1
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Bobrovnikov D, Makurath MA, Wolfe CH, Chemla YR, Ha T. Helicase Activity Modulation with On-Demand Light-Based Conformational Control. J Am Chem Soc 2023; 145:21253-21262. [PMID: 37739407 PMCID: PMC10557133 DOI: 10.1021/jacs.3c05254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 09/24/2023]
Abstract
Engineering a protein variant with a desired role relies on deep knowledge of the relationship between a protein's native structure and function. Using our structural understanding of a regulatory subdomain found in a family of DNA helicases, we engineered novel helicases for which the subdomain orientation is designed to switch between unwinding-inactive and -active conformations upon trans-cis isomerization of an azobenzene-based crosslinker. This on-demand light-based conformational control directly alters helicase activity as demonstrated by both bulk phase experiments and single-molecule optical tweezers analysis of one of the engineered helicases. The "opto-helicase" may be useful in future applications that require spatiotemporal control of DNA hybridization states.
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Affiliation(s)
- Dmitriy Bobrovnikov
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Monika A. Makurath
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Clara H. Wolfe
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Yann R. Chemla
- Department
of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Taekjip Ha
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Department
of Biophysics, Department of Biological Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard Hughes
Medical Institute, Baltimore, Maryland 21205, United States
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2
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Yin Y, Xu ZY, Liu YJ, Huang W, Zhang Q, Li JP, Zou X. Identification and Validation in a Novel Classification of Helicase Patterns for the Prediction of Tumor Proliferation and Prognosis. J Hepatocell Carcinoma 2022; 9:885-900. [PMID: 36061235 PMCID: PMC9432388 DOI: 10.2147/jhc.s378175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Helicases have been classified as a class of enzymes that determine the stability of the cellular genome. There is growing evidence that helicases can help tumor cells resist drug killing by repairing Deoxyribose Nucleic Acid (DNA) or stabilizing transcription, which may contribute to the understanding of drug resistance. Currently, identifying cancer biomarkers among helicases and stratifying patients according to helicase activity will be able to guide treatment well. Methods We clustered 371 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) by consensus clustering based on helicase expression profiles to identify potential molecular subtypes. The Multiscale Embedded Gene Co-Expression Network Analysis (MEGENA) algorithm was used to find core differential gene modules between different molecular subtypes, and single-cell analysis was utlized to explore the potential function of hub gene. Immunohistochemical (IHC) staining was used to verify the diagnostic value of DDX56 and its ability to reflect the proliferation efficiency of cancer cells. Results We identified two subtypes associated with helicase. High helicase subtype was associated with poor clinical outcome, massive M0 macrophage infiltration, and highly active cell proliferation features. In addition, we identified a new biomarker, DDX56, which has not been reported in HCC, was highly expressed in HCC tissues, associated with poor prognosis, and was also shown to be associated with high cell proliferative activity. Conclusion In conclusion, based on helicase expression profiles, we have developed a new classification system for HCC, which is a proliferation-related system, and has clinical significance in evaluating prognosis and treating HCC patients, including immunotherapy and chemotherapy. In addition, we identified a new biomarker, DDX 56, which is overexpressed in HCC tissues, predicts a poor prognosis and is a validated index of tumor cell proliferation.
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Affiliation(s)
- Yi Yin
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Zi-Yuan Xu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Yuan-jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Wei Huang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Qian Zhang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
| | - Jie-pin Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing, Jiangsu, 210029, People’s Republic of China
- Correspondence: Xi Zou; Jie-pin Li, Email ;
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3
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Singh A, Patel SS. Quantitative methods to study helicase, DNA polymerase, and exonuclease coupling during DNA replication. Methods Enzymol 2022; 672:75-102. [PMID: 35934486 PMCID: PMC9933136 DOI: 10.1016/bs.mie.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genome replication is accomplished by highly regulated activities of enzymes in a multi-protein complex called the replisome. Two major enzymes, DNA polymerase and helicase, catalyze continuous DNA synthesis on the leading strand of the parental DNA duplex while the lagging strand is synthesized discontinuously. The helicase and DNA polymerase on their own are catalytically inefficient and weak motors for unwinding/replicating double-stranded DNA. However, when a helicase and DNA polymerase are functionally and physically coupled, they catalyze fast and highly processive leading strand DNA synthesis. DNA polymerase has a 3'-5' exonuclease activity, which removes nucleotides misincorporated in the nascent DNA. DNA synthesis kinetics, processivity, and accuracy are governed by the interplay of the helicase, DNA polymerase, and exonuclease activities within the replisome. This chapter describes quantitative biochemical and biophysical methods to study the coupling of these three critical activities during DNA replication. The methods include real-time quantitation of kinetics of DNA unwinding-synthesis by a coupled helicase-DNA polymerase complex, a 2-aminopurine fluorescence-based assay to map the precise positions of helicase and DNA polymerase with respect to the replication fork junction, and a radiometric assay to study the coupling of DNA polymerase, exonuclease, and helicase activities during processive leading strand DNA synthesis. These methods are presented here with bacteriophage T7 replication proteins as an example but can be applied to other systems with appropriate modifications.
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4
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Spinks RR, Spenkelink LM, Dixon NE, van Oijen AM. Single-Molecule Insights Into the Dynamics of Replicative Helicases. Front Mol Biosci 2021; 8:741718. [PMID: 34513934 PMCID: PMC8426354 DOI: 10.3389/fmolb.2021.741718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Helicases are molecular motors that translocate along single-stranded DNA and unwind duplex DNA. They rely on the consumption of chemical energy from nucleotide hydrolysis to drive their translocation. Specialized helicases play a critically important role in DNA replication by unwinding DNA at the front of the replication fork. The replicative helicases of the model systems bacteriophages T4 and T7, Escherichia coli and Saccharomyces cerevisiae have been extensively studied and characterized using biochemical methods. While powerful, their averaging over ensembles of molecules and reactions makes it challenging to uncover information related to intermediate states in the unwinding process and the dynamic helicase interactions within the replisome. Here, we describe single-molecule methods that have been developed in the last few decades and discuss the new details that these methods have revealed about replicative helicases. Applying methods such as FRET and optical and magnetic tweezers to individual helicases have made it possible to access the mechanistic aspects of unwinding. It is from these methods that we understand that the replicative helicases studied so far actively translocate and then passively unwind DNA, and that these hexameric enzymes must efficiently coordinate the stepping action of their subunits to achieve unwinding, where the size of each step is prone to variation. Single-molecule fluorescence microscopy methods have made it possible to visualize replicative helicases acting at replication forks and quantify their dynamics using multi-color colocalization, FRAP and FLIP. These fluorescence methods have made it possible to visualize helicases in replication initiation and dissect this intricate protein-assembly process. In a similar manner, single-molecule visualization of fluorescent replicative helicases acting in replication identified that, in contrast to the replicative polymerases, the helicase does not exchange. Instead, the replicative helicase acts as the stable component that serves to anchor the other replication factors to the replisome.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
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5
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Jayalath IM, Gerken MM, Mantel G, Hartley CS. Substituent Effects on Transient, Carbodiimide-Induced Geometry Changes in Diphenic Acids. J Org Chem 2021; 86:12024-12033. [PMID: 34409831 DOI: 10.1021/acs.joc.1c01385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nucleotide-induced conformational changes in motor proteins are key to many important cell functions. Inspired by this biological behavior, we report a simple chemically fueled system that exhibits carbodiimide-induced geometry changes. Bridging via transient anhydride formation leads to a significant reduction of the twist about the biaryl bond of substituted diphenic acids, giving a simple molecular clamp. The kinetics are well-described by a simple mechanism, allowing structure-property effects to be determined. The kinetic parameters can be used to derive important characteristics of the system such as the efficiencies (anhydride yields), maximum anhydride concentrations, and overall lifetimes. Transient diphenic anhydrides tolerate steric hindrance ortho to the biaryl bond but are significantly affected by electronic effects, with electron-deficient substituents giving lower yields, peak conversions, and lifetimes. The results provide useful guidelines for the design of functional systems incorporating diphenic acid units.
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Affiliation(s)
- Isuru M Jayalath
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Madelyn M Gerken
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Georgia Mantel
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - C Scott Hartley
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
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6
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Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT). Essays Biochem 2021; 65:109-127. [PMID: 33491732 DOI: 10.1042/ebc20200027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT's spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT's ability to discern an enzyme's nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
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7
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Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV, Williams LD. Water and Life: The Medium is the Message. J Mol Evol 2021; 89:2-11. [PMID: 33427903 PMCID: PMC7884305 DOI: 10.1007/s00239-020-09978-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology, but is much more than that. Water is the most frequent actor in the chemistry of metabolism. Our quantitation here reveals that water accounts for 99.4% of metabolites in Escherichia coli by molar concentration. Between a third and a half of known biochemical reactions involve consumption or production of water. We calculated the chemical flux of water and observed that in the life of a cell, a given water molecule frequently and repeatedly serves as a reaction substrate, intermediate, cofactor, and product. Our results show that as an E. coli cell replicates in the presence of molecular oxygen, an average in vivo water molecule is chemically transformed or is mechanistically involved in catalysis ~ 3.7 times. We conclude that, for biological water, there is no distinction between medium and chemical participant. Chemical transformations of water provide a basis for understanding not only extant biochemistry, but the origins of life. Because the chemistry of water dominates metabolism and also drives biological synthesis and degradation, it seems likely that metabolism co-evolved with biopolymers, which helps to reconcile polymer-first versus metabolism-first theories for the origins of life.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Vahab Rajaei
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, USA
- School of Earth and Atmospheric Science, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0340, USA
| | - Nicholas V Hud
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, USA.
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA.
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8
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Feng Y, Liu S, Chen R, Xie A. Target binding and residence: a new determinant of DNA double-strand break repair pathway choice in CRISPR/Cas9 genome editing. J Zhejiang Univ Sci B 2021; 22:73-86. [PMID: 33448189 PMCID: PMC7818014 DOI: 10.1631/jzus.b2000282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/24/2020] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms, and holds tremendous promise in clinical applications. The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA (sgRNA) at a given site. However, little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks (DSBs). We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target, contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing. Here, we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing, and the opportunity this presents to optimize Cas9-based technology.
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Affiliation(s)
- Yili Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310019, China.
- Department of Biochemistry and Molecular Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China.
| | - Sicheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310019, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - Ruodan Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310019, China
- Department of Biochemistry and Molecular Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China
| | - Anyong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310019, China.
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China.
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9
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Joo S, Chung BH, Lee M, Ha TH. Ring-shaped replicative helicase encircles double-stranded DNA during unwinding. Nucleic Acids Res 2020; 47:11344-11354. [PMID: 31665506 PMCID: PMC6868380 DOI: 10.1093/nar/gkz893] [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: 06/18/2019] [Revised: 09/29/2019] [Accepted: 10/23/2019] [Indexed: 11/14/2022] Open
Abstract
Ring-shaped replicative helicases are hexameric and play a key role in cellular DNA replication. Despite their importance, our understanding of the unwinding mechanism of replicative helicases is far from perfect. Bovine papillomavirus E1 is one of the best-known model systems for replicative helicases. E1 is a multifunctional initiator that senses and melts the viral origin and unwinds DNA. Here, we study the unwinding mechanism of E1 at the single-molecule level using magnetic tweezers. The result reveals that E1 as a single hexamer is a poorly processive helicase with a low unwinding rate. Tension on the DNA strands impedes unwinding, indicating that the helicase interacts strongly with both DNA strands at the junction. While investigating the interaction at a high force (26–30 pN), we discovered that E1 encircles dsDNA. By comparing with the E1 construct without a DNA binding domain, we propose two possible encircling modes of E1 during active unwinding.
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Affiliation(s)
- Sihwa Joo
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong H Chung
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.,BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
| | - Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Tai H Ha
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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10
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Peter B, Falkenberg M. TWINKLE and Other Human Mitochondrial DNA Helicases: Structure, Function and Disease. Genes (Basel) 2020; 11:genes11040408. [PMID: 32283748 PMCID: PMC7231222 DOI: 10.3390/genes11040408] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022] Open
Abstract
Mammalian mitochondria contain a circular genome (mtDNA) which encodes subunits of the oxidative phosphorylation machinery. The replication and maintenance of mtDNA is carried out by a set of nuclear-encoded factors—of which, helicases form an important group. The TWINKLE helicase is the main helicase in mitochondria and is the only helicase required for mtDNA replication. Mutations in TWINKLE cause a number of human disorders associated with mitochondrial dysfunction, neurodegeneration and premature ageing. In addition, a number of other helicases with a putative role in mitochondria have been identified. In this review, we discuss our current knowledge of TWINKLE structure and function and its role in diseases of mtDNA maintenance. We also briefly discuss other potential mitochondrial helicases and postulate on their role(s) in mitochondria.
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11
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Perera HM, Behrmann MS, Hoang JM, Griffin WC, Trakselis MA. Contacts and context that regulate DNA helicase unwinding and replisome progression. Enzymes 2019; 45:183-223. [PMID: 31627877 DOI: 10.1016/bs.enz.2019.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hexameric DNA helicases involved in the separation of duplex DNA at the replication fork have a universal architecture but have evolved from two separate protein families. The consequences are that the regulation, translocation polarity, strand specificity, and architectural orientation varies between phage/bacteria to that of archaea/eukaryotes. Once assembled and activated for single strand DNA translocation and unwinding, the DNA polymerase couples tightly to the helicase forming a robust replisome complex. However, this helicase-polymerase interaction can be challenged by various forms of endogenous or exogenous agents that can stall the entire replisome or decouple DNA unwinding from synthesis. The consequences of decoupling can be severe, leading to a build-up of ssDNA requiring various pathways for replication fork restart. All told, the hexameric helicase sits prominently at the front of the replisome constantly responding to a variety of obstacles that require transient unwinding/reannealing, traversal of more stable blocks, and alternations in DNA unwinding speed that regulate replisome progression.
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Affiliation(s)
- Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Joy M Hoang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
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12
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Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure 2017; 25:157-166. [PMID: 28052235 DOI: 10.1016/j.str.2016.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. Two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerase binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. Our collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.
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Affiliation(s)
- Jamie R Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA.
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Caroline Weis
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brittni M Foster
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA
| | - Chris M W Ho
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX 77054, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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13
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Dehghani-Tafti S, Sanders CM. DNA substrate recognition and processing by the full-length human UPF1 helicase. Nucleic Acids Res 2017; 45:7354-7366. [PMID: 28541562 PMCID: PMC5499549 DOI: 10.1093/nar/gkx478] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 05/16/2017] [Indexed: 12/31/2022] Open
Abstract
UPF1 is a conserved helicase required for nonsense-mediated decay (NMD) regulating mRNA stability in the cytoplasm. Human UPF1 (hUPF1) is also needed for nuclear DNA replication. While loss of NMD is tolerated, loss of hUPF1 induces a DNA damage response and cell cycle arrest. We have analysed nucleic acid (NA) binding and processing by full-length hUPF1. hUPF1 unwinds non-B and B-form DNA and RNA substrates in vitro. Unlike many helicases involved in genome stability no hUPF1 binding to DNA structures stabilized by inter-base-pair hydrogen bonding was observed. Alternatively, hUPF1 binds to single-stranded NAs (ssNA) with apparent affinity increasing with substrate length and with no preference for binding RNA or DNA or purine compared to pyrimidine polynucleotides. However, the data show a pronounced nucleobase bias with a preference for binding poly (U) or d(T) while d(A) polymers bind with low affinity. Although the data indicate that hUPF1 must bind a ssNA segments to initiate unwinding they also raise the possibility that hUPF1 has significantly reduced affinity for ssNA structures with stacked bases. Overall, the NA processing activities of hUPF1 are consistent with its function in mRNA regulation and suggest that roles in DNA replication could also be influenced by base sequence.
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Affiliation(s)
- Saba Dehghani-Tafti
- Department of Oncology & Metabolism, Academic Unit of Molecular oncology, University of Sheffield Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK
| | - Cyril M Sanders
- Department of Oncology & Metabolism, Academic Unit of Molecular oncology, University of Sheffield Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK
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14
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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand J, Bensimon D, Croquette V. A mechanistic study of helicases with magnetic traps. Protein Sci 2017; 26:1314-1336. [PMID: 28474797 PMCID: PMC5477542 DOI: 10.1002/pro.3187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023]
Abstract
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
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Affiliation(s)
- Samar Hodeib
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Saurabh Raj
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Maria Manosas
- Departament de Física FonamentalFacultat de Física, Universitat de BarcelonaBarcelona08028Spain
- CIBER‐BBN de BioingenieriaBiomateriales y Nanomedicina, Instituto de Sanidad Carlos IIIMadridSpain
| | - Weiting Zhang
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Debjani Bagchi
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Present address: Physics DepartmentFaculty of Science, The M.S. University of BarodaVadodaraGujarat390002India
| | - Bertrand Ducos
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Francesca Fiorini
- Univ Lyon, Molecular Microbiology and Structural Biochemistry, MMSB‐IBCP UMR5086 CNRS/Lyon1Lyon Cedex 769367France
| | - Joanne Kanaan
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Jean‐François Allemand
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - David Bensimon
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia90095
| | - Vincent Croquette
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
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15
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Hedglin M, Benkovic SJ. Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle. Chem Rev 2017; 117:7857-7877. [PMID: 28497687 PMCID: PMC5662946 DOI: 10.1021/acs.chemrev.7b00046] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During S-phase, minor DNA damage may be overcome by DNA damage tolerance (DDT) pathways that bypass such obstacles, postponing repair of the offending damage to complete the cell cycle and maintain cell survival. In translesion DNA synthesis (TLS), specialized DNA polymerases replicate the damaged DNA, allowing stringent DNA synthesis by a replicative polymerase to resume beyond the offending damage. Dysregulation of this DDT pathway in human cells leads to increased mutation rates that may contribute to the onset of cancer. Furthermore, TLS affords human cancer cells the ability to counteract chemotherapeutic agents that elicit cell death by damaging DNA in actively replicating cells. Currently, it is unclear how this critical pathway unfolds, in particular, where and when TLS occurs on each template strand. Given the semidiscontinuous nature of DNA replication, it is likely that TLS on the leading and lagging strand templates is unique for each strand. Since the discovery of DDT in the late 1960s, most studies on TLS in eukaryotes have focused on DNA lesions resulting from ultraviolet (UV) radiation exposure. In this review, we revisit these and other related studies to dissect the step-by-step intricacies of this complex process, provide our current understanding of TLS on leading and lagging strand templates, and propose testable hypotheses to gain further insights.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Stephen J. Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, U.S.A
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16
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Zhang Z, Hu F, Sung MW, Shu C, Castillo-González C, Koiwa H, Tang G, Dickman M, Li P, Zhang X. RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana. eLife 2017; 6. [PMID: 28463111 PMCID: PMC5451212 DOI: 10.7554/elife.24466] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/29/2017] [Indexed: 01/01/2023] Open
Abstract
RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5’ products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC. DOI:http://dx.doi.org/10.7554/eLife.24466.001 DNA contains all the information needed to build a body, yet molecules of RNA carry these instructions to the sites in the cell where they can be used. Cells must control how much RNA they produce in order to ensure that they develop properly and can respond well to their environment. RNA silencing refers to a collection of mechanisms that use smaller RNA molecules called microRNAs to incapacitate certain RNA molecules and selectively switch off the genes that encode them to stop more from being made. One key player in RNA silencing is the multi-protein complex called RISC, which contains microRNA and a group of proteins called AGOs. Once the microRNA has identified its RNA target, the AGOs cut the RNA into two pieces, known as the 5’ cleavage fragment and 3’ cleavage fragment. The two resulting fragments need to be cleared away swiftly, so that the RISC can move on to the next target. While it was known how the 3’ cleavage fragment was removed, it was less clear how the 5’ cleavage fragment was dealt with. Previous studies had shown that the 5’ cleavage fragment was marked with a chemical called uridine, which somehow signals to the RISC that this fragment needs to be destroyed. Now, using biochemical techniques, Zhang et al. have identified two new proteins in the model plant Arabidopsis that attach to the AGO proteins and degrade the 5’ cleavage fragments that are marked with uridine. The two proteins are named RICE1 and RICE2. Zhang et al. then analyzed the three-dimensional shape of RICE1 and identified the ‘active’ region that is responsible for degrading the RNA fragments. When these active regions were blocked, the microRNA levels were low, but the uridine-marked 5’ cleavage fragments were high. Also, the RISC complex could not work properly, which lead to problems during the development of the plant. These results suggest that RICE proteins degrade 5’ cleavage fragments modified with uridine to activate RISC. RICE proteins are conserved between plants and animals, and it is likely that their counterparts in humans will have a similar role to the plant proteins. The next challenge will be to explore how RICE proteins work in more details, which may lead to new ways to manipulate the levels of microRNAs to change the architecture of the plant and to improve their tolerance to various stress conditions. DOI:http://dx.doi.org/10.7554/eLife.24466.002
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Affiliation(s)
- Zhonghui Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Fuqu Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Min Woo Sung
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Hisashi Koiwa
- Department of Horticulture, Texas A&M University, College Station, United States
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, United States
| | - Martin Dickman
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, United States
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17
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Chang HW, Pandey M, Kulaeva OI, Patel SS, Studitsky VM. Overcoming a nucleosomal barrier to replication. SCIENCE ADVANCES 2016; 2:e1601865. [PMID: 27847876 PMCID: PMC5106197 DOI: 10.1126/sciadv.1601865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/11/2016] [Indexed: 05/05/2023]
Abstract
Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro. Nucleosomes present a strong, sequence-dependent barrier for replication, with particularly strong pausing of DNA polymerase at the +(31-40) and +(41-65) regions of the nucleosomal DNA. The exonuclease activity of T7 DNA polymerase increases the overall rate of progression of the replisome through a nucleosome, likely by resolving nonproductive complexes. The presence of nucleosome-free DNA upstream of the replication fork facilitates the progression of DNA polymerase through the nucleosome. After replication, at least 50% of the nucleosomes assume an alternative conformation, maintaining their original positions on the DNA. Our data suggest a previously unpublished mechanism for nucleosome maintenance during replication, likely involving transient formation of an intranucleosomal DNA loop.
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Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | | | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Corresponding author. (S.S.P.); (V.M.S.)
| | - Vasily M. Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Corresponding author. (S.S.P.); (V.M.S.)
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18
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Nandakumar D, Patel SS. Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork. Methods 2016; 108:65-78. [PMID: 27173619 DOI: 10.1016/j.ymeth.2016.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/26/2023] Open
Abstract
Replicative helicases work closely with the replicative DNA polymerases to ensure that the genomic DNA is copied in a timely and error free manner. In the replisomes of prokaryotes, mitochondria, and eukaryotes, the helicase and DNA polymerase enzymes are functionally and physically coupled at the leading strand replication fork and rely on each other for optimal DNA strand separation and synthesis activities. In this review, we describe pre-steady state kinetic methods to quantify the base pair unwinding-synthesis rate constant, a fundamental parameter to understand how the helicase and polymerase help each other during leading strand replication. We describe a robust method to measure the chemical step size of the helicase-polymerase complex that determines how the two motors are energetically coupled while tracking along the DNA. The 2-aminopurine fluorescence-based method provide structural information on the leading strand helicase-polymerase complex, such as the distance between the two enzymes, their relative positions at the replication fork, and their roles in fork junction melting. The combined information garnered from these methods informs on the mutual dependencies between the helicase and DNA polymerase enzymes, their stepping mechanism, and their individual functions at the replication fork during leading strand replication.
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Affiliation(s)
- Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway 08854, NJ, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway 08854, NJ, USA.
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19
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20
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Chodavarapu S, Jones AD, Feig M, Kaguni JM. DnaC traps DnaB as an open ring and remodels the domain that binds primase. Nucleic Acids Res 2015; 44:210-20. [PMID: 26420830 PMCID: PMC4705694 DOI: 10.1093/nar/gkv961] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/11/2015] [Indexed: 11/23/2022] Open
Abstract
Helicase loading at a DNA replication origin often requires the dynamic interactions between the DNA helicase and an accessory protein. In E. coli, the DNA helicase is DnaB and DnaC is its loading partner. We used the method of hydrogen/deuterium exchange mass spectrometry to address the importance of DnaB–DnaC complex formation as a prerequisite for helicase loading. Our results show that the DnaB ring opens and closes, and that specific amino acids near the N-terminus of DnaC interact with a site in DnaB's C-terminal domain to trap it as an open ring. This event correlates with conformational changes of the RecA fold of DnaB that is involved in nucleotide binding, and of the AAA+ domain of DnaC. DnaC also causes an alteration of the helical hairpins in the N-terminal domain of DnaB, presumably occluding this region from interacting with primase. Hence, DnaC controls the access of DnaB by primase.
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Affiliation(s)
- Sundari Chodavarapu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824-1319, USA
| | - Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
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21
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Pandey M, Elshenawy MM, Jergic S, Takahashi M, Dixon NE, Hamdan SM, Patel SS. Two mechanisms coordinate replication termination by the Escherichia coli Tus-Ter complex. Nucleic Acids Res 2015; 43:5924-35. [PMID: 26007657 PMCID: PMC4499146 DOI: 10.1093/nar/gkv527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/10/2015] [Indexed: 11/28/2022] Open
Abstract
The Escherichia coli replication terminator protein (Tus) binds to Ter sequences to block replication forks approaching from one direction. Here, we used single molecule and transient state kinetics to study responses of the heterologous phage T7 replisome to the Tus–Ter complex. The T7 replisome was arrested at the non-permissive end of Tus–Ter in a manner that is explained by a composite mousetrap and dynamic clamp model. An unpaired C(6) that forms a lock by binding into the cytosine binding pocket of Tus was most effective in arresting the replisome and mutation of C(6) removed the barrier. Isolated helicase was also blocked at the non-permissive end, but unexpectedly the isolated polymerase was not, unless C(6) was unpaired. Instead, the polymerase was blocked at the permissive end. This indicates that the Tus–Ter mechanism is sensitive to the translocation polarity of the DNA motor. The polymerase tracking along the template strand traps the C(6) to prevent lock formation; the helicase tracking along the other strand traps the complementary G(6) to aid lock formation. Our results are consistent with the model where strand separation by the helicase unpairs the GC(6) base pair and triggers lock formation immediately before the polymerase can sequester the C(6) base.
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Affiliation(s)
- Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mohamed M Elshenawy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, New South Wales 2522, Australia
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, New South Wales 2522, Australia
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, the State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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22
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Nandakumar D, Pandey M, Patel SS. Cooperative base pair melting by helicase and polymerase positioned one nucleotide from each other. eLife 2015; 4. [PMID: 25970034 PMCID: PMC4460406 DOI: 10.7554/elife.06562] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/13/2015] [Indexed: 12/19/2022] Open
Abstract
Leading strand DNA synthesis requires functional coupling between replicative helicase and DNA polymerase (DNAP) enzymes, but the structural and mechanistic basis of coupling is poorly understood. This study defines the precise positions of T7 helicase and T7 DNAP at the replication fork junction with single-base resolution to create a structural model that explains the mutual stimulation of activities. Our 2-aminopurine studies show that helicase and polymerase both participate in DNA melting, but each enzyme melts the junction base pair partially. When combined, the junction base pair is melted cooperatively provided the helicase is located one nucleotide ahead of the primer-end. The synergistic shift in equilibrium of junction base pair melting by combined enzymes explains the cooperativity, wherein helicase stimulates the polymerase by promoting dNTP binding (decreasing dNTP Km), polymerase stimulates the helicase by increasing the unwinding rate-constant (kcat), consequently the combined enzymes unwind DNA with kinetic parameters resembling enzymes translocating on single-stranded DNA. DOI:http://dx.doi.org/10.7554/eLife.06562.001 DNA replication is the process whereby a molecule of DNA is copied to form two identical molecules. First, an enzyme called a DNA helicase separates the two strands of the DNA double helix. This forms a structure called a replication fork that has two exposed single strands. Other enzymes called DNA polymerases then use each strand as a template to build a new matching DNA strand. DNA polymerases build the new DNA strands by joining together smaller molecules called nucleotides. One of the new DNA strands—called the ‘leading strand’—is built continuously, while the other—the ‘lagging strand’—is made as a series of short fragments that are later joined together. Building the leading strand requires the helicase and DNA polymerase to work closely together. However, it was not clear how these two enzymes coordinate their activity. Now, Nandakumar et al. have studied the helicase and DNA polymerase from a virus that infects bacteria and have pinpointed the exact positions of the enzymes at a replication fork. The experiments revealed that both the polymerase and helicase contribute to the separating of the DNA strands, and that this process is most efficient when the helicase is only a single nucleotide ahead of the polymerase. Further experiments showed that the helicase stimulates the polymerase by helping it to bind to nucleotides, and that the polymerase stimulates the helicase by helping it to separate the DNA strands at a faster rate. The next challenge is to investigate the molecular setup that allows the helicase and polymerase to increase each other's activities. DOI:http://dx.doi.org/10.7554/eLife.06562.002
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Affiliation(s)
- Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, United States
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, United States
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, United States
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23
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Abstract
The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.
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24
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Tan KW, Pham TM, Furukohri A, Maki H, Akiyama MT. Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells. Nucleic Acids Res 2015; 43:1714-25. [PMID: 25628359 PMCID: PMC4330395 DOI: 10.1093/nar/gkv044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The SOS response is a DNA damage response pathway that serves as a general safeguard of genome integrity in bacteria. Extensive studies of the SOS response in Escherichia coli have contributed to establishing the key concepts of cellular responses to DNA damage. However, how the SOS response impacts on the dynamics of DNA replication fork movement remains unknown. We found that inducing the SOS response decreases the mean speed of individual replication forks by 30–50% in E. coli cells, leading to a 20–30% reduction in overall DNA synthesis. dinB and recA belong to a group of genes that are upregulated during the SOS response, and encode the highly conserved proteins DinB (also known as DNA polymerase IV) and RecA, which, respectively, specializes in translesion DNA synthesis and functions as the central recombination protein. Both genes were independently responsible for the SOS-dependent slowdown of replication fork progression. Furthermore, fork speed was reduced when each gene was ectopically expressed in SOS-uninduced cells to the levels at which they are expressed in SOS-induced cells. These results clearly indicate that the increased expression of dinB and recA performs a novel role in restraining the progression of an unperturbed replication fork during the SOS response.
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Affiliation(s)
- Kang Wei Tan
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tuan Minh Pham
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masahiro Tatsumi Akiyama
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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25
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Abstract
Replicative polymerases (pols) cannot accommodate damaged template bases, and these pols stall when such offenses are encountered during S phase. Rather than repairing the damaged base, replication past it may proceed via one of two DNA damage tolerance (DDT) pathways, allowing replicative DNA synthesis to resume. In translesion DNA synthesis (TLS), a specialized TLS pol is recruited to catalyze stable, yet often erroneous, nucleotide incorporation opposite damaged template bases. In template switching, the newly synthesized sister strand is used as a damage-free template to synthesize past the lesion. In eukaryotes, both pathways are regulated by the conjugation of ubiquitin to the PCNA sliding clamp by distinct E2/E3 pairs. Whereas monoubiquitination by Rad6/Rad18 mediates TLS, extension of this ubiquitin to a polyubiquitin chain by Ubc13-Mms2/Rad5 routes DDT to the template switching pathway. In this review, we focus on the monoubiquitination of PCNA by Rad6/Rad18 and summarize the current knowledge of how this process is regulated.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802; ,
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26
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Liu S, Chistol G, Bustamante C. Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophys J 2014; 106:1844-58. [PMID: 24806916 DOI: 10.1016/j.bpj.2014.03.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
Ring NTPases represent a large and diverse group of proteins that couple their nucleotide hydrolysis activity to a mechanical task involving force generation and some type of transport process in the cell. Because of their shape, these enzymes often operate as gates that separate distinct cellular compartments to control and regulate the passage of chemical species across them. In this manner, ions and small molecules are moved across membranes, biopolymer substrates are segregated between cells or moved into confined spaces, double-stranded nucleic acids are separated into single strands to provide access to the genetic information, and polypeptides are unfolded and processed for recycling. Here we review the recent advances in the characterization of these motors using single-molecule manipulation and detection approaches. We describe the various mechanisms by which ring motors convert chemical energy to mechanical force or torque and coordinate the activities of individual subunits that constitute the ring. We also examine how single-molecule studies have contributed to a better understanding of the structural elements involved in motor-substrate interaction, mechanochemical coupling, and intersubunit coordination. Finally, we discuss how these molecular motors tailor their operation-often through regulation by other cofactors-to suit their unique biological functions.
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Affiliation(s)
- Shixin Liu
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Gheorghe Chistol
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; California Institute for Quantitative Biosciences, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Physics, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California; Department of Molecular and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, and Kavli Energy NanoSciences Institute, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, California.
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27
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CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication. Proc Natl Acad Sci U S A 2014; 111:15390-5. [PMID: 25313033 DOI: 10.1073/pnas.1418334111] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.
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28
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Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. BIOMED RESEARCH INTERNATIONAL 2014; 2014:195162. [PMID: 25136561 PMCID: PMC4129139 DOI: 10.1155/2014/195162] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/20/2014] [Accepted: 07/01/2014] [Indexed: 01/31/2023]
Abstract
Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome in Escherichia coli is composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.
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29
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Blastyák A. DNA replication: damage tolerance at the assembly line. Trends Biochem Sci 2014; 39:301-4. [PMID: 24957737 DOI: 10.1016/j.tibs.2014.05.004] [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: 03/31/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
Damage tolerance mechanisms ensure resumption of DNA synthesis at damage-replisome encounters. Replication fork reversal (RFR) is one such widely recognized mechanism that acts on replisomes where lagging strand synthesis continues upon leading strand synthesis block. The possibility to form such a structure is highly counter to our current understanding of the replisome dynamics of single replisomes. Here, I suggest a model that takes coupled bidirectional replisome organization into account to solve this apparent contradiction.
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Affiliation(s)
- András Blastyák
- Department of Biochemistry and Molecular Biology, University of Szeged, Faculty of Science and Informatics, H-6726 Szeged, Hungary.
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30
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Pandey M, Patel SS. Helicase and polymerase move together close to the fork junction and copy DNA in one-nucleotide steps. Cell Rep 2014; 6:1129-1138. [PMID: 24630996 DOI: 10.1016/j.celrep.2014.02.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/10/2014] [Accepted: 02/16/2014] [Indexed: 01/25/2023] Open
Abstract
By simultaneously measuring DNA synthesis and dNTP hydrolysis, we show that T7 DNA polymerase and T7 gp4 helicase move in sync during leading-strand synthesis, taking one-nucleotide steps and hydrolyzing one dNTP per base-pair unwound/copied. The cooperative catalysis enables the helicase and polymerase to move at a uniformly fast rate without guanine:cytosine (GC) dependency or idling with futile NTP hydrolysis. We show that the helicase and polymerase are located close to the replication fork junction. This architecture enables the polymerase to use its strand-displacement synthesis to increase the unwinding rate, whereas the helicase aids this process by translocating along single-stranded DNA and trapping the unwound bases. Thus, in contrast to the helicase-only unwinding model, our results suggest a model in which the helicase and polymerase are moving in one-nucleotide steps, DNA synthesis drives fork unwinding, and a role of the helicase is to trap the unwound bases and prevent DNA reannealing.
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Affiliation(s)
- Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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31
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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32
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Huang YH, Huang CY. The N-terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self-trimerization. Biochem Biophys Res Commun 2013; 442:147-52. [PMID: 24280305 DOI: 10.1016/j.bbrc.2013.11.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 10/26/2022]
Abstract
DnaT and PriB are replication restart primosomal proteins required for re-initiating chromosomal DNA replication in bacteria. Although the interaction of DnaT with PriB has been proposed, which region of DnaT is involved in PriB binding and self-trimerization remains unknown. In this study, we identified the N-terminal domain in DnaT (aa 1-83) that is important in PriB binding and self-trimerization but not in single-stranded DNA (ssDNA) binding. DnaT and the deletion mutant DnaT42-179 protein can bind to PriB according to native polyacrylamide gel electrophoresis, Western blot analysis, and pull-down assay, whereas DnaT84-179 cannot bind to PriB. In contrast to DnaT, DnaT26-179, and DnaT42-179 proteins, which form distinct complexes with ssDNA of different lengths, DnaT84-179 forms only a single complex with ssDNA. Analysis of DnaT84-179 protein by gel filtration chromatography showed a stable monomer in solution rather than a trimer, such as DnaT, DnaT26-179, and DnaT42-179 proteins. These results constitute a pioneering study of the domain definition of DnaT. Further research can directly focus on determining how DnaT binds to the PriA-PriB-DNA tricomplex in replication restart by the hand-off mechanism.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd., Taichung City, Taiwan
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33
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Vaithiyalingam S, Arnett DR, Aggarwal A, Eichman BF, Fanning E, Chazin WJ. Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase. J Mol Biol 2013; 426:558-69. [PMID: 24239947 DOI: 10.1016/j.jmb.2013.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 11/25/2022]
Abstract
DNA replication in all organisms requires polymerases to synthesize copies of the genome. DNA polymerases are unable to function on a bare template and require a primer. Primases are crucial RNA polymerases that perform the initial de novo synthesis, generating the first 8-10 nucleotides of the primer. Although structures of archaeal and bacterial primases have provided insights into general priming mechanisms, these proteins are not well conserved with heterodimeric (p48/p58) primases in eukaryotes. Here, we present X-ray crystal structures of the catalytic engine of a eukaryotic primase, which is contained in the p48 subunit. The structures of p48 reveal that eukaryotic primases maintain the conserved catalytic prim fold domain, but with a unique subdomain not found in the archaeal and bacterial primases. Calorimetry experiments reveal that Mn(2+) but not Mg(2+) significantly enhances the binding of nucleotide to primase, which correlates with higher catalytic efficiency in vitro. The structure of p48 with bound UTP and Mn(2+) provides insights into the mechanism of nucleotide synthesis by primase. Substitution of conserved residues involved in either metal or nucleotide binding alter nucleotide binding affinities, and yeast strains containing the corresponding Pri1p substitutions are not viable. Our results reveal that two residues (S160 and H166) in direct contact with the nucleotide were previously unrecognized as critical to the human primase active site. Comparing p48 structures to those of similar polymerases in different states of action suggests changes that would be required to attain a catalytically competent conformation capable of initiating dinucleotide synthesis.
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Affiliation(s)
- Sivaraja Vaithiyalingam
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Diana R Arnett
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
| | - Amit Aggarwal
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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34
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Im JS, Lee KY, Dillon LW, Dutta A. Human Primpol1: a novel guardian of stalled replication forks. EMBO Rep 2013; 14:1032-3. [PMID: 24189099 DOI: 10.1038/embor.2013.171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jun-Sub Im
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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35
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He Q, Shumate CK, White MA, Molineux IJ, Yin YW. Exonuclease of human DNA polymerase gamma disengages its strand displacement function. Mitochondrion 2013; 13:592-601. [PMID: 23993955 PMCID: PMC5017585 DOI: 10.1016/j.mito.2013.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/15/2013] [Accepted: 08/15/2013] [Indexed: 12/21/2022]
Abstract
Pol γ, the only DNA polymerase found in human mitochondria, functions in both mtDNA repair and replication. During mtDNA base-excision repair, gaps are created after damaged base excision. Here we show that Pol γ efficiently gap-fills except when the gap is only a single nucleotide. Although wild-type Pol γ has very limited ability for strand displacement DNA synthesis, exo(-) (3'-5' exonuclease-deficient) Pol γ has significantly high activity and rapidly unwinds downstream DNA, synthesizing DNA at a rate comparable to that of the wild-type enzyme on a primer-template. The catalytic subunit Pol γA alone, even when exo(-), is unable to synthesize by strand displacement, making this the only known reaction of Pol γ holoenzyme that has an absolute requirement for the accessory subunit Pol γB.
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Affiliation(s)
- Quan He
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Christie K. Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
| | - Mark A White
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ian J. Molineux
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555
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36
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Huang YH, Lin MJ, Huang CY. DnaT is a single-stranded DNA binding protein. Genes Cells 2013; 18:1007-19. [PMID: 24118681 DOI: 10.1111/gtc.12095] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/11/2013] [Indexed: 01/26/2023]
Abstract
DnaT is one of the replication restart primosomal proteins required for reinitiating chromosomal DNA replication in bacteria. In this study, we identified and characterized the single-stranded DNA (ssDNA)-binding properties of DnaT using electrophoretic mobility shift analysis (EMSA), bioinformatic tools and two deletion mutant proteins, namely, DnaT26-179 and DnaT42-179. ConSurf analysis indicated that the N-terminal region of DnaT is highly variable. The analysis of purified DnaT and the deletion mutant protein DnaT42-179 by gel filtration chromatography showed a stable trimer in solution, indicating that the N-terminal region, amino acid 1-41, is not crucial for the oligomerization of DnaT. Contrary to PriB, which forms a single complex with a series of ssDNA homopolymers, DnaT, DnaT26-179 and DnaT42-179 form distinct complexes with ssDNA of different lengths and the size of binding site of 26 ± 2 nucleotides (nt). Using bioinformatic programs (ps)(2) and the analysis of the positively charged/hydrophobic residue distribution, as well as the biophysical results in this study, we propose a binding model for the DnaT trimer-ssDNA complex, in which 25-nt-long ssDNA is tethered on the surface groove located in the highly conserved C-terminal domain of DnaT. These results constitute the first study regarding ssDNA-binding activity of DnaT. Consequently, a hand-off mechanism for primosome assembly was modified.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Rd, Taichung, Taiwan
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37
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38
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Pham TM, Tan KW, Sakumura Y, Okumura K, Maki H, Akiyama MT. A single-molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed. Mol Microbiol 2013; 90:584-96. [PMID: 23998701 DOI: 10.1111/mmi.12386] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 11/26/2022]
Abstract
The replisome catalyses DNA synthesis at a DNA replication fork. The molecular behaviour of the individual replisomes, and therefore the dynamics of replication fork movements, in growing Escherichia coli cells remains unknown. DNA combing enables a single-molecule approach to measuring the speed of replication fork progression in cells pulse-labelled with thymidine analogues. We constructed a new thymidine-requiring strain, eCOMB (E. coli for combing), that rapidly and sufficiently incorporates the analogues into newly synthesized DNA chains for the DNA-combing method. In combing experiments with eCOMB, we found the speed of most replication forks in the cells to be within the narrow range of 550-750 nt s(-1) and the average speed to be 653 ± 9 nt s(-1) (± SEM). We also found the average speed of the replication fork to be only 264 ± 9 nt s(-1) in a dnaE173-eCOMB strain producing a mutant-type of the replicative DNA polymerase III (Pol III) with a chain elongation rate (300 nt s(-1) ) much lower than that of the wild-type Pol III (900 nt s(-1) ). This indicates that the speed of chain elongation by Pol III is a major determinant of replication fork speed in E. coli cells.
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Affiliation(s)
- Tuan Minh Pham
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
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39
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Yeast Two-Hybrid Analysis of PriB-Interacting Proteins in Replication Restart Primosome: A Proposed PriB–SSB Interaction Model. Protein J 2013; 32:477-83. [DOI: 10.1007/s10930-013-9509-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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You Z, De Falco M, Kamada K, Pisani FM, Masai H. The mini-chromosome maintenance (Mcm) complexes interact with DNA polymerase α-primase and stimulate its ability to synthesize RNA primers. PLoS One 2013; 8:e72408. [PMID: 23977294 PMCID: PMC3748026 DOI: 10.1371/journal.pone.0072408] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 07/16/2013] [Indexed: 01/14/2023] Open
Abstract
The Mini-chromosome maintenance (Mcm) proteins are essential as central components for the DNA unwinding machinery during eukaryotic DNA replication. DNA primase activity is required at the DNA replication fork to synthesize short RNA primers for DNA chain elongation on the lagging strand. Although direct physical and functional interactions between helicase and primase have been known in many prokaryotic and viral systems, potential interactions between helicase and primase have not been explored in eukaryotes. Using purified Mcm and DNA primase complexes, a direct physical interaction is detected in pull-down assays between the Mcm2∼7 complex and the hetero-dimeric DNA primase composed of the p48 and p58 subunits. The Mcm4/6/7 complex co-sediments with the primase and the DNA polymerase α-primase complex in glycerol gradient centrifugation and forms a Mcm4/6/7-primase-DNA ternary complex in gel-shift assays. Both the Mcm4/6/7 and Mcm2∼7 complexes stimulate RNA primer synthesis by DNA primase in vitro. However, primase inhibits the Mcm4/6/7 helicase activity and this inhibition is abolished by the addition of competitor DNA. In contrast, the ATP hydrolysis activity of Mcm4/6/7 complex is not affected by primase. Mcm and primase proteins mutually stimulate their DNA-binding activities. Our findings indicate that a direct physical interaction between primase and Mcm proteins may facilitate priming reaction by the former protein, suggesting that efficient DNA synthesis through helicase-primase interactions may be conserved in eukaryotic chromosomes.
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Affiliation(s)
- Zhiying You
- Genome Dynamics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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41
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Weller SK, Kuchta RD. The DNA helicase-primase complex as a target for herpes viral infection. Expert Opin Ther Targets 2013; 17:1119-32. [PMID: 23930666 DOI: 10.1517/14728222.2013.827663] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION The Herpesviridae are responsible for debilitating acute and chronic infections, and some members of this family are associated with human cancers. Conventional anti-herpesviral therapy targets the viral DNA polymerase and has been extremely successful; however, the emergence of drug-resistant virus strains, especially in neonates and immunocompromised patients, underscores the need for continued development of anti-herpes drugs. In this article, we explore an alternative target for antiviral therapy, the HSV helicase/primase complex. AREAS COVERED This review addresses the current state of knowledge of HSV DNA replication and the important roles played by the herpesvirus helicase- primase complex. In the last 10 years several helicase/primase inhibitors (HPIs) have been described, and in this article, we discuss and contrast these new agents with established inhibitors. EXPERT OPINION The outstanding safety profile of existing nucleoside analogues for α-herpesvirus infection make the development of new therapeutic agents a challenge. Currently used nucleoside analogues exhibit few side effects and have low occurrence of clinically relevant resistance. For HCMV, however, existing drugs have significant toxicity issues and the frequency of drug resistance is high, and no antiviral therapies are available for EBV and KSHV. The development of new anti-herpesvirus drugs is thus well worth pursuing especially for immunocompromised patients and those who develop drug-resistant infections. Although the HPIs are promising, limitations to their development into a successful drug strategy remain.
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Affiliation(s)
- Sandra K Weller
- University of Connecticut Health Center, Department of Molecular Microbial and Structural Biology , Farmington CT 06030 , USA +1 860 679 2310 ;
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42
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Geertsema HJ, van Oijen AM. A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed. Curr Opin Struct Biol 2013; 23:788-93. [PMID: 23890728 DOI: 10.1016/j.sbi.2013.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 06/21/2013] [Indexed: 01/31/2023]
Abstract
Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such tools have been applied to study the dynamic nature of large multi-protein complexes that support multiple enzymatic activities. In this review, we will discuss single-molecule studies of the replisome, the protein complex responsible for the coordinated replication of double-stranded DNA. In particular, we will focus on new insights obtained into the dynamic nature of the composition of the DNA-replication machinery and how the dynamic replacement of components plays a role in the regulation of the DNA-replication process.
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Affiliation(s)
- Hylkje J Geertsema
- Zernike Institute for Advanced Materials, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
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Bell SP, Kaguni JM. Helicase loading at chromosomal origins of replication. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a010124. [PMID: 23613349 DOI: 10.1101/cshperspect.a010124] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Loading of the replicative DNA helicase at origins of replication is of central importance in DNA replication. As the first of the replication fork proteins assemble at chromosomal origins of replication, the loaded helicase is required for the recruitment of the rest of the replication machinery. In this work, we review the current knowledge of helicase loading at Escherichia coli and eukaryotic origins of replication. In each case, this process requires both an origin recognition protein as well as one or more additional proteins. Comparison of these events shows intriguing similarities that suggest a similar underlying mechanism, as well as critical differences that likely reflect the distinct processes that regulate helicase loading in bacterial and eukaryotic cells.
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Affiliation(s)
- Stephen P Bell
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Wallen JR, Majka J, Ellenberger T. Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase. Biochemistry 2013; 52:4026-36. [PMID: 23675753 DOI: 10.1021/bi400284j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replisomes are multiprotein complexes that coordinate the synthesis of leading and lagging DNA strands to increase the replication efficiency and reduce DNA strand breaks caused by stalling of replication forks. The bacteriophage T7 replisome is an economical machine that requires only four proteins for processive, coupled synthesis of two DNA strands. Here we characterize a complex between T7 primase-helicase and DNA polymerase on DNA that was trapped during the initiation of Okazaki fragment synthesis from an RNA primer. This priming complex consists of two DNA polymerases and a primase-helicase hexamer that assemble on the DNA template in an RNA-dependent manner. The zinc binding domain of the primase-helicase is essential for trapping the RNA primer in complex with the polymerase, and a unique loop located on the thumb of the polymerase also stabilizes this primer extension complex. Whereas one of the polymerases engages the primase-helicase and RNA primer on the lagging strand of a model replication fork, the second polymerase in the complex is also functional and can bind a primed template DNA. These results indicate that the T7 primase-helicase specifically engages two copies of DNA polymerase, which would allow the coordination of leading and lagging strand synthesis at a replication fork. Assembly of the T7 replisome is driven by intimate interactions between the DNA polymerase and multiple subunits of the primase-helicase hexamer.
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Affiliation(s)
- Jamie R Wallen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Rannou O, Le Chatelier E, Larson MA, Nouri H, Dalmais B, Laughton C, Jannière L, Soultanas P. Functional interplay of DnaE polymerase, DnaG primase and DnaC helicase within a ternary complex, and primase to polymerase hand-off during lagging strand DNA replication in Bacillus subtilis. Nucleic Acids Res 2013; 41:5303-20. [PMID: 23563155 PMCID: PMC3664799 DOI: 10.1093/nar/gkt207] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacillus subtilis has two replicative DNA polymerases. PolC is a processive high-fidelity replicative polymerase, while the error-prone DnaEBs extends RNA primers before hand-off to PolC at the lagging strand. We show that DnaEBs interacts with the replicative helicase DnaC and primase DnaG in a ternary complex. We characterize their activities and analyse the functional significance of their interactions using primase, helicase and primer extension assays, and a ‘stripped down’ reconstituted coupled assay to investigate the coordinated displacement of the parental duplex DNA at a replication fork, synthesis of RNA primers along the lagging strand and hand-off to DnaEBs. The DnaG–DnaEBs hand-off takes place after de novo polymerization of only two ribonucleotides by DnaG, and does not require other replication proteins. Furthermore, the fidelity of DnaEBs is improved by DnaC and DnaG, likely via allosteric effects induced by direct protein–protein interactions that lower the efficiency of nucleotide mis-incorporations and/or the efficiency of extension of mis-aligned primers in the catalytic site of DnaEBs. We conclude that de novo RNA primer synthesis by DnaG and initial primer extension by DnaEBs are carried out by a lagging strand–specific subcomplex comprising DnaG, DnaEBs and DnaC, which stimulates chromosomal replication with enhanced fidelity.
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Affiliation(s)
- Olivier Rannou
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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Perera RL, Torella R, Klinge S, Kilkenny ML, Maman JD, Pellegrini L. Mechanism for priming DNA synthesis by yeast DNA polymerase α. eLife 2013; 2:e00482. [PMID: 23599895 PMCID: PMC3628110 DOI: 10.7554/elife.00482] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/18/2013] [Indexed: 11/23/2022] Open
Abstract
The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate in the production of RNA-DNA oligonucleotides that prime synthesis of new DNA. Here we report crystal structures of the catalytic core of yeast Pol α in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with deoxynucleotides. We combine the structural analysis with biochemical and computational data to demonstrate that Pol α specifically recognizes the A-form RNA/DNA helix and that the ensuing synthesis of B-form DNA terminates primer synthesis. The spontaneous release of the completed RNA-DNA primer by the Pol α/primase complex simplifies current models of primer transfer to leading- and lagging strand polymerases. The proposed mechanism of nucleotide polymerization by Pol α might contribute to genomic stability by limiting the amount of inaccurate DNA to be corrected at the start of each Okazaki fragment. DOI:http://dx.doi.org/10.7554/eLife.00482.001 During mitosis, a cell duplicates its DNA and then divides, ultimately generating two genetically identical daughter cells. In eukaryotes, the process of DNA duplication occurs at multiple sites throughout the genome: at each site, the antiparallel strands of the parental DNA separate and provide a template for DNA polymerase (Pol), the enzyme that synthesizes the two new DNA strands. Duplication of the DNA proceeds in both directions from each site through the polymerization of nucleotides to form new strands of DNA that are complementary to the template strands. However, since DNA polymerases can only polymerize nucleotides in one direction, the 5′ to 3′ direction, synthesis of the so-called leading strand proceeds continuously, whereas the other, lagging strand is synthesized in fragments. The task of duplicating the bulk of the DNA is shared between Pol δ, which is primarily responsible for synthesis of the lagging strand, and Pol ε, which fulfils the same role for the leading strand. However, Pols δ and ε cannot initiate DNA synthesis by themselves; short RNA-DNA chains called primers must also be paired to each template strand. Production of the primers requires the concerted action of two more enzymes: an RNA polymerase known as primase, and another DNA polymerase called Pol α. It is known that completion of the RNA-DNA primer requires Pol α to increase the length of the RNA segment by adding extra nucleotides, but the details of this process are poorly understood. Perera et al. combined crystallographic, biochemical and computational evidence to describe how Pol α first recognizes and then extends the RNA strand in the primer. They found that Pol α recognizes the particular shape of double helix—an A-form helix—that is formed by the DNA template and the RNA primer. The geometry of this helix prompts the Pol α enzyme to start adding nucleotides to the RNA in the primer. Perera et al. determined that once a full turn of double-helix DNA has been synthesized, Pol α is no longer in direct contact with the A-form helix, which causes the enzyme to disengage and terminate polymerization, leaving behind the now complete RNA-DNA primer. Perera et al. offer a new paradigm for understanding the initiation of DNA synthesis in eukaryotic replication. Their work suggests that Pol α has the ability to discriminate between different shapes of the primer-template helix, thus providing a mechanistic understanding of primer release. The spontaneous release of the primer offers a simple and elegant way to limit DNA synthesis by Pol α, a polymerase that is prone to error, and to make the RNA-DNA primer directly available for extension by Pol δ and Pol ε. DOI:http://dx.doi.org/10.7554/eLife.00482.002
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Affiliation(s)
- Rajika L Perera
- Department of Biochemistry , University of Cambridge , Cambridge , United Kingdom
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Strong subunit coordination drives a powerful viral DNA packaging motor. Proc Natl Acad Sci U S A 2013; 110:5909-14. [PMID: 23530228 DOI: 10.1073/pnas.1222820110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Terminase enzymes are viral motors that package DNA into a preformed capsid and are of interest both therapeutically and as potential nano-machines. The enzymes excise a single genome from a concatemeric precursor (genome maturation) and then package the duplex to near-crystalline density (genome packaging). The functional motors are oligomers of protomeric subunits and are the most powerful motors currently known. Here, we present mechanistic studies on the terminase motor from bacteriophage λ. We identify a mutant (K76R) that is specifically deficient in packaging activity. Biochemical analysis of this enzyme provides insight into the linkage between ATP hydrolysis and motor translocation. We further use this mutant to assemble chimeric motors with WT enzyme and characterize the catalytic activity of the complexes. The data demonstrate that strong coordination between the motor protomers is required for DNA packaging and that incorporation of even a single mutant protomer poisons motor activity. Significant coordination is similarly observed in the genome maturation reaction; however, although the motor is composed of a symmetric tetramer of protomers, the maturation complex is better described as a "dimer-of-dimers" with half-site reactivity. We describe a model for how the motor alternates between a stable genome maturation complex and a dynamic genome packaging complex. The fundamental features of coordinated ATP hydrolysis, DNA movement, and tight association between the motor and the duplex during translocation are recapitulated in all of the viral motors. This work is thus of relevance to all terminase enzymes, both prokaryotic and eukaryotic.
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SHARMA AJEETK, CHOWDHURY DEBASHISH. TEMPLATE-DIRECTED BIOPOLYMERIZATION: TAPE-COPYING TURING MACHINES. ACTA ACUST UNITED AC 2013. [DOI: 10.1142/s1793048012300083] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA, RNA and proteins are among the most important macromolecules in a living cell. These molecules are polymerized by molecular machines. These natural nano-machines polymerize such macromolecules, adding one monomer at a time, using another linear polymer as the corresponding template. The machine utilizes input chemical energy to move along the template which also serves as a track for the movements of the machine. In the Alan Turing year 2012, it is worth pointing out that these machines are "tape-copying Turing machines". We review the operational mechanisms of the polymerizer machines and their collective behavior from the perspective of statistical physics, emphasizing their common features in spite of the crucial differences in their biological functions. We also draw the attention of the physics community to another class of modular machines that carry out a different type of template-directed polymerization. We hope this review will inspire new kinetic models for these modular machines.
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Affiliation(s)
- AJEET K. SHARMA
- Department of Physics, Indian Institute of Technology, Kanpur 208016, India
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Deshayes S, Divita G. Fluorescence technologies for monitoring interactions between biological molecules in vitro. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:109-43. [PMID: 23244790 DOI: 10.1016/b978-0-12-386932-6.00004-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last two centuries, the discovery and understanding of the principle of fluorescence have provided new means of characterizing physical/biological/chemical processes in a noninvasive manner. Fluorescence spectroscopy has become one of the most powerful and widely applied methods in the life sciences, from fundamental research to clinical applications. In vitro, fluorescence approaches offer the potential to sense in real-time extra and intracellular molecular interactions and enzymatic reactions, which constitutes a major advantage over other approaches to the study of biomolecular interactions. This technology has been used for the characterization of protein/protein, protein/nucleic acid, protein/substrate, and biomembrane/biomolecule interactions, which play crucial roles in the regulation of cellular pathways. This chapter reviews the different fluorescence strategies that have been developed for sensing molecular interactions in vitro at both steady- and pre-steady-state levels.
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Affiliation(s)
- Sebastien Deshayes
- Centre de Recherches de Biochimie Macromoléculaire, Department of Chemical Biology and Nanotechnology for Therapeutics, CRBM-CNRS, UMR-5237, UM1-UM2, University of Montpellier, 1919 Route de Mende, Montpellier, France
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Medagli B, Onesti S. Structure and mechanism of hexameric helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:75-95. [PMID: 23161007 DOI: 10.1007/978-1-4614-5037-5_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hexameric helicases are responsible for many biological processes, ranging from DNA replication in various life domains to DNA repair, transcriptional regulation and RNA metabolism, and encompass superfamilies 3-6 (SF3-6).To harness the chemical energy from ATP hydrolysis for mechanical work, hexameric helicases have a conserved core engine, called ASCE, that belongs to a subdivision of the P-loop NTPases. Some of the ring helicases (SF4 and SF5) use a variant of ASCE known as RecA-like, while some (SF3 and SF6) use another variant known as AAA+ fold. The NTP-binding sites are located at the interface between monomers and include amino-acid residues coming from neighbouring subunits, providing a mean for small structural changes within the ATP-binding site to be amplified into large inter-subunit movement.The ring structure has a central channel which encircles the nucleic acid. The topological link between the protein and the nucleic acid substrate increases the stability and processivity of the enzyme. This is probably the reason why within cellular systems the critical step of unwinding dsDNA ahead of the replication fork seems to be almost invariably carried out by a toroidal helicase, whether in bacteria, archaea or eukaryotes, as well as in some viruses.Over the last few years, a large number of biochemical, biophysical and structural data have thrown new light onto the architecture and function of these remarkable machines. Although the evidence is still limited to a couple of systems, biochemical and structural results suggest that motors based on RecA and AAA+ folds have converged on similar mechanisms to couple ATP-driven conformational changes to movement along nucleic acids.
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Affiliation(s)
- Barbara Medagli
- Structural Biology, Sincrotrone Trieste (Elettra), Area Science Pk, Basovizza, Trieste, Italy,
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