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Grimes SL, Denison MR. The Coronavirus helicase in replication. Virus Res 2024; 346:199401. [PMID: 38796132 PMCID: PMC11177069 DOI: 10.1016/j.virusres.2024.199401] [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: 11/30/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
The coronavirus nonstructural protein (nsp) 13 encodes an RNA helicase (nsp13-HEL) with multiple enzymatic functions, including unwinding and nucleoside phosphatase (NTPase) activities. Attempts for enzymatic inactivation have defined the nsp13-HEL as a critical enzyme for viral replication and a high-priority target for antiviral development. Helicases have been shown to play numerous roles beyond their canonical ATPase and unwinding activities, though these functions are just beginning to be explored in coronavirus biology. Recent genetic and biochemical studies, as well as work in structurally-related helicases, have provided evidence that supports new hypotheses for the helicase's potential role in coronavirus replication. Here, we review several aspects of the coronavirus nsp13-HEL, including its reported and proposed functions in viral replication and highlight fundamental areas of research that may aid the development of helicase inhibitors.
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Affiliation(s)
- Samantha L Grimes
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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2
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Klarić ML, Marić T, Žunić L, Trgovec-Greif L, Rokić F, Fiolić A, Šorgić AM, Ježek D, Vugrek O, Jakovčević A, Barbalić M, Belužić R, Katušić Bojanac A. FANCM Gene Variants in a Male Diagnosed with Sertoli Cell-Only Syndrome and Diffuse Astrocytoma. Genes (Basel) 2024; 15:707. [PMID: 38927643 PMCID: PMC11202954 DOI: 10.3390/genes15060707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Azoospermia is a form of male infertility characterized by a complete lack of spermatozoa in the ejaculate. Sertoli cell-only syndrome (SCOS) is the most severe form of azoospermia, where no germ cells are found in the tubules. Recently, FANCM gene variants were reported as novel genetic causes of spermatogenic failure. At the same time, FANCM variants are known to be associated with cancer predisposition. We performed whole-exome sequencing on a male patient diagnosed with SCOS and a healthy father. Two compound heterozygous missense mutations in the FANCM gene were found in the patient, both being inherited from his parents. After the infertility assessment, the patient was diagnosed with diffuse astrocytoma. Immunohistochemical analyses in the testicular and tumor tissues of the patient and adequate controls showed, for the first time, not only the existence of a cytoplasmic and not nuclear pattern of FANCM in astrocytoma but also in non-mitotic neurons. In the testicular tissue of the SCOS patient, cytoplasmic anti-FANCM staining intensity appeared lower than in the control. Our case report raises a novel possibility that the infertile carriers of FANCM gene missense variants could also be prone to cancer development.
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Affiliation(s)
| | - Tihana Marić
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Lucija Žunić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Lovro Trgovec-Greif
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Filip Rokić
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Ana Fiolić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Ana Merkler Šorgić
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Davor Ježek
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Oliver Vugrek
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Antonia Jakovčević
- Department of Pathology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Maja Barbalić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
- Faculty of Science, University of Split, Rudjera Bošković 33, 21000 Split, Croatia
| | - Robert Belužić
- Laboratory for Metabolism and Aging, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Ana Katušić Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
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3
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Amundsen SK, Smith GR. Chi hotspot Control of RecBCD Helicase-nuclease: Enzymatic Tests Support the Intramolecular Signal-transduction Model. J Mol Biol 2024; 436:168482. [PMID: 38331210 PMCID: PMC10947171 DOI: 10.1016/j.jmb.2024.168482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/11/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Repair of broken DNA is essential for life; the reactions involved can also promote genetic recombination to aid evolution. In Escherichia coli, RecBCD enzyme is required for the major pathway of these events. RecBCD is a complex ATP-dependent DNA helicase with nuclease activity controlled by Chi recombination hotspots (5'-GCTGGTGG-3'). During rapid DNA unwinding, when Chi is in a RecC tunnel, RecB nuclease nicks DNA at Chi. Here, we test our signal transduction model - upon binding Chi (step 1), RecC signals RecD helicase to stop unwinding (step 2); RecD then signals RecB (step 3) to nick at Chi (step 4) and to begin loading RecA DNA strand-exchange protein (step 5). We discovered that ATP-γ-S, like the small molecule RecBCD inhibitor NSAC1003, causes RecBCD to nick DNA, independent of Chi, at novel positions determined by the DNA substrate length. Two RecB ATPase-site mutants nick at novel positions determined by their RecB:RecD helicase rate ratios. In each case, we find that nicking at the novel position requires steps 3 and 4 but not step 1 or 2, as shown by mutants altered at the intersubunit contacts specific for each step; nicking also requires RecD helicase and RecB nuclease activities. Thus, altering the RecB ATPase site, by small molecules or mutation, sensitizes RecD to signal RecB to nick DNA (steps 4 and 3, respecitvely) without the signal from RecC or Chi (steps 1 and 2). These new, enzymatic results strongly support the signal transduction model and provide a paradigm for studying other complex enzymes.
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Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Farview Avenue North, A1-162, Seattle, WA 98109, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Farview Avenue North, A1-162, Seattle, WA 98109, USA.
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4
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Fazio NT, Mersch KN, Hao L, Lohman TM. E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity. J Mol Biol 2024; 436:168381. [PMID: 38081382 PMCID: PMC11131135 DOI: 10.1016/j.jmb.2023.168381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as occurring by the ATPase motors mechanically pulling the DNA duplex across a wedge domain in the helicase, biochemical data show that processive DNA unwinding by E. coli RecBCD helicase can occur in the absence of ssDNA translocation by the canonical RecB and RecD motors. Here we show that DNA unwinding is not a simple consequence of ssDNA translocation by the motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecBΔNucCD) unwinds dsDNA at significantly slower rates than RecBCD, while the ssDNA translocation rate is unaffected. This effect is primarily due to the absence of the nuclease domain since a nuclease-dead mutant (RecBD1080ACD), which retains the nuclease domain, showed no change in ssDNA translocation or dsDNA unwinding rates relative to RecBCD on short DNA substrates (≤60 base pairs). Hence, ssDNA translocation is not rate-limiting for DNA unwinding. RecBΔNucCD also initiates unwinding much slower than RecBCD from a blunt-ended DNA. RecBΔNucCD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecBD1080ACD unwinding are intermediate between RecBCD and RecBΔNucCD. Surprisingly, significant pauses in DNA unwinding occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, possibly allosterically and that RecBΔNucCD may mimic a post-chi state of RecBCD.
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Affiliation(s)
- Nicole T Fazio
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Kacey N Mersch
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
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Amundsen SK, Smith GR. RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiol Mol Biol Rev 2023; 87:e0004123. [PMID: 38047637 PMCID: PMC10732027 DOI: 10.1128/mmbr.00041-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYRecBCD enzyme is a multi-functional protein that initiates the major pathway of homologous genetic recombination and DNA double-strand break repair in Escherichia coli. It is also required for high cell viability and aids proper DNA replication. This 330-kDa, three-subunit enzyme is one of the fastest, most processive helicases known and contains a potent nuclease controlled by Chi sites, hotspots of recombination, in DNA. RecBCD undergoes major changes in activity and conformation when, during DNA unwinding, it encounters Chi (5'-GCTGGTGG-3') and nicks DNA nearby. Here, we discuss the multitude of mutations in each subunit that affect one or another activity of RecBCD and its control by Chi. These mutants have given deep insights into how the multiple activities of this complex enzyme are coordinated and how it acts in living cells. Similar studies could help reveal how other complex enzymes are controlled by inter-subunit interactions and conformational changes.
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Affiliation(s)
| | - Gerald R. Smith
- Fred Hutchinson Cancer Center Seattle, Seattle, Washington, USA
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6
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Fazio N, Mersch KN, Hao L, Lohman TM. E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.561901. [PMID: 37905078 PMCID: PMC10614803 DOI: 10.1101/2023.10.13.561901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as a consequence of mechanically pulling the DNA duplex across a wedge domain in the helicase by the single stranded (ss)DNA translocase activity of the ATPase motors, biochemical data indicate that processive DNA unwinding by the E. coli RecBCD helicase can occur in the absence of ssDNA translocation of the canonical RecB and RecD motors. Here, we present evidence that dsDNA unwinding is not a simple consequence of ssDNA translocation by the RecBCD motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecB ΔNuc CD) unwinds dsDNA at significantly slower rates than RecBCD, while the rate of ssDNA translocation is unaffected. This effect is primarily due to the absence of the nuclease domain and not the absence of the nuclease activity, since a nuclease-dead mutant (RecB D1080A CD), which retains the nuclease domain, showed no significant change in rates of ssDNA translocation or dsDNA unwinding relative to RecBCD on short DNA substrates (≤ 60 base pairs). This indicates that ssDNA translocation is not rate-limiting for DNA unwinding. RecB ΔNuc CD also initiates unwinding much slower than RecBCD from a blunt-ended DNA, although it binds with higher affinity than RecBCD. RecB ΔNuc CD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecB D1080A CD unwinding are intermediate between RecBCD and RecB ΔNuc CD. Surprisingly, significant pauses occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, rather than DNA translocation, possibly allosterically. Since the rate of DNA unwinding by RecBCD also slows after it recognizes a chi sequence, RecB ΔNuc CD may mimic a post- chi state of RecBCD.
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7
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Islam F, Purkait D, Mishra PP. Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective. J Phys Chem B 2023; 127:4351-4363. [PMID: 37163679 DOI: 10.1021/acs.jpcb.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase-DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.
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Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Debayan Purkait
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS. Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. eLife 2022; 11:e83409. [PMID: 36533901 PMCID: PMC9836394 DOI: 10.7554/elife.83409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022] Open
Abstract
Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Oliver J Wilkinson
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Connie Feyerherm
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Emma E Fletcher
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Mark S Dillingham
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
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Craig JM, Mills M, Kim HC, Huang JR, Abell S, Mount J, Gundlach J, Neuman K, Laszlo A. Nanopore tweezers measurements of RecQ conformational changes reveal the energy landscape of helicase motion. Nucleic Acids Res 2022; 50:10601-10613. [PMID: 36165957 PMCID: PMC9561376 DOI: 10.1093/nar/gkac837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/13/2022] Open
Abstract
Helicases are essential for nearly all nucleic acid processes across the tree of life, yet detailed understanding of how they couple ATP hydrolysis to translocation and unwinding remains incomplete because their small (∼300 picometer), fast (∼1 ms) steps are difficult to resolve. Here, we use Nanopore Tweezers to observe single Escherichia coli RecQ helicases as they translocate on and unwind DNA at ultrahigh spatiotemporal resolution. Nanopore Tweezers simultaneously resolve individual steps of RecQ along the DNA and conformational changes of the helicase associated with stepping. Our data reveal the mechanochemical coupling between physical domain motions and chemical reactions that together produce directed motion of the helicase along DNA. Nanopore Tweezers measurements are performed under either assisting or opposing force applied directly on RecQ, shedding light on how RecQ responds to such forces in vivo. Determining the rates of translocation and physical conformational changes under a wide range of assisting and opposing forces reveals the underlying dynamic energy landscape that drives RecQ motion. We show that RecQ has a highly asymmetric energy landscape that enables RecQ to maintain velocity when encountering molecular roadblocks such as bound proteins and DNA secondary structures. This energy landscape also provides a mechanistic basis making RecQ an 'active helicase,' capable of unwinding dsDNA as fast as it translocates on ssDNA. Such an energy landscape may be a general strategy for molecular motors to maintain consistent velocity despite opposing loads or roadblocks.
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Affiliation(s)
- Jonathan M Craig
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics & Astronomy, University of Missouri, 701 S College Ave, Physics Building Rm 223, Columbia, MO 65211, USA
| | - Hwanhee C Kim
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Jesse R Huang
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Sarah J Abell
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Jonathan W Mount
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, 3910 15th Ave NE, Seattle, WA, USA
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Purkait D, Islam F, Mishra PP. A single-molecule approach to unravel the molecular mechanism of the action of Deinococcus radiodurans RecD2 and its interaction with SSB and RecA in DNA repair. Int J Biol Macromol 2022; 221:653-664. [PMID: 36096248 DOI: 10.1016/j.ijbiomac.2022.09.043] [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: 06/01/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022]
Abstract
Helicases are ATP-driven molecular machines that directionally remodel nucleic acid polymers in all three domains of life. They are responsible for resolving double-stranded DNA (dsDNA) into single-strands, which is essential for DNA replication, nucleotide excision repair, and homologous recombination. RecD2 from Deinococcus radiodurans (DrRecD2) has important contributions to the organism's unusually high tolerance to gamma radiation and hydrogen peroxide. Although the results from X-ray Crystallography studies have revealed the structural characteristics of the protein, direct experimental evidence regarding the dynamics of the DNA unwinding process by DrRecD2 in the context of other accessory proteins is yet to be found. In this study, we have probed the exact binding event and processivity of DrRecD2 at single-molecule resolution using Protein-induced fluorescence enhancement (smPIFE) and Forster resonance energy transfer (smFRET). We have found that the protein prefers to bind at the 5' terminal end of the single-stranded DNA (ssDNA) by Drift and has helicase activity even in absence of ATP. However, a faster and iterative mode of DNA unwinding was evident in presence of ATP. The rate of translocation of the protein was found to be slower on dsDNA compared to ssDNA. We also showed that DrRecD2 is recruited at the binding site by the single-strand binding protein (SSB) and during the unwinding, it can displace RecA from ssDNA.
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Affiliation(s)
- Debayan Purkait
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India
| | - Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India
| | - Padmaja P Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhaba National Institute, Mumbai, India.
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11
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Comparative Genomics Revealed Wide Intra-Species Genetic Heterogeneity and Lineage-Specific Genes of Akkermansia muciniphila. Microbiol Spectr 2022; 10:e0243921. [PMID: 35536024 PMCID: PMC9241678 DOI: 10.1128/spectrum.02439-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Akkermansia muciniphila has potential as a next-generation probiotic, but few previous studies attempted to analyze its intraspecies population diversity. In this study, we performed a comparative genomic analysis of 112 filtered genomes from the NCBI database. The populations formed three clades (A-C) on the phylogenetic tree, suggesting the existence of three genetic lineages though clades B and C were phylogenetically closer than clade A. The three clades also showed geographic-based clustering, different genetic characteristics, and clade-specific genes. Two putative functional genes (RecD2 and xerD) were specific to clade C due to genomic islands. These lineage-specific genes might be associated with differences in genomic features (number of phages/genomic islands, pan-core genome, recombination rate, genetic diversity) between genetic lineages. The carbohydrate utilization gene profile (particularly for glycolytic hydrolases and carbohydrate esterases) also varied between clades, suggesting different carbohydrate metabolism potential/requirements between genetic lineages. Our findings provide important implications for future research on A. muciniphila. IMPORTANCEAkkermansia muciniphila has been widely accepted as part of the next generation of probiotics. However, most current studies on A. muciniphila have focused on the application of type strain BAA835T in the treatment of diseases, while few studies have reported on the genomic specificity, population structure, and functional characteristics of A. muciniphila species. By comparing the genomes of 112 strains from NCBI which met the quality control conditions, we found that the A. muciniphila population could be divided into three main clades (clades A to C) and presented a certain regional aggregation. There are significant differences among the three clades in their genetic characteristics and functional genes (the type strain BAA835T was located in clade A), especially in genes related to carbohydrate metabolism. It should be mentioned that probiotics should be a concept at the strain level rather than at the gut species level, so the probiotic properties of A. muciniphila need to be carefully interpreted.
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Hormeno S, Wilkinson OJ, Aicart-Ramos C, Kuppa S, Antony E, Dillingham MS, Moreno-Herrero F. Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA. Proc Natl Acad Sci U S A 2022; 119:e2112376119. [PMID: 35385349 PMCID: PMC9169624 DOI: 10.1073/pnas.2112376119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/01/2022] [Indexed: 01/17/2023] Open
Abstract
Human DNA helicase B (HELB) is a poorly characterized helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single-molecule approaches to characterize the biochemical activities of HELB protein with a particular focus on its interactions with Replication Protein A (RPA) and RPA–single-stranded DNA (ssDNA) filaments. HELB is a monomeric protein that binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5′ to 3′ direction accompanied by the formation of DNA loops. HELB also displays classical helicase activity, but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from ssDNA. This activity, which can allow other proteins access to ssDNA intermediates despite their shielding by RPA, may underpin the diverse roles of HELB in cellular DNA transactions.
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Affiliation(s)
- Silvia Hormeno
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Oliver J. Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Sahiti Kuppa
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Edwin Antony
- Department of Biochemistry, Saint Louis University, St. Louis, MO 63104
| | - Mark S. Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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13
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Ramos C, Hernández-Tamayo R, López-Sanz M, Carrasco B, Serrano E, Alonso JC, Graumann PL, Ayora S. The RecD2 helicase balances RecA activities. Nucleic Acids Res 2022; 50:3432-3444. [PMID: 35234892 PMCID: PMC8989531 DOI: 10.1093/nar/gkac131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
DNA helicases of the RecD2 family are ubiquitous. Bacillus subtilis RecD2 in association with the single-stranded binding protein SsbA may contribute to replication fork progression, but its detailed action remains unknown. In this work, we explore the role of RecD2 during DNA replication and its interaction with the RecA recombinase. RecD2 inhibits replication restart, but this effect is not observed in the absence of SsbA. RecD2 slightly affects replication elongation. RecA inhibits leading and lagging strand synthesis, and RecD2, which physically interacts with RecA, counteracts this negative effect. In vivo results show that recD2 inactivation promotes RecA–ssDNA accumulation at low mitomycin C levels, and that RecA threads persist for a longer time after induction of DNA damage. In vitro, RecD2 modulates RecA-mediated DNA strand-exchange and catalyzes branch migration. These findings contribute to our understanding of how RecD2 may contribute to overcome a replicative stress, removing RecA from the ssDNA and, thus, it may act as a negative modulator of RecA filament growth.
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Affiliation(s)
- Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
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14
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Aicart-Ramos C, Hormeno S, Wilkinson OJ, Dillingham MS, Moreno-Herrero F. Long DNA constructs to study helicases and nucleic acid translocases using optical tweezers. Methods Enzymol 2022; 673:311-358. [DOI: 10.1016/bs.mie.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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16
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The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end. Mol Cell 2021; 81:4271-4286.e4. [PMID: 34403695 DOI: 10.1016/j.molcel.2021.07.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022]
Abstract
Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions.
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17
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Meir A, Greene EC. Srs2 and Pif1 as Model Systems for Understanding Sf1a and Sf1b Helicase Structure and Function. Genes (Basel) 2021; 12:1319. [PMID: 34573298 PMCID: PMC8469786 DOI: 10.3390/genes12091319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/19/2023] Open
Abstract
Helicases are enzymes that convert the chemical energy stored in ATP into mechanical work, allowing them to move along and manipulate nucleic acids. The helicase superfamily 1 (Sf1) is one of the largest subgroups of helicases and they are required for a range of cellular activities across all domains of life. Sf1 helicases can be further subdivided into two classes called the Sf1a and Sf1b helicases, which move in opposite directions on nucleic acids. The results of this movement can range from the separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. Here, we describe the characteristics of the Sf1a helicase Srs2 and the Sf1b helicase Pif1, both from the model organism Saccharomyces cerevisiae, focusing on the roles that they play in homologous recombination, a DNA repair pathway that is necessary for maintaining genome integrity.
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Affiliation(s)
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA;
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18
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Hao L, Zhang R, Lohman TM. Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting. J Mol Biol 2021; 433:167147. [PMID: 34246654 DOI: 10.1016/j.jmb.2021.167147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/14/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022]
Abstract
E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17-18 nucleotides and can melt at least 10-11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecBNuc) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecBNuc, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecBNuc. This suggests that the RecBNuc domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecBNuc is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecBNuc is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.
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Affiliation(s)
- Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, United States.
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19
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Targeting the bacterial SOS response for new antimicrobial agents: drug targets, molecular mechanisms and inhibitors. Future Med Chem 2021; 13:143-155. [PMID: 33410707 DOI: 10.4155/fmc-2020-0310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is a pressing threat to global health, with multidrug-resistant pathogens becoming increasingly prevalent. The bacterial SOS pathway functions in response to DNA damage that occurs during infection, initiating several pro-survival and resistance mechanisms, such as DNA repair and hypermutation. This makes SOS pathway components potential targets that may combat drug-resistant pathogens and decrease resistance emergence. This review discusses the mechanism of the SOS pathway; the structure and function of potential targets AddAB, RecBCD, RecA and LexA; and efforts to develop selective small-molecule inhibitors of these proteins. These inhibitors may serve as valuable tools for target validation and provide the foundations for desperately needed novel antibacterial therapeutics.
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20
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Amundsen SK, Taylor AF, Smith GR. Chi hotspot control of RecBCD helicase-nuclease by long-range intramolecular signaling. Sci Rep 2020; 10:19415. [PMID: 33154402 PMCID: PMC7644769 DOI: 10.1038/s41598-020-73078-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022] Open
Abstract
Repair of broken DNA by homologous recombination requires coordinated enzymatic reactions to prepare it for interaction with intact DNA. The multiple activities of enterobacterial RecBCD helicase-nuclease are coordinated by Chi recombination hotspots (5′ GCTGGTGG 3′) recognized during DNA unwinding. Chi is recognized in a tunnel in RecC but activates the RecB nuclease, > 25 Ǻ away. How the Chi-dependent signal travels this long distance has been unknown. We found a Chi hotspot-deficient mutant in the RecB helicase domain located > 45 Ǻ from both the Chi-recognition site and the nuclease active site. This unexpected observation led us to find additional mutations that reduced or eliminated Chi hotspot activity in each subunit and widely scattered throughout RecBCD. Each mutation alters the intimate contact between one or another pair of subunits in crystal or cryoEM structures of RecBCD bound to DNA. Collectively, these mutations span a path about 185 Ǻ long from the Chi recognition site to the nuclease active site. We discuss these surprising results in the context of an intramolecular signal transduction accounting for many previous observations.
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Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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21
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Xue ZY, Wu WQ, Zhao XC, Kumar A, Ran X, Zhang XH, Zhang Y, Guo LJ. Single-molecule probing the duplex and G4 unwinding patterns of a RecD family helicase. Int J Biol Macromol 2020; 164:902-910. [PMID: 32693146 DOI: 10.1016/j.ijbiomac.2020.07.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
RecD family helicases play an important role in prokaryotic genome stability and serve as the structural models for studying superfamily 1B (SF1B) helicases. However, RecD-catalyzed duplex DNA unwinding behavior and the underlying mechanism are still elusive. RecD family helicases share a common proto-helicase with eukaryotic Pif1 family helicases, which are well known for their outstanding G-quadruplex (G4) unwinding ability. However, there are still controversial points as to whether and how RecD helicases unfold G4 structures. Here, single-molecule fluorescence resonance energy transfer (smFRET) and magnetic tweezers (MT) were used to study Deinococcus radiodurans RecD2 (DrRecD2)-mediated duplex DNA unwinding and resolution of G4 structures. A symmetric, repetitive unwinding phenomenon was observed on duplex DNA, revealed from the strand switch and translocation of one monomer. Furthermore, we found that DrRecD2 was able to unwind both parallel and antiparallel G4 structures without obvious topological preferences. Surprisingly, the unwinding properties of RecD on duplex and G4 DNA are different from those of Pif1. The findings provide an example, in which the patterns of two molecules derived from a common ancestor deviate during evolution, and they are of significance for understanding the unwinding mechanism and function of SF1B helicases.
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Affiliation(s)
- Zhen-Yong Xue
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Wen-Qiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China.
| | - Xiao-Cong Zhao
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Arvind Kumar
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Xia Ran
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Yu Zhang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Li-Jun Guo
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China.
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22
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Piña MDLN, Frontera A, Bauzá A. Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study. ACS Chem Biol 2020; 15:1942-1948. [PMID: 32469201 DOI: 10.1021/acschembio.0c00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
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23
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A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair. Nat Struct Mol Biol 2020; 27:71-77. [PMID: 31907455 PMCID: PMC7000243 DOI: 10.1038/s41594-019-0355-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/21/2019] [Indexed: 12/04/2022]
Abstract
The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognised and others in which it is not. The Chi-recognised structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognised and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair.
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24
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Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection. Proc Natl Acad Sci U S A 2019; 116:24507-24516. [PMID: 31740608 DOI: 10.1073/pnas.1913546116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain. Here we report cryoelectron microscopy (cryo-EM) structures of AdnAB in three functional states: in the absence of DNA and in complex with forked duplex DNAs before and after cleavage of the 5' single-strand DNA (ssDNA) tail by the AdnA nuclease. The structures reveal the path of the 5' ssDNA through the AdnA nuclease domain and the mechanism of 5' strand cleavage; the path of the 3' tracking strand through the AdnB motor and the DNA contacts that couple ATP hydrolysis to mechanical work; the position of the AdnA iron-sulfur cluster subdomain at the Y junction and its likely role in maintaining the split trajectories of the unwound 5' and 3' strands. Single-molecule DNA curtain analysis of DSB resection reveals that AdnAB is highly processive but prone to spontaneous pausing at random sites on duplex DNA. A striking property of AdnAB is that the velocity of DSB resection slows after the enzyme experiences a spontaneous pause. Our results highlight shared as well as distinctive properties of AdnAB vis-à-vis the RecBCD and AddAB clades of bacterial DSB-resecting motor nucleases.
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25
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Amundsen SK, Smith GR. The RecB helicase-nuclease tether mediates Chi hotspot control of RecBCD enzyme. Nucleic Acids Res 2019; 47:197-209. [PMID: 30445486 PMCID: PMC6326792 DOI: 10.1093/nar/gky1132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/29/2018] [Indexed: 11/25/2022] Open
Abstract
In bacteria, repair of DNA double-strand breaks uses a highly conserved helicase–nuclease complex to unwind DNA from a broken end and cut it at specific DNA sequences called Chi. In Escherichia coli the RecBCD enzyme also loads the DNA strand-exchange protein RecA onto the newly formed end, resulting in a recombination hotspot at Chi. Chi hotspots regulate multiple RecBCD activities by altering RecBCD’s conformation, which is proposed to include the swinging of the RecB nuclease domain on the 19-amino-acid tether connecting the helicase and nuclease domains. Here, we altered the tether and tested multiple RecBCD activities, genetically in cells and enzymatically in cell-free extracts. Randomizing the amino-acid sequence or lengthening it had little effect. However, shortening it by as little as two residues or making substitutions of ≥10 proline or ≥9 glycine residues dramatically lowered Chi-dependent activities. These results indicate that proper control of RecBCD by Chi requires that the tether be long enough and appropriately flexible. We discuss a model in which the swing-time of the nuclease domain determines the position of Chi-dependent and Chi-independent cuts and Chi hotspot activity.
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Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
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26
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Kosuri P, Altheimer BD, Dai M, Yin P, Zhuang X. Rotation tracking of genome-processing enzymes using DNA origami rotors. Nature 2019; 572:136-140. [PMID: 31316204 PMCID: PMC7036295 DOI: 10.1038/s41586-019-1397-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 06/17/2019] [Indexed: 11/24/2022]
Abstract
Many genome-processing reactions, such as transcription, replication and repair, generate DNA rotation. Methods that directly measure DNA rotation, including rotor bead tracking1–3, angular optical trap4, and magnetic tweezers5 have helped unravel the action mechanisms of a range of genome-processing enzymes, such as RNA polymerase (RNAP)6, gyrase2, viral DNA packaging motor7, and DNA recombination enzymes8. However, despite the potential of rotation measurements to transform our understanding of genome-processing reactions, measuring DNA rotation remains a difficult task. The time resolution of existing methods is insufficient to track rotation induced by many enzymes under physiological conditions, and the measurement throughput is typically low. Here we introduce Origami-Rotor-Based Imaging and Tracking (ORBIT), a method that uses fluorescently labeled DNA origami rotors to track DNA rotation at the single-molecule level with millisecond time resolution. We used ORBIT to track DNA rotation resulted from unwinding by RecBCD, a helicase involved in DNA repair9, and transcription by RNAP. We characterized a series of events during RecBCD-induced DNA unwinding, including initiation, processive translocation, pausing and backtracking, and revealed an initiation mechanism that involves reversible, ATP-independent DNA unwinding and engagement of the RecB motor. During transcription by RNAP, we directly observed rotational steps corresponding to single-base-pair unwinding. We envision ORBIT will enable studies of a wide range of protein-DNA interactions.
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Affiliation(s)
- Pallav Kosuri
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
| | - Benjamin D Altheimer
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Mingjie Dai
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Department of Physics, Harvard University, Cambridge, MA, USA.
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27
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Gowravaram M, Bonneau F, Kanaan J, Maciej VD, Fiorini F, Raj S, Croquette V, Le Hir H, Chakrabarti S. A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner. Nucleic Acids Res 2019; 46:2648-2659. [PMID: 29378013 PMCID: PMC5861435 DOI: 10.1093/nar/gky040] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
The RNA helicase UPF1 is a key component of the nonsense mediated mRNA decay (NMD) pathway. Previous X-ray crystal structures of UPF1 elucidated the molecular mechanisms of its catalytic activity and regulation. In this study, we examine features of the UPF1 core and identify a structural element that adopts different conformations in the various nucleotide- and RNA-bound states of UPF1. We demonstrate, using biochemical and single molecule assays, that this structural element modulates UPF1 catalytic activity and thereby refer to it as the regulatory loop. Interestingly, there are two alternatively spliced isoforms of UPF1 in mammals which differ only in the lengths of their regulatory loops. The loop in isoform 1 (UPF11) is 11 residues longer than that of isoform 2. We find that this small insertion in UPF11 leads to a two-fold increase in its translocation and ATPase activities. To determine the mechanistic basis of this differential catalytic activity, we have determined the X-ray crystal structure of the helicase core of UPF11 in its apo-state. Our results point toward a novel mechanism of regulation of RNA helicases, wherein alternative splicing leads to subtle structural rearrangements within the protein that are critical to modulate enzyme movements and catalytic activity.
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Affiliation(s)
- Manjeera Gowravaram
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Fabien Bonneau
- Max Planck Institute of Biochemistry, Structural Cell Biology Department, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Joanne Kanaan
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Vincent D Maciej
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
| | - Francesca Fiorini
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Saurabh Raj
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,LPS, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, F-75005 Paris, France
| | - Vincent Croquette
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,LPS, Département de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, F-75005 Paris, France
| | - Hervé Le Hir
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Sutapa Chakrabarti
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 6, D-14195 Berlin, Germany
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28
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Dehghani-Tafti S, Levdikov V, Antson AA, Bax B, Sanders CM. Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Nucleic Acids Res 2019; 47:3208-3222. [PMID: 30698796 PMCID: PMC6451128 DOI: 10.1093/nar/gkz028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 01/06/2023] Open
Abstract
Pif1 is a multifunctional helicase and DNA processing enzyme that has roles in genome stability. The enzyme is conserved in eukaryotes and also found in some prokaryotes. The functions of human PIF1 (hPIF1) are also critical for survival of certain tumour cell lines during replication stress, making it an important target for cancer therapy. Crystal structures of hPIF1 presented here explore structural events along the chemical reaction coordinate of ATP hydrolysis at an unprecedented level of detail. The structures for the apo as well as the ground and transition states reveal conformational adjustments in defined protein segments that can trigger larger domain movements required for helicase action. Comparisons with the structures of yeast and bacterial Pif1 reveal a conserved ssDNA binding channel in hPIF1 that we show is critical for single-stranded DNA binding during unwinding, but not the binding of G quadruplex DNA. Mutational analysis suggests that while the ssDNA-binding channel is important for helicase activity, it is not used in DNA annealing. Structural differences, in particular in the DNA strand separation wedge region, highlight significant evolutionary divergence of the human PIF1 protein from bacterial and yeast orthologues.
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Affiliation(s)
- Saba Dehghani-Tafti
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
| | - Vladimir Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Ben Bax
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
- Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Cyril M Sanders
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
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29
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Zananiri R, Malik O, Rudnizky S, Gaydar V, Kreiserman R, Henn A, Kaplan A. Synergy between RecBCD subunits is essential for efficient DNA unwinding. eLife 2019; 8:e40836. [PMID: 30601118 PMCID: PMC6338465 DOI: 10.7554/elife.40836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/01/2019] [Indexed: 12/12/2022] Open
Abstract
The subunits of the bacterial RecBCD act in coordination, rapidly and processively unwinding DNA at the site of a double strand break. RecBCD is able to displace DNA-binding proteins, suggesting that it generates high forces, but the specific role of each subunit in the force generation is unclear. Here, we present a novel optical tweezers assay that allows monitoring the activity of RecBCD's individual subunits, when they are part of an intact full complex. We show that RecBCD and its subunits are able to generate forces up to 25-40 pN without a significant effect on their velocity. Moreover, the isolated RecD translocates fast but is a weak helicase with limited processivity. Experiments at a broad range of [ATP] and forces suggest that RecD unwinds DNA as a Brownian ratchet, rectified by ATP binding, and that the presence of the other subunits shifts the ratchet equilibrium towards the post-translocation state.
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Affiliation(s)
- Rani Zananiri
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Omri Malik
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Russell Berrie Nanotechnology InstituteTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Sergei Rudnizky
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Vera Gaydar
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Roman Kreiserman
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
- Faculty of PhysicsTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Arnon Henn
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
| | - Ariel Kaplan
- Faculty of BiologyTechnion – Israel Institute of TechnologyHaifaIsrael
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30
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Ligat G, Da Re S, Alain S, Hantz S. Identification of Amino Acids Essential for Viral Replication in the HCMV Helicase-Primase Complex. Front Microbiol 2018; 9:2483. [PMID: 30405556 PMCID: PMC6205958 DOI: 10.3389/fmicb.2018.02483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Promising new inhibitors that target the viral helicase-primase complex have been reported to block replication of herpes simplex and varicella-zoster viruses, but they have no activity against human cytomegalovirus (HCMV), another herpesvirus. The HCMV helicase-primase complex (pUL105-pUL102-pUL70) is essential for viral DNA replication and could thus be a relevant antiviral target. The roles of the individual subunits composing this complex remain to be defined. By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis.
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Affiliation(s)
- Gaetan Ligat
- U1092, RESINFIT, CHU Limoges, INSERM, University of Limoges, Limoges, France.,CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, National Reference Center for Herpesviruses, Limoges, France
| | - Sandra Da Re
- U1092, RESINFIT, CHU Limoges, INSERM, University of Limoges, Limoges, France
| | - Sophie Alain
- U1092, RESINFIT, CHU Limoges, INSERM, University of Limoges, Limoges, France.,CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, National Reference Center for Herpesviruses, Limoges, France
| | - Sébastien Hantz
- U1092, RESINFIT, CHU Limoges, INSERM, University of Limoges, Limoges, France.,CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, National Reference Center for Herpesviruses, Limoges, France
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31
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Lohman TM, Fazio NT. How Does a Helicase Unwind DNA? Insights from RecBCD Helicase. Bioessays 2018; 40:e1800009. [PMID: 29603305 DOI: 10.1002/bies.201800009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/26/2018] [Indexed: 01/06/2023]
Abstract
DNA helicases are a class of molecular motors that catalyze processive unwinding of double stranded DNA. In spite of much study, we know relatively little about the mechanisms by which these enzymes carry out the function for which they are named. Most current views are based on inferences from crystal structures. A prominent view is that the canonical ATPase motor exerts a force on the ssDNA resulting in "pulling" the duplex across a "pin" or "wedge" in the enzyme leading to a mechanical separation of the two DNA strands. In such models, DNA base pair separation is tightly coupled to ssDNA translocation of the motors. However, recent studies of the Escherichia coli RecBCD helicase suggest an alternative model in which DNA base pair melting and ssDNA translocation occur separately. In this view, the enzyme-DNA binding free energy is used to melt multiple DNA base pairs in an ATP-independent manner, followed by ATP-dependent translocation of the canonical motors along the newly formed ssDNA tracks. Repetition of these two steps results in processive DNA unwinding. We summarize recent evidence suggesting this mechanism for RecBCD helicase action.
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Affiliation(s)
- Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Nicole T Fazio
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
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32
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Wilkinson M, Chaban Y, Wigley DB. Mechanism for nuclease regulation in RecBCD. eLife 2016; 5. [PMID: 27644322 PMCID: PMC5030088 DOI: 10.7554/elife.18227] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/29/2016] [Indexed: 11/30/2022] Open
Abstract
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5’-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves a SH3 domain that binds to a region of the RecB subunit in a binding mode that is distinct from others observed previously in SH3 domains and, to our knowledge, this is the first example of peptide-binding of an SH3 domain in a bacterial system. DOI:http://dx.doi.org/10.7554/eLife.18227.001
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yuriy Chaban
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
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33
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Simon MJ, Sokoloski JE, Hao L, Weiland E, Lohman TM. Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation. J Mol Biol 2016; 428:2997-3012. [PMID: 27422010 DOI: 10.1016/j.jmb.2016.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/13/2016] [Accepted: 07/06/2016] [Indexed: 11/25/2022]
Abstract
Escherichia coli RecBCD is a DNA helicase/nuclease that functions in double-stranded DNA break repair. RecBCD possesses two motors (RecB, a 3' to 5' translocase, and RecD, a 5' to 3' translocase). Current DNA unwinding models propose that motor translocation is tightly coupled to base pair melting. However, some biochemical evidence suggests that DNA melting of multiple base pairs may occur separately from single-stranded DNA translocation. To test this hypothesis, we designed DNA substrates containing reverse backbone polarity linkages that prevent ssDNA translocation of the canonical RecB and RecD motors. Surprisingly, we find that RecBCD can processively unwind DNA for at least 80bp beyond the reverse polarity linkages. This ability requires an ATPase active RecB motor, the RecB "arm" domain, and also the RecB nuclease domain, but not its nuclease activity. These results indicate that RecBCD can unwind duplex DNA processively in the absence of ssDNA translocation by the canonical motors and that the nuclease domain regulates the helicase activity of RecBCD.
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Affiliation(s)
- Michael J Simon
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Joshua E Sokoloski
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, Saint Louis, MO 63110, USA.
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34
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RecBCD Enzyme "Chi Recognition" Mutants Recognize Chi Recombination Hotspots in the Right DNA Context. Genetics 2016; 204:139-52. [PMID: 27401752 DOI: 10.1534/genetics.116.191056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/23/2016] [Indexed: 11/18/2022] Open
Abstract
RecBCD enzyme is a complex, three-subunit protein machine essential for the major pathway of DNA double-strand break repair and homologous recombination in Escherichia coli Upon encountering a Chi recombination-hotspot during DNA unwinding, RecBCD nicks DNA to produce a single-stranded DNA end onto which it loads RecA protein. Conformational changes that regulate RecBCD's helicase and nuclease activities are induced upon its interaction with Chi, defined historically as 5' GCTGGTGG 3'. Chi is thought to be recognized as single-stranded DNA passing through a tunnel in RecC. To define the Chi recognition-domain in RecC and thus the mechanism of the RecBCD-Chi interaction, we altered by random mutagenesis eight RecC amino acids lining the tunnel. We screened for loss of Chi activity with Chi at one site in bacteriophage λ. The 25 recC mutants analyzed thoroughly had undetectable or strongly reduced Chi-hotspot activity with previously reported Chi sites. Remarkably, most of these mutants had readily detectable, and some nearly wild-type, activity with Chi at newly generated Chi sites. Like wild-type RecBCD, these mutants had Chi activity that responded dramatically (up to fivefold, equivalent to Chi's hotspot activity) to nucleotide changes flanking 5' GCTGGTGG 3'. Thus, these and previously published RecC mutants thought to be Chi-recognition mutants are actually Chi context-dependence mutants. Our results fundamentally alter the view that Chi is a simple 8-bp sequence recognized by the RecC tunnel. We propose that Chi hotspots have dual nucleotide sequence interactions, with both the RecC tunnel and the RecB nuclease domain.
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35
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Abstract
Chromatin remodeling motors play essential roles in all DNA-based processes. These motors catalyze diverse outcomes ranging from sliding the smallest units of chromatin, known as nucleosomes, to completely disassembling chromatin. The broad range of actions carried out by these motors on the complex template presented by chromatin raises many stimulating mechanistic questions. Other well-studied nucleic acid motors provide examples of the depth of mechanistic understanding that is achievable from detailed biophysical studies. We use these studies as a guiding framework to discuss the current state of knowledge of chromatin remodeling mechanisms and highlight exciting open questions that would continue to benefit from biophysical analyses.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Nathan I Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
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36
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Timmins J, Moe E. A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges. Comput Struct Biotechnol J 2016; 14:168-176. [PMID: 27924191 PMCID: PMC5128194 DOI: 10.1016/j.csbj.2016.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 10/27/2022] Open
Affiliation(s)
- Joanna Timmins
- Université Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Elin Moe
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Av da Republica (EAN), 2780-157 Oeiras, Portugal
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37
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Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H. Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1. Cell Rep 2016; 14:2030-9. [PMID: 26904952 DOI: 10.1016/j.celrep.2016.02.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 11/27/2022] Open
Abstract
Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the β hairpin in other SF1B DNA helicases folds into an extended loop followed by an α helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.
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Affiliation(s)
- Xianglian Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Wendan Ren
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Yang He
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Chen Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Zhou Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Dewang Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Haiwei Song
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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38
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Chen WF, Dai YX, Duan XL, Liu NN, Shi W, Li N, Li M, Dou SX, Dong YH, Rety S, Xi XG. Crystal structures of the BsPif1 helicase reveal that a major movement of the 2B SH3 domain is required for DNA unwinding. Nucleic Acids Res 2016; 44:2949-61. [PMID: 26809678 PMCID: PMC4824106 DOI: 10.1093/nar/gkw033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/11/2016] [Indexed: 11/14/2022] Open
Abstract
Pif1 helicases are ubiquitous members of the SF1B family and are essential for maintaining genome stability. It was speculated that Pif1-specific motifs may fold in specific structures, conferring distinct activities upon it. Here, we report the crystal structures of the Pif1 helicase from Bacteroides spp with and without adenosine triphosphate (ATP) analog/ssDNA. BsPif1 shares structural similarities with RecD2 and Dda helicases but has specific features in the 1B and 2B domains. The highly conserved Pif1 family specific sequence motif interacts with and constraints a putative pin-loop in domain 1B in a precise conformation. More importantly, we found that the 2B domain which contains a specific extended hairpin undergoes a significant rotation and/or movement upon ATP and DNA binding, which is absolutely required for DNA unwinding. We therefore propose a mechanism for DNA unwinding in which the 2B domain plays a predominant role. The fact that the conformational change regulates Pif1 activity may provide insight into the puzzling observation that Pif1 becomes highly processive during break-induced replication in association with Polδ, while the isolated Pif1 has low processivity.
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Affiliation(s)
- Wei-Fei Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang-Xue Dai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Lei Duan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na Li
- National Center for Protein Science Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shou-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yu-Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Stephane Rety
- Institut de Biochimie et Chimie des Protéines, CNRS UMR 5086, 7 passage du Vercors, 69367 Lyon, France
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China LBPA, Institut d'Alembert, ENS de Cachan, Université Paris-Saclay, CNRS, 61, avenue du Président Wilson, F-94235 Cachan, France
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39
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Abstract
AddAB and RecBCD-type helicase-nuclease complexes control the first stage of bacterial homologous recombination (HR) – the resection of double strand DNA breaks. A switch in the activities of the complexes to initiate repair by HR is regulated by a short, species-specific DNA sequence known as a Crossover Hotspot Instigator (Chi) site. It has been shown that, upon encountering Chi, AddAB and RecBCD pause translocation before resuming at a reduced rate. Recently, the structure of B.subtilis AddAB in complex with its regulatory Chi sequence revealed the nature of Chi binding and the paused translocation state. Here the structural features associated with Chi binding are described in greater detail and discussed in relation to the related E.coli RecBCD system.
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Affiliation(s)
- Martin Wilkinson
- a Division of Structural Biology; Institute of Cancer Research; Chester Beatty Laboratories ; London , UK
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40
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Dewhare SS, Umesh TG, Muniyappa K. Molecular and Functional Characterization of RecD, a Novel Member of the SF1 Family of Helicases, from Mycobacterium tuberculosis. J Biol Chem 2015; 290:11948-68. [PMID: 25802334 DOI: 10.1074/jbc.m114.619395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 01/14/2023] Open
Abstract
The annotated whole-genome sequence of Mycobacterium tuberculosis revealed the presence of a putative recD gene; however, the biochemical characteristics of its encoded protein product (MtRecD) remain largely unknown. Here, we show that MtRecD exists in solution as a stable homodimer. Protein-DNA binding assays revealed that MtRecD binds efficiently to single-stranded DNA and linear duplexes containing 5' overhangs relative to the 3' overhangs but not to blunt-ended duplex. Furthermore, MtRecD bound more robustly to a variety of Y-shaped DNA structures having ≥18-nucleotide overhangs but not to a similar substrate containing 5-nucleotide overhangs. MtRecD formed more salt-tolerant complexes with Y-shaped structures compared with linear duplex having 3' overhangs. The intrinsic ATPase activity of MtRecD was stimulated by single-stranded DNA. Site-specific mutagenesis of Lys-179 in motif I abolished the ATPase activity of MtRecD. Interestingly, although MtRecD-catalyzed unwinding showed a markedly higher preference for duplex substrates with 5' overhangs, it could also catalyze significant unwinding of substrates containing 3' overhangs. These results support the notion that MtRecD is a bipolar helicase with strong 5' → 3' and weak 3' → 5' unwinding activities. The extent of unwinding of Y-shaped DNA structures was ∼3-fold lower compared with duplexes with 5' overhangs. Notably, direct interaction between MtRecD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA. Altogether, these studies provide the first detailed characterization of MtRecD and present important insights into the type of DNA structure the enzyme is likely to act upon during the processes of DNA repair or homologous recombination.
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Affiliation(s)
| | - T G Umesh
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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41
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Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases. Proc Natl Acad Sci U S A 2015; 112:4292-7. [PMID: 25831501 DOI: 10.1073/pnas.1416746112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.
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42
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Lehmann KC, Snijder EJ, Posthuma CC, Gorbalenya AE. What we know but do not understand about nidovirus helicases. Virus Res 2014; 202:12-32. [PMID: 25497126 PMCID: PMC7114383 DOI: 10.1016/j.virusres.2014.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The ubiquitous nidovirus helicase is a multi-functional enzyme of superfamily 1. Its unique N-terminal domain is most similar to the Upf1 multinuclear zinc-binding domain. It has been implicated in replication, transcription, virion biogenesis, translation and post-transcriptional viral RNA processing. Four different classes of antiviral compounds targeting the helicase have been identified.
Helicases are versatile NTP-dependent motor proteins of monophyletic origin that are found in all kingdoms of life. Their functions range from nucleic acid duplex unwinding to protein displacement and double-strand translocation. This explains their participation in virtually every metabolic process that involves nucleic acids, including DNA replication, recombination and repair, transcription, translation, as well as RNA processing. Helicases are encoded by all plant and animal viruses with a positive-sense RNA genome that is larger than 7 kb, indicating a link to genome size evolution in this virus class. Viral helicases belong to three out of the six currently recognized superfamilies, SF1, SF2, and SF3. Despite being omnipresent, highly conserved and essential, only a few viral helicases, mostly from SF2, have been studied extensively. In general, their specific roles in the viral replication cycle remain poorly understood at present. The SF1 helicase protein of viruses classified in the order Nidovirales is encoded in replicase open reading frame 1b (ORF1b), which is translated to give rise to a large polyprotein following a ribosomal frameshift from the upstream ORF1a. Proteolytic processing of the replicase polyprotein yields a dozen or so mature proteins, one of which includes a helicase. Its hallmark is the presence of an N-terminal multi-nuclear zinc-binding domain, the nidoviral genetic marker and one of the most conserved domains across members of the order. This review summarizes biochemical, structural, and genetic data, including drug development studies, obtained using helicases originating from several mammalian nidoviruses, along with the results of the genomics characterization of a much larger number of (putative) helicases of vertebrate and invertebrate nidoviruses. In the context of our knowledge of related helicases of cellular and viral origin, it discusses the implications of these results for the protein's emerging critical function(s) in nidovirus evolution, genome replication and expression, virion biogenesis, and possibly also post-transcriptional processing of viral RNAs. Using our accumulated knowledge and highlighting gaps in our data, concepts and approaches, it concludes with a perspective on future research aimed at elucidating the role of helicases in the nidovirus replication cycle.
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Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
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43
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Taylor AF, Amundsen SK, Guttman M, Lee KK, Luo J, Ranish J, Smith GR. Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes. J Mol Biol 2014; 426:3479-99. [PMID: 25073102 DOI: 10.1016/j.jmb.2014.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/02/2014] [Accepted: 07/20/2014] [Indexed: 11/28/2022]
Abstract
Faithful repair of DNA double-strand breaks by homologous recombination is crucial to maintain functional genomes. The major Escherichia coli pathway of DNA break repair requires RecBCD enzyme, a complex protein machine with multiple activities. Upon encountering a Chi recombination hotspot (5' GCTGGTGG 3') during DNA unwinding, RecBCD's unwinding, nuclease, and RecA-loading activities change dramatically, but the physical basis for these changes is unknown. Here, we identify, during RecBCD's DNA unwinding, two Chi-stimulated conformational changes involving RecC. One produced a marked, long-lasting, Chi-dependent increase in protease sensitivity of a small patch, near the Chi recognition domain, on the solvent-exposed RecC surface. The other change was identified by crosslinking of an artificial amino acid inserted in this RecC patch to RecB. Small-angle X-ray scattering analysis confirmed a major conformational change upon binding of DNA to the enzyme and is consistent with these two changes. We propose that, upon DNA binding, the RecB nuclease domain swings from one side of RecC to the other; when RecBCD encounters Chi, the nuclease domain returns to its initial position determined by crystallography, where it nicks DNA exiting from RecC and loads RecA onto the newly generated 3'-ended single-stranded DNA during continued unwinding; a crevice between RecB and RecC increasingly narrows during these steps. This model provides a physical basis for the intramolecular "signal transduction" from Chi to RecC to RecD to RecB inferred previously from genetic and enzymatic analyses, and it accounts for the enzymatic changes that accompany Chi's stimulation of recombination.
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Affiliation(s)
- Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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44
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Unique helicase determinants in the essential conjugative TraI factor from Salmonella enterica serovar Typhimurium plasmid pCU1. J Bacteriol 2014; 196:3082-90. [PMID: 24936053 DOI: 10.1128/jb.01496-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread development of multidrug-resistant bacteria is a major health emergency. Conjugative DNA plasmids, which harbor a wide range of antibiotic resistance genes, also encode the protein factors necessary to orchestrate the propagation of plasmid DNA between bacterial cells through conjugative transfer. Successful conjugative DNA transfer depends on key catalytic components to nick one strand of the duplex DNA plasmid and separate the DNA strands while cell-to-cell transfer occurs. The TraI protein from the conjugative Salmonella plasmid pCU1 fulfills these key catalytic roles, as it contains both single-stranded DNA-nicking relaxase and ATP-dependent helicase domains within a single, 1,078-residue polypeptide. In this work, we unraveled the helicase determinants of Salmonella pCU1 TraI through DNA binding, ATPase, and DNA strand separation assays. TraI binds DNA substrates with high affinity in a manner influenced by nucleic acid length and the presence of a DNA hairpin structure adjacent to the nick site. TraI selectively hydrolyzes ATP, and mutations in conserved helicase motifs eliminate ATPase activity. Surprisingly, the absence of a relatively short (144-residue) domain at the extreme C terminus of the protein severely diminishes ATP-dependent strand separation. Collectively, these data define the helicase motifs of the conjugative factor TraI from Salmonella pCU1 and reveal a previously uncharacterized C-terminal functional domain that uncouples ATP hydrolysis from strand separation activity.
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45
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Raney KD. Chemical modifications of DNA for study of helicase mechanisms. Bioorg Med Chem 2014; 22:4399-406. [PMID: 24931273 DOI: 10.1016/j.bmc.2014.05.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 12/28/2022]
Abstract
Helicases are ubiquitous enzymes that are required for virtually all processes in DNA and RNA metabolism including replication, repair, recombination, transcription, and translation. The mechanisms for helicase-catalyzed unwinding of double-stranded DNA or remodeling of RNA have been the subject of intense investigation for more than two decades. The central function of these enzymes is to transduce the energy available from ATP binding and hydrolysis to alter the conformation of nucleic acids. Specific interactions between helicases and nucleic acids have been investigated by chemical approaches in which the nucleic acid substrate has been modified in order to provide specific insight into the enzymatic mechanism.
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Affiliation(s)
- Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W. Markham St., Slot 516, Little Rock, AR 72205, USA.
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46
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Abstract
DNA helicases have important roles in genome maintenance. The RecD helicase has been well studied as a component of the heterotrimeric RecBCD helicase-nuclease enzyme important for double-strand break repair in Escherichia coli. Interestingly, many bacteria lack RecBC and instead contain a RecD2 helicase, which is not known to function as part of a larger complex. Depending on the organism studied, RecD2 has been shown to provide resistance to a broad range of DNA-damaging agents while also contributing to mismatch repair (MMR). Here we investigated the importance of Bacillus subtilis RecD2 helicase to genome integrity. We show that deletion of recD2 confers a modest increase in the spontaneous mutation rate and that the mutational signature in ΔrecD2 cells is not consistent with an MMR defect, indicating a new function for RecD2 in B. subtilis. To further characterize the role of RecD2, we tested the deletion strain for sensitivity to DNA-damaging agents. We found that loss of RecD2 in B. subtilis sensitized cells to several DNA-damaging agents that can block or impair replication fork movement. Measurement of replication fork progression in vivo showed that forks collapse more frequently in ΔrecD2 cells, supporting the hypothesis that RecD2 is important for normal replication fork progression. Biochemical characterization of B. subtilis RecD2 showed that it is a 5'-3' helicase and that it directly binds single-stranded DNA binding protein. Together, our results highlight novel roles for RecD2 in DNA replication which help to maintain replication fork integrity during normal growth and when forks encounter DNA damage.
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47
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Protein-DNA complexes are the primary sources of replication fork pausing in Escherichia coli. Proc Natl Acad Sci U S A 2013; 110:7252-7. [PMID: 23589869 DOI: 10.1073/pnas.1303890110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replication fork pausing drives genome instability, because any loss of paused replisome activity creates a requirement for reloading of the replication machinery, a potentially mutagenic process. Despite this importance, the relative contributions to fork pausing of different replicative barriers remain unknown. We show here that Deinococcus radiodurans RecD2 helicase inactivates Escherichia coli replisomes that are paused but still functional in vitro, preventing continued fork movement upon barrier removal or bypass, but does not inactivate elongating forks. Using RecD2 to probe replisome pausing in vivo, we demonstrate that most pausing events do not lead to replisome inactivation, that transcription complexes are the primary sources of this pausing, and that an accessory replicative helicase is critical for minimizing the frequency and/or duration of replisome pauses. These findings reveal the hidden potential for replisome inactivation, and hence genome instability, inside cells. They also demonstrate that efficient chromosome duplication requires mechanisms that aid resumption of replication by paused replisomes, especially those halted by protein-DNA barriers such as transcription complexes.
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48
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Abstract
First discovered in the 1970s, DNA helicases were initially described as enzymes that use chemical energy to separate (i.e., to unwind) the complementary strands of DNA. Because helicases are ubiquitous, display a range of fascinating biochemical activities, and are involved in all aspects of DNA metabolism, defects in human helicases are linked to a variety of genetic disorders, and helicase research continues to be important in understanding the molecular basis of DNA replication, recombination, and repair. The purpose of this book is to organize this information and to update the traditional view of these enzymes, because it is now evident that not all helicases possess bona fide strand separation activity and may function instead as energy-dependent switches or translocases. In this chapter, we will first discuss the biochemical and structural features of DNA-the lattice on which helicases operate-and its cellular organization. We will then provide a historical overview of helicases, starting from their discovery and classification, leading to their structures, mechanisms, and biomedical significance. Finally, we will highlight several key advances and developments in helicase research, and summarize some remaining questions and active areas of investigation. The subsequent chapters will discuss these topics and others in greater detail and are written by experts of these respective fields.
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Affiliation(s)
- Colin G Wu
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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Structure and Mechanisms of SF1 DNA Helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:17-46. [PMID: 23161005 DOI: 10.1007/978-1-4614-5037-5_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.
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50
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Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 2012. [DOI: 10.1038/nrmicro2917] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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