1
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Chen HW, Yeh HY, Chang CC, Kuo WC, Lin SW, Vrielynck N, Grelon M, Chan NL, Chi P. Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana. Nucleic Acids Res 2024; 52:4541-4555. [PMID: 38499490 PMCID: PMC11077084 DOI: 10.1093/nar/gkae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Formation of programmed DNA double-strand breaks is essential for initiating meiotic recombination. Genetic studies on Arabidopsis thaliana and Mus musculus have revealed that assembly of a type IIB topoisomerase VI (Topo VI)-like complex, composed of SPO11 and MTOPVIB, is a prerequisite for generating DNA breaks. However, it remains enigmatic if MTOPVIB resembles its Topo VI subunit B (VIB) ortholog in possessing robust ATPase activity, ability to undergo ATP-dependent dimerization, and activation of SPO11-mediated DNA cleavage. Here, we successfully prepared highly pure A. thaliana MTOPVIB and MTOPVIB-SPO11 complex. Contrary to expectations, our findings highlight that MTOPVIB differs from orthologous Topo VIB by lacking ATP-binding activity and independently forming dimers without ATP. Most significantly, our study reveals that while MTOPVIB lacks the capability to stimulate SPO11-mediated DNA cleavage, it functions as a bona fide DNA-binding protein and plays a substantial role in facilitating the dsDNA binding capacity of the MOTOVIB-SPO11 complex. Thus, we illustrate mechanistic divergence between the MTOPVIB-SPO11 complex and classical type IIB topoisomerases.
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Affiliation(s)
- Hsin-Wen Chen
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Chih-Chiang Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Wei-Chen Kuo
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
| | - Nathalie Vrielynck
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Mathilde Grelon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
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2
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Yu Y, Wang J, Liu K, Zheng Z, Arter M, Bouuaert CC, Pu S, Patel DJ, Keeney S. Cryo-EM structure of the Spo11 core complex bound to DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564985. [PMID: 37961437 PMCID: PMC10634984 DOI: 10.1101/2023.10.31.564985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The DNA double-strand breaks that initiate meiotic recombination are formed by topoisomerase relative Spo11, supported by conserved auxiliary factors. Because high-resolution structural data are lacking, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-EM structures at up to 3.3 Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104, and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3'-OH and first 5' overhanging nucleotide, definitively establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.
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Affiliation(s)
- You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Kaixian Liu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhi Zheng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Corentin Claeys Bouuaert
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Stephen Pu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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3
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Mazur AK, Gladyshev E. C-DNA may facilitate homologous DNA pairing. Trends Genet 2023:S0168-9525(23)00023-9. [PMID: 36804168 DOI: 10.1016/j.tig.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Recombination-independent homologous pairing represents a prominent yet largely enigmatic feature of chromosome biology. As suggested by studies in the fungus Neurospora crassa, this process may be based on the direct pairing of homologous DNA molecules. Theoretical search for the DNA structures consistent with those genetic results has led to an all-atom model in which the B-DNA conformation of the paired double helices is strongly shifted toward C-DNA. Coincidentally, C-DNA also features a very shallow major groove that could permit initial homologous contacts without atom-atom clashes. The hereby conjectured role of C-DNA in homologous pairing should encourage the efforts to discover its biological functions and may also clarify the mechanism of recombination-independent recognition of DNA homology.
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Affiliation(s)
- Alexey K Mazur
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris, France; Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
| | - Eugene Gladyshev
- Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
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4
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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5
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McKie SJ, Desai P, Seol Y, Allen AM, Maxwell A, Neuman KC. Topoisomerase VI is a chirally-selective, preferential DNA decatenase. eLife 2022; 11:67021. [PMID: 35076393 PMCID: PMC8837201 DOI: 10.7554/elife.67021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase; however, robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a significant increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.
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Affiliation(s)
- Shannon J McKie
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Parth Desai
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Adam Mb Allen
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Anthony Maxwell
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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6
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A Novel Spo11 Homologue Functions as a Positive Regulator in Cyst Differentiation in Giardia lamblia. Int J Mol Sci 2021; 22:ijms222111902. [PMID: 34769330 PMCID: PMC8584520 DOI: 10.3390/ijms222111902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Giardia lamblia persists in a dormant state with a protective cyst wall for transmission. It is incompletely known how three cyst wall proteins (CWPs) are coordinately synthesized during encystation. Meiotic recombination is required for sexual reproduction in animals, fungi, and plants. It is initiated by formation of double-stranded breaks by a topoisomerase-like Spo11. It has been shown that exchange of genetic material in the fused nuclei occurs during Giardia encystation, suggesting parasexual recombination processes of this protozoan. Giardia possesses an evolutionarily conserved Spo11 with typical domains for cleavage reaction and an upregulated expression pattern during encystation. In this study, we asked whether Spo11 can activate encystation process, like other topoisomerases we previously characterized. We found that Spo11 was capable of binding to both single-stranded and double-stranded DNA in vitro and that it could also bind to the cwp promoters in vivo as accessed in chromatin immunoprecipitation assays. Spo11 interacted with WRKY and MYB2 (named from myeloblastosis), transcription factors that can activate cwp gene expression during encystation. Interestingly, overexpression of Spo11 resulted in increased expression of cwp1-3 and myb2 genes and cyst formation. Mutation of the Tyr residue for the active site or two conserved residues corresponding to key DNA-binding residues for Arabidopsis Spo11 reduced the levels of cwp1-3 and myb2 gene expression and cyst formation. Targeted disruption of spo11 gene with CRISPR/Cas9 system led to a significant decrease in cwp1-3 and myb2 gene expression and cyst number. Our results suggest that Spo11 acts as a positive regulator for Giardia differentiation into cyst.
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7
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Yamamoto T, Sakaue T, Schiessel H. Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates. Nucleic Acids Res 2021; 49:5017-5027. [PMID: 33885786 PMCID: PMC8136786 DOI: 10.1093/nar/gkab275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 04/20/2021] [Indexed: 01/17/2023] Open
Abstract
Enhancers are DNA sequences at a long genomic distance from target genes. Recent experiments suggest that enhancers are anchored to the surfaces of condensates of transcription machinery and that the loop extrusion process enhances the transcription level of their target genes. Here, we theoretically study the polymer dynamics driven by the loop extrusion of the linker DNA between an enhancer and the promoter of its target gene to calculate the contact probability of the promoter to the transcription machinery in the condensate. Our theory predicts that when the loop extrusion process is active, the contact probability increases with increasing linker DNA length. This finding reflects the fact that the relaxation time, with which the promoter stays in proximity to the surface of the transcriptional condensate, increases as the length of the linker DNA increases. This contrasts the equilibrium case for which the contact probability between the promoter and the transcription machineries is smaller for longer linker DNA lengths.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1, Fuchinobe,Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
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8
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Prieler S, Chen D, Huang L, Mayrhofer E, Zsótér S, Vesely M, Mbogning J, Klein F. Spo11 generates gaps through concerted cuts at sites of topological stress. Nature 2021; 594:577-582. [PMID: 34108684 DOI: 10.1038/s41586-021-03632-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/11/2021] [Indexed: 02/08/2023]
Abstract
Meiotic recombination is essential for chromosome segregation at meiosis and fertility. It is initiated by programmed DNA double-strand breaks (DSBs) introduced by Spo11, a eukaryotic homologue of an archaeal topoisomerase (Topo VIA)1. Here we describe previously uncharacterized Spo11-induced lesions, 34 to several hundred base pair-long gaps, which are generated by coordinated pairs of DSBs termed double DSBs. Isolation and genome-wide mapping of the resulting fragments with single base-pair precision revealed enrichment at DSB hotspots but also a widely dispersed distribution across the genome. Spo11 prefers to cut sequences with similarity to a DNA-bending motif2, which indicates that bendability contributes to the choice of cleavage site. Moreover, fragment lengths have a periodicity of approximately (10.4n + 3) base pairs, which indicates that Spo11 favours cleavage on the same face of underwound DNA. Consistently, double DSB signals overlap and correlate with topoisomerase II-binding sites, which points to a role for topological stress and DNA crossings in break formation, and suggests a model for the formation of DSBs and double DSBs in which Spo11 traps two DNA strands. Double DSB gaps, which make up an estimated 20% of all initiation events, can account for full gene conversion events that are independent of both Msh2-dependent heteroduplex repair3,4 and the MutLγ endonuclease4. Because non-homologous gap repair results in deletions, and ectopically re-integrated double DSB fragments result in insertions, the formation of double DSBs is a potential source of evolutionary diversity and pathogenic germline aberrations.
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Affiliation(s)
- Silvia Prieler
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Doris Chen
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Lingzhi Huang
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Elisa Mayrhofer
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,Austrian Research Institute for Chemistry and Technology, Microbiology and Cell Culture, Vienna, Austria
| | - Soma Zsótér
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,Humboldt University of Berlin, IRI Life Sciences, Berlin, Germany
| | - Magdalena Vesely
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Jean Mbogning
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,McGill University, Department of Pharmacology and Therapeutics, Montréal, Canada
| | - Franz Klein
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.
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9
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McKie SJ, Neuman KC, Maxwell A. DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 2021; 43:e2000286. [PMID: 33480441 PMCID: PMC7614492 DOI: 10.1002/bies.202000286] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.
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Affiliation(s)
- Shannon J. McKie
- Department Biological Chemistry, John Innes Centre, Norwich, UK
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich, UK
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10
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Yadav VK, Claeys Bouuaert C. Mechanism and Control of Meiotic DNA Double-Strand Break Formation in S. cerevisiae. Front Cell Dev Biol 2021; 9:642737. [PMID: 33748134 PMCID: PMC7968521 DOI: 10.3389/fcell.2021.642737] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Developmentally programmed formation of DNA double-strand breaks (DSBs) by Spo11 initiates a recombination mechanism that promotes synapsis and the subsequent segregation of homologous chromosomes during meiosis. Although DSBs are induced to high levels in meiosis, their formation and repair are tightly regulated to minimize potentially dangerous consequences for genomic integrity. In S. cerevisiae, nine proteins participate with Spo11 in DSB formation, but their molecular functions have been challenging to define. Here, we describe our current view of the mechanism of meiotic DSB formation based on recent advances in the characterization of the structure and function of DSB proteins and discuss regulatory pathways in the light of recent models.
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Affiliation(s)
| | - Corentin Claeys Bouuaert
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-La-Neuve, Belgium
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11
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Structural and functional characterization of the Spo11 core complex. Nat Struct Mol Biol 2021; 28:92-102. [PMID: 33398171 PMCID: PMC7855791 DOI: 10.1038/s41594-020-00534-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/08/2020] [Indexed: 12/19/2022]
Abstract
Spo11, which makes DNA double-strand breaks (DSBs) essential for meiotic recombination, has long been recalcitrant to biochemical study. We provide molecular analysis of S. cerevisiae Spo11 purified with partners Rec102, Rec104 and Ski8. Rec102 and Rec104 jointly resemble the B subunit of archaeal Topoisomerase VI, with Rec104 occupying a position similar to the Top6B GHKL-type ATPase domain. Unexpectedly, the Spo11 complex is monomeric (1:1:1:1 stoichiometry), consistent with dimerization controlling DSB formation. Reconstitution of DNA binding reveals topoisomerase-like preferences for duplex-duplex junctions and bent DNA. Spo11 also binds noncovalently but with high affinity to DNA ends mimicking cleavage products, suggesting a mechanism to cap DSB ends. Mutations that reduce DNA binding in vitro attenuate DSB formation, alter DSB processing, and reshape the DSB landscape in vivo. Our data reveal structural and functional similarities between the Spo11 core complex and Topo VI, but also highlight differences reflecting their distinct biological roles.
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12
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Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS. Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function. Nucleic Acids Res 2020; 48:3962-3974. [PMID: 32095813 PMCID: PMC7144941 DOI: 10.1093/nar/gkaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/07/2023] Open
Abstract
Modified DNA bases functionally distinguish the taxonomic forms of life—5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an α-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C–H < S–H < O–H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.
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Affiliation(s)
- Crystal M Vander Zanden
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ethan N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Adam B Robertson
- Department of Molecular Microbiology, Oslo University Hospital, Sognsvannsveien 20, NO-0027 Oslo, Norway
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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13
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Sexual reproduction potential implied by functional analysis of SPO11 in Phaeodactylum tricornutum. Gene 2020; 757:144929. [PMID: 32622990 DOI: 10.1016/j.gene.2020.144929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 01/05/2023]
Abstract
Phaeodactylum tricornutum is a model microalgae that is widely used to study diatom physiology and ecology. Since the meiotic process and sexual cycle have never been observed directly, P. tricornutum has been considered to be an asexual species. However, phylogenetic analysis of the P. tricornutum genome has revealed a series of meiosis-specific gene homologues in this species. We identified two copies of differently transcribed SPO11 homologs that contain the conserved motifs of Winged-helix and Toprim domains. The homolog PtSPO11-3 interacts with TopoVIB in yeast two-hybrid analysis, whereas the homolog PtSPO11-2 could rescue the sporulation defect of a Spo11 yeast mutant strain. PtSPO11-2 was also found to be significantly up-regulated at low temperatures in P. tricornutum and its key catalytic residue was important to the homolog's function in sporulation. The results herein provide positive clue that meiosis and sexual reproduction could exist in this diatom.
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14
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Takahashi TS, Da Cunha V, Krupovic M, Mayer C, Forterre P, Gadelle D. Expanding the type IIB DNA topoisomerase family: identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements. NAR Genom Bioinform 2019; 2:lqz021. [PMID: 33575570 PMCID: PMC7671362 DOI: 10.1093/nargab/lqz021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/12/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
The control of DNA topology by DNA topoisomerases is essential for virtually all DNA transactions in the cell. These enzymes, present in every organism, exist as several non-homologous families. We previously identified a small group of atypical type IIB topoisomerases, called Topo VIII, mainly encoded by plasmids. Here, taking advantage of the rapid expansion of sequence databases, we identified new putative Topo VIII homologs. Our analyses confirm the exclusivity of the corresponding genes to mobile genetic elements (MGE) and extend their distribution to nine different bacterial phyla and one archaeal superphylum. Notably, we discovered another subfamily of topoisomerases, dubbed ‘Mini-A’, including distant homologs of type IIB topoisomerases and encoded by extrachromosomal and integrated bacterial and archaeal viruses. Interestingly, a short, functionally uncharacterized motif at the C-terminal extremity of type IIB topoisomerases appears sufficient to discriminate between Mini-A, Topo VI and Topo VIII subfamilies. This motif could be a key element for understanding the differences between the three subfamilies. Collectively, this work leads to an updated model for the origin and evolution of the type IIB topoisomerase family and raises questions regarding the role of topoisomerases during replication of MGE in bacteria and archaea.
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Affiliation(s)
- Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, 75015 Paris, France
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France.,Université de Paris, Paris Diderot, F-75013 Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Institut Pasteur, F-75015 Paris, France
| | - Danièle Gadelle
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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