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Martin CA, Sarlós K, Logan CV, Thakur RS, Parry DA, Bizard AH, Leitch A, Cleal L, Ali NS, Al-Owain MA, Allen W, Altmüller J, Aza-Carmona M, Barakat BA, Barraza-García J, Begtrup A, Bogliolo M, Cho MT, Cruz-Rojo J, Mundi Dhahrabi HA, Elcioglu NH, GOSgene, Gorman GS, Jobling R, Kesterton I, Kishita Y, Kohda M, Le Quesne Stabej P, Malallah AJ, Nürnberg P, Ohtake A, Okazaki Y, Pujol R, Ramirez MJ, Revah-Politi A, Shimura M, Stevens P, Taylor RW, Turner L, Williams H, Wilson C, Yigit G, Zahavich L, Alkuraya FS, Surralles J, Iglesias A, Murayama K, Wollnik B, Dattani M, Heath KE, Hickson ID, Jackson AP. Mutations in TOP3A Cause a Bloom Syndrome-like Disorder. Am J Hum Genet 2024; 111:996. [PMID: 38701747 PMCID: PMC11080603 DOI: 10.1016/j.ajhg.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
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2
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Meijering AEC, Sarlós K, Nielsen CF, Witt H, Harju J, Kerklingh E, Haasnoot GH, Bizard AH, Heller I, Broedersz CP, Liu Y, Peterman EJG, Hickson ID, Wuite GJL. Nonlinear mechanics of human mitotic chromosomes. Nature 2022; 605:545-550. [PMID: 35508652 PMCID: PMC9117150 DOI: 10.1038/s41586-022-04666-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/26/2022]
Abstract
In preparation for mitotic cell division, the nuclear DNA of human cells is compacted into individualized, X-shaped chromosomes1. This metamorphosis is driven mainly by the combined action of condensins and topoisomerase IIα (TOP2A)2,3, and has been observed using microscopy for over a century. Nevertheless, very little is known about the structural organization of a mitotic chromosome. Here we introduce a workflow to interrogate the organization of human chromosomes based on optical trapping and manipulation. This allows high-resolution force measurements and fluorescence visualization of native metaphase chromosomes to be conducted under tightly controlled experimental conditions. We have used this method to extensively characterize chromosome mechanics and structure. Notably, we find that under increasing mechanical load, chromosomes exhibit nonlinear stiffening behaviour, distinct from that predicted by classical polymer models4. To explain this anomalous stiffening, we introduce a hierarchical worm-like chain model that describes the chromosome as a heterogeneous assembly of nonlinear worm-like chains. Moreover, through inducible degradation of TOP2A5 specifically in mitosis, we provide evidence that TOP2A has a role in the preservation of chromosome compaction. The methods described here open the door to a wide array of investigations into the structure and dynamics of both normal and disease-associated chromosomes.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian F Nielsen
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Witt
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Janni Harju
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Emma Kerklingh
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Guus H Haasnoot
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Iddo Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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3
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Bizard AH, Allemand JF, Hassenkam T, Paramasivam M, Sarlós K, Singh MI, Hickson ID. PICH and TOP3A cooperate to induce positive DNA supercoiling. Nat Struct Mol Biol 2019; 26:267-274. [PMID: 30936532 DOI: 10.1038/s41594-019-0201-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
All known eukaryotic topoisomerases are only able to relieve torsional stress in DNA. Nevertheless, it has been proposed that the introduction of positive DNA supercoiling is required for efficient sister-chromatid disjunction by Topoisomerase 2a during mitosis. Here we identify a eukaryotic enzymatic activity that introduces torsional stress into DNA. We show that the human Plk1-interacting checkpoint helicase (PICH) and Topoisomerase 3a proteins combine to create an extraordinarily high density of positive DNA supercoiling. This activity, which is analogous to that of a reverse-gyrase, is apparently driven by the ability of PICH to progressively extrude hypernegatively supercoiled DNA loops that are relaxed by Topoisomerase 3a. We propose that this positive supercoiling provides an optimal substrate for the rapid disjunction of sister centromeres by Topoisomerase 2a at the onset of anaphase in eukaryotic cells.
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Affiliation(s)
- Anna H Bizard
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jean-Francois Allemand
- Laboratoire de Physique de l'Ecole Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Tue Hassenkam
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Manikandan Paramasivam
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kata Sarlós
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Manika Indrajit Singh
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability & Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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4
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Martin CA, Sarlós K, Logan CV, Thakur RS, Parry DA, Bizard AH, Leitch A, Cleal L, Ali NS, Al-Owain MA, Allen W, Altmüller J, Aza-Carmona M, Barakat BA, Barraza-García J, Begtrup A, Bogliolo M, Cho MT, Cruz-Rojo J, Dhahrabi HAM, Elcioglu NH, Gorman GS, Jobling R, Kesterton I, Kishita Y, Kohda M, Le Quesne Stabej P, Malallah AJ, Nürnberg P, Ohtake A, Okazaki Y, Pujol R, Ramirez MJ, Revah-Politi A, Shimura M, Stevens P, Taylor RW, Turner L, Williams H, Wilson C, Yigit G, Zahavich L, Alkuraya FS, Surralles J, Iglesias A, Murayama K, Wollnik B, Dattani M, Heath KE, Hickson ID, Jackson AP, Jackson AP. Mutations in TOP3A Cause a Bloom Syndrome-like Disorder. Am J Hum Genet 2018; 103:456. [PMID: 30193137 PMCID: PMC6128302 DOI: 10.1016/j.ajhg.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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5
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Martin CA, Sarlós K, Logan CV, Thakur RS, Parry DA, Bizard AH, Leitch A, Cleal L, Ali NS, Al-Owain MA, Allen W, Altmüller J, Aza-Carmona M, Barakat BAY, Barraza-García J, Begtrup A, Bogliolo M, Cho MT, Cruz-Rojo J, Dhahrabi HAM, Elcioglu NH, Gorman GS, Jobling R, Kesterton I, Kishita Y, Kohda M, Le Quesne Stabej P, Malallah AJ, Nürnberg P, Ohtake A, Okazaki Y, Pujol R, Ramirez MJ, Revah-Politi A, Shimura M, Stevens P, Taylor RW, Turner L, Williams H, Wilson C, Yigit G, Zahavich L, Alkuraya FS, Surralles J, Iglesias A, Murayama K, Wollnik B, Dattani M, Heath KE, Hickson ID, Jackson AP. Mutations in TOP3A Cause a Bloom Syndrome-like Disorder. Am J Hum Genet 2018; 103:221-231. [PMID: 30057030 PMCID: PMC6080766 DOI: 10.1016/j.ajhg.2018.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/29/2018] [Indexed: 11/21/2022] Open
Abstract
Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatal-onset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIα), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIα, and consequently subjects' cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIα in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis.
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Affiliation(s)
- Carol-Anne Martin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Clare V Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Roshan Singh Thakur
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - David A Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Andrea Leitch
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Louise Cleal
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Mohammed A Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Miriam Aza-Carmona
- Institute of Medical and Molecular Genetics and Skeletal dysplasia multidisciplinary Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPaz, Madrid 28046, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain
| | | | - Jimena Barraza-García
- Institute of Medical and Molecular Genetics and Skeletal dysplasia multidisciplinary Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPaz, Madrid 28046, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain
| | - Amber Begtrup
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Massimo Bogliolo
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Jaime Cruz-Rojo
- Department of Pediatric Endocrinology & Dysmorphology, Hospital 12 Octubre, Madrid 28041, Spain
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34722, Turkey
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, School of Medical Education, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Ian Kesterton
- Cytogenetics Department, Viapath Analytics, Guy's Hospital, London SE1 9RT, UK
| | - Yoshihito Kishita
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masakazu Kohda
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | | | | | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495, Japan
| | - Yasushi Okazaki
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Roser Pujol
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Maria José Ramirez
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Masaru Shimura
- Center for Medical Genetics, Department of Metabolism, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
| | - Paul Stevens
- Cytogenetics Department, Viapath Analytics, Guy's Hospital, London SE1 9RT, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, School of Medical Education, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lesley Turner
- Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Hywel Williams
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | | | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Laura Zahavich
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Jordi Surralles
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department of Genetics and Biomedical Research Institute Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona 08041, Spain
| | - Alejandro Iglesias
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Medical Center, New York, NY 10032, USA
| | - Kei Murayama
- Center for Medical Genetics, Department of Metabolism, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mehul Dattani
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Karen E Heath
- Institute of Medical and Molecular Genetics and Skeletal dysplasia multidisciplinary Unit, Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPaz, Madrid 28046, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid 28029, Spain
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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Sarlós K, Biebricher A, Petermann EJG, Wuite GJL, Hickson ID. Knotty Problems during Mitosis: Mechanistic Insight into the Processing of Ultrafine DNA Bridges in Anaphase. Cold Spring Harb Symp Quant Biol 2017; 82:187-195. [PMID: 29167280 DOI: 10.1101/sqb.2017.82.033647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation. A failure to accurately unlink UFB DNA results in chromosome segregation errors and binucleation. This, in turn, compromises genome integrity, which is a hallmark of cancer. UFBs are actively removed during anaphase, and most known UFB-associated proteins are enzymes involved in DNA repair in interphase. However, little is known about the mitotic activities of these enzymes or the exact DNA structures present on UFBs. We focus on the biology of UFBs, with special emphasis on their underlying DNA structure and the decatenation machineries that process UFBs.
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Affiliation(s)
- Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Biebricher
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Erwin J G Petermann
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
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7
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Newman JA, Savitsky P, Allerston CK, Bizard AH, Özer Ö, Sarlós K, Liu Y, Pardon E, Steyaert J, Hickson ID, Gileadi O. Crystal structure of the Bloom's syndrome helicase indicates a role for the HRDC domain in conformational changes. Nucleic Acids Res 2015; 43:5221-35. [PMID: 25901030 PMCID: PMC4446433 DOI: 10.1093/nar/gkv373] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/03/2015] [Indexed: 01/16/2023] Open
Abstract
Bloom's syndrome helicase (BLM) is a member of the RecQ family of DNA helicases, which play key roles in the maintenance of genome integrity in all organism groups. We describe crystal structures of the BLM helicase domain in complex with DNA and with an antibody fragment, as well as SAXS and domain association studies in solution. We show an unexpected nucleotide-dependent interaction of the core helicase domain with the conserved, poorly characterized HRDC domain. The BLM–DNA complex shows an unusual base-flipping mechanism with unique positioning of the DNA duplex relative to the helicase core domains. Comparison with other crystal structures of RecQ helicases permits the definition of structural transitions underlying ATP-driven helicase action, and the identification of a nucleotide-regulated tunnel that may play a role in interactions with complex DNA substrates.
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Affiliation(s)
- Joseph A Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Pavel Savitsky
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Charles K Allerston
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Özgün Özer
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 , 1050 Brussels, Belgium Structural Biology Research Center, VIB, Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2 , 1050 Brussels, Belgium Structural Biology Research Center, VIB, Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Building 18.1, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
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Sarlós K, Gyimesi M, Kele Z, Kovács M. Mechanism of RecQ helicase mechanoenzymatic coupling reveals that the DNA interactions of the ADP-bound enzyme control translocation run terminations. Nucleic Acids Res 2014; 43:1090-7. [PMID: 25539922 PMCID: PMC4333385 DOI: 10.1093/nar/gku1333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The processing of various DNA structures by RecQ helicases is crucial for genome maintenance in both bacteria and eukaryotes. RecQ helicases perform active destabilization of DNA duplexes, based on tight coupling of their ATPase activity to moderately processive translocation along DNA strands. Here, we determined the ATPase kinetic mechanism of E. coli RecQ helicase to reveal how mechanoenzymatic coupling is achieved. We found that the interaction of RecQ with DNA results in a drastic acceleration of the rate-limiting ATP cleavage step, which occurs productively due to subsequent rapid phosphate release. ADP release is not rate-limiting and ADP-bound RecQ molecules make up a small fraction during single-stranded DNA translocation. However, the relatively rapid release of the ADP-bound enzyme from DNA causes the majority of translocation run terminations (i.e. detachment from the DNA track). Thus, the DNA interactions of ADP-bound RecQ helicase, probably dependent on DNA structure, will mainly determine translocation processivity and may control the outcome of DNA processing. Comparison with human Bloom's syndrome (BLM) helicase reveals that similar macroscopic parameters are achieved by markedly different underlying mechanisms of RecQ homologs, suggesting diversity in enzymatic tuning.
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Affiliation(s)
- Kata Sarlós
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
| | - Zoltán Kele
- Department of Medical Chemistry, University of Szeged, Dóm sqr. 8. Szeged, H-6720, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA 'Momentum' Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, Budapest, H-1117, Hungary
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Kocsis ZS, Sarlós K, Harami GM, Martina M, Kovács M. A nucleotide-dependent and HRDC domain-dependent structural transition in DNA-bound RecQ helicase. J Biol Chem 2014; 289:5938-49. [PMID: 24403069 DOI: 10.1074/jbc.m113.530741] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The allosteric communication between the ATP- and DNA-binding sites of RecQ helicases enables efficient coupling of ATP hydrolysis to translocation along single-stranded DNA (ssDNA) and, in turn, the restructuring of multistranded DNA substrates during genome maintenance processes. In this study, we used the tryptophan fluorescence signal of Escherichia coli RecQ helicase to decipher the kinetic mechanism of the interaction of the enzyme with ssDNA. Rapid kinetic experiments revealed that ssDNA binding occurs in a two-step mechanism in which the initial binding step is followed by a structural transition of the DNA-bound helicase. We found that the nucleotide state of RecQ greatly influences the kinetics of the detected structural transition, which leads to a high affinity DNA-clamped state in the presence of the nucleotide analog ADP-AlF4. The DNA binding mechanism is largely independent of ssDNA length, indicating the independent binding of RecQ molecules to ssDNA and the lack of significant DNA end effects. The structural transition of DNA-bound RecQ was not detected when the ssDNA binding capability of the helicase-RNase D C-terminal domain was abolished or the domain was deleted. The results shed light on the nature of conformational changes leading to processive ssDNA translocation and multistranded DNA processing by RecQ helicases.
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Affiliation(s)
- Zsuzsa S Kocsis
- From the Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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Gyimesi M, Pires RH, Billington N, Sarlós K, Kocsis ZS, Módos K, Kellermayer MSZ, Kovács M. Visualization of human Bloom's syndrome helicase molecules bound to homologous recombination intermediates. FASEB J 2013; 27:4954-64. [PMID: 24005907 DOI: 10.1096/fj.13-234088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Homologous recombination (HR) is a key process in the repair of double-stranded DNA breaks (DSBs) that can initiate cancer or cell death. Human Bloom's syndrome RecQ-family DNA helicase (BLM) exerts complex activities to promote DSB repair while avoiding illegitimate HR. The oligomeric assembly state of BLM has been a key unresolved aspect of its activities. In this study we assessed the structure and oligomeric state of BLM, in the absence and presence of key HR-intermediate DNA structures, by using single-molecule visualization (electron microscopic and atomic force microscopic single-particle analysis) and solution biophysical (dynamic light scattering, kinetic and equilibrium binding) techniques. Besides full-length BLM, we used a previously characterized truncated construct (BLM(642-1290)) as a monomeric control. Contrary to previous models proposing a ring-forming oligomer, we found the majority of BLM molecules to be monomeric in all examined conditions. However, BLM showed a tendency to form dimers when bound to branched HR intermediates. Our results suggest that HR activities requiring single-stranded DNA translocation are performed by monomeric BLM, while complex DNA structures encountered and dissolved by BLM in later stages of HR induce partial oligomerization of the helicase.
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Affiliation(s)
- Máté Gyimesi
- 3Department of Biochemistry, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary.
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Sun Y, In J, Seol Y, Sarkar S, Strub MP, Sarlós K, Kovács M, Neuman K. Sequence Specific pausing of RecQ Helicase. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Gyimesi M, Harami GM, Sarlós K, Hazai E, Bikádi Z, Kovács M. Complex activities of the human Bloom's syndrome helicase are encoded in a core region comprising the RecA and Zn-binding domains. Nucleic Acids Res 2012; 40:3952-63. [PMID: 22253018 PMCID: PMC3351180 DOI: 10.1093/nar/gks008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bloom's syndrome DNA helicase (BLM), a member of the RecQ family, is a key player in homologous recombination (HR)-based error-free DNA repair processes. During HR, BLM exerts various biochemical activities including single-stranded (ss) DNA translocation, separation and annealing of complementary DNA strands, disruption of complex DNA structures (e.g. displacement loops) and contributes to quality control of HR via clearance of Rad51 nucleoprotein filaments. We performed a quantitative mechanistic analysis of truncated BLM constructs that are shorter than the previously identified minimal functional module. Surprisingly, we found that a BLM construct comprising only the two conserved RecA domains and the Zn2+-binding domain (residues 642–1077) can efficiently perform all mentioned HR-related activities. The results demonstrate that the Zn2+-binding domain is necessary for functional interaction with DNA. We show that the extensions of this core, including the winged-helix domain and the strand separation hairpin identified therein in other RecQ-family helicases, are not required for mechanochemical activity per se and may instead play modulatory roles and mediate protein–protein interactions.
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Affiliation(s)
- Máté Gyimesi
- Department of Biochemistry, ELTE-MTA Momentum Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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Abstract
BLM, one of the human RecQ helicases, plays a fundamental role in homologous recombination-based error-free DNA repair pathways, which require its translocation and DNA unwinding activities. Although translocation is essential in vivo during DNA repair processes and it provides a framework for more complex activities of helicases, including strand separation and nucleoprotein displacement, its mechanism has not been resolved for any human DNA helicase. Here, we present a quantitative model for the translocation of a monomeric form of BLM along ssDNA. We show that BLM performs translocation at a low adenosine triphosphate (ATP) coupling ratio (1 ATP consumed/1 nucleotide traveled) and moderate processivity (with a mean number of 50 nucleotides traveled in a single run). We also show that the rate-limiting step of the translocation cycle is a transition between two ADP-bound enzyme states. Via opening of the helicase core, this structural change may drive the stepping of BLM along the DNA track by a directed inchworm mechanism. The data also support the conclusion that BLM performs double-stranded DNA unwinding by fully active duplex destabilization.
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Affiliation(s)
- Máté Gyimesi
- Department of Biochemistry, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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Gyimesi M, Sarlós K, Derényi I, Kovács M. Streamlined determination of processive run length and mechanochemical coupling of nucleic acid motor activities. Nucleic Acids Res 2010; 38:e102. [PMID: 20123728 PMCID: PMC2853143 DOI: 10.1093/nar/gkq014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Quantitative determination of enzymatic rates, processivity and mechanochemical coupling is a key aspect in characterizing nucleotide triphosphate (NTP)-driven nucleic acid motor enzymes, for both basic research and technological applications. Here, we present a streamlined analytical method suitable for the determination of all key functional parameters based on measurement of NTP hydrolysis during interaction of motor enzymes with the nucleic acid track. The proposed method utilizes features of kinetic time courses of NTP hydrolysis that have not been addressed in previous analyses, and also accounts for the effect of protein traps used in kinetic experiments on processivity. This analysis is suitable for rapid and precise assessment of the effects of mutations, physical conditions, binding partners and other effectors on the functioning of translocases, helicases, polymerases and other NTP-consuming processive nucleic acid motors.
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Affiliation(s)
- Máté Gyimesi
- Department of Biochemistry, Eötvös University, Budapest, Hungary
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Gyimesi M, Sarlós K, Kovács M. Working Mechanism of the Human Bloom's Syndrome Helicase. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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