1
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Zhang Z, Chen J, Yao M, Wang G. Structural Insight Into the Function of DnaB Helicase in Bacterial DNA Replication. Proteins 2024. [PMID: 39230358 DOI: 10.1002/prot.26746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/16/2024] [Accepted: 08/26/2024] [Indexed: 09/05/2024]
Abstract
In bacteria, chromosome replication is achieved by the coordinations of more than a dozen replisome enzymes. Replication initiation protein DnaA melts DNA duplex at replication origin (oriC) and forms a replication bubble, followed by loading of helicase DnaB with the help of loader protein DnaC. Then the DnaB helicase unwinds the dsDNA and supports the priming of DnaG and the polymerizing of DNA polymerase. The DnaB helicase functions as a platform coupling unwinding, priming, and polymerizing events. The multiple roles of DnaB helicase are underlined by its distinctive architecture and dynamics conformations. In this review, we will discuss the assembling of DnaB hexamer and the conformational changes upon binding of various partners, DnaB in states of closed dilated (CD), closed constricted (CC), closed helical (CH), and open helical (OH) are discussed. These multiple interfaces among DnaB and partners are potential targets for inhibitors design and novel peptide antibiotics development.
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Affiliation(s)
- Zhiming Zhang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiang Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Maochun Yao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ganggang Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, China
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2
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Carrasco B, Torres R, Moreno-del Álamo M, Ramos C, Ayora S, Alonso JC. Processing of stalled replication forks in Bacillus subtilis. FEMS Microbiol Rev 2024; 48:fuad065. [PMID: 38052445 PMCID: PMC10804225 DOI: 10.1093/femsre/fuad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
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3
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. Nat Commun 2023; 14:4396. [PMID: 37474605 PMCID: PMC10359460 DOI: 10.1038/s41467-023-40106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer length is defined are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates. We show that gp41 alone is an open spiral, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the ring closure and activates the helicase. Helicase activation exposes a cryptic hydrophobic surface to recruit the gp61 primase. The primase binds the helicase in a bipartite mode in which the N-terminal Zn-binding domain and the C-terminal RNA polymerase domain each contain a helicase-interacting motif that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Our study reveals the T4 primosome assembly process and sheds light on the RNA primer synthesis mechanism.
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Affiliation(s)
- Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michelle M Spiering
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | | | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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4
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Inoue S, Ikeda Y, Fujiyama S, Ueda T, Abe Y. Oligomeric state of the N-terminal domain of DnaT for replication restart in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023:140929. [PMID: 37328019 DOI: 10.1016/j.bbapap.2023.140929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Abstract
DNA replication stops when chemical or physical damage occurs to the DNA. Repairing genomic DNA and reloading the replication helicase are crucial steps for restarting DNA replication. The Escherichia coli primosome is a complex of proteins and DNA responsible for reloading the replication helicase DnaB. DnaT, a protein found in the primosome complex, contains two functional domains. The C-terminal domain (89-179) forms an oligomeric complex with single-stranded DNA. Although the N-terminal domain (1-88) forms an oligomer, the specific residues responsible for this oligomeric structure have not yet been identified. In this study, we proposed that the N-terminal domain of DnaT has a dimeric antitoxin structure based on its primary sequence. Based on the proposed model, we confirmed the site of oligomerization in the N-terminal domain of DnaT through site-directed mutagenesis. The molecular masses and thermodynamic stabilities of the site-directed mutants located at the dimer interface, namely Phe42, Tyr43, Leu50, Leu53, and Leu54, were found to be lower than those of the wild-type. Moreover, we observed a decrease in the molecular masses of the V10S and F35S mutants compared to the wild-type DnaT. NMR analysis of the V10S mutant revealed that the secondary structure of the N-terminal domain of DnaT was consistent with the proposed model. Additionally, we have demonstrated that the stability of the oligomer formed by the N-terminal domain of DnaT is crucial for its function. Based on these findings, we propose that the DnaT oligomer plays a role in replication restart in Escherichia coli.
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Affiliation(s)
- Shogo Inoue
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yohei Ikeda
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Saki Fujiyama
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tadashi Ueda
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshito Abe
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Department of Pharmaceutical Sciences, School of Pharmacy at Fukuoka, International University of Health and Welfare, Okawa 831-8501, Japan.
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5
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539249. [PMID: 37205424 PMCID: PMC10187150 DOI: 10.1101/2023.05.03.539249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 Å. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.
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6
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Blaine HC, Simmons LA, Stallings CL. Diverse Mechanisms of Helicase Loading during DNA Replication Initiation in Bacteria. J Bacteriol 2023; 205:e0048722. [PMID: 36877032 PMCID: PMC10128896 DOI: 10.1128/jb.00487-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Initiation of DNA replication is required for cell viability and passage of genetic information to the next generation. Studies in Escherichia coli and Bacillus subtilis have established ATPases associated with diverse cellular activities (AAA+) as essential proteins required for loading of the replicative helicase at replication origins. AAA+ ATPases DnaC in E. coli and DnaI in B. subtilis have long been considered the paradigm for helicase loading during replication in bacteria. Recently, it has become increasingly clear that most bacteria lack DnaC/DnaI homologs. Instead, most bacteria express a protein homologous to the newly described DciA (dnaC/dnaI antecedent) protein. DciA is not an ATPase, and yet it serves as a helicase operator, providing a function analogous to that of DnaC and DnaI across diverse bacterial species. The recent discovery of DciA and of other alternative mechanisms of helicase loading in bacteria has changed our understanding of DNA replication initiation. In this review, we highlight recent discoveries, detailing what is currently known about the replicative helicase loading process across bacterial species, and we discuss the critical questions that remain to be investigated.
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Affiliation(s)
- Helen C. Blaine
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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7
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Cargemel C, Marsin S, Noiray M, Legrand P, Bounoua H, Li de la Sierra-Gallay I, Walbott H, Quevillon-Cheruel S. The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders. Acta Crystallogr D Struct Biol 2023; 79:177-187. [PMID: 36762863 PMCID: PMC9912922 DOI: 10.1107/s2059798323000281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data showed that the VcDciA binding site on VcDnaB is the conserved module formed by the linker helix LH of one monomer and the determinant helix DH of the second monomer. Interestingly, DnaC from Escherichia coli also targets this module onto EcDnaB. Thanks to their common target site, it was shown that VcDciA and EcDnaC could be functionally interchanged in vitro despite sharing no structural similarity. This represents a milestone in understanding the mechanism employed by phage helicase loaders to hijack bacterial replicative helicases during evolution.
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Affiliation(s)
- Claire Cargemel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Stéphanie Marsin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Magali Noiray
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Halil Bounoua
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Inès Li de la Sierra-Gallay
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Hélène Walbott
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91180 Gif-sur-Yvette, France
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8
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Li Z, Kaur P, Lo CY, Chopra N, Smith J, Wang H, Gao Y. Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase. Nucleic Acids Res 2022; 50:11965-11978. [PMID: 36400570 PMCID: PMC9723800 DOI: 10.1093/nar/gkac1089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022] Open
Abstract
Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the important role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain directly contacts the C-terminal helicase domain, and the contact interface is a hotspot for disease-related mutations. Mutations at the interface destabilize Twinkle hexamer and reduce helicase activity. With HS-AFM, we observed that a highly dynamic Twinkle domain, which is likely to be the N-terminal domain, can protrude ∼5 nm to transiently capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which is distinct from related helicases from bacteriophages.
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Affiliation(s)
- Zhuo Li
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Chen-Yu Lo
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Neil Chopra
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Jamie Smith
- BioSciences Department, Rice University, Houston, TX 77005, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Yang Gao
- BioSciences Department, Rice University, Houston, TX 77005, USA
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9
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TMT-based proteomic analysis of the inactivation effect of high voltage atmospheric cold plasma treatment on Pseudomonas aeruginosa. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Jin S, Bueno C, Lu W, Wang Q, Chen M, Chen X, Wolynes PG, Gao Y. Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA. Proc Natl Acad Sci U S A 2022; 119:e2202239119. [PMID: 35914145 PMCID: PMC9371691 DOI: 10.1073/pnas.2202239119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/05/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteriophage T7 gp4 helicase has served as a model system for understanding mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how nucleoside 5'-triphosphate hydrolysis and translocation of gp4 helicase are coupled is not fully resolved. Here, we used a thermodynamically benchmarked coarse-grained protein force field, Associative memory, Water mediated, Structure and Energy Model (AWSEM), with the single-stranded DNA (ssDNA) force field 3SPN.2C to investigate gp4 translocation. We found that the adenosine 5'-triphosphate (ATP) at the subunit interface stabilizes the subunit-subunit interaction and inhibits subunit translocation. Hydrolysis of ATP to adenosine 5'-diphosphate enables the translocation of one subunit, and new ATP binding at the new subunit interface finalizes the subunit translocation. The LoopD2 and the N-terminal primase domain provide transient protein-protein and protein-DNA interactions that facilitate the large-scale subunit movement. The simulations of gp4 helicase both validate our coarse-grained protein-ssDNA force field and elucidate the molecular basis of replicative helicase translocation.
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Affiliation(s)
- Shikai Jin
- Department of Biosciences, Rice University, Houston, TX 77005
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Carlos Bueno
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics, Rice University, Houston, TX 77005
| | - Qian Wang
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
| | - Mingchen Chen
- Department of Research and Development, neoX Biotech, Beijing 100206, China
| | - Xun Chen
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Peter G Wolynes
- Department of Biosciences, Rice University, Houston, TX 77005
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX 77005
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11
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Cargemel C, Walbott H, Durand D, Legrand P, Ould Ali M, Ferat JL, Marsin S, Quevillon-Cheruel S. The apo-form of the Vibrio cholerae replicative helicase DnaB is a labile and inactive planar trimer of dimers. FEBS Lett 2022; 596:2031-2040. [PMID: 35568982 DOI: 10.1002/1873-3468.14403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022]
Abstract
To enable chromosomal replication, DNA is unwound by the ATPase molecular motor replicative helicase. The bacterial helicase DnaB is a ring-shaped homo-hexamer whose conformational dynamics are being studied through its different 3D structural states adopted along its functional cycle. Our findings describe a new crystal structure for the apo-DnaB from Vibrio cholerae, forming a planar hexamer with pseudo-symmetry, constituted by a trimer of dimers in which the C-terminal domains delimit a triskelion-shaped hole. This hexamer is labile and inactive. We suggest that it represents an intermediate state allowing the formation of the active NTP-bound hexamer from dimers.
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Affiliation(s)
- Claire Cargemel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Hélène Walbott
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif-sur-Yvette, France
| | - Malika Ould Ali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Luc Ferat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stéphanie Marsin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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12
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Chmielewska-Jeznach M, Steczkiewicz K, Kobyłecki K, Bardowski JK, Szczepankowska AK. An Adenosine Triphosphate- Dependent 5'-3' DNA Helicase From sk1-Like Lactococcus lactis F13 Phage. Front Microbiol 2022; 13:840219. [PMID: 35369496 PMCID: PMC8965321 DOI: 10.3389/fmicb.2022.840219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Here, we describe functional characterization of an early gene (gp46) product of a virulent Lactococcus lactis sk1-like phage, vB_Llc_bIBBF13 (abbr. F13). The GP46F13 protein carries a catalytically active RecA-like domain belonging to the P-loop NTPase superfamily. It also retains features characteristic for ATPases forming oligomers. In order to elucidate its detailed molecular function, we cloned and overexpressed the gp46 gene in Escherichia coli. Purified GP46F13 protein binds to DNA and exhibits DNA unwinding activity on branched substrates in the presence of adenosine triphosphate (ATP). Size exclusion chromatography with multi-angle light scattering (SEC-MALS) experiments demonstrate that GP46F13 forms oligomers, and further pull-down assays show that GP46F13 interacts with host proteins involved in replication (i.e., DnaK, DnaJ, topoisomerase I, and single-strand binding protein). Taking together the localization of the gene and the obtained results, GP46F13 is the first protein encoded in the early-expressed gene region with helicase activity that has been identified among lytic L. lactis phages up to date.
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Affiliation(s)
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Kobyłecki
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Jacek K Bardowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
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13
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Periago J, Mason C, Griep MA. Theoretical Development of DnaG Primase as a Novel Narrow-Spectrum Antibiotic Target. ACS OMEGA 2022; 7:8420-8428. [PMID: 35309427 PMCID: PMC8928506 DOI: 10.1021/acsomega.1c05928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/01/2022] [Indexed: 06/01/2023]
Abstract
The widespread use of antibiotics to treat infections is one of the reasons that global mortality rates have fallen over the past 80 years. However, antibiotic use is also responsible for the concomitant rise in antibiotic resistance because it results in dysbiosis in which commensal and pathogenic bacteria are both greatly reduced. Therefore, narrow-range antibiotics are a promising direction for reducing antibiotic resistance because they are more discriminate. As a step toward addressing this problem, the goal of this study was to identify sites on DnaG primase that are conserved within Gram-positive bacteria and different from the equivalent sites in Gram-negative bacteria. Based on sequence and structural analysis, the primase C-terminal helicase-binding domain (CTD) was identified as most promising. Although the primase CTD sequences are very poorly conserved, they have highly conserved protein folds, and Gram-positive bacterial primases fold into a compact state that creates a small molecule binding site adjacent to a groove. The small molecule would stabilize the protein in its compact state, which would interfere with the helicase binding. This is important because primase CTD must be in its open conformation to bind to its cognate helicase at the replication fork.
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14
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Horikoshi N, Kurumizaka H. Structural insight into replicative helicase loading in Escherichia coli. J Biochem 2022; 171:605-607. [PMID: 35238386 DOI: 10.1093/jb/mvac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
DNA replication is an essential, precisely regulated process that occurs once in a cell cycle. In the Gram-negative bacterium Escherichia coli, the replicative helicase EcDnaB and the helicase loader EcDnaC play key roles in the initiation step at the replication origin, oriC. EcDnaB and EcDnaC form a heterododecamer, in which hexameric EcDnaB is bound to hexameric EcDnaC. Using genetic, biochemical, and structural biology approaches, many groups have probed the mechanism of replicative helicase loading, using helicases and helicase loaders from various species. Recent X-ray crystallography and cryo-EM structural studies of the EcDnaB-EcDnaC complex revealed that the interaction of DnaC with DnaB triggers distortion accumulation on the closed ring of hexameric DnaB, inducing DnaB subunits to adopt the open helical form for replication progression. The high-resolution crystal structure of the DnaB-DnaC complex solved by Nagata et al. contributed to a better understanding of the conformational rearrangement of the DnaB ring. In addition to the structural alterations in DnaB subunits by DnaC, the binding of single stranded DNA (ssDNA) substrates alters the ATP- and ADP-bound forms of DnaB and DnaC. These studies have proposed mechanisms by which DnaC regulates helicase loading onto ssDNA.
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Affiliation(s)
- Naoki Horikoshi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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15
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Convergent evolution in two bacterial replicative helicase loaders. Trends Biochem Sci 2022; 47:620-630. [DOI: 10.1016/j.tibs.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
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16
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Tharappel AM, Li Z, Li H. Inteins as Drug Targets and Therapeutic Tools. Front Mol Biosci 2022; 9:821146. [PMID: 35211511 PMCID: PMC8861304 DOI: 10.3389/fmolb.2022.821146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Multidrug-resistant pathogens are of significant concern in recent years. Hence new antifungal and anti-bacterial drug targets are urgently needed before the situation goes beyond control. Inteins are polypeptides that self-splice from exteins without the need for cofactors or external energy, resulting in joining of extein fragments. Inteins are present in many organisms, including human pathogens such as Mycobacterium tuberculosis, Cryptococcus neoformans, C. gattii, and Aspergillus fumigatus. Because intein elements are not present in human genes, they are attractive drug targets to develop antifungals and antibiotics. Thus far, a few inhibitors of intein splicing have been reported. Metal-ions such as Zn2+ and Cu2+, and platinum-containing compound cisplatin inhibit intein splicing in M. tuberculosis and C. neoformans by binding to the active site cysteines. A small-molecule inhibitor 6G-318S and its derivative 6G-319S are found to inhibit intein splicing in C. neoformans and C. gattii with a MIC in nanomolar concentrations. Inteins have also been used in many other applications. Intein can be used in activating a protein inside a cell using small molecules. Moreover, split intein can be used to deliver large genes in experimental gene therapy and to kill selected species in a mixed population of microbes by taking advantage of the toxin-antitoxin system. Furthermore, split inteins are used in synthesizing cyclic peptides and in developing cell culture model to study infectious viruses including SARS-CoV-2 in the biosafety level (BSL) 2 facility. This mini-review discusses the recent research developments of inteins in drug discovery and therapeutic research.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- *Correspondence: Hongmin Li,
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17
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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18
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Gaimster H, Winterhalter C, Koh A, Murray H. Visualizing the Replisome, Chromosome Breaks, and Replication Restart in Bacillus subtilis. Methods Mol Biol 2022; 2476:263-276. [PMID: 35635709 DOI: 10.1007/978-1-0716-2221-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Research over the last two decades has revealed that bacterial genomes are highly organized and that bacteria have sophisticated mechanisms in place to ensure their correct replication and segregation into progeny cells. Here we discuss techniques that can be used with live bacterial cells to analyze DNA replisome dynamics, double-strand chromosome breaks, and restart of repaired replication forks.
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Affiliation(s)
- Hannah Gaimster
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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19
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The alarmone (p)ppGpp regulates primer extension by bacterial primase. J Mol Biol 2021; 433:167189. [PMID: 34389317 DOI: 10.1016/j.jmb.2021.167189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/22/2021] [Accepted: 08/02/2021] [Indexed: 11/21/2022]
Abstract
Primase is an essential component of the DNA replication machinery, responsible for synthesizing RNA primers that initiate leading and lagging strand DNA synthesis. Bacterial primase activity can be regulated by the starvation-inducible nucleotide (p)ppGpp. This regulation contributes to a timely inhibition of DNA replication upon amino acid starvation in the Gram-positive bacterium Bacillus subtilis. Here, we characterize the effect of (p)ppGpp on B. subtilis DnaG primase activity in vitro. Using a single-nucleotide resolution primase assay, we dissected the effect of ppGpp on the initiation, extension, and fidelity of B. subtilis primase. We found that ppGpp has a mild effect on initiation, but strongly inhibits primer extension and reduces primase processivity, promoting termination of primer extension. High (p)ppGpp concentration, together with low GTP concentration, additively inhibit primase activity. This explains the strong inhibition of replication elongation during starvation which induces high levels of (p)ppGpp and depletion of GTP in B. subtilis. Finally, we found that lowering GTP concentration results in mismatches in primer base pairing that allow priming readthrough, and that ppGpp reduces readthrough to protect priming fidelity. These results highlight the importance of (p)ppGpp in protecting replisome integrity and genome stability in fluctuating nucleotide concentrations upon onset of environmental stress.
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20
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Spinks RR, Spenkelink LM, Stratmann SA, Xu ZQ, Stamford NPJ, Brown SE, Dixon NE, Jergic S, van Oijen AM. DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies. Nucleic Acids Res 2021; 49:6804-6816. [PMID: 34139009 PMCID: PMC8266626 DOI: 10.1093/nar/gkab493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 01/09/2023] Open
Abstract
In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.
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Affiliation(s)
- Richard R Spinks
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Sarah A Stratmann
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - N Patrick J Stamford
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Susan E Brown
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
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21
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Marsin S, Adam Y, Cargemel C, Andreani J, Baconnais S, Legrand P, Li de la Sierra-Gallay I, Humbert A, Aumont-Nicaise M, Velours C, Ochsenbein F, Durand D, Le Cam E, Walbott H, Possoz C, Quevillon-Cheruel S, Ferat JL. Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Nucleic Acids Res 2021; 49:6569-6586. [PMID: 34107018 PMCID: PMC8216460 DOI: 10.1093/nar/gkab463] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/I. While the DciA structure from Vibrio cholerae shares no homology with DnaC, it reveals similarities with DnaA and DnaX, two proteins involved during replication initiation. As other bacterial replicative helicases, VcDnaB adopts a toroid-shaped homo-hexameric structure, but with a slightly open dynamic conformation in the free state. We show that VcDnaB can load itself on DNA in vitro and that VcDciA stimulates this function, resulting in an increased DNA unwinding. VcDciA interacts with VcDnaB with a 3/6 stoichiometry and we show that a determinant residue, which discriminates DciA- and DnaC/I-helicases, is critical in vivo. Our work is the first step toward the understanding of the ancestral mode of loading of bacterial replicative helicases on DNA. It sheds light on the strategy employed by phage helicase loaders to hijack bacterial replicative helicases and may explain the recurrent domestication of dnaC/I through evolution in bacteria.
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Affiliation(s)
| | | | | | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sonia Baconnais
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Ines Li de la Sierra-Gallay
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Adeline Humbert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Hélène Walbott
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christophe Possoz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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22
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Single-Molecule Dynamics at a Bacterial Replication Fork after Nutritional Downshift or Chemically Induced Block in Replication. mSphere 2021; 6:6/1/e00948-20. [PMID: 33504660 PMCID: PMC7885319 DOI: 10.1128/msphere.00948-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replication forks must respond to changes in nutrient conditions, especially in bacterial cells. By investigating the single-molecule dynamics of replicative helicase DnaC, DNA primase DnaG, and lagging-strand polymerase DnaE in the model bacterium Bacillus subtilis, we show that proteins react differently to stress conditions in response to transient replication blocks due to DNA damage, to inhibition of the replicative polymerase, or to downshift of serine availability. DnaG appears to be recruited to the forks by a diffusion and capture mechanism, becomes more statically associated after the arrest of polymerase, but binds less frequently after fork blocks due to DNA damage or to nutritional downshift. These results indicate that binding of the alarmone (p)ppGpp due to stringent response prevents DnaG from binding to forks rather than blocking bound primase. Dissimilar behavior of DnaG and DnaE suggests that both proteins are recruited independently to the forks rather than jointly. Turnover of all three proteins was increased during replication block after nutritional downshift, different from the situation due to DNA damage or polymerase inhibition, showing high plasticity of forks in response to different stress conditions. Forks persisted during all stress conditions, apparently ensuring rapid return to replication extension.IMPORTANCE All cells need to adjust DNA replication, which is achieved by a well-orchestrated multiprotein complex, in response to changes in physiological and environmental conditions. For replication forks, it is extremely challenging to meet with conditions where amino acids are rapidly depleted from cells, called the stringent response, to deal with the inhibition of one of the centrally involved proteins or with DNA modifications that arrest the progression of forks. By tracking helicase (DnaC), primase (DnaG), and polymerase (DnaE), central proteins of Bacillus subtilis replication forks, at a single molecule level in real time, we found that interactions of the three proteins with replication forks change in different manners under different stress conditions, revealing an intriguing plasticity of replication forks in dealing with replication obstacles. We have devised a new tool to determine rates of exchange between static movement (binding to a much larger complex) and free diffusion, showing that during stringent response, all proteins have highly increased exchange rates, slowing down overall replication, while inactivation of polymerase or replication roadblocks leaves forks largely intact, allowing rapid restart once obstacles are removed.
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23
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ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter. Molecules 2020; 25:molecules25225268. [PMID: 33198135 PMCID: PMC7698047 DOI: 10.3390/molecules25225268] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases.
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24
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Bebel A, Walsh MA, Mir-Sanchis I, Rice PA. A novel DNA primase-helicase pair encoded by SCC mec elements. eLife 2020; 9:55478. [PMID: 32945259 PMCID: PMC7581432 DOI: 10.7554/elife.55478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/17/2020] [Indexed: 01/18/2023] Open
Abstract
Mobile genetic elements (MGEs) are a rich source of new enzymes, and conversely, understanding the activities of MGE-encoded proteins can elucidate MGE function. Here, we biochemically characterize three proteins encoded by a conserved operon carried by the Staphylococcal Cassette Chromosome (SCCmec), an MGE that confers methicillin resistance to Staphylococcus aureus, creating MRSA strains. The first of these proteins, CCPol, is an active A-family DNA polymerase. The middle protein, MP, binds tightly to CCPol and confers upon it the ability to synthesize DNA primers de novo. The CCPol-MP complex is therefore a unique primase-polymerase enzyme unrelated to either known primase family. The third protein, Cch2, is a 3’-to-5’ helicase. Cch2 additionally binds specifically to a dsDNA sequence downstream of its gene that is also a preferred initiation site for priming by CCPol-MP. Taken together, our results suggest that this is a functional replication module for SCCmec.
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Affiliation(s)
- Aleksandra Bebel
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Melissa A Walsh
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
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25
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Hayashi C, Miyazaki E, Ozaki S, Abe Y, Katayama T. DnaB helicase is recruited to the replication initiation complex via binding of DnaA domain I to the lateral surface of the DnaB N-terminal domain. J Biol Chem 2020; 295:11131-11143. [PMID: 32540966 DOI: 10.1074/jbc.ra120.014235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/10/2020] [Indexed: 01/09/2023] Open
Abstract
The DNA replication protein DnaA in Escherichia coli constructs higher-order complexes on the origin, oriC, to unwind this region. DnaB helicase is loaded onto unwound oriC via interactions with the DnaC loader and the DnaA complex. The DnaB-DnaC complex is recruited to the DnaA complex via stable binding of DnaB to DnaA domain I. The DnaB-DnaC complex is then directed to unwound oriC via a weak interaction between DnaB and DnaA domain III. Previously, we showed that Phe46 in DnaA domain I binds to DnaB. Here, we searched for the DnaA domain I-binding site in DnaB. The DnaB L160A variant was impaired in binding to DnaA complex on oriC but retained its DnaC-binding and helicase activities. DnaC binding moderately stimulated DnaA binding of DnaB L160A, and loading of DnaB L160A onto oriC was consistently and moderately inhibited. In a helicase assay with partly single-stranded DNA bearing a DnaA-binding site, DnaA stimulated DnaB loading, which was strongly inhibited in DnaB L160A even in the presence of DnaC. DnaB L160A was functionally impaired in vivo On the basis of these findings, we propose that DnaB Leu160 interacts with DnaA domain I Phe46 DnaB Leu160 is exposed on the lateral surface of the N-terminal domain, which can explain unobstructed interactions of DnaA domain I-bound DnaB with DnaC, DnaG primase, and DnaA domain III. We propose a probable structure for the DnaA-DnaB-DnaC complex, which could be relevant to the process of DnaB loading onto oriC.
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Affiliation(s)
- Chihiro Hayashi
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka, Japan
| | - Erika Miyazaki
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka, Japan
| | - Shogo Ozaki
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka, Japan
| | - Yoshito Abe
- Department of Protein Structure, Function, and Design, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka, Japan.,Department of Pharmaceutical Sciences, International University of Health and Welfare, Okawa, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka, Japan
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26
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Monachino E, Jergic S, Lewis JS, Xu ZQ, Lo ATY, O'Shea VL, Berger JM, Dixon NE, van Oijen AM. A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome. Mol Cell 2020; 79:140-154.e7. [PMID: 32464091 DOI: 10.1016/j.molcel.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/12/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly found plasticity lies in the 500-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
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Affiliation(s)
- Enrico Monachino
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747, the Netherlands
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Allen T Y Lo
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Valerie L O'Shea
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
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27
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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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28
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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29
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Brosh RM, Matson SW. History of DNA Helicases. Genes (Basel) 2020; 11:genes11030255. [PMID: 32120966 PMCID: PMC7140857 DOI: 10.3390/genes11030255] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Since the discovery of the DNA double helix, there has been a fascination in understanding the molecular mechanisms and cellular processes that account for: (i) the transmission of genetic information from one generation to the next and (ii) the remarkable stability of the genome. Nucleic acid biologists have endeavored to unravel the mysteries of DNA not only to understand the processes of DNA replication, repair, recombination, and transcription but to also characterize the underlying basis of genetic diseases characterized by chromosomal instability. Perhaps unexpectedly at first, DNA helicases have arisen as a key class of enzymes to study in this latter capacity. From the first discovery of ATP-dependent DNA unwinding enzymes in the mid 1970's to the burgeoning of helicase-dependent pathways found to be prevalent in all kingdoms of life, the story of scientific discovery in helicase research is rich and informative. Over four decades after their discovery, we take this opportunity to provide a history of DNA helicases. No doubt, many chapters are left to be written. Nonetheless, at this juncture we are privileged to share our perspective on the DNA helicase field - where it has been, its current state, and where it is headed.
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Affiliation(s)
- Robert M. Brosh
- Section on DNA Helicases, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
| | - Steven W. Matson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (R.M.B.J.); (S.W.M.); Tel.: +1-410-558-8578 (R.M.B.J.); +1-919-962-0005 (S.W.M.)
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30
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Nagata K, Okada A, Ohtsuka J, Ohkuri T, Akama Y, Sakiyama Y, Miyazaki E, Horita S, Katayama T, Ueda T, Tanokura M. Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding. J Biochem 2020; 167:1-14. [PMID: 31665315 DOI: 10.1093/jb/mvz087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 02/03/2023] Open
Abstract
Loading the bacterial replicative helicase DnaB onto DNA requires a specific loader protein, DnaC/DnaI, which creates the loading-competent state by opening the DnaB hexameric ring. To understand the molecular mechanism by which DnaC/DnaI opens the DnaB ring, we solved 3.1-Å co-crystal structure of the interaction domains of Escherichia coli DnaB-DnaC. The structure reveals that one N-terminal domain (NTD) of DnaC interacts with both the linker helix of a DnaB molecule and the C-terminal domain (CTD) of the adjacent DnaB molecule by forming a three α-helix bundle, which fixes the relative orientation of the two adjacent DnaB CTDs. The importance of the intermolecular interface in the crystal structure was supported by the mutational data of DnaB and DnaC. Based on the crystal structure and other available information on DnaB-DnaC structures, we constructed a molecular model of the hexameric DnaB CTDs bound by six DnaC NTDs. This model suggested that the binding of a DnaC would cause a distortion in the hexameric ring of DnaB. This distortion of the DnaB ring might accumulate by the binding of up to six DnaC molecules, resulting in the DnaB ring to open.
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Affiliation(s)
- Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akitoshi Okada
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Jun Ohtsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takatoshi Ohkuri
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Yusuke Akama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Yukari Sakiyama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Erika Miyazaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Shoichiro Horita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tadashi Ueda
- Department of Protein Structure, Function and Design, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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31
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Torres R, Serrano E, Alonso JC. Bacillus subtilis RecA interacts with and loads RadA/Sms to unwind recombination intermediates during natural chromosomal transformation. Nucleic Acids Res 2019; 47:9198-9215. [PMID: 31350886 PMCID: PMC6755099 DOI: 10.1093/nar/gkz647] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 02/01/2023] Open
Abstract
During natural transformation Bacillus subtilis RecA, polymerized onto the incoming single-stranded (ss) DNA, catalyses DNA strand invasion resulting in a displacement loop (D-loop) intermediate. A null radA mutation impairs chromosomal transformation, and RadA/Sms unwinds forked DNA in the 5′→3′ direction. We show that in the absence of RadA/Sms competent cells require the RecG translocase for natural chromosomal transformation. RadA/Sms tetracysteine motif (C13A and C13R) variants, which fail to interact with RecA, are also deficient in plasmid transformation, but this defect is suppressed by inactivating recA. The RadA/Sms C13A and C13R variants bind ssDNA, and this interaction stimulates their ATPase activity. Wild-type (wt) RadA/Sms interacts with and inhibits the ATPase activity of RecA, but RadA/Sms C13A fails to do it. RadA/Sms and its variants, C13A and C13R, bound to the 5′-tail of a DNA substrate, unwind DNA in the 5′→3′ direction. RecA interacts with and loads wt RadA/Sms to promote unwinding of a non-cognate 3′-tailed or 5′-fork DNA substrate, but RadA/Sms C13A or C13R fail to do it. We propose that wt RadA/Sms interaction with RecA is crucial to recruit the former onto D-loop DNA, and both proteins in concert catalyse D-loop extension to favour integration of ssDNA during chromosomal transformation.
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Affiliation(s)
- Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91585 4546; Fax: +34 91585 4506;
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32
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Helicobacter pylori helicase loader protein Hp0897 shows unique functions of N- and C-terminal regions. Biochem J 2019; 476:3261-3279. [PMID: 31548270 DOI: 10.1042/bcj20190430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022]
Abstract
Helicase loaders are required for the loading of helicases at the vicinity of replication origins. In Helicobacter pylori, Hp0897 has been shown to be a potential helicase loader for replicative helicase (HpDnaB) although it does not show any sequence homology with conventional DnaC like helicase loader proteins. Therefore, it is important to investigate the in vivo role of Hp0897 and structure-function analysis with respect to domain mapping of Hp0897 and HpDnaB. Although HporiC is divided into oriC1 and oriC2, the latter has been assigned as functional origin based on loading of initiator protein HpDnaA. Using chromatin immunoprecipitation (ChIP) experiment, we show preferential binding of Hp0897 at oriC2 over oriC1 like HpDnaA highlighting its helicase loader function in vivo. Furthermore, we generated series of deletion mutants for HpDnaB and Hp0897 that enabled us to map the domains of interaction between these two proteins. Interestingly, the C-terminal domain of Hp0897 (Hp0897CTD) shows stronger interaction with HpDnaB over the N-terminal region of Hp0897 (Hp0897NTD). Similar to the full-length protein, Hp0897CTD also stimulates the DNA binding activity of HpDnaB. Furthermore, overexpression of Hp0897 full-length protein in H. pylori leads to an elongated cell phenotype. While the overexpression of Hp0897CTD does not show a phenotype of cell elongation, overexpression of Hp0897NTD shows extensive cell elongation. These results highlight the possible role of Hp0897CTD in helicase loading and Hp0897NTD's unique function linked to cell division that make Hp0897 as a potential drug target against H. pylori.
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33
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Bergsch J, Allain FHT, Lipps G. Recent advances in understanding bacterial and archaeoeukaryotic primases. Curr Opin Struct Biol 2019; 59:159-167. [PMID: 31585372 DOI: 10.1016/j.sbi.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/05/2019] [Accepted: 08/26/2019] [Indexed: 11/16/2022]
Abstract
DNA replication in all forms of life relies upon the initiation of synthesis on a single strand template by formation of a short oligonucleotide primer, which is subsequently elongated by DNA polymerases. Two structurally distinct classes of enzymes have evolved to perform this function, namely the bacterial DnaG-type primases and the Archaeal and Eukaryotic primases (AEP). Structural and mechanistic insights have provided a clear understanding of the role of the different domains of these enzymes in the context of the replisome and recent work sheds light upon primase-substrate interactions. We herein review the emerging picture of the primase mechanism on the basis of the structural knowledge obtained to date and propose future directions of this essential aspect of DNA replication.
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Affiliation(s)
- Jan Bergsch
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland; Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland.
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34
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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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35
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Yang W, Seidman MM, Rupp WD, Gao Y. Replisome structure suggests mechanism for continuous fork progression and post-replication repair. DNA Repair (Amst) 2019; 81:102658. [PMID: 31303546 DOI: 10.1016/j.dnarep.2019.102658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
What happens to DNA replication when it encounters a damaged or nicked DNA template has been under investigation for five decades. Initially it was thought that DNA polymerase, and thus the replication-fork progression, would stall at road blocks. After the discovery of replication-fork helicase and replication re-initiation factors by the 1990s, it became clear that the replisome can "skip" impasses and finish replication with single-stranded gaps and double-strand breaks in the product DNA. But the mechanism for continuous fork progression after encountering roadblocks is entangled with translesion synthesis, replication fork reversal and recombination repair. The recently determined structure of the bacteriophage T7 replisome offers the first glimpse of how helicase, primase, leading-and lagging-strand DNA polymerases are organized around a DNA replication fork. The tightly coupled leading-strand polymerase and lagging-strand helicase provides a scaffold to consolidate data accumulated over the past five decades and offers a fresh perspective on how the replisome may skip lesions and complete discontinuous DNA synthesis. Comparison of the independently evolved bacterial and eukaryotic replisomes suggests that repair of discontinuous DNA synthesis occurs post replication in both.
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Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute of Aging, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - W Dean Rupp
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520-8040, USA
| | - Yang Gao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
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36
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Peter B, Farge G, Pardo-Hernandez C, Tångefjord S, Falkenberg M. Structural basis for adPEO-causing mutations in the mitochondrial TWINKLE helicase. Hum Mol Genet 2019; 28:1090-1099. [PMID: 30496414 PMCID: PMC6423418 DOI: 10.1093/hmg/ddy415] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
TWINKLE is the helicase involved in replication and maintenance of mitochondrial DNA (mtDNA) in mammalian cells. Structurally, TWINKLE is closely related to the bacteriophage T7 gp4 protein and comprises a helicase and primase domain joined by a flexible linker region. Mutations in and around this linker region are responsible for autosomal dominant progressive external ophthalmoplegia (adPEO), a neuromuscular disorder associated with deletions in mtDNA. The underlying molecular basis of adPEO-causing mutations remains unclear, but defects in TWINKLE oligomerization are thought to play a major role. In this study, we have characterized these disease variants by single-particle electron microscopy and can link the diminished activities of the TWINKLE variants to altered oligomeric properties. Our results suggest that the mutations can be divided into those that (i) destroy the flexibility of the linker region, (ii) inhibit ring closure and (iii) change the number of subunits within a helicase ring. Furthermore, we demonstrate that wild-type TWINKLE undergoes large-scale conformational changes upon nucleoside triphosphate binding and that this ability is lost in the disease-causing variants. This represents a substantial advancement in the understanding of the molecular basis of adPEO and related pathologies and may aid in the development of future therapeutic strategies.
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Affiliation(s)
- Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Sweden
| | - Geraldine Farge
- Centre Nacionale de la Recherche Scientifique/Institut National de Physique Nucléaire et des Particules, Laboratoire de Physique de Clermont, Université Clermont Auvergne, BP 10448, Clermont-Ferrand, France
| | | | - Stefan Tångefjord
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Sweden
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37
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Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
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Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
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38
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Oakley AJ. A structural view of bacterial DNA replication. Protein Sci 2019; 28:990-1004. [PMID: 30945375 DOI: 10.1002/pro.3615] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 11/11/2022]
Abstract
DNA replication mechanisms are conserved across all organisms. The proteins required to initiate, coordinate, and complete the replication process are best characterized in model organisms such as Escherichia coli. These include nucleotide triphosphate-driven nanomachines such as the DNA-unwinding helicase DnaB and the clamp loader complex that loads DNA-clamps onto primer-template junctions. DNA-clamps are required for the processivity of the DNA polymerase III core, a heterotrimer of α, ε, and θ, required for leading- and lagging-strand synthesis. DnaB binds the DnaG primase that synthesizes RNA primers on both strands. Representative structures are available for most classes of DNA replication proteins, although there are gaps in our understanding of their interactions and the structural transitions that occur in nanomachines such as the helicase, clamp loader, and replicase core as they function. Reviewed here is the structural biology of these bacterial DNA replication proteins and prospects for future research.
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Affiliation(s)
- Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
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39
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Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM. Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Mol Cell 2019; 74:173-184.e4. [PMID: 30797687 DOI: 10.1016/j.molcel.2019.01.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 02/02/2023]
Abstract
In cells, dedicated AAA+ ATPases deposit hexameric, ring-shaped helicases onto DNA to initiate chromosomal replication. To better understand the mechanisms by which helicase loading can occur, we used cryo-EM to determine sub-4-Å-resolution structures of the E. coli DnaB⋅DnaC helicase⋅loader complex with nucleotide in pre- and post-DNA engagement states. In the absence of DNA, six DnaC protomers latch onto and crack open a DnaB hexamer using an extended N-terminal domain, stabilizing this conformation through nucleotide-dependent ATPase interactions. Upon binding DNA, DnaC hydrolyzes ATP, allowing DnaB to isomerize into a topologically closed, pre-translocation state competent to bind primase. Our data show how DnaC opens the DnaB ring and represses the helicase prior to DNA binding and how DnaC ATPase activity is reciprocally regulated by DnaB and DNA. Comparative analyses reveal how the helicase loading mechanism of DnaC parallels and diverges from homologous AAA+ systems involved in DNA replication and transposition.
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Affiliation(s)
- Ernesto Arias-Palomo
- Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC 28040 Madrid, Spain.
| | - Neha Puri
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valerie L O'Shea Murray
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qianyun Yan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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40
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Wiegand T, Cadalbert R, Lacabanne D, Timmins J, Terradot L, Böckmann A, Meier BH. The conformational changes coupling ATP hydrolysis and translocation in a bacterial DnaB helicase. Nat Commun 2019; 10:31. [PMID: 30604765 PMCID: PMC6318325 DOI: 10.1038/s41467-018-07968-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/10/2018] [Indexed: 11/08/2022] Open
Abstract
DnaB helicases are motor proteins that couple ATP-hydrolysis to the loading of the protein onto DNA at the replication fork and to translocation along DNA to separate double-stranded DNA into single strands during replication. Using a network of conformational states, arrested by nucleotide mimics, we herein characterize the reaction coordinates for ATP hydrolysis, DNA loading and DNA translocation using solid-state NMR spectroscopy. AMP-PCP is used as pre-hydrolytic, ADP:AlF4- as transition state, and ADP as post-hydrolytic ATP mimic. 31P and 13C NMR spectra reveal conformational and dynamic responses to ATP hydrolysis and the resulting DNA loading and translocation with single amino-acid resolution. This allows us to identify residues guiding the DNA translocation process and to explain the high binding affinities for DNA observed for ADP:AlF4-, which turns out to be optimally preconfigured to bind DNA.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Denis Lacabanne
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Joanna Timmins
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France.
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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41
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Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
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Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
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42
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Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis. Biochem J 2018; 475:3493-3509. [DOI: 10.1042/bcj20180673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022]
Abstract
The helicase–primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase–primase interaction in M. tuberculosis, a complex was modeled using the MtDnaG-CTD and MtDnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of MtDnaG were identified as potential key residues interacting with MtDnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of MtDnaB-NTD with the Ile605Ala mutant of MtDnaG-CTD compared with native MtDnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB–DnaG complex. Also, MtDnaB-NTD showed micromolar affinity with DnaG-CTDs from Escherichia coli and Helicobacter pylori and unstable binding with DnaG-CTD from Vibrio cholerae. The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.
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43
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Kelley DS, Lennon CW, Li Z, Miller MR, Banavali NK, Li H, Belfort M. Mycobacterial DnaB helicase intein as oxidative stress sensor. Nat Commun 2018; 9:4363. [PMID: 30341292 PMCID: PMC6195587 DOI: 10.1038/s41467-018-06554-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H2O2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.
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Affiliation(s)
- Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
| | - Christopher W Lennon
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Michael R Miller
- Department of Chemistry, University at Albany, Albany, NY, 12222, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA
| | - Hongmin Li
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208, USA.
| | - Marlene Belfort
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, NY, 12222, USA.
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44
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Hou C, Biswas T, Tsodikov OV. Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events. Biochemistry 2018; 57:2084-2093. [PMID: 29558114 DOI: 10.1021/acs.biochem.8b00036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear due to the paucity of structural information on DnaG in complexes with other replisome components. Here we report the first crystal structures of noncovalent DnaG-DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase.
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Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States
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45
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Kaguni JM. The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery. Antibiotics (Basel) 2018. [PMID: 29538288 PMCID: PMC5872134 DOI: 10.3390/antibiotics7010023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
DNA replication is an essential process. Although the fundamental strategies to duplicate chromosomes are similar in all free-living organisms, the enzymes of the three domains of life that perform similar functions in DNA replication differ in amino acid sequence and their three-dimensional structures. Moreover, the respective proteins generally utilize different enzymatic mechanisms. Hence, the replication proteins that are highly conserved among bacterial species are attractive targets to develop novel antibiotics as the compounds are unlikely to demonstrate off-target effects. For those proteins that differ among bacteria, compounds that are species-specific may be found. Escherichia coli has been developed as a model system to study DNA replication, serving as a benchmark for comparison. This review summarizes the functions of individual E. coli proteins, and the compounds that inhibit them.
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Affiliation(s)
- Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.
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46
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PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection. Genes (Basel) 2018; 9:genes9020091. [PMID: 29443925 PMCID: PMC5852587 DOI: 10.3390/genes9020091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/24/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Protein quaternary structure complex is also known as a multimer, which plays an important role in a cell. The dimer structure of transcription factors is involved in gene regulation, but the trimer structure of virus-infection-associated glycoproteins is related to the human immunodeficiency virus. The classification of the protein quaternary structure complex for the post-genome era of proteomics research will be of great help. Classification systems among protein quaternary structures have not been widely developed. Therefore, we designed the architecture of a two-layer machine learning technique in this study, and developed the classification system PClass. The protein quaternary structure of the complex is divided into five categories, namely, monomer, dimer, trimer, tetramer, and other subunit classes. In the framework of the bootstrap method with a support vector machine, we propose a new model selection method. Each type of complex is classified based on sequences, entropy, and accessible surface area, thereby generating a plurality of feature modules. Subsequently, the optimal model of effectiveness is selected as each kind of complex feature module. In this stage, the optimal performance can reach as high as 70% of Matthews correlation coefficient (MCC). The second layer of construction combines the first-layer module to integrate mechanisms and the use of six machine learning methods to improve the prediction performance. This system can be improved over 10% in MCC. Finally, we analyzed the performance of our classification system using transcription factors in dimer structure and virus-infection-associated glycoprotein in trimer structure. PClass is available via a web interface at http://predictor.nchu.edu.tw/PClass/.
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47
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The ring-shaped hexameric helicases that function at DNA replication forks. Nat Struct Mol Biol 2018; 25:122-130. [PMID: 29379175 DOI: 10.1038/s41594-018-0024-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/27/2017] [Indexed: 11/08/2022]
Abstract
DNA replication requires separation of genomic duplex DNA strands, an operation that is performed by a hexameric ring-shaped helicase in all domains of life. The structures and chemomechanical actions of these fascinating machines are coming into sharper focus. Although there is no evolutionary relationship between the hexameric helicases of bacteria and those of archaea and eukaryotes, they share many fundamental features. Here we review recent studies of these two groups of hexameric helicases and the unexpected distinctions they have also unveiled.
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48
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van Eijk E, Paschalis V, Green M, Friggen AH, Larson MA, Spriggs K, Briggs GS, Soultanas P, Smits WK. Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen Clostridium difficile. Open Biol 2017; 6:rsob.160272. [PMID: 28003473 PMCID: PMC5204125 DOI: 10.1098/rsob.160272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022] Open
Abstract
DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. difficile, and reconstitute helicase and primase activities in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase in vitro. The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile Aquifex aeolicus. However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader–helicase–primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in C. difficile from that of the well-studied Gram-positive Bacillus subtilis model.
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Affiliation(s)
- Erika van Eijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Vasileios Paschalis
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Matthew Green
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Annemieke H Friggen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marilynn A Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, USA.,National Strategic Research Institute, Omaha, NE 68105, USA
| | | | - Geoffrey S Briggs
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Panos Soultanas
- School of Chemistry, Center for Biomolecular Sciences, University of Nottingham, UK
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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49
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Felczak MM, Chodavarapu S, Kaguni JM. DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase. J Biol Chem 2017; 292:20871-20882. [PMID: 29070678 DOI: 10.1074/jbc.m117.807644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/11/2017] [Indexed: 11/06/2022] Open
Abstract
Former studies relying on hydrogen/deuterium exchange analysis suggest that DnaC bound to DnaB alters the conformation of the N-terminal domain (NTD) of DnaB to impair the ability of this DNA helicase to interact with primase. Supporting this idea, the work described herein based on biosensor experiments and enzyme-linked immunosorbent assays shows that the DnaB-DnaC complex binds poorly to primase in comparison with DnaB alone. Using a structural model of DnaB complexed with the C-terminal domain of primase, we found that Ile-85 is located at the interface in the NTD of DnaB that contacts primase. An alanine substitution for Ile-85 specifically interfered with this interaction and impeded DnaB function in DNA replication, but not its activity as a DNA helicase or its ability to bind to ssDNA. By comparison, substitutions of Asn for Ile-136 (I136N) and Thr for Ile-142 (I142T) in a subdomain previously named the helical hairpin in the NTD of DnaB altered the conformation of the helical hairpin and/or compromised its pairwise arrangement with the companion subdomain in each brace of protomers of the DnaB hexamer. In contrast with the I85A mutant, the latter were defective in DNA replication due to impaired binding to both ssDNA and primase. In view of these findings, we propose that DnaC controls the ability of DnaB to interact with primase by modifying the conformation of the NTD of DnaB.
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Affiliation(s)
- Magdalena M Felczak
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Sundari Chodavarapu
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
| | - Jon M Kaguni
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319
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50
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Li YC, Naveen V, Lin MG, Hsiao CD. Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein. J Biol Chem 2017; 292:15744-15757. [PMID: 28808061 PMCID: PMC5612107 DOI: 10.1074/jbc.m117.792002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/08/2017] [Indexed: 11/06/2022] Open
Abstract
The DnaB primosomal protein from Gram-positive bacteria plays a key role in DNA replication and restart as a loader protein for the recruitment of replisome cascade proteins. Previous investigations have established that DnaB is composed of an N-terminal domain, a middle domain, and a C-terminal domain. However, structural evidence for how DnaB functions at the atomic level is lacking. Here, we report the crystal structure of DnaB, encompassing the N-terminal and middle domains (residues 1-300), from Geobacillus stearothermophilus (GstDnaB1-300) at 2.8 Å resolution. Our structure revealed that GstDnaB1-300 forms a tetramer with two basket-like architectures, a finding consistent with those from solution studies using analytical ultracentrifugation. Furthermore, our results from both GST pulldown assays and analytical ultracentrifugation show that GstDnaB1-300 is sufficient to form a complex with PriA, the primosomal reinitiation protein. Moreover, with the aid of small angle X-ray scattering experiments, we also determined the structural envelope of full-length DnaB (GstDnaBFL) in solution. These small angle X-ray scattering studies indicated that GstDnaBFL has an elongated conformation and that the protruding density envelopes originating from GstDnaB1-300 could completely accommodate the GstDnaB C-terminal domain (residues 301-461). Taken together with biochemical assays, our results suggest that GstDnaB uses different domains to distinguish the PriA interaction and single-stranded DNA binding. These findings can further extend our understanding of primosomal assembly in replication restart.
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Affiliation(s)
- Yi-Ching Li
- From the Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan and
| | - Vankadari Naveen
- From the Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan and
| | - Min-Guan Lin
- From the Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan and
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- From the Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan and
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