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Yokota H. Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD. Int J Mol Sci 2021; 22:ijms22031018. [PMID: 33498436 PMCID: PMC7864180 DOI: 10.3390/ijms22031018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, The Graduate School for the Creation of New Photonics Industries, 1955-1, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan
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2
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Teng FY, Wang TT, Guo HL, Xin BG, Sun B, Dou SX, Xi XG, Hou XM. The HRDC domain oppositely modulates the unwinding activity of E. coli RecQ helicase on duplex DNA and G-quadruplex. J Biol Chem 2020; 295:17646-17658. [PMID: 33454004 DOI: 10.1074/jbc.ra120.015492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/09/2020] [Indexed: 12/17/2022] Open
Abstract
RecQ family helicases are highly conserved from bacteria to humans and have essential roles in maintaining genome stability. Mutations in three human RecQ helicases cause severe diseases with the main features of premature aging and cancer predisposition. Most RecQ helicases shared a conserved domain arrangement which comprises a helicase core, an RecQ C-terminal domain, and an auxiliary element helicase and RNaseD C-terminal (HRDC) domain, the functions of which are poorly understood. In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3'-partial duplex and fork DNA with a moderate processivity and periodically patrols on the ssDNA in the 5'-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core- and ssDNA-binding modes after RecQ association with DNA, we proposed a model to explain the modulation mechanism of the HRDC domain. Our findings not only provide new insights into the activities of RecQ on different substrates but also highlight the novel functions of the HRDC domain in DNA metabolisms.
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Affiliation(s)
- Fang-Yuan Teng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China; Department of Endocrinology and Metabolism, and Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Ting-Ting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hai-Lei Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ben-Ge Xin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Bo Sun
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China; LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette, France.
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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Chennoufi R, Trinh ND, Simon F, Bordeau G, Naud-Martin D, Moussaron A, Cinquin B, Bougherara H, Rambaud B, Tauc P, Frochot C, Teulade-Fichou MP, Mahuteau-Betzer F, Deprez E. Interplay between Cellular Uptake, Intracellular Localization and the Cell Death Mechanism in Triphenylamine-Mediated Photoinduced Cell Death. Sci Rep 2020; 10:6881. [PMID: 32327691 PMCID: PMC7181850 DOI: 10.1038/s41598-020-63991-9] [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: 04/08/2019] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
Triphenylamines (TPAs) were previously shown to trigger cell death under prolonged one- or two-photon illumination. Their initial subcellular localization, before prolonged illumination, is exclusively cytoplasmic and they translocate to the nucleus upon photoactivation. However, depending on their structure, they display significant differences in terms of precise initial localization and subsequent photoinduced cell death mechanism. Here, we investigated the structural features of TPAs that influence cell death by studying a series of molecules differing by the number and chemical nature of vinyl branches. All compounds triggered cell death upon one-photon excitation, however to different extents, the nature of the electron acceptor group being determinant for the overall cell death efficiency. Photobleaching susceptibility was also an important parameter for discriminating efficient/inefficient compounds in two-photon experiments. Furthermore, the number of branches, but not their chemical nature, was crucial for determining the cellular uptake mechanism of TPAs and their intracellular fate. The uptake of all TPAs is an active endocytic process but two- and three-branch compounds are taken up via distinct endocytosis pathways, clathrin-dependent or -independent (predominantly caveolae-dependent), respectively. Two-branch TPAs preferentially target mitochondria and photoinduce both apoptosis and a proper necrotic process, whereas three-branch TPAs preferentially target late endosomes and photoinduce apoptosis only.
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Affiliation(s)
- Rahima Chennoufi
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Ngoc-Duong Trinh
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Françoise Simon
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Guillaume Bordeau
- UMR9187, CNRS, INSERM, Institut Curie, PSL Research University, Université Paris-Saclay, F-91405, Orsay, France.,Laboratoire des IMRCP, Université de Toulouse, CNRS UMR5623, Université Toulouse-III - Paul Sabatier, F-31400, Toulouse, France
| | - Delphine Naud-Martin
- UMR9187, CNRS, INSERM, Institut Curie, PSL Research University, Université Paris-Saclay, F-91405, Orsay, France
| | - Albert Moussaron
- LRGP, UMR7274 CNRS-Université de Lorraine, F-54000, Nancy, France
| | - Bertrand Cinquin
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Houcine Bougherara
- Institut Cochin, INSERM U1016-CNRS UMR8104-Université Paris Descartes, Sorbonne Paris Cité, F-75014, Paris, France.,Institut de Recherches Servier SA, F-78290, Croissy-sur-Seine, France
| | - Béatrice Rambaud
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Patrick Tauc
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France
| | - Céline Frochot
- LRGP, UMR7274 CNRS-Université de Lorraine, F-54000, Nancy, France
| | - Marie-Paule Teulade-Fichou
- UMR9187, CNRS, INSERM, Institut Curie, PSL Research University, Université Paris-Saclay, F-91405, Orsay, France.
| | - Florence Mahuteau-Betzer
- UMR9187, CNRS, INSERM, Institut Curie, PSL Research University, Université Paris-Saclay, F-91405, Orsay, France.
| | - Eric Deprez
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France.
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4
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Mechanistic insight into cadmium-induced inactivation of the Bloom protein. Sci Rep 2016; 6:26225. [PMID: 27194376 PMCID: PMC4872126 DOI: 10.1038/srep26225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/25/2016] [Indexed: 11/08/2022] Open
Abstract
Cadmium is a toxic metal that inactivates DNA-repair proteins via multiple mechanisms, including zinc substitution. In this study, we investigated the effect of Cd(2+) on the Bloom protein (BLM), a DNA-repair helicase carrying a zinc-binding domain (ZBD) and playing a critical role to ensure genomic stability. One characteristics of BLM-deficient cells is the elevated rate of sister chromatid exchanges, a phenomenon that is also induced by Cd(2+). Here, we show that Cd(2+) strongly inhibits both ATPase and helicase activities of BLM. Cd(2+) primarily prevents BLM-DNA interaction via its binding to sulfhydryl groups of solvent-exposed cysteine residues and, concomitantly, promotes the formation of large BLM multimers/aggregates. In contrast to previously described Cd(2+) effects on other zinc-containing DNA-repair proteins, the ZBD appears to play a minor role in the Cd(2+)-mediated inhibition. While the Cd(2+)-dependent formation of inactive multimers and the defect of DNA-binding were fully reversible upon addition of EDTA, the inhibition of the DNA unwinding activity was not counteracted by EDTA, indicating another mechanism of inhibition by Cd(2+) relative to the targeting of a catalytic residue. Altogether, our results provide new clues for understanding the mechanism behind the ZBD-independent inactivation of BLM by Cd(2+) leading to accumulation of DNA double-strand breaks.
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Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding. Proc Natl Acad Sci U S A 2015; 112:E6852-61. [PMID: 26540728 DOI: 10.1073/pnas.1518028112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40-60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.
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7
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Liu NN, Duan XL, Ai X, Yang YT, Li M, Dou SX, Rety S, Deprez E, Xi XG. The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase. Nucleic Acids Res 2015; 43:8942-54. [PMID: 26384418 PMCID: PMC4605326 DOI: 10.1093/nar/gkv916] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/04/2015] [Indexed: 11/24/2022] Open
Abstract
ScPif1 DNA helicase is the prototypical member of a 5′-to-3′ helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis. While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown. Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1). BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5′-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation. Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA–RNA hybrids. Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes. Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions. Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action. These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo.
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Affiliation(s)
- Na-Nv Liu
- 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
| | - Xia Ai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yan-Tao Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ming Li
- CAS Key Laboratory of Soft Matter Physics, International Associated Laboratory of CNRS-Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- CAS Key Laboratory of Soft Matter Physics, International Associated Laboratory of CNRS-Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Stephane Rety
- Institut de Biochimie et Chimie des protéines, CNRS UMR5086, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Eric Deprez
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS UMR8113, IDA FR3242, F-94235 Cachan, France
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS UMR8113, IDA FR3242, F-94235 Cachan, France
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8
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Mikuni S, Kodama K, Sasaki A, Kohira N, Maki H, Munetomo M, Maenaka K, Kinjo M. Screening for FtsZ Dimerization Inhibitors Using Fluorescence Cross-Correlation Spectroscopy and Surface Resonance Plasmon Analysis. PLoS One 2015; 10:e0130933. [PMID: 26154290 PMCID: PMC4496089 DOI: 10.1371/journal.pone.0130933] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/01/2015] [Indexed: 01/16/2023] Open
Abstract
FtsZ is an attractive target for antibiotic research because it is an essential bacterial cell division protein that polymerizes in a GTP-dependent manner. To find the seed chemical structure, we established a high-throughput, quantitative screening method combining fluorescence cross-correlation spectroscopy (FCCS) and surface plasmon resonance (SPR). As a new concept for the application of FCCS to polymerization-prone protein, Staphylococcus aureus FtsZ was fragmented into the N-terminal and C-terminal, which were fused with GFP and mCherry (red fluorescent protein), respectively. By this fragmentation, the GTP-dependent head-to-tail dimerization of each fluorescent labeled fragment of FtsZ could be observed, and the inhibitory processes of chemicals could be monitored by FCCS. In the first round of screening by FCCS, 28 candidates were quantitatively and statistically selected from 495 chemicals determined by in silico screening. Subsequently, in the second round of screening by FCCS, 71 candidates were also chosen from 888 chemicals selected via an in silico structural similarity search of the chemicals screened in the first round of screening. Moreover, the dissociation constants between the highest inhibitory chemicals and Staphylococcus aureus FtsZ were determined by SPR. Finally, by measuring the minimum inhibitory concentration, it was confirmed that the screened chemical had antibacterial activity against Staphylococcus aureus, including methicillin-resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kota Kodama
- Creative Research Institution, Hokkaido University, Sapporo, Japan
| | - Akira Sasaki
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Naoki Kohira
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Hideki Maki
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Masaharu Munetomo
- Information Initiative Center and Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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9
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Hamoudi MC, Henry E, Zerrouk N, Scherman D, Arnaud P, Deprez E, Escriou V. Enhancement of siRNA lipid-based vector stability and siRNA integrity in human serum with addition of anionic polymer adjuvant. J Drug Deliv Sci Technol 2015. [DOI: 10.1016/j.jddst.2015.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Insight into the cooperative DNA binding of the O⁶-alkylguanine DNA alkyltransferase. DNA Repair (Amst) 2014; 20:14-22. [PMID: 24553127 DOI: 10.1016/j.dnarep.2014.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/18/2014] [Indexed: 11/22/2022]
Abstract
The O(6)-alkylguanine DNA alkyltransferase (AGT) is a highly conserved protein responsible for direct repair of alkylated guanine and to a lesser degree thymine bases. While specific DNA lesion-bound complexes in crystal structures consist of monomeric AGT, several solution studies have suggested that cooperative DNA binding plays a role in the physiological activities of AGT. Cooperative AGT-DNA complexes have been described by theoretical models, which can be tested by atomic force microscopy (AFM). Direct access to structural features of AGT-DNA complexes at the single molecule level by AFM imaging revealed non-specifically bound, cooperative complexes with limited cluster length. Implications of cooperative binding in AGT-DNA interactions are discussed.
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11
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Kocsis ZS, Sarlós K, Harami GM, Martina M, Kovács M. A nucleotide-dependent and HRDC domain-dependent structural transition in DNA-bound RecQ helicase. J Biol Chem 2014; 289:5938-49. [PMID: 24403069 DOI: 10.1074/jbc.m113.530741] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The allosteric communication between the ATP- and DNA-binding sites of RecQ helicases enables efficient coupling of ATP hydrolysis to translocation along single-stranded DNA (ssDNA) and, in turn, the restructuring of multistranded DNA substrates during genome maintenance processes. In this study, we used the tryptophan fluorescence signal of Escherichia coli RecQ helicase to decipher the kinetic mechanism of the interaction of the enzyme with ssDNA. Rapid kinetic experiments revealed that ssDNA binding occurs in a two-step mechanism in which the initial binding step is followed by a structural transition of the DNA-bound helicase. We found that the nucleotide state of RecQ greatly influences the kinetics of the detected structural transition, which leads to a high affinity DNA-clamped state in the presence of the nucleotide analog ADP-AlF4. The DNA binding mechanism is largely independent of ssDNA length, indicating the independent binding of RecQ molecules to ssDNA and the lack of significant DNA end effects. The structural transition of DNA-bound RecQ was not detected when the ssDNA binding capability of the helicase-RNase D C-terminal domain was abolished or the domain was deleted. The results shed light on the nature of conformational changes leading to processive ssDNA translocation and multistranded DNA processing by RecQ helicases.
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Affiliation(s)
- Zsuzsa S Kocsis
- From the Department of Biochemistry, ELTE-MTA "Momentum" Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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12
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Fiorini F, Boudvillain M, Le Hir H. Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains. Nucleic Acids Res 2012; 41:2404-15. [PMID: 23275559 PMCID: PMC3575847 DOI: 10.1093/nar/gks1320] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The RNA helicase Upf1 is a multifaceted eukaryotic enzyme involved in DNA replication, telomere metabolism and several mRNA degradation pathways. Upf1 plays a central role in nonsense-mediated mRNA decay (NMD), a surveillance process in which it links premature translation termination to mRNA degradation with its conserved partners Upf2 and Upf3. In human, both the ATP-dependent RNA helicase activity and the phosphorylation of Upf1 are essential for NMD. Upf1 activation occurs when Upf2 binds its N-terminal domain, switching the enzyme to the active form. Here, we uncovered that the C-terminal domain of Upf1, conserved in higher eukaryotes and containing several essential phosphorylation sites, also inhibits the flanking helicase domain. With different biochemical approaches we show that this domain, named SQ, directly interacts with the helicase domain to impede ATP hydrolysis and RNA unwinding. The phosphorylation sites in the distal half of the SQ domain are not directly involved in this inhibition. Therefore, in the absence of multiple binding partners, Upf1 is securely maintained in an inactive state by two intramolecular inhibition mechanisms. This study underlines the tight and intricate regulation pathways required to activate multifunctional RNA helicases like Upf1.
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Affiliation(s)
- Francesca Fiorini
- Institut de Biologie de l'Ecole Normale Supérieure, Functional Genomics, CNRS UMR8197-INSERM U1024, 46 rue d'Ulm, 75230 Paris cedex 05, France
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13
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Parisse P, Vindigni A, Scoles G, Casalis L. In Vitro Enzyme Comparative Kinetics: Unwinding of Surface-Bound DNA Nanostructures by RecQ and RecQ1. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2012; 3:3532-7. [PMID: 26290984 DOI: 10.1021/jz3018682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Pietro Parisse
- Sincrotrone Trieste S.C.p.A., s.s.14 km163,5 in Area Science Park, Trieste
34149, Italy
| | - Alessandro Vindigni
- Sincrotrone Trieste S.C.p.A., s.s.14 km163,5 in Area Science Park, Trieste
34149, Italy
- International Centre for Genetic Engineering and Biotechnology, Padriciano
99, Trieste 34149, Italy
- Department of Biochemistry and
Molecular Biology, St. Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Giacinto Scoles
- Sincrotrone Trieste S.C.p.A., s.s.14 km163,5 in Area Science Park, Trieste
34149, Italy
- Department of Biological and
Medical Science, University of Udine, Ospedale
della Misericordia, Udine 33100, Italy
| | - Loredana Casalis
- Sincrotrone Trieste S.C.p.A., s.s.14 km163,5 in Area Science Park, Trieste
34149, Italy
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14
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RecQ helicase translocates along single-stranded DNA with a moderate processivity and tight mechanochemical coupling. Proc Natl Acad Sci U S A 2012; 109:9804-9. [PMID: 22665805 DOI: 10.1073/pnas.1114468109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maintenance of genome integrity is the major biological role of RecQ-family helicases via their participation in homologous recombination (HR)-mediated DNA repair processes. RecQ helicases exert their functions by using the free energy of ATP hydrolysis for mechanical movement along DNA tracks (translocation). In addition to the importance of translocation per se in recombination processes, knowledge of its mechanism is necessary for the understanding of more complex translocation-based activities, including nucleoprotein displacement, strand separation (unwinding), and branch migration. Here, we report the key properties of the ssDNA translocation mechanism of Escherichia coli RecQ helicase, the prototype of the RecQ family. We monitored the pre-steady-state kinetics of ATP hydrolysis by RecQ and the dissociation of the enzyme from ssDNA during single-round translocation. We also gained information on the translocation mechanism from the ssDNA length dependence of the steady-state ssDNA-activated ATPase activity. We show that RecQ occludes 18 ± 2 nt on ssDNA during translocation. The hydrolysis of ATP is noncooperative in the presence of ssDNA, indicating that RecQ active sites work independently during translocation. In the applied conditions, the enzyme hydrolyzes 35 ± 4 ATP molecules per second during ssDNA translocation. RecQ translocates at a moderate processivity, with a mean run length of 100-320 nt on ssDNA. The determined tight mechanochemical coupling of 1.1 ± 0.2 ATP consumed per nucleotide traveled indicates an inchworm-type mechanism.
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15
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Wu Y, Brosh RM. DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster. Nucleic Acids Res 2012; 40:4247-60. [PMID: 22287629 PMCID: PMC3378879 DOI: 10.1093/nar/gks039] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Conserved Iron-Sulfur (Fe-S) clusters are found in a growing family of metalloproteins that are implicated in prokaryotic and eukaryotic DNA replication and repair. Among these are DNA helicase and helicase-nuclease enzymes that preserve chromosomal stability and are genetically linked to diseases characterized by DNA repair defects and/or a poor response to replication stress. Insight to the structural and functional importance of the conserved Fe-S domain in DNA helicases has been gleaned from structural studies of the purified proteins and characterization of Fe-S cluster site-directed mutants. In this review, we will provide a current perspective of what is known about the Fe-S cluster helicases, with an emphasis on how the conserved redox active domain may facilitate mechanistic aspects of helicase function. We will discuss testable models for how the conserved Fe-S cluster might operate in helicase and helicase-nuclease enzymes to conduct their specialized functions that help to preserve the integrity of the genome.
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Affiliation(s)
- Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada.
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16
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Fluorescence Correlation and Cross-Correlation Spectroscopy Using Fluorescent Proteins for Measurements of Biomolecular Processes in Living Organisms. FLUORESCENT PROTEINS II 2011. [DOI: 10.1007/4243_2011_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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17
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Fairman-Williams ME, Guenther UP, Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 2010; 20:313-24. [PMID: 20456941 DOI: 10.1016/j.sbi.2010.03.011] [Citation(s) in RCA: 662] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 03/29/2010] [Indexed: 12/25/2022]
Abstract
Helicases of the superfamily (SF) 1 and 2 are involved in virtually all aspects of RNA and DNA metabolism. SF1 and SF2 helicases share a catalytic core with high structural similarity, but different enzymes even within each SF perform a wide spectrum of distinct functions on diverse substrates. To rationalize similarities and differences between these helicases, we outline a classification based on protein families that are characterized by typical sequence, structural, and mechanistic features. This classification complements and extends existing SF1 and SF2 helicase categorizations and highlights major structural and functional themes for these proteins. We discuss recent data in the context of this unifying view of SF1 and SF2 helicases.
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Affiliation(s)
- Margaret E Fairman-Williams
- Center for RNA Molecular Biology & Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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18
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Xi XG, Deprez E. Monitoring helicase-catalyzed DNA unwinding by fluorescence anisotropy and fluorescence cross-correlation spectroscopy. Methods 2010; 51:289-94. [PMID: 20219681 DOI: 10.1016/j.ymeth.2010.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/28/2022] Open
Abstract
In order to elucidate molecular mechanism of helicases, we have developed two new rapid and sensitive fluorescence assays to measure helicase-mediated DNA unwinding. The fluorescence anisotropy (FA) assay takes the advantage of the substantial change in fluorescence polarization upon helicase binding to DNA and DNA unwinding. The extent of depolarization depends on the rate of tumbling of the fluorescently labeled DNA molecule, which decreases with increasing size. This assay therefore can simultaneously monitor the DNA binding of helicase and the subsequent helicase-catalyzed DNA unwinding in real-time. For size limitation reasons, the FA approach is more suitable for single-turnover kinetic studies. A fluorescence cross-correlation spectroscopy method (FCCS) is also described for measuring DNA unwinding. This assay is based on the degree of concomitant diffusion of the two complementary DNA strands in a small excitation volume, each labeled by a different color. The decrease in the amplitude of the cross-correlation signal is then directly related to the unwinding activity. By contrast with FA, the FCCS-based assay can be used to measure the unwinding activity under both single- and multiple-turnover conditions, with no limitation related to the size of the DNA strands constituting the DNA substrate. These methods used together have proven to be useful for studying molecular mechanism underlying efficient motor function of helicases. Here, we describe the theoretical basis and framework of FA and FCCS and some practical implications for measuring DNA binding and unwinding. We discuss sample preparation and potential troubleshooting. Special attention is paid to instrumentation, data acquisition and analysis.
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Affiliation(s)
- Xu Guang Xi
- Laboratoire de Stress Génotoxiques et Cancer, CNRS UMR3348, Institut Curie-Section de Recherche, Centre Universitaire, Bat 110, 91405 Orsay, France.
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