K4 methylation-defective mutants are defective in SC elongation, although they seem to have moderate reduction of DSBs. This suggests that high levels of DSBs mediated by histone H3K4 methylation promote SC elongation.
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191
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Chinone A, Matsumoto M. DrRad51 is required for chiasmata formation in meiosis in planarian Dugesia ryukyuensis. Mol Reprod Dev 2014; 81:409-21. [PMID: 24488935 DOI: 10.1002/mrd.22308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/28/2014] [Indexed: 01/01/2023]
Abstract
Rad51, a conserved eukaryotic protein, mediates the homologous-recombination repair of DNA double-strand breaks that occur during both mitosis and meiosis. During prophase I of meiosis, homologous recombination enhances the linkage between homologous chromosomes to increase the accuracy of segregation at anaphase I. In polyploidy situations, however, difficulties with homologous chromosome segregation often disrupt meiosis. Yet, triploid individuals of the planarian Dugesia ryukyuensis are able to produce functional gametes through a specialized form of meiosis. To shed light on the molecular mechanisms that promote successful meiosis in triploid D. ryukyuensis, we investigated rad51 gene function. We isolated three genes of the Rad51 family, the Rad51 homolog Dr-rad51 and the Rad51 paralogs Dr-rad51B and Dr-rad51C. Dr-rad51 was expressed in germ-line and presumably in somatic stem cells, but was not necessary for the regeneration of somatic tissue. RNA-interference (RNAi) depletion of Dr-rad51 during sexualization did not affect chromosome behavior in zygotene oocytes, but did result in the loss of chiasmata at the diplotene stage. Thus, homologous recombination does not appear to be necessary for synapsis, but is needed for crossover and proper segregation in D. ryukyuensis.
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Affiliation(s)
- Ayako Chinone
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
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192
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Rao DECS, Luo Y. pH-dependent activities and structural stability of loop-2-anchoring helix of RadA recombinase from Methanococcus voltae. Protein Pept Lett 2014; 21:679-87. [PMID: 24654848 PMCID: PMC4150490 DOI: 10.2174/0929866521666140320103512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/25/2014] [Accepted: 02/27/2014] [Indexed: 11/22/2022]
Abstract
RadA is an archaeal orthologue of human recombinase Rad51. This superfamily of recombinases, which also includes eukaryal meiosis-specific DMC1 and remotely related bacterial RecA, form filaments on single-stranded DNA in the presence of ATP and promote a strand exchange reaction between the single-stranded DNA and a homologous double-stranded DNA. Due to its feasibility of getting crystals and similarity (> 40% sequence identity) to eukaryal homologues, we have studied RadA from Methanococcus voltae (MvRadA) as a structural model for understanding the molecular mechanism of homologous strand exchange. Here we show this protein’s ATPase and strand exchange activities are minimal at pH 6.0. Interestingly, MvRadA’s pH dependence is similar to the properties of human Rad51 but dissimilar to that of the well-studied E. coli RecA. A structure subsequently determined at pH 6.0 reveals features indicative of an ATPase-inactive form with a disordered L2 loop. Comparison with a previously determined ATPase-active form at pH 7.5 implies that the stability of the ATPase-active conformation is reduced at the acidic pH. We interpret these results as further suggesting an ordered disposition of the DNA-binding L2 region, similar to what has been observed in the previously observed ATPase-active conformation, is required for promoting hydrolysis of ATP and strand exchange between single- and double-stranded DNA. His-276 in the mobile L2 region was observed to be partially responsible for the pH-dependent activities of MvRadA.
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Affiliation(s)
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 2D01 Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.
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193
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Frykholm K, Alizadehheidari M, Fritzsche J, Wigenius J, Modesti M, Persson F, Westerlund F. Probing physical properties of a DNA-protein complex using nanofluidic channels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:884-7. [PMID: 24382826 DOI: 10.1002/smll.201302028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/08/2013] [Indexed: 05/28/2023]
Abstract
A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
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Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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194
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Holt JE, Pye V, Boon E, Stewart JL, García-Higuera I, Moreno S, Rodríguez R, Jones KT, McLaughlin EA. The APC/C activator FZR1 is essential for meiotic prophase I in mice. Development 2014; 141:1354-65. [PMID: 24553289 DOI: 10.1242/dev.104828] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fizzy-related 1 (FZR1) is an activator of the Anaphase promoting complex/cyclosome (APC/C) and an important regulator of the mitotic cell division cycle. Using a germ-cell-specific conditional knockout model we examined its role in entry into meiosis and early meiotic events in both sexes. Loss of APC/C(FZR1) activity in the male germline led to both a mitotic and a meiotic testicular defect resulting in infertility due to the absence of mature spermatozoa. Spermatogonia in the prepubertal testes of such mice had abnormal proliferation and delayed entry into meiosis. Although early recombination events were initiated, male germ cells failed to progress beyond zygotene and underwent apoptosis. Loss of APC/C(FZR1) activity was associated with raised cyclin B1 levels, suggesting that CDK1 may trigger apoptosis. By contrast, female FZR1Δ mice were subfertile, with premature onset of ovarian failure by 5 months of age. Germ cell loss occurred embryonically in the ovary, around the time of the zygotene-pachytene transition, similar to that observed in males. In addition, the transition of primordial follicles into the growing follicle pool in the neonatal ovary was abnormal, such that the primordial follicles were prematurely depleted. We conclude that APC/C(FZR1) is an essential regulator of spermatogonial proliferation and early meiotic prophase I in both male and female germ cells and is therefore important in establishing the reproductive health of adult male and female mammals.
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Affiliation(s)
- Janet E Holt
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
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195
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Pan Y, Yang H, Claret FX. Emerging roles of Jab1/CSN5 in DNA damage response, DNA repair, and cancer. Cancer Biol Ther 2014; 15:256-62. [PMID: 24495954 DOI: 10.4161/cbt.27823] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Jab1/CSN5 is a multifunctional protein that plays an important role in integrin signaling, cell proliferation, apoptosis, and the regulation of genomic instability and DNA repair. Dysregulation of Jab1/CSN5 activity has been shown to contribute to oncogenesis by functionally inactivating several key negative regulatory proteins and tumor suppressors. In this review, we discuss our current understanding of the relationship between Jab1/CSN5 and DNA damage and summarize recent findings regarding opportunities for and challenges to therapeutic intervention.
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Affiliation(s)
- Yunbao Pan
- Department of Systems Biology; The University of Texas MD Anderson Cancer Center; Houston, TX USA; Department of Pathophysiology; Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou, Guangdong, PR China; Breast Tumor Center; Sun Yat-Sen Memorial Hospital; Sun Yat-Sen University; Guangzhou, Guangdong, PR China
| | - Huiling Yang
- Department of Pathophysiology; Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou, Guangdong, PR China
| | - Francois X Claret
- Department of Systems Biology; The University of Texas MD Anderson Cancer Center; Houston, TX USA; Experimental Therapeutic Academic Program and Cancer Biology Program; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX USA
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196
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Kobayashi W, Sekine S, Machida S, Kurumizaka H. Green fluorescent protein fused to the C terminus of RAD51 specifically interferes with secondary DNA binding by the RAD51-ssDNA complex. Genes Genet Syst 2014; 89:169-79. [DOI: 10.1266/ggs.89.169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University
| | - Satoshi Sekine
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University
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197
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Marston AL. Chromosome segregation in budding yeast: sister chromatid cohesion and related mechanisms. Genetics 2014; 196:31-63. [PMID: 24395824 PMCID: PMC3872193 DOI: 10.1534/genetics.112.145144] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/28/2022] Open
Abstract
Studies on budding yeast have exposed the highly conserved mechanisms by which duplicated chromosomes are evenly distributed to daughter cells at the metaphase-anaphase transition. The establishment of proteinaceous bridges between sister chromatids, a function provided by a ring-shaped complex known as cohesin, is central to accurate segregation. It is the destruction of this cohesin that triggers the segregation of chromosomes following their proper attachment to microtubules. Since it is irreversible, this process must be tightly controlled and driven to completion. Furthermore, during meiosis, modifications must be put in place to allow the segregation of maternal and paternal chromosomes in the first division for gamete formation. Here, I review the pioneering work from budding yeast that has led to a molecular understanding of the establishment and destruction of cohesion.
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Affiliation(s)
- Adele L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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198
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De Storme N, Geelen D. The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms. PLANT, CELL & ENVIRONMENT 2014; 37:1-18. [PMID: 23731015 PMCID: PMC4280902 DOI: 10.1111/pce.12142] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/30/2013] [Accepted: 05/08/2013] [Indexed: 05/18/2023]
Abstract
In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved.
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Affiliation(s)
- Nico De Storme
- Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links, 653, B-9000, Ghent, Belgium
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199
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Lao JP, Cloud V, Huang CC, Grubb J, Thacker D, Lee CY, Dresser ME, Hunter N, Bishop DK. Meiotic crossover control by concerted action of Rad51-Dmc1 in homolog template bias and robust homeostatic regulation. PLoS Genet 2013; 9:e1003978. [PMID: 24367271 PMCID: PMC3868528 DOI: 10.1371/journal.pgen.1003978] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022] Open
Abstract
During meiosis, repair of programmed DNA double-strand breaks (DSBs) by recombination promotes pairing of homologous chromosomes and their connection by crossovers. Two DNA strand-exchange proteins, Rad51 and Dmc1, are required for meiotic recombination in many organisms. Studies in budding yeast imply that Rad51 acts to regulate Dmc1's strand exchange activity, while its own exchange activity is inhibited. However, in a dmc1 mutant, elimination of inhibitory factor, Hed1, activates Rad51's strand exchange activity and results in high levels of recombination without participation of Dmc1. Here we show that Rad51-mediated meiotic recombination is not subject to regulatory processes associated with high-fidelity chromosome segregation. These include homolog bias, a process that directs strand exchange between homologs rather than sister chromatids. Furthermore, activation of Rad51 does not effectively substitute for Dmc1's chromosome pairing activity, nor does it ensure formation of the obligate crossovers required for accurate homolog segregation. We further show that Dmc1's dominance in promoting strand exchange between homologs involves repression of Rad51's strand-exchange activity. This function of Dmc1 is independent of Hed1, but requires the meiotic kinase, Mek1. Hed1 makes a relatively minor contribution to homolog bias, but nonetheless this is important for normal morphogenesis of synaptonemal complexes and efficient crossing-over especially when DSB numbers are decreased. Super-resolution microscopy shows that Dmc1 also acts to organize discrete complexes of a Mek1 partner protein, Red1, into clusters along lateral elements of synaptonemal complexes; this activity may also contribute to homolog bias. Finally, we show that when interhomolog bias is defective, recombination is buffered by two feedback processes, one that increases the fraction of events that yields crossovers, and a second that we propose involves additional DSB formation in response to defective homolog interactions. Thus, robust crossover homeostasis is conferred by integrated regulation at initiation, strand-exchange and maturation steps of meiotic recombination. Meiosis is the specialized cell division that produces gametes by precisely reducing the chromosome copy number from two to one. Accurate segregation of homologous chromosome pairs requires they be connected by crossing-over, the precise breakage and exchange of chromosome arms that is carried out by a process called recombination. Recombination is regulated so each pair of homologous chromosomes becomes connected by at least one crossover. We studied the roles of two recombination proteins, Rad51 and Dmc1, which can act directly to join homologous DNA molecules. Our evidence supports the idea that Dmc1 is the dominant joining activity, while Rad51 acts indirectly with other proteins to support and regulate Dmc1. Furthermore, Hed1, an inhibitor of Rad51's DNA joining activity, is also shown to enhance the efficiency of crossing-over. Cells in which Rad51 is activated to promote DNA joining in place of Dmc1 have unregulated and inefficient crossing-over that often leaves chromosome pairs without the requisite crossover. Despite these defects, most cells that use Rad51 in place of Dmc1 complete meiosis and produce high levels of crossovers. Our results indicate that compensatory processes ensure that meiotic cells accumulate high levels of crossover intermediates before progressing to the first round of chromosome segregation.
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Affiliation(s)
- Jessica P. Lao
- Howard Hughes Medical Institute and Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, United States of America
- Genetics Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Veronica Cloud
- Committee on Genetics, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Chu-Chun Huang
- Howard Hughes Medical Institute and Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, United States of America
| | - Jennifer Grubb
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Drew Thacker
- Weil Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Chih-Ying Lee
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Michael E. Dresser
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Neil Hunter
- Howard Hughes Medical Institute and Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, California, United States of America
- Genetics Graduate Group, University of California, Davis, Davis, California, United States of America
- Department of Molecular & Cellular Biology, University of California, Davis, Davis, California, United States of America
- Department of Cell Biology & Human Anatomy, University of California, Davis, Davis, California, United States of America
- * E-mail: (NH); (DKB)
| | - Douglas K. Bishop
- Committee on Genetics, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- * E-mail: (NH); (DKB)
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200
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Xu X, Ball L, Chen W, Tian X, Lambrecht A, Hanna M, Xiao W. The yeast Shu complex utilizes homologous recombination machinery for error-free lesion bypass via physical interaction with a Rad51 paralogue. PLoS One 2013; 8:e81371. [PMID: 24339919 PMCID: PMC3855272 DOI: 10.1371/journal.pone.0081371] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/11/2013] [Indexed: 12/20/2022] Open
Abstract
DNA-damage tolerance (DDT) is defined as a mechanism by which eukaryotic cells resume DNA synthesis to fill the single-stranded DNA gaps left by replication-blocking lesions. Eukaryotic cells employ two different means of DDT, namely translesion DNA synthesis (TLS) and template switching, both of which are coordinately regulated through sequential ubiquitination of PCNA at the K164 residue. In the budding yeast Saccharomyces cerevisiae, the same PCNA-K164 residue can also be sumoylated, which recruits the Srs2 helicase to prevent undesired homologous recombination (HR). While the mediation of TLS by PCNA monoubiquitination has been extensively characterized, the method by which K63-linked PCNA polyubiquitination leads to template switching remains unclear. We recently identified a yeast heterotetrameric Shu complex that couples error-free DDT to HR as a critical step of template switching. Here we report that the Csm2 subunit of Shu physically interacts with Rad55, an accessory protein involved in HR. Rad55 and Rad57 are Rad51 paralogues and form a heterodimer to promote Rad51-ssDNA filament formation by antagonizing Srs2 activity. Although Rad55-Rad57 and Shu function in the same pathway and both act to inhibit Srs2 activity, Shu appears to be dedicated to error-free DDT while the Rad55-Rad57 complex is also involved in double-strand break repair. This study reveals the detailed steps of error-free lesion bypass and also brings to light an intrinsic interplay between error-free DDT and Srs2-mediated inhibition of HR.
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Affiliation(s)
- Xin Xu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Lindsay Ball
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Wangyang Chen
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xuelei Tian
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Amanda Lambrecht
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Michelle Hanna
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, China
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
- * E-mail:
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