1
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Moon KW, Ryu JK. Current working models of SMC-driven DNA-loop extrusion. Biochem Soc Trans 2023; 51:1801-1810. [PMID: 37767565 DOI: 10.1042/bst20220898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Structural maintenance of chromosome (SMC) proteins play a key roles in the chromosome organization by condensing two meters of DNA into cell-sized structures considered as the SMC protein extrudes DNA loop. Recent sequencing-based high-throughput chromosome conformation capture technique (Hi-C) and single-molecule experiments have provided direct evidence of DNA-loop extrusion. However, the molecular mechanism by which SMCs extrude a DNA loop is still under debate. Here, we review DNA-loop extrusion studies with single-molecule assays and introduce recent structural studies of how the ATP-hydrolysis cycle is coupled to the conformational changes of SMCs for DNA-loop extrusion. In addition, we explain the conservation of the DNA-binding sites that are vital for dynamic DNA-loop extrusion by comparing Cryo-EM structures of SMC complexes. Based on this information, we compare and discuss four compelling working models that explain how the SMC complex extrudes a DNA loop.
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Affiliation(s)
- Kyoung-Wook Moon
- Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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2
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Taschner M, Gruber S. DNA segment capture by Smc5/6 holocomplexes. Nat Struct Mol Biol 2023; 30:619-628. [PMID: 37012407 DOI: 10.1038/s41594-023-00956-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Three distinct structural maintenance of chromosomes (SMC) complexes facilitate chromosome folding and segregation in eukaryotes, presumably by DNA loop extrusion. How SMCs interact with DNA to extrude loops is not well understood. Among the SMC complexes, Smc5/6 has dedicated roles in DNA repair and preventing a buildup of aberrant DNA junctions. In the present study, we describe the reconstitution of ATP-dependent DNA loading by yeast Smc5/6 rings. Loading strictly requires the Nse5/6 subcomplex which opens the kleisin neck gate. We show that plasmid molecules are topologically entrapped in the kleisin and two SMC subcompartments, but not in the full SMC compartment. This is explained by the SMC compartment holding a looped DNA segment and by kleisin locking it in place when passing between the two flanks of the loop for neck-gate closure. Related segment capture events may provide the power stroke in subsequent DNA extrusion steps, possibly also in other SMC complexes, thus providing a unifying principle for DNA loading and extrusion.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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3
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Martínez‐García B, Dyson S, Segura J, Ayats A, Cutts EE, Gutierrez‐Escribano P, Aragón L, Roca J. Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage. EMBO J 2023; 42:e111913. [PMID: 36533296 PMCID: PMC9890231 DOI: 10.15252/embj.2022111913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain positive DNA supercoils. However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of -0.4. This ∆Lk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. We propose that this loop is the feeding segment of DNA that is subsequently merged to enlarge an extruding loop. Such a "pinch and merge" mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop.
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Affiliation(s)
| | - Sílvia Dyson
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Joana Segura
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Alba Ayats
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Erin E Cutts
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | | | - Luís Aragón
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | - Joaquim Roca
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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4
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Freitag M, Jaklin S, Padovani F, Radzichevici E, Zernia S, Schmoller KM, Stigler J. Single-molecule experiments reveal the elbow as an essential folding guide in SMC coiled-coil arms. Biophys J 2022; 121:4702-4713. [PMID: 36242515 PMCID: PMC9748247 DOI: 10.1016/j.bpj.2022.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/16/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Structural maintenance of chromosome (SMC) complexes form ring-like structures through exceptional elongated coiled-coils (CCs). Recent studies found that variable CC conformations, including open and collapsed forms, which might result from discontinuities in the CC, facilitate the diverse functions of SMCs in DNA organization. However, a detailed description of the SMC CC architecture is still missing. Here, we study the structural composition and mechanical properties of SMC proteins with optical tweezers unfolding experiments using the isolated Psm3 CC as a model system. We find a comparatively unstable protein with three unzipping intermediates, which we could directly assign to CC features by crosslinking experiments and state-of-the-art prediction software. Particularly, the CC elbow is shown to be a flexible, potentially non-structured feature, which divides the CC into sections, induces a pairing shift from one CC strand to the other and could facilitate large-scale conformational changes, most likely via thermal fluctuations of the flanking CC sections. A replacement of the elbow amino acids hinders folding of the consecutive CC region and frequently leads to non-native misalignments, revealing the elbow as a guide for proper folding. Additional in vivo manipulation of the elbow flexibility resulted in impaired cohesin complexes, which directly link the sensitive CC architecture to the biological function of cohesin.
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Affiliation(s)
- Marvin Freitag
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sigrun Jaklin
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
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5
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Bock FP, Liu HW, Anchimiuk A, Diebold-Durand ML, Gruber S. A joint-ParB interface promotes Smc DNA recruitment. Cell Rep 2022; 40:111273. [PMID: 36044845 PMCID: PMC9449133 DOI: 10.1016/j.celrep.2022.111273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomes readily unlink and segregate to daughter cells during cell division, highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes promote DNA organization by loop extrusion. In most bacteria, chromosome folding initiates at dedicated start sites marked by the ParB/parS partition complexes. Whether SMC complexes recognize a specific DNA structure in the partition complex or a protein component is unclear. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate foreign chromosomes. Using chimeric proteins and chemical cross-linking, we find that ParB directly binds the Smc subunit. We map an interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex, presumably to initiate DNA loop extrusion. The bacterial DNA-binding protein ParB interacts with the condensin-like Smc-ScpAB Genetic mapping and structure predictions reveal an Smc joint-ParB binding interface Mutating the binding interface hampers Smc recruitment but not other ParB functions ParB and Smc-ScpAB form a transplantable unit for chromosome segregation in bacteria
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Affiliation(s)
- Florian P Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Anchimiuk
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Marie-Laure Diebold-Durand
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland.
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A walk through the SMC cycle: From catching DNAs to shaping the genome. Mol Cell 2022; 82:1616-1630. [PMID: 35477004 DOI: 10.1016/j.molcel.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes such as transcription, recombination, repair, and mitosis.
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7
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Bürmann F, Funke LFH, Chin JW, Löwe J. Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites. Mol Cell 2021; 81:4891-4906.e8. [PMID: 34739874 PMCID: PMC8669397 DOI: 10.1016/j.molcel.2021.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022]
Abstract
The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
| | - Louise F H Funke
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jason W Chin
- MRC Laboratory of Molecular Biology, Protein and Nucleic Acid Chemistry Division, Cambridge Biomedical Campus, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, UK.
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8
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Taschner M, Basquin J, Steigenberger B, Schäfer IB, Soh YM, Basquin C, Lorentzen E, Räschle M, Scheltema RA, Gruber S. Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. EMBO J 2021; 40:e107807. [PMID: 34191293 PMCID: PMC8327961 DOI: 10.15252/embj.2021107807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo‐complex. We found that the Nse5/6 sub‐complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross‐linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross‐linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non‐productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jérôme Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Steigenberger
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Young-Min Soh
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Claire Basquin
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
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