1
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Pradhan B, Deep A, König J, Baaske MD, Corbett KD, Kim E. Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580791. [PMID: 38405785 PMCID: PMC10889018 DOI: 10.1101/2024.02.17.580791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes play pivotal roles in genome organization and maintenance across all domains of life. In prokaryotes, SMC family Wadjet complexes structurally resemble the widespread MukBEF genome-organizing complexes but serve a defensive role by inhibiting plasmid transformation. We previously showed that Wadjet specifically cleaves circular DNA; however, the molecular mechanism underlying DNA substrate recognition remains unclear. Here, we use in vitro single-molecule imaging to directly visualize DNA loop extrusion and plasmid cleavage by Wadjet. We find that Wadjet is a symmetric DNA loop extruder that simultaneously reels in DNA from both sides of a growing loop and that this activity requires a dimeric JetABC supercomplex containing two dimers of the JetC motor subunit. On surface-anchored plasmid DNAs, Wadjet extrudes the full length of a 44 kilobase pair plasmid, stalls, and then cleaves DNA. Our findings reveal the role of loop extrusion in the specific recognition and elimination of plasmids by Wadjet, and establish loop extrusion as an evolutionarily conserved mechanism among SMC complexes across kingdoms of life.
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Affiliation(s)
- Biswajit Pradhan
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
| | - Jessica König
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | | | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Eugene Kim
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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2
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Deep A, Gu Y, Gao YQ, Ego KM, Herzik MA, Zhou H, Corbett KD. The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. Mol Cell 2022; 82:4145-4159.e7. [PMID: 36206765 PMCID: PMC9637719 DOI: 10.1016/j.molcel.2022.09.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/19/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022]
Abstract
Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yong-Qi Gao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kaori M Ego
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark A Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Zhou M. DNA sliding and loop formation by E. coli SMC complex: MukBEF. Biochem Biophys Rep 2022; 31:101297. [PMID: 35770038 PMCID: PMC9234588 DOI: 10.1016/j.bbrep.2022.101297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/08/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022] Open
Abstract
SMC (structural maintenance of chromosomes) complexes share conserved architectures and function in chromosome maintenance via an unknown mechanism. Here we have used single-molecule techniques to study MukBEF, the SMC complex in Escherichia coli. Real-time movies show MukB alone can compact DNA and ATP inhibits DNA compaction by MukB. We observed that DNA unidirectionally slides through MukB, potentially by a ratchet mechanism, and the sliding speed depends on the elastic energy stored in the DNA. MukE, MukF and ATP binding stabilize MukB and DNA interaction, and ATP hydrolysis regulates the loading/unloading of MukBEF from DNA. Our data suggests a new model for how MukBEF organizes the bacterial chromosome in vivo; and this model will be relevant for other SMC proteins. ATP-independent DNA compaction by MukB. DNA unidirectionally slides through MukB, potentially by a ratchet mechanism. MukE, MukF and ATP binding stabilize MukB and DNA interaction. DNA sliding via ratchet driven by entropic force model for chromosome organization by SMC complex.
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4
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Nomidis SK, Carlon E, Gruber S, Marko JF. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nucleic Acids Res 2022; 50:4974-4987. [PMID: 35474142 PMCID: PMC9122525 DOI: 10.1093/nar/gkac268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 12/19/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced 'power stroke' to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site ('safety belt'), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.
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Affiliation(s)
- Stefanos K Nomidis
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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5
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Qian JW, Wang XY, Deng K, Li DF, Guo L. Crystal structure of the chromosome partition protein MukE homodimer. Biochem Biophys Res Commun 2021; 589:229-233. [PMID: 34929446 DOI: 10.1016/j.bbrc.2021.12.032] [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: 12/04/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 11/15/2022]
Abstract
The SMC (structural maintenance of chromosomes) proteins are known to be involved in chromosome pairing or aggregation and play an important role in cell cycle and division. Different from SMC-ScpAB complex maintaining chromosome structure in most bacteria, the MukB-MukE-MukF complex is responsible for chromosome condensation in E. coli and some γ-proteobacter. Though different models were proposed to illustrate the mechanism of how the MukBEF complex worked, the assembly of the MukBEF complex is a key. The MukE dimer interacted with the middle region of one MukF molecule, and was clamped by the N- and C-terminal domain of the latter, and then was involved in the interaction with the head domain of MukB. To reveal the structural basis of MukE involved in the dynamic equilibrium of potential different MukBEF assemblies, we determined the MukE structure at 2.44 Å resolution. We found that the binding cavity for the α10, β4 and β5 of MukF (residues 296-327) in the MukE dimer has been occupied by the α9 and β7 strand of MukE. We proposed that the highly dynamic C-terminal region (173-225) was important for the MukE-F assembly and then involved in the MukBEF complex formation.
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Affiliation(s)
- Jia-Wei Qian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China
| | - Xiao-Yan Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Kai Deng
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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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: 36] [Impact Index Per Article: 12.0] [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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7
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Prince JP, Bolla JR, Fisher GLM, Mäkelä J, Fournier M, Robinson CV, Arciszewska LK, Sherratt DJ. Acyl carrier protein promotes MukBEF action in Escherichia coli chromosome organization-segregation. Nat Commun 2021; 12:6721. [PMID: 34795302 PMCID: PMC8602292 DOI: 10.1038/s41467-021-27107-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes act ubiquitously to compact DNA linearly, thereby facilitating chromosome organization-segregation. SMC proteins have a conserved architecture, with a dimerization hinge and an ATPase head domain separated by a long antiparallel intramolecular coiled-coil. Dimeric SMC proteins interact with essential accessory proteins, kleisins that bridge the two subunits of an SMC dimer, and HAWK/KITE proteins that interact with kleisins. The ATPase activity of the Escherichia coli SMC protein, MukB, which is essential for its in vivo function, requires its interaction with the dimeric kleisin, MukF that in turn interacts with the KITE protein, MukE. Here we demonstrate that, in addition, MukB interacts specifically with Acyl Carrier Protein (AcpP) that has essential functions in fatty acid synthesis. We characterize the AcpP interaction at the joint of the MukB coiled-coil and show that the interaction is necessary for MukB ATPase and for MukBEF function in vivo.
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Affiliation(s)
- Josh P. Prince
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK ,grid.14105.310000000122478951Present Address: Meiosis Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN UK
| | - Jani R. Bolla
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ UK ,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU UK ,grid.4991.50000 0004 1936 8948Present Address: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Gemma L. M. Fisher
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK ,grid.14105.310000000122478951Present Address: DNA Motors Group, Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN UK
| | - Jarno Mäkelä
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK ,grid.168010.e0000000419368956Present Address: ChEM-H Institute, Stanford University, 290 Jane Stanford Way, Stanford, CA 94305 USA
| | - Marjorie Fournier
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Carol V. Robinson
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ UK ,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU UK
| | - Lidia K. Arciszewska
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - David J. Sherratt
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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8
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Fisher GL, Bolla JR, Rajasekar KV, Mäkelä J, Baker R, Zhou M, Prince JP, Stracy M, Robinson CV, Arciszewska LK, Sherratt DJ. Competitive binding of MatP and topoisomerase IV to the MukB hinge domain. eLife 2021; 10:70444. [PMID: 34585666 PMCID: PMC8523169 DOI: 10.7554/elife.70444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes have ubiquitous roles in compacting DNA linearly, thereby promoting chromosome organization-segregation. Interaction between the Escherichia coli SMC complex, MukBEF, and matS-bound MatP in the chromosome replication termination region, ter, results in depletion of MukBEF from ter, a process essential for efficient daughter chromosome individualization and for preferential association of MukBEF with the replication origin region. Chromosome-associated MukBEF complexes also interact with topoisomerase IV (ParC2E2), so that their chromosome distribution mirrors that of MukBEF. We demonstrate that MatP and ParC have an overlapping binding interface on the MukB hinge, leading to their mutually exclusive binding, which occurs with the same dimer to dimer stoichiometry. Furthermore, we show that matS DNA competes with the MukB hinge for MatP binding. Cells expressing MukBEF complexes that are mutated at the ParC/MatP binding interface are impaired in ParC binding and have a mild defect in MukBEF function. These data highlight competitive binding as a means of globally regulating MukBEF-topoisomerase IV activity in space and time.
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Affiliation(s)
- Gemma Lm Fisher
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.,The Kavli Institute for Nanoscience Discovery, Oxford, United Kingdom
| | | | - Jarno Mäkelä
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rachel Baker
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Man Zhou
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Josh P Prince
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mathew Stracy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.,The Kavli Institute for Nanoscience Discovery, Oxford, United Kingdom
| | | | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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9
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Abstract
Since the nucleoid was isolated from bacteria in the 1970s, two fundamental questions emerged and are still in the spotlight: how bacteria organize their chromosomes to fit inside the cell and how nucleoid organization enables essential biological processes. During the last decades, knowledge of bacterial chromosome organization has advanced considerably, and today, such chromosomes are considered to be highly organized and dynamic structures that are shaped by multiple factors in a multiscale manner. Here we review not only the classical well-known factors involved in chromosome organization but also novel components that have recently been shown to dynamically shape the 3D structuring of the bacterial genome. We focus on the different functional elements that control short-range organization and describe how they collaborate in the establishment of the higher-order folding and disposition of the chromosome. Recent advances have opened new avenues for a deeper understanding of the principles and mechanisms of chromosome organization in bacteria. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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10
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Karaboja X, Ren Z, Brandão HB, Paul P, Rudner DZ, Wang X. XerD unloads bacterial SMC complexes at the replication terminus. Mol Cell 2021; 81:756-766.e8. [PMID: 33472056 DOI: 10.1016/j.molcel.2020.12.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/11/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022]
Abstract
Bacillus subtilis structural maintenance of chromosomes (SMC) complexes are topologically loaded at centromeric sites adjacent to the replication origin by the partitioning protein ParB. These ring-shaped ATPases then translocate down the left and right chromosome arms while tethering them together. Here, we show that the site-specific recombinase XerD, which resolves chromosome dimers, is required to unload SMC tethers when they reach the terminus. We identify XerD-specific binding sites in the terminus region and show that they dictate the site of unloading in a manner that depends on XerD but not its catalytic residue, its partner protein XerC, or the recombination site dif. Finally, we provide evidence that ParB and XerD homologs perform similar functions in Staphylococcus aureus. Thus, two broadly conserved factors that act at the origin and terminus have second functions in loading and unloading SMC complexes that travel between them.
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Affiliation(s)
- Xheni Karaboja
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Payel Paul
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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11
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Matityahu A, Onn I. Hit the brakes - a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes. J Cell Sci 2021; 134:jcs247577. [PMID: 33419949 DOI: 10.1242/jcs.247577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.
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Affiliation(s)
- Avi Matityahu
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
| | - Itay Onn
- 8 Henrietta Szold St., The Azrieli Faculty of Medicine, Bar-Ilan University, P.O. Box 1589 Safed, Israel
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12
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Krishnan A, Burroughs AM, Iyer LM, Aravind L. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Nucleic Acids Res 2020; 48:10045-10075. [PMID: 32894288 DOI: 10.1093/nar/gkaa726] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
ABC ATPases form one of the largest clades of P-loop NTPase fold enzymes that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from transport to nucleoprotein dynamics. Using sensitive sequence and structure analysis with comparative genomics, for the first time we provide a comprehensive classification of the ABC ATPase superfamily. ABC ATPases developed structural hallmarks that unambiguously distinguish them from other P-loop NTPases such as an alternative to arginine-finger-based catalysis. At least five and up to eight distinct clades of ABC ATPases are reconstructed as being present in the last universal common ancestor. They underwent distinct phases of structural innovation with the emergence of inserts constituting conserved binding interfaces for proteins or nucleic acids and the adoption of a unique dimeric toroidal configuration for DNA-threading. Specifically, several clades have also extensively radiated in counter-invader conflict systems where they serve as nodal nucleotide-dependent sensory and energetic components regulating a diversity of effectors (including some previously unrecognized) acting independently or together with restriction-modification systems. We present a unified mechanism for ABC ATPase function across disparate systems like RNA editing, translation, metabolism, DNA repair, and biological conflicts, and some unexpected recruitments, such as MutS ATPases in secondary metabolism.
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Affiliation(s)
- Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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13
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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14
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SMC complexes organize the bacterial chromosome by lengthwise compaction. Curr Genet 2020; 66:895-899. [PMID: 32300862 PMCID: PMC7497336 DOI: 10.1007/s00294-020-01076-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 11/13/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes are ancient and conserved molecular machines that organize chromosomes in all domains of life. We propose that the principles of chromosome folding needed to accommodate DNA inside a cell in an accessible form will follow similar principles in prokaryotes and eukaryotes. However, the exact contributions of SMC complexes to bacterial chromosome organization have been elusive. Recently, it was shown that the SMC homolog, MukBEF, organizes and individualizes the Escherichia coli chromosome by forming a filamentous axial core from which DNA loops emanate, similar to the action of condensin in mitotic chromosome formation. MukBEF action, along with its interaction with the partner protein, MatP, also facilitates chromosome individualization by directing opposite chromosome arms (replichores) to different cell halves. This contrasts with the situation in many other bacteria, where SMC complexes organise chromosomes in a way that the opposite replichores are aligned along the long axis of the cell. We highlight the similarities and differences of SMC complex contributions to chromosome organization in bacteria and eukaryotes, and summarize the current mechanistic understanding of the processes.
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15
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Organization of the Escherichia coli Chromosome by a MukBEF Axial Core. Mol Cell 2020; 78:250-260.e5. [PMID: 32097603 PMCID: PMC7163298 DOI: 10.1016/j.molcel.2020.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/03/2019] [Accepted: 02/03/2020] [Indexed: 01/22/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes organize chromosomes ubiquitously, thereby contributing to their faithful segregation. We demonstrate that under conditions of increased chromosome occupancy of the Escherichia coli SMC complex, MukBEF, the chromosome is organized as a series of loops around a thin (<130 nm) MukBEF axial core, whose length is ∼1,100 times shorter than the chromosomal DNA. The linear order of chromosomal loci is maintained in the axial cores, whose formation requires MukBEF ATP hydrolysis. Axial core structure in non-replicating chromosomes is predominantly linear (1 μm) but becomes circular (1.5 μm) in the absence of MatP because of its failure to displace MukBEF from the 800 kbp replication termination region (ter). Displacement of MukBEF from ter by MatP in wild-type cells directs MukBEF colocalization with the replication origin. We conclude that MukBEF individualizes and compacts the chromosome lengthwise, demonstrating a chromosome organization mechanism similar to condensin in mitotic chromosome formation. MukBEF forms a chromosome axial core dependent on ATP hydrolysis MukBEF compacts the chromosome lengthwise while avoiding links between replichores MatP determines the shape of the axial core by displacing MukBEF from ter The displacement by MatP directs MukBEF colocalization with the replication origin
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