101
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Argunhan B, Leung WK, Afshar N, Terentyev Y, Subramanian VV, Murayama Y, Hochwagen A, Iwasaki H, Tsubouchi T, Tsubouchi H. Fundamental cell cycle kinases collaborate to ensure timely destruction of the synaptonemal complex during meiosis. EMBO J 2017; 36:2488-2509. [PMID: 28694245 DOI: 10.15252/embj.201695895] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 01/07/2023] Open
Abstract
The synaptonemal complex (SC) is a proteinaceous macromolecular assembly that forms during meiotic prophase I and mediates adhesion of paired homologous chromosomes along their entire lengths. Although prompt disassembly of the SC during exit from prophase I is a landmark event of meiosis, the underlying mechanism regulating SC destruction has remained elusive. Here, we show that DDK (Dbf4-dependent Cdc7 kinase) is central to SC destruction. Upon exit from prophase I, Dbf4, the regulatory subunit of DDK, directly associates with and is phosphorylated by the Polo-like kinase Cdc5. In parallel, upregulated CDK1 activity also targets Dbf4. An enhanced Dbf4-Cdc5 interaction pronounced phosphorylation of Dbf4 and accelerated SC destruction, while reduced/abolished Dbf4 phosphorylation hampered destruction of SC proteins. SC destruction relieved meiotic inhibition of the ubiquitous recombinase Rad51, suggesting that the mitotic recombination machinery is reactivated following prophase I exit to repair any persisting meiotic DNA double-strand breaks. Taken together, we propose that the concerted action of DDK, Polo-like kinase, and CDK1 promotes efficient SC destruction at the end of prophase I to ensure faithful inheritance of the genome.
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Affiliation(s)
- Bilge Argunhan
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Wing-Kit Leung
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK
| | - Negar Afshar
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Yaroslav Terentyev
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK
| | | | - Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Tomomi Tsubouchi
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK .,National Institute for Basic Biology, Okazaki, Japan
| | - Hideo Tsubouchi
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton, East Sussex, UK .,National Institute for Basic Biology, Okazaki, Japan
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102
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Abstract
The exchange of DNA strands between broken and intact molecules lies at the heart of fundamental cellular processes ranging from repairing DNA damage by homologous recombination to generation of genetic diversity during sexual reproduction. New work by Lee and colleagues utilizes the DNA curtain method, an elegant single-molecule technique, to demonstrate common and idiosyncratic features in the DNA strand exchange mechanisms of three RecA-family recombinases, bacterial RecA, and eukaryotic Rad51 and Dmc1 proteins.
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Affiliation(s)
- Maria Spies
- From the Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
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103
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Kong M, Beckwitt EC, Springall L, Kad NM, Van Houten B. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time. Methods Enzymol 2017; 592:213-257. [PMID: 28668122 DOI: 10.1016/bs.mie.2017.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair.
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Affiliation(s)
- Muwen Kong
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Emily C Beckwitt
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Luke Springall
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Bennett Van Houten
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States.
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104
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Lee JY, Steinfeld JB, Qi Z, Kwon Y, Sung P, Greene EC. Sequence imperfections and base triplet recognition by the Rad51/RecA family of recombinases. J Biol Chem 2017; 292:11125-11135. [PMID: 28476890 DOI: 10.1074/jbc.m117.787614] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/27/2017] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination plays key roles in double-strand break repair, rescue, and repair of stalled replication forks and meiosis. The broadly conserved Rad51/RecA family of recombinases catalyzes the DNA strand invasion reaction that takes place during homologous recombination. We have established single-stranded (ss)DNA curtain assays for measuring individual base triplet steps during the early stages of strand invasion. Here, we examined how base triplet stepping by RecA, Rad51, and Dmc1 is affected by DNA sequence imperfections, such as single and multiple mismatches, abasic sites, and single nucleotide insertions. Our work reveals features of base triplet stepping that are conserved among these three phylogenetic lineages of the Rad51/RecA family and also reveals lineage-specific behaviors reflecting properties that are unique to each recombinase. These findings suggest that Dmc1 is tolerant of single mismatches, multiple mismatches, and even abasic sites, whereas RecA and Rad51 are not. Interestingly, the presence of single nucleotide insertion abolishes recognition of an adjacent base triplet by all three recombinases. On the basis of these findings, we describe models for how sequence imperfections may affect base triplet recognition by Rad51/RecA family members, and we discuss how these models and our results may relate to the different biological roles of RecA, Rad51, and Dmc1.
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Affiliation(s)
- Ja Yil Lee
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Justin B Steinfeld
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Zhi Qi
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - YoungHo Kwon
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
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105
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Anand R, Beach A, Li K, Haber J. Rad51-mediated double-strand break repair and mismatch correction of divergent substrates. Nature 2017; 544:377-380. [PMID: 28405019 PMCID: PMC5544500 DOI: 10.1038/nature22046] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/06/2017] [Indexed: 01/14/2023]
Abstract
The Rad51 (also known as RecA) family of recombinases executes the critical step in homologous recombination: the search for homologous DNA to serve as a template during the repair of DNA double-strand breaks (DSBs). Although budding yeast Rad51 has been extensively characterized in vitro, the stringency of its search and sensitivity to mismatched sequences in vivo remain poorly defined. Here, in Saccharomyces cerevisiae, we analysed Rad51-dependent break-induced replication in which the invading DSB end and its donor template share a 108-base-pair homology region and the donor carries different densities of single-base-pair mismatches. With every eighth base pair mismatched, repair was about 14% of that of completely homologous sequences. With every sixth base pair mismatched, repair was still more than 5%. Thus, completing break-induced replication in vivo overcomes the apparent requirement for at least 6-8 consecutive paired bases that has been inferred from in vitro studies. When recombination occurs without a protruding nonhomologous 3' tail, the mismatch repair protein Msh2 does not discourage homeologous recombination. However, when the DSB end contains a 3' protruding nonhomologous tail, Msh2 promotes the rejection of mismatched substrates. Mismatch correction of strand invasion heteroduplex DNA is strongly polar, favouring correction close to the DSB end. Nearly all mismatch correction depends on the proofreading activity of DNA polymerase-δ, although the repair proteins Msh2, Mlh1 and Exo1 influence the extent of correction.
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Affiliation(s)
| | - Annette Beach
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110
| | - Kevin Li
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110
| | - James Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02254-9110
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106
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Reichman R, Alleva B, Smolikove S. Prophase I: Preparing Chromosomes for Segregation in the Developing Oocyte. Results Probl Cell Differ 2017; 59:125-173. [PMID: 28247048 DOI: 10.1007/978-3-319-44820-6_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Formation of an oocyte involves a specialized cell division termed meiosis. In meiotic prophase I (the initial stage of meiosis), chromosomes undergo elaborate events to ensure the proper segregation of their chromosomes into gametes. These events include processes leading to the formation of a crossover that, along with sister chromatid cohesion, forms the physical link between homologous chromosomes. Crossovers are formed as an outcome of recombination. This process initiates with programmed double-strand breaks that are repaired through the use of homologous chromosomes as a repair template. The accurate repair to form crossovers takes place in the context of the synaptonemal complex, a protein complex that links homologous chromosomes in meiotic prophase I. To allow proper execution of meiotic prophase I events, signaling processes connect different steps in recombination and synapsis. The events occurring in meiotic prophase I are a prerequisite for proper chromosome segregation in the meiotic divisions. When these processes go awry, chromosomes missegregate. These meiotic errors are thought to increase with aging and may contribute to the increase in aneuploidy observed in advanced maternal age female oocytes.
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Affiliation(s)
- Rachel Reichman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Benjamin Alleva
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.
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107
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Ma CJ, Gibb B, Kwon Y, Sung P, Greene EC. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 2016; 45:749-761. [PMID: 27903895 PMCID: PMC5314761 DOI: 10.1093/nar/gkw1125] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly.
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Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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108
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Abstract
Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.
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109
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Greene EC. On the influence of protein-DNA register during homologous recombination. Cell Cycle 2016; 15:172-5. [PMID: 26652653 DOI: 10.1080/15384101.2015.1121352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Homologous recombination enables the exchange of genetic information between related DNA molecules and is a driving force in evolution. Using single-molecule optical microscopy we have recently shown that members of the Rad51/RecA family of recombinases stabilize paired homologous strand of DNA in precise 3-nt increments. Here we discuss an interesting conceptual implication of these results, which is that the recombinases may actively sense and reorganize their alignment register relative to the bound DNA sequences to ensure optimal base triplet pairing interactions during the early stages of recombination.
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Affiliation(s)
- Eric C Greene
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
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110
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Abstract
Double-strand breaks (DSBs) pose a severe challenge to genome integrity; consequently, cells have developed efficient mechanisms to repair DSBs through several pathways of homologous recombination and other nonhomologous end-joining processes. Much of our understanding of these pathways has come from the analysis of site-specific DSBs created by the HO endonuclease in the budding yeast Saccharomyces cerevisiae. I was fortunate to get in on the ground floor of analyzing the fate of synchronously induced DSBs through the study of what I coined "in vivo biochemistry." I have had the remarkable good fortune to profit from the development of new techniques that have permitted an ever more detailed dissection of these repair mechanisms, which are described here.
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Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02453;
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111
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A general solution for opening double-stranded DNA for isothermal amplification. Sci Rep 2016; 6:34582. [PMID: 27687498 PMCID: PMC5043356 DOI: 10.1038/srep34582] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/15/2016] [Indexed: 01/13/2023] Open
Abstract
Nucleic acid amplification is the core technology of molecular biology and genetic
engineering. Various isothermal amplification techniques have been developed as
alternatives to polymerase chain reaction (PCR). However, most of these
methods can only detect single stranded nucleic acid. Herein, we put forward a
simple solution for opening double-stranded DNA for isothermal detection methods.
The strategy employs recombination protein from E. coli (RecA) to form
nucleoprotein complex with single-stranded DNA, which could scan double-stranded
template for homologous sites. Then, the nucleoprotein can invade the
double-stranded template to form heteroduplex in the presence of ATP, resulting in
the strand exchange. The ATP regeneration system could be eliminated by using high
concentration of ATP, and the 3′-OH terminal of the invasion strand can
be recognized by other DNA modifying enzymes such as DNA polymerase or DNA ligase.
Moreover, dATP was found to be a better cofactor for RecA, which make the
system more compatible to DNA polymerase. The method described here is a general
solution to open dsDNA, serving as a platform to develop more isothermal nucleic
acids detection methods for real DNA samples based on it.
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112
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Abstract
Comparisons among a variety of eukaryotes have revealed considerable variability in the structures and processes involved in their meiosis. Nevertheless, conventional forms of meiosis occur in all major groups of eukaryotes, including early-branching protists. This finding confirms that meiosis originated in the common ancestor of all eukaryotes and suggests that primordial meiosis may have had many characteristics in common with conventional extant meiosis. However, it is possible that the synaptonemal complex and the delicate crossover control related to its presence were later acquisitions. Later still, modifications to meiotic processes occurred within different groups of eukaryotes. Better knowledge on the spectrum of derived and uncommon forms of meiosis will improve our understanding of many still mysterious aspects of the meiotic process and help to explain the evolutionary basis of functional adaptations to the meiotic program.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology and Vienna Biocenter, University of Vienna, A-1030 Vienna, Austria;
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113
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Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. Proc Natl Acad Sci U S A 2016; 113:E6045-E6054. [PMID: 27671650 DOI: 10.1073/pnas.1604807113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The DNA strand exchange protein RAD51 facilitates the central step in homologous recombination, a process fundamentally important for accurate repair of damaged chromosomes, restart of collapsed replication forks, and telomere maintenance. The active form of RAD51 is a nucleoprotein filament that assembles on single-stranded DNA (ssDNA) at the sites of DNA damage. The c-Abl tyrosine kinase and its oncogenic counterpart BCR-ABL fusion kinase phosphorylate human RAD51 on tyrosine residues 54 and 315. We combined biochemical reconstitutions of the DNA strand exchange reactions with total internal reflection fluorescence microscopy to determine how the two phosphorylation events affect the biochemical activities of human RAD51 and properties of the RAD51 nucleoprotein filament. By mimicking RAD51 tyrosine phosphorylation with a nonnatural amino acid, p-carboxymethyl-l-phenylalanine (pCMF), we demonstrated that Y54 phosphorylation enhances the RAD51 recombinase activity by at least two different mechanisms, modifies the RAD51 nucleoprotein filament formation, and allows RAD51 to compete efficiently with ssDNA binding protein RPA. In contrast, Y315 phosphorylation has little effect on the RAD51 activities. Based on our work and previous cellular studies, we propose a mechanism underlying RAD51 activation by c-Abl/BCR-ABL kinases.
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114
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Zhang YW, Nong DG, Dou SX, Li W, Yan Y, Xi XG, Xu CH, Li M. Iterative homology checking and non-uniform stepping during RecA-mediated strand exchange. Biochem Biophys Res Commun 2016; 478:1153-7. [PMID: 27543204 DOI: 10.1016/j.bbrc.2016.08.084] [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: 07/24/2016] [Accepted: 08/14/2016] [Indexed: 12/11/2022]
Abstract
Recombinase-mediated homologous recombination (HR) in which strands are exchanged between two similar or identical DNA molecules is essential for maintaining genome fidelity and generating genetic diversity. It is believed that HR comprises two distinct stages: an initial alignment with stringent homology checking followed by stepwise heteroduplex expansion. If and how homology checking takes place during heteroduplex expansion, however, remains unknown. In addition, the number of base pairs (bp) involved in each step is still under debate. By using single-molecule approaches to catch transient intermediates in RecA-mediated HR with different degrees of homology, we show that (i) the expansion proceeds with step sizes of multiples of 3 bp, (ii) the step sizes follow wide distributions that are similar to that of initial alignment lengths, and (iii) each distribution can be divided into a short-scale and a long-scale part irrespective of the degree of homology. Our results suggest an iterative mechanism of strand exchange in which ssDNA-RecA filament interrogates double-stranded DNA using a short tract (6-15 bp) for quick checking and a long tract (>18 bp) for stringent sequence comparison. The present work provides novel insights into the physical and structural bases of DNA recombination.
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Affiliation(s)
- Yu-Wei Zhang
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Da-Guan Nong
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yan Yan
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China; Department of Physics, Emory University, Atlanta, GA, 30322, USA
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A & F University, Xi'an, Shaanxi, 712100, China; LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, F-94235, Cachan, France
| | - Chun-Hua Xu
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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115
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Singh D, Sternberg SH, Fei J, Doudna JA, Ha T. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun 2016; 7:12778. [PMID: 27624851 PMCID: PMC5027287 DOI: 10.1038/ncomms12778] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Binding specificity of Cas9-guide RNA complexes to DNA is important for genome-engineering applications; however, how mismatches influence target recognition/rejection kinetics is not well understood. Here we used single-molecule FRET to probe real-time interactions between Cas9-RNA and DNA targets. The bimolecular association rate is only weakly dependent on sequence; however, the dissociation rate greatly increases from <0.006 s(-1) to >2 s(-1) upon introduction of mismatches proximal to protospacer-adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 11 base pairs in length, which prevent DNA cleavage, still allow formation of a stable complex (dissociation rate <0.006 s(-1)), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome-editing, thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading.
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Affiliation(s)
- Digvijay Singh
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Samuel H. Sternberg
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jingyi Fei
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA
| | - Taekjip Ha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
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116
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Lee JY, Qi Z, Greene EC. ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex. J Biol Chem 2016; 291:22218-22230. [PMID: 27587394 DOI: 10.1074/jbc.m116.740563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 01/13/2023] Open
Abstract
Homologous recombination is an important DNA repair pathway that plays key roles in maintaining genome stability. Escherichia coli RecA is an ATP-dependent DNA-binding protein that catalyzes the DNA strand exchange reactions in homologous recombination. RecA assembles into long helical filaments on single-stranded DNA, and these presynaptic complexes are responsible for locating and pairing with a homologous duplex DNA. Recent single molecule studies have provided new insights into RecA behavior, but the potential influence of ATP in the reactions remains poorly understood. Here we examine how ATP influences the ability of the RecA presynaptic complex to interact with homologous dsDNA. We demonstrate that over short time regimes, RecA presynaptic complexes sample heterologous dsDNA similarly in the presence of either ATP or ATPγS, suggesting that initial interactions do not depend on ATP hydrolysis. In addition, RecA stabilizes pairing intermediates in three-base steps, and stepping energetics is seemingly unaltered in the presence of ATP. However, the overall dissociation rate of these paired intermediates with ATP is ∼4-fold higher than with ATPγS. These experiments suggest that ATP plays an unanticipated role in promoting the turnover of captured duplex DNA intermediates as RecA attempts to align homologous sequences during the early stages of recombination.
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Affiliation(s)
- Ja Yil Lee
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Zhi Qi
- the Center of Quantitative Biology & Center of Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
| | - Eric C Greene
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
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117
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Mek1 Down Regulates Rad51 Activity during Yeast Meiosis by Phosphorylation of Hed1. PLoS Genet 2016; 12:e1006226. [PMID: 27483004 PMCID: PMC4970670 DOI: 10.1371/journal.pgen.1006226] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 11/24/2022] Open
Abstract
During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In dmc1Δ mutants, Rad51 is actively inhibited, thereby resulting in prophase arrest due to unrepaired DSBs triggering the meiotic recombination checkpoint. This inhibition is dependent upon the meiosis-specific kinase Mek1 and occurs through two different mechanisms that prevent complex formation with the Rad51 accessory factor Rad54: (i) phosphorylation of Rad54 by Mek1 and (ii) binding of Rad51 by the meiosis-specific protein Hed1. An open question has been why inhibition of Mek1 affects Hed1 repression of Rad51. This work shows that Hed1 is a direct substrate of Mek1. Phosphorylation of Hed1 at threonine 40 helps suppress Rad51 activity in dmc1Δ mutants by promoting Hed1 protein stability. Rad51-mediated recombination occurring in the absence of Hed1 phosphorylation results in a significant increase in non-exchange chromosomes despite wild-type levels of crossovers, confirming previous results indicating a defect in crossover assurance. We propose that Rad51 function in meiosis is regulated in part by the coordinated phosphorylation of Rad54 and Hed1 by Mek1. Sexual reproduction requires the formation of haploid gametes by a highly conserved, specialized cell division called meiosis. Failures in meiotic chromosome segregation lead to chromosomally imbalanced gametes that cause infertility and birth defects such as Trisomy 21 in humans. Meiotic crossovers, initiated by programmed double strand breaks (DSBs), are critical for proper chromosome segregation. Interhomolog strand invasion requires the presence of Rad51, and the strand invasion activity of the meiosis-specific recombinase Dmc1. The meiosis-specific kinase, Mek1, is a key regulator of meiotic recombination, promoting interhomolog strand invasion and recombination pathway choice. Rad51 activity during meiosis is inhibited by preventing the Rad51 protein from forming complexes with an accessory factor, Rad54, in two ways: (1) Mek1 phosphorylation of Rad54 and (2) binding of Rad51 by a meiosis-specific protein, Hed1. Why inactivation of Mek1 affects Hed1-mediated repression of Rad51 was previously unknown. This work demonstrates that Mek1 regulates the ability of Hed1 to inhibit Rad51 by direct phosphorylation of Hed1. Therefore in meiosis, Rad51 activity is regulated in part by the coordinated phosphorylation of both Rad54 and Hed1 by Mek1.
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118
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Bell JC, Kowalczykowski SC. RecA: Regulation and Mechanism of a Molecular Search Engine. Trends Biochem Sci 2016; 41:491-507. [PMID: 27156117 PMCID: PMC4892382 DOI: 10.1016/j.tibs.2016.04.002] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/19/2022]
Abstract
Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
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119
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Wang H, Hu Q, Tang D, Liu X, Du G, Shen Y, Li Y, Cheng Z. OsDMC1 Is Not Required for Homologous Pairing in Rice Meiosis. PLANT PHYSIOLOGY 2016; 171:230-41. [PMID: 26960731 PMCID: PMC4854709 DOI: 10.1104/pp.16.00167] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/07/2016] [Indexed: 05/13/2023]
Abstract
Meiotic homologous recombination is pivotal to sexual reproduction. DMC1, a conserved recombinase, is involved in directing single-end invasion between interhomologs during meiotic recombination. In this study, we identified OsDMC1A and OsDMC1B, two closely related proteins in rice (Oryza sativa) with high sequence similarity to DMC1 proteins from other species. Analysis of Osdmc1a and Osdmc1b Tos17 insertion mutants indicated that these genes are functionally redundant. Immunolocalization analysis revealed OsDMC1 foci occurred at leptotene, which disappeared from late pachytene chromosomes in wild-type meiocytes. According to cytological analyses, homologous pairing is accomplished in the Osdmc1a Osdmc1b double mutant, but synapsis is seriously disrupted. The reduced number of bivalents and abnormal OsHEI10 foci in Osdmc1a Osdmc1b establishes an essential role for OsDMC1 in crossover formation. In the absence of OsDMC1, early recombination events probably occur normally, leading to normal localization of γH2AX, PAIR3, OsMRE11, OsCOM1, and OsRAD51C. Moreover, OsDMC1 was not detected in pairing-defective mutants, such as pair2, pair3, Oscom1, and Osrad51c, while it was loaded onto meiotic chromosomes in zep1, Osmer3, Oszip4, and Oshei10 Taken together, these results suggest that during meiosis, OsDMC1 is dispensable for homologous pairing in rice, which is quite different from the DMC1 homologs identified so far in other organisms.
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Affiliation(s)
- Hongjun Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Hu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofei Liu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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120
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Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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121
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Abstract
Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination.
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Affiliation(s)
- Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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122
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Godin SK, Sullivan MR, Bernstein KA. Novel insights into RAD51 activity and regulation during homologous recombination and DNA replication. Biochem Cell Biol 2016; 94:407-418. [PMID: 27224545 DOI: 10.1139/bcb-2016-0012] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this review we focus on new insights that challenge our understanding of homologous recombination (HR) and Rad51 regulation. Recent advances using high-resolution microscopy and single molecule techniques have broadened our knowledge of Rad51 filament formation and strand invasion at double-strand break (DSB) sites and at replication forks, which are one of most physiologically relevant forms of HR from yeast to humans. Rad51 filament formation and strand invasion is regulated by many mediator proteins such as the Rad51 paralogues and the Shu complex, consisting of a Shu2/SWS1 family member and additional Rad51 paralogues. Importantly, a novel RAD51 paralogue was discovered in Caenorhabditis elegans, and its in vitro characterization has demonstrated a new function for the worm RAD51 paralogues during HR. Conservation of the human RAD51 paralogues function during HR and repair of replicative damage demonstrate how the RAD51 mediators play a critical role in human health and genomic integrity. Together, these new findings provide a framework for understanding RAD51 and its mediators in DNA repair during multiple cellular contexts.
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Affiliation(s)
- Stephen K Godin
- University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, and the Department of Microbiology and Molecular Genetics.,University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, and the Department of Microbiology and Molecular Genetics
| | - Meghan R Sullivan
- University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, and the Department of Microbiology and Molecular Genetics.,University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, and the Department of Microbiology and Molecular Genetics
| | - Kara A Bernstein
- University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, and the Department of Microbiology and Molecular Genetics
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123
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Visualizing recombination intermediates with single-stranded DNA curtains. Methods 2016; 105:62-74. [PMID: 27038747 DOI: 10.1016/j.ymeth.2016.03.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 01/23/2023] Open
Abstract
Homologous recombination (HR) is a critical cellular process for repairing double-stranded DNA breaks (DSBs) - a toxic type of DNA lesion that can result in chromosomal rearrangements and cancer. During the early stages of HR, members from the Rad51/RecA family of recombinases assemble into long filaments on the single-stranded DNA overhangs that are present at processed DSBs. These nucleoprotein filaments are referred to as presynaptic complexes, and these presynaptic complexes must align and pair homologous DNA sequences during HR. Traditional ensemble methods cannot easily access the transient and often heterogeneous intermediates that are typical of DNA recombination reactions, and as a consequence, there remain many open questions with respect to the molecular details of this pathway. Novel single-molecule approaches that are capable of directly visualizing reaction intermediates in solution and in real time offer the potential for new insights into the mechanism of homologous DNA recombination. Here we highlight recently developed single stranded DNA curtain methods for studying the properties of individual Rad51 presynaptic complexes and other related recombination intermediates at the single-molecule level.
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124
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Loidl J, Lorenz A. DNA double-strand break formation and repair in Tetrahymena meiosis. Semin Cell Dev Biol 2016; 54:126-34. [PMID: 26899715 DOI: 10.1016/j.semcdb.2016.02.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022]
Abstract
The molecular details of meiotic recombination have been determined for a small number of model organisms. From these studies, a general picture has emerged that shows that most, if not all, recombination is initiated by a DNA double-strand break (DSB) that is repaired in a recombinogenic process using a homologous DNA strand as a template. However, the details of recombination vary between organisms, and it is unknown which variant is representative of evolutionarily primordial meiosis or most prevalent among eukaryotes. To answer these questions and to obtain a better understanding of the range of recombination processes among eukaryotes, it is important to study a variety of different organisms. Here, the ciliate Tetrahymena thermophila is introduced as a versatile meiotic model system, which has the additional bonus of having the largest phylogenetic distance to all of the eukaryotes studied to date. Studying this organism can contribute to our understanding of the conservation and diversification of meiotic recombination processes.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
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125
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Forsdyke DR. Chargaff’s GC rule. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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126
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Borgogno MV, Monti MR, Zhao W, Sung P, Argaraña CE, Pezza RJ. Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange. J Biol Chem 2015; 291:4928-38. [PMID: 26709229 DOI: 10.1074/jbc.m115.704718] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 12/30/2022] Open
Abstract
Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity.
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Affiliation(s)
- María V Borgogno
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Mariela R Monti
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Weixing Zhao
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Carlos E Argaraña
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Roberto J Pezza
- the Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, and the Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, Oklahoma 73126
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