1
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Cezanne A, Foo S, Kuo YW, Baum B. The Archaeal Cell Cycle. Annu Rev Cell Dev Biol 2024; 40:1-23. [PMID: 38748857 DOI: 10.1146/annurev-cellbio-111822-120242] [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: 10/04/2024]
Abstract
Since first identified as a separate domain of life in the 1970s, it has become clear that archaea differ profoundly from both eukaryotes and bacteria. In this review, we look across the archaeal domain and discuss the diverse mechanisms by which archaea control cell cycle progression, DNA replication, and cell division. While the molecular and cellular processes archaea use to govern these critical cell biological processes often differ markedly from those described in bacteria and eukaryotes, there are also striking similarities that highlight both unique and common principles of cell cycle control across the different domains of life. Since much of the eukaryotic cell cycle machinery has its origins in archaea, exploration of the mechanisms of archaeal cell division also promises to illuminate the evolution of the eukaryotic cell cycle.
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Affiliation(s)
- Alice Cezanne
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom; , , ,
| | - Sherman Foo
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom; , , ,
| | - Yin-Wei Kuo
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom; , , ,
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom; , , ,
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2
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Liman GLS, Lennon CW, Mandley JL, Galyon AM, Zatopek KM, Gardner AF, Santangelo TJ. Intein splicing efficiency and RadA levels can control the mode of archaeal DNA replication. SCIENCE ADVANCES 2024; 10:eadp4995. [PMID: 39292776 PMCID: PMC11409957 DOI: 10.1126/sciadv.adp4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/08/2024] [Indexed: 09/20/2024]
Abstract
Inteins (intervening proteins), mobile genetic elements removed through protein splicing, often interrupt proteins required for DNA replication, recombination, and repair. An abundance of in vitro evidence implies that inteins may act as regulatory elements, whereby reduced splicing inhibits production of the mature protein lacking the intein, but in vivo evidence of regulatory intein excision in the native host is absent. The model archaeon Thermococcus kodakarensis encodes 15 inteins, and we establish the impacts of intein splicing inhibition on host physiology and replication in vivo. We report that a decrease in intein splicing efficiency of the recombinase RadA, a Rad51/RecA homolog, has widespread physiological consequences, including a general growth defect, increased sensitivity to DNA damage, and a switch in the mode of DNA replication from recombination-dependent replication toward origin-dependent replication.
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Affiliation(s)
- Geraldy L. S. Liman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Jaylin L. Mandley
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Alina M. Galyon
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | | | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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3
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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4
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Juhas M. The World of Microorganisms. BRIEF LESSONS IN MICROBIOLOGY 2023:1-16. [DOI: 10.1007/978-3-031-29544-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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5
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Marín‐Tovar Y, Serrano‐Posada H, Díaz‐Vilchis A, Rudiño‐Piñera E. PCNA from
Thermococcus gammatolerans
: A protein involved in chromosomal
DNA
metabolism intrinsically resistant at high levels of ionizing radiation. Proteins 2022; 90:1684-1698. [DOI: 10.1002/prot.26346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Yerli Marín‐Tovar
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
| | - Hugo Serrano‐Posada
- Consejo Nacional de Ciencia y Tecnología (CONACyT), Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ Universidad de Colima Colima Mexico
| | - Adelaida Díaz‐Vilchis
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
| | - Enrique Rudiño‐Piñera
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos Instituto de Biotecnología (IBt), Universidad Nacional Autónoma de México (UNAM) Cuernavaca Mexico
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6
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Huang QY, Song D, Wang WW, Peng L, Chen HF, Xiao X, Liu XP. Mechanism Underlying the Bypass of Apurinic/Pyrimidinic Site Analogs by Sulfolobus acidocaldarius DNA Polymerase IV. Int J Mol Sci 2022; 23:ijms23052729. [PMID: 35269871 PMCID: PMC8910976 DOI: 10.3390/ijms23052729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/10/2022] Open
Abstract
The spontaneous depurination of genomic DNA occurs frequently and generates apurinic/pyrimidinic (AP) site damage that is mutagenic or lethal to cells. Error-prone DNA polymerases are specifically responsible for the translesion synthesis (TLS) of specific DNA damage, such as AP site damage, generally with relatively low fidelity. The Y-family DNA polymerases are the main error-prone DNA polymerases, and they employ three mechanisms to perform TLS, including template-skipping, dNTP-stabilized misalignment, and misincorporation-misalignment. The bypass mechanism of the dinB homolog (Dbh), an archaeal Y-family DNA polymerase from Sulfolobus acidocaldarius, is unclear and needs to be confirmed. In this study, we show that the Dbh primarily uses template skipping accompanied by dNTP-stabilized misalignment to bypass AP site analogs, and the incorporation of the first nucleotide across the AP site is the most difficult. Furthermore, based on the reported crystal structures, we confirmed that three conserved residues (Y249, R333, and I295) in the little finger (LF) domain and residue K78 in the palm subdomain of the catalytic core domain are very important for TLS. These results deepen our understanding of how archaeal Y-family DNA polymerases deal with intracellular AP site damage and provide a biochemical basis for elucidating the intracellular function of these polymerases.
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Affiliation(s)
- Qin-Ying Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Wei-Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Li Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
- Correspondence: (X.X.); (X.-P.L.)
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; (Q.-Y.H.); (D.S.); (W.-W.W.); (L.P.); (H.-F.C.)
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
- Correspondence: (X.X.); (X.-P.L.)
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7
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Grogan DW. Editorial: Mechanisms of Preservation and Change in Archaeal Genomes. Front Microbiol 2021; 12:722509. [PMID: 34394067 PMCID: PMC8358315 DOI: 10.3389/fmicb.2021.722509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dennis W Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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8
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Oki K, Yamagami T, Nagata M, Mayanagi K, Shirai T, Adachi N, Numata T, Ishino S, Ishino Y. DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen. Nucleic Acids Res 2021; 49:4599-4612. [PMID: 33849056 PMCID: PMC8096248 DOI: 10.1093/nar/gkab243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
The eukaryotic replisome is comprised of three family-B DNA polymerases (Polα, δ and ϵ). Polα forms a stable complex with primase to synthesize short RNA-DNA primers, which are subsequently elongated by Polδ and Polϵ in concert with proliferating cell nuclear antigen (PCNA). In some species of archaea, family-D DNA polymerase (PolD) is the only DNA polymerase essential for cell viability, raising the question of how it alone conducts the bulk of DNA synthesis. We used a hyperthermophilic archaeon, Thermococcus kodakarensis, to demonstrate that PolD connects primase to the archaeal replisome before interacting with PCNA. Whereas PolD stably connects primase to GINS, a component of CMG helicase, cryo-EM analysis indicated a highly flexible PolD-primase complex. A conserved hydrophobic motif at the C-terminus of the DP2 subunit of PolD, a PIP (PCNA-Interacting Peptide) motif, was critical for the interaction with primase. The dissociation of primase was induced by DNA-dependent binding of PCNA to PolD. Point mutations in the alternative PIP-motif of DP2 abrogated the molecular switching that converts the archaeal replicase from de novo to processive synthesis mode.
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Affiliation(s)
- Keisuke Oki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kouta Mayanagi
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan
| | - Naruhiko Adachi
- Structure Biology Research Center, Institute of Materials Structural Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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9
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Li H, Zheng F, O'Donnell M. Water skating: How polymerase sliding clamps move on DNA. FEBS J 2021; 288:7256-7262. [PMID: 33523561 DOI: 10.1111/febs.15740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/19/2021] [Accepted: 01/24/2021] [Indexed: 11/30/2022]
Abstract
Polymerase sliding clamps are ring-shaped proteins that encircle duplex DNA and hold polymerases to DNA for high processivity during synthesis. The crystal structure of clamp-DNA complex reveals that the DNA is highly tilted through the clamp with extensive interaction with the clamp inner surface. In contrast to the tilted clamp-DNA interaction without DNA polymerases, recent structures of replicative polymerases of bacteria, eukaryotes, and archaea that are bound to the clamp and DNA show that the polymerase positions DNA straight through the clamp without direct protein-DNA contacts. Instead, the clamp-to-DNA interaction is mediated by one or two layers of water. Hence, clamps 'water skate' on DNA during function with replicative polymerases from all domains of life, providing a nearly frictionless bearing for fast and processive DNA synthesis.
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Affiliation(s)
- Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Mike O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA.,HHMI, The Rockefeller University, New York, NY, USA
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10
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Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
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Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
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11
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Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA. Proc Natl Acad Sci U S A 2020; 117:30344-30353. [PMID: 33203675 PMCID: PMC7720213 DOI: 10.1073/pnas.2017637117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The structure of the eukaryotic chromosomal replicase, DNA polymerase (Pol) δ, was determined in complex with its cognate proliferating cell nuclear antigen (PCNA) sliding clamp on primed DNA. The results show that the Pol3 catalytic subunit binds atop the PCNA ring, and the two regulatory subunits of Pol δ, Pol31, and Pol32, are positioned off to the side of the Pol3 clamp. The catalytic Pol3 binds DNA and PCNA such as to thread the DNA straight through the circular PCNA clamp. Considering the large diameter of the PCNA clamp, there is room for water between DNA and the inner walls of PCNA, indicating the clamp “waterskates” on DNA during function with polymerase. The DNA polymerase (Pol) δ of Saccharomyces cerevisiae (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and functions in genome replication, repair, and recombination. Unique among DNA polymerases, the Pol3 catalytic subunit contains a 4Fe-4S cluster that may sense the cellular redox state. Here we report the 3.2-Å cryo-EM structure of S.c. Pol δ in complex with primed DNA, an incoming ddTTP, and the PCNA clamp. Unexpectedly, Pol δ binds only one subunit of the PCNA trimer. This singular yet extensive interaction holds DNA such that the 2-nm-wide DNA threads through the center of the 3-nm interior channel of the clamp without directly contacting the protein. Thus, a water-mediated clamp and DNA interface enables the PCNA clamp to “waterskate” along the duplex with minimum drag. Pol31 and Pol32 are positioned off to the side of the catalytic Pol3-PCNA-DNA axis. We show here that Pol31-Pol32 binds single-stranded DNA that we propose underlies polymerase recycling during lagging strand synthesis, in analogy to Escherichia coli replicase. Interestingly, the 4Fe-4S cluster in the C-terminal CysB domain of Pol3 forms the central interface to Pol31-Pol32, and this strategic location may explain the regulation of the oxidation state on Pol δ activity, possibly useful during cellular oxidative stress. Importantly, human cancer and other disease mutations map to nearly every domain of Pol3, suggesting that all aspects of Pol δ replication are important to human health and disease.
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12
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Darnell CL, Zheng J, Wilson S, Bertoli RM, Bisson-Filho AW, Garner EC, Schmid AK. The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea. mBio 2020; 11:e01007-20. [PMID: 32788376 PMCID: PMC7439475 DOI: 10.1128/mbio.01007-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022] Open
Abstract
Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. Here, we use genetics, functional genomics, and quantitative imaging to identify and characterize the novel CdrSL gene regulatory network in a model species of archaea. We demonstrate the central role of these ribbon-helix-helix family transcription factors in the regulation of cell division through specific transcriptional control of the gene encoding FtsZ2, a putative tubulin homolog. Using time-lapse fluorescence microscopy in live cells cultivated in microfluidics devices, we further demonstrate that FtsZ2 is required for cell division but not elongation. The cdrS-ftsZ2 locus is highly conserved throughout the archaeal domain, and the central function of CdrS in regulating cell division is conserved across hypersaline adapted archaea. We propose that the CdrSL-FtsZ2 transcriptional network coordinates cell division timing with cell growth in archaea.IMPORTANCE Healthy cell growth and division are critical for individual organism survival and species long-term viability. However, it remains unknown how cells of the domain Archaea maintain a healthy cell cycle. Understanding the archaeal cell cycle is of paramount evolutionary importance given that an archaeal cell was the host of the endosymbiotic event that gave rise to eukaryotes. Here, we identify and characterize novel molecular players needed for regulating cell division in archaea. These molecules dictate the timing of cell septation but are dispensable for growth between divisions. Timing is accomplished through transcriptional control of the cell division ring. Our results shed light on mechanisms underlying the archaeal cell cycle, which has thus far remained elusive.
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Affiliation(s)
| | - Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan M Bertoli
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Alexandre W Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy K Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
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13
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Varga M, Csályi K, Bertyák I, Menyhárd DK, Poole RJ, Cerveny KL, Kövesdi D, Barátki B, Rouse H, Vad Z, Hawkins TA, Stickney HL, Cavodeassi F, Schwarz Q, Young RM, Wilson SW. Tissue-Specific Requirement for the GINS Complex During Zebrafish Development. Front Cell Dev Biol 2020; 8:373. [PMID: 32548116 PMCID: PMC7270345 DOI: 10.3389/fcell.2020.00373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Efficient and accurate DNA replication is particularly critical in stem and progenitor cells for successful proliferation and survival. The replisome, an amalgam of protein complexes, is responsible for binding potential origins of replication, unwinding the double helix, and then synthesizing complimentary strands of DNA. According to current models, the initial steps of DNA unwinding and opening are facilitated by the CMG complex, which is composed of a GINS heterotetramer that connects Cdc45 with the mini-chromosome maintenance (Mcm) helicase. In this work, we provide evidence that in the absence of GINS function DNA replication is cell autonomously impaired, and we also show that gins1 and gins2 mutants exhibit elevated levels of apoptosis restricted to actively proliferating regions of the central nervous system (CNS). Intriguingly, our results also suggest that the rapid cell cycles during early embryonic development in zebrafish may not require the function of the canonical GINS complex as neither zygotic Gins1 nor Gins2 isoforms seem to be present during these stages.
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Affiliation(s)
- Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.,Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kitti Csályi
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Bertyák
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dóra K Menyhárd
- HAS-ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Richard J Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kara L Cerveny
- Biology Department, Reed College, Portland, OR, United States
| | - Dorottya Kövesdi
- Office of Supported Research Groups of the Hungarian Academy of Sciences, Budapest, Hungary.,Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Barátki
- Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Hannah Rouse
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Zsuzsa Vad
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom.,Institute of Medical and Biomedical Education, St. George's University of London, London, United Kingdom
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rodrigo M Young
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
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14
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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15
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Gong P, Lei P, Wang S, Zeng A, Lou H. Post-Translational Modifications Aid Archaeal Survival. Biomolecules 2020; 10:biom10040584. [PMID: 32290118 PMCID: PMC7226565 DOI: 10.3390/biom10040584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
- Correspondence: (P.G.); (H.L.)
| | - Ping Lei
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Ao Zeng
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
- Correspondence: (P.G.); (H.L.)
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16
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Abstract
Replicative DNA helicases are essential cellular enzymes that unwind duplex DNA in front of the replication fork during chromosomal DNA replication. Replicative helicases were discovered, beginning in the 1970s, in bacteria, bacteriophages, viruses, and eukarya, and, in the mid-1990s, in archaea. This year marks the 20th anniversary of the first report on the archaeal replicative helicase, the minichromosome maintenance (MCM) protein. This minireview summarizes 2 decades of work on the archaeal MCM.
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17
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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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18
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Hogrel G, Lu Y, Laurent S, Henry E, Etienne C, Phung DK, Dulermo R, Bossé A, Pluchon PF, Clouet-d'Orval B, Flament D. Physical and functional interplay between PCNA DNA clamp and Mre11-Rad50 complex from the archaeon Pyrococcus furiosus. Nucleic Acids Res 2019; 46:5651-5663. [PMID: 29741662 PMCID: PMC6009593 DOI: 10.1093/nar/gky322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/18/2018] [Indexed: 01/10/2023] Open
Abstract
Several archaeal species prevalent in extreme environments are particularly exposed to factors likely to cause DNA damages. These include hyperthermophilic archaea (HA), living at temperatures >70°C, which arguably have efficient strategies and robust genome guardians to repair DNA damage threatening their genome integrity. In contrast to Eukarya and other archaea, homologous recombination appears to be a vital pathway in HA, and the Mre11–Rad50 complex exerts a broad influence on the initiation of this DNA damage response process. In a previous study, we identified a physical association between the Proliferating Cell Nuclear Antigen (PCNA) and the Mre11–Rad50 (MR) complex. Here, by performing co-immunoprecipitation and SPR analyses, we identified a short motif in the C- terminal portion of Pyrococcus furiosus Mre11 involved in the interaction with PCNA. Through this work, we revealed a PCNA-interaction motif corresponding to a variation on the PIP motif theme which is conserved among Mre11 sequences of Thermococcale species. Additionally, we demonstrated functional interplay in vitro between P. furiosus PCNA and MR enzymatic functions in the DNA end resection process. At physiological ionic strength, PCNA stimulates MR nuclease activities for DNA end resection and promotes an endonucleolytic incision proximal to the 5′ strand of double strand DNA break.
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Affiliation(s)
- Gaëlle Hogrel
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Yang Lu
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Etienne Henry
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Clarisse Etienne
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Duy Khanh Phung
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Rémi Dulermo
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Pierre-François Pluchon
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Béatrice Clouet-d'Orval
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
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19
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Coleman GA, Pancost RD, Williams TA. Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting. Genome Biol Evol 2019; 11:883-898. [PMID: 30753429 PMCID: PMC6431249 DOI: 10.1093/gbe/evz034] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
One of the key differences between Bacteria and Archaea is their canonical membrane phospholipids, which are synthesized by distinct biosynthetic pathways with nonhomologous enzymes. This “lipid divide” has important implications for the early evolution of cells and the type of membrane phospholipids present in the last universal common ancestor. One of the main challenges in studies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved. This poses major challenges for traditional rooting methods because the only available outgroups are distantly related. Here, we address this issue by using the best available substitution models for single-gene trees, by expanding our analyses to the diversity of uncultivated prokaryotes recently revealed by environmental genomics, and by using two complementary approaches to rooting that do not depend on outgroups. Consistent with some previous analyses, our rooted gene trees support extensive interdomain horizontal transfer of membrane phospholipid biosynthetic genes, primarily from Archaea to Bacteria. They also suggest that the capacity to make archaeal-type membrane phospholipids was already present in last universal common ancestor.
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Affiliation(s)
- Gareth A Coleman
- School of Biological Sciences, University of Bristol, United Kingdom
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
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20
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Gardner AF, Kelman Z. Editorial: The DNA Replication Machinery as Therapeutic Targets. Front Mol Biosci 2019; 6:35. [PMID: 31179285 PMCID: PMC6537510 DOI: 10.3389/fmolb.2019.00035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/02/2019] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, United States.,National Institute of Standards and Technology, Rockville, MD, United States
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21
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The archaeal RecJ-like proteins: nucleases and ex-nucleases with diverse roles in replication and repair. Emerg Top Life Sci 2018; 2:493-501. [PMID: 33525824 DOI: 10.1042/etls20180017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 11/17/2022]
Abstract
RecJ proteins belong to the DHH superfamily of phosphoesterases that has members in all three domains of life. In bacteria, the archetypal RecJ is a 5' → 3' ssDNA exonuclease that functions in homologous recombination, base excision repair and mismatch repair, while in eukaryotes, the RecJ-like protein Cdc45 (which has lost its nuclease activity) is a key component of the CMG (Cdc45-MCM-GINS) complex, the replicative DNA helicase that unwinds double-stranded DNA at the replication fork. In archaea, database searching identifies genes encoding one or more RecJ family proteins in almost all sequenced genomes. Biochemical analysis has confirmed that some but not all of these proteins are components of archaeal CMG complexes and has revealed a surprising diversity in mode of action and substrate preference. In addition to this, some archaea encode catalytically inactive RecJ-like proteins, and others a mix of active and inactive proteins, with the inactive proteins being confined to structural roles only. Here, I summarise current knowledge of the structure and function of the archaeal RecJ-like proteins, focusing on similarities and differences between proteins from different archaeal species, between proteins within species and between the archaeal proteins and their bacterial and eukaryotic relatives. Models for RecJ-like function are described and key areas for further study highlighted.
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22
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Zatopek KM, Gardner AF, Kelman Z. Archaeal DNA replication and repair: new genetic, biophysical and molecular tools for discovering and characterizing enzymes, pathways and mechanisms. FEMS Microbiol Rev 2018; 42:477-488. [PMID: 29912309 DOI: 10.1093/femsre/fuy017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/17/2018] [Indexed: 01/03/2023] Open
Abstract
DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, archaea, bacteria and eukarya, the proteins and complexes involved differ. The genetic and biophysical tools developed for archaea in the last several years have accelerated the study of DNA replication and repair in this domain. In this review, the current knowledge of DNA replication and repair processes in archaea will be summarized, with emphasis on the contribution of genetics and other recently developed biophysical and molecular tools, including capillary gel electrophoresis, next-generation sequencing and single-molecule approaches. How these new tools will continue to drive archaeal DNA replication and repair research will also be discussed.
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Affiliation(s)
| | | | - Zvi Kelman
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
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23
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Kelman LM, Kelman Z. Do Archaea Need an Origin of Replication? Trends Microbiol 2018; 26:172-174. [PMID: 29268981 DOI: 10.1016/j.tim.2017.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 11/16/2022]
Abstract
Chromosomal DNA replication starts at a specific region called an origin of replication. Until recently, all organisms were thought to require origins to replicate their chromosomes. It was recently discovered that some archaeal species do not utilize origins of replication under laboratory growth conditions.
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Affiliation(s)
- Lori M Kelman
- Program in Biotechnology, Montgomery College, 20200 Observation Drive, Germantown, MD 20876, USA
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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24
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Willkomm S, Makarova KS, Grohmann D. DNA silencing by prokaryotic Argonaute proteins adds a new layer of defense against invading nucleic acids. FEMS Microbiol Rev 2018; 42:376-387. [PMID: 29579258 PMCID: PMC5995195 DOI: 10.1093/femsre/fuy010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 01/05/2023] Open
Abstract
Argonaute (Ago) proteins are encoded in all three domains of life and are responsible for the regulation of intracellular nucleic acid levels. Whereas some Ago variants are able to cleave target nucleic acids by their endonucleolytic activity, others only bind to their target nucleic acids while target cleavage is mediated by other effector proteins. Although all Ago proteins show a high degree of overall structural homology, the nature of the nucleic acid binding partners differs significantly. Recent structural and functional data have provided intriguing new insights into the mechanisms of archaeal and bacterial Ago variants demonstrating the mechanistic diversity within the prokaryotic Ago family with astonishing differences in nucleic acid selection and nuclease specificity. In this review, we provide an overview of the structural organisation of archaeal Ago variants and discuss the current understanding of their biological functions that differ significantly from their eukaryotic counterparts.
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Affiliation(s)
- Sarah Willkomm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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25
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Andis NM, Sausen CW, Alladin A, Bochman ML. The WYL Domain of the PIF1 Helicase from the Thermophilic Bacterium Thermotoga elfii is an Accessory Single-Stranded DNA Binding Module. Biochemistry 2018; 57:1108-1118. [PMID: 29341597 DOI: 10.1021/acs.biochem.7b01233] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PIF1 family helicases are conserved from bacteria to man. With the exception of the well-studied yeast PIF1 helicases (e.g., ScPif1 and ScRrm3), however, very little is known about how these enzymes help maintain genome stability. Indeed, we lack a basic understanding of the protein domains found N- and C-terminal to the characteristic central PIF1 helicase domain in these proteins. Here, using chimeric constructs, we show that the ScPif1 and ScRrm3 helicase domains are interchangeable and that the N-terminus of ScRrm3 is important for its function in vivo. This suggests that PIF1 family helicases evolved functional modules fused to a generic motor domain. To investigate this hypothesis, we characterized the biochemical activities of the PIF1 helicase from the thermophilic bacterium Thermotoga elfii (TePif1), which contains a C-terminal WYL domain of unknown function. Like helicases from other thermophiles, recombinant TePif1 was easily prepared, thermostable in vitro, and displayed activities similar to its eukaryotic homologues. We also found that the WYL domain was necessary for high-affinity single-stranded DNA (ssDNA) binding and affected both ATPase and helicase activities. Deleting the WYL domain from TePif1 or mutating conserved residues in the predicted ssDNA binding site uncoupled ATPase activity and DNA unwinding, leading to higher rates of ATP hydrolysis but less efficient DNA helicase activity. Our findings suggest that the domains of unknown function found in eukaryotic PIF1 helicases may also confer functional specificity and additional activities to these enzymes, which should be investigated in future work.
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Affiliation(s)
- Nicholas M Andis
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Christopher W Sausen
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Ashna Alladin
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
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26
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Marques CA, McCulloch R. Conservation and Variation in Strategies for DNA Replication of Kinetoplastid Nuclear Genomes. Curr Genomics 2018; 19:98-109. [PMID: 29491738 PMCID: PMC5814967 DOI: 10.2174/1389202918666170815144627] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/19/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Introduction: Understanding how the nuclear genome of kinetoplastid parasites is replicated received experimental stimulus from sequencing of the Leishmania major, Trypanosoma brucei and Trypanosoma cruzi genomes around 10 years ago. Gene annotations suggested key players in DNA replication initiation could not be found in these organisms, despite considerable conservation amongst characterised eukaryotes. Initial studies that indicated trypanosomatids might possess an archaeal-like Origin Recognition Complex (ORC), composed of only a single factor termed ORC1/CDC6, have been supplanted by the more recent identification of an ORC in T. brucei. However, the constituent subunits of T. brucei ORC are highly diverged relative to other eukaryotic ORCs and the activity of the complex appears subject to novel, positive regulation. The availability of whole genome sequences has also allowed the deployment of genome-wide strategies to map DNA replication dynamics, to date in T. brucei and Leishmania. ORC1/CDC6 binding and function in T. brucei displays pronounced overlap with the unconventional organisation of gene expression in the genome. Moreover, mapping of sites of replication initiation suggests pronounced differences in replication dynamics in Leishmania relative to T. brucei. Conclusion: Here we discuss what implications these emerging data may have for parasite and eukaryotic biology of DNA replication.
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Affiliation(s)
- Catarina A Marques
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, Dow Street, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, University of Glasgow, Glasgow, G12 8TA, UK
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27
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Eun YJ, Ho PY, Kim M, LaRussa S, Robert L, Renner LD, Schmid A, Garner E, Amir A. Archaeal cells share common size control with bacteria despite noisier growth and division. Nat Microbiol 2017; 3:148-154. [PMID: 29255255 DOI: 10.1038/s41564-017-0082-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 11/21/2017] [Indexed: 01/23/2023]
Abstract
In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model 2-6 ). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution. Given that archaeal cells share characteristics with both bacteria and eukaryotes, we investigated whether and how archaeal cells exhibit control over cell size. To this end, we developed a soft-lithography method of growing the archaeal cells to enable quantitative time-lapse imaging and single-cell analysis, which would be useful for other microorganisms. Using this method, we demonstrated that Halobacterium salinarum, a hypersaline-adapted archaeal organism, grows exponentially at the single-cell level and maintains a narrow-size distribution by adding a constant length between cell division events. Interestingly, the archaeal cells exhibited greater variability in cell division placement and exponential growth rate across individual cells in a population relative to those observed in Escherichia coli 6-9 . Here, we present a theoretical framework that explains how these larger fluctuations in archaeal cell cycle events contribute to cell size variability and control.
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Affiliation(s)
- Ye-Jin Eun
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Po-Yi Ho
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Minjeong Kim
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | | | - Lydia Robert
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France.,AgroParisTech, UMR Micalis, Jouy-en-Josas, France.,Laboratoire Jean Perrin, UPMC-CNRS, UMR 8237, UPMC, Paris, France
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Amy Schmid
- Biology Department, Center for Genomics and Computational Biology, Duke University, Durham, NC, USA.
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA.
| | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
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28
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Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef. Sci Rep 2017; 7:16949. [PMID: 29209094 PMCID: PMC5717133 DOI: 10.1038/s41598-017-17306-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/20/2017] [Indexed: 01/03/2023] Open
Abstract
RecJ was originally identified in Escherichia coli and plays an important role in the DNA repair and recombination pathways. Thermococcus kodakarensis, a hyperthermophilic archaeon, has two RecJ-like nucleases. These proteins are designated as GAN (GINS-associated nuclease) and HAN (Hef-associated nuclease), based on the protein they interact with. GAN is probably a counterpart of Cdc45 in the eukaryotic CMG replicative helicase complex. HAN is considered mainly to function with Hef for restoration of the stalled replication fork. In this study, we characterized HAN to clarify its functions in Thermococcus cells. HAN showed single-strand specific 3′ to 5′ exonuclease activity, which was stimulated in the presence of Hef. A gene disruption analysis revealed that HAN was non-essential for viability, but the ΔganΔhan double mutant did not grow under optimal conditions at 85 °C. This deficiency was not fully recovered by introducing the mutant han gene, encoding the nuclease-deficient HAN protein, back into the genome. These results suggest that the unstable replicative helicase complex without GAN performs ineffective fork progression, and thus the stalled fork repair system including HAN becomes more important. The nuclease activity of HAN is required for the function of this protein in T. kodakarensis.
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Demey LM, Miller CR, Manzella MP, Spurbeck RR, Sandhu SK, Reguera G, Kashefi K. The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction. Stand Genomic Sci 2017; 12:47. [PMID: 28814988 PMCID: PMC5556600 DOI: 10.1186/s40793-017-0260-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023] Open
Abstract
Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.
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Affiliation(s)
- Lucas M. Demey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Caitlin R. Miller
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Michael P Manzella
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
- Present address: Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Rachel R. Spurbeck
- Applied Genomics and Biology Group, Department of CBRNE Defense, Battelle Memorial Institute, Columbus, OH USA
| | | | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis. J Bacteriol 2017; 199:JB.00141-17. [PMID: 28416706 DOI: 10.1128/jb.00141-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/07/2017] [Indexed: 11/20/2022] Open
Abstract
Many aspects of and factors required for DNA replication are conserved across all three domains of life, but there are some significant differences surrounding lagging-strand synthesis. In Archaea, a 5'-to-3' exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS was identified and designated GAN (for GINS-associated nuclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation, and as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, and GINS) replication complex. We demonstrate here that, individually, either Fen1 or GAN can be deleted, with no discernible effects on viability and growth. However, deletion of both Fen1 and GAN was not possible, consistent with both enzymes catalyzing the same step in primer removal from Okazaki fragments in vivo RNase HII has also been proposed to participate in primer processing during Okazaki fragment maturation. Strains with both Fen1 and RNase HII deleted grew well. GAN activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it was not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. The ability to delete GAN demonstrates that GAN is not required for the activation or stability of the archaeal MCM replicative helicase.IMPORTANCE The mechanisms used to remove primer sequences from Okazaki fragments during lagging-strand DNA replication differ in the biological domains. Bacteria use the exonuclease activity of DNA polymerase I, whereas eukaryotes and archaea encode a flap endonuclease (Fen1) that cleaves displaced primer sequences. RNase HII and the GINS-associated exonuclease GAN have also been hypothesized to assist in primer removal in Archaea Here we demonstrate that in Thermococcus kodakarensis, either Fen1 or GAN activity is sufficient for viability. Furthermore, GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN.
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Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2. J Virol 2017; 91:JVI.00486-17. [PMID: 28424282 DOI: 10.1128/jvi.00486-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Viral factories are compartmentalized centers for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by prototypical archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in the model archaeon Sulfolobus This rod-shaped virus belongs to the viral family Rudiviridae, carrying linear double-stranded DNA (dsDNA) genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus. Furthermore, we show that of the four host DNA polymerases (DNA polymerase I [Dpo1] to Dpo4), only Dpo1 participates in viral DNA synthesis. This constitutes the first report of the formation of a viral replication focus in archaeal cells, suggesting that organization of viral replication in foci is a widespread strategy employed by viruses of the three domains of life.IMPORTANCE The organization of viral replication in foci or viral factories has been mostly described for different eukaryotic viruses and for several bacteriophages. This work constitutes the first report of the formation of a viral replication center by a virus infecting members of the Archaea domain.
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Yurieva O, O'Donnell M. Reconstitution of a eukaryotic replisome reveals the mechanism of asymmetric distribution of DNA polymerases. Nucleus 2017; 7:360-8. [PMID: 27416113 PMCID: PMC5039002 DOI: 10.1080/19491034.2016.1205774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotes require 3 DNA polymerases for normal replisome operations, DNA polymerases (Pol) α, delta and epsilon. Recent biochemical and structural studies support the asymmetric use of these polymerases on the leading and lagging strands. Pol epsilon interacts with the 11-subunit CMG helicase, forming a 15-protein leading strand complex that acts processively in leading strand synthesis in vitro, but Pol epsilon is inactive on the lagging strand. The opposite results are observed for Pol delta with CMG. Pol delta is highly active on the lagging strand in vitro, but has only feeble activity with CMG on the leading strand. Pol α also functions with CMG to prime both strands, and is even capable of extending both strands with CMG present. However, extensive DNA synthesis by Pol α is sharply curtailed by the presence of either Pol epsilon or Pol delta, which limits the role of the low fidelity Pol α to the initial priming of synthesis.
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Affiliation(s)
- Olga Yurieva
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
| | - Mike O'Donnell
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
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Prioleau MN. G-Quadruplexes and DNA Replication Origins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:273-286. [DOI: 10.1007/978-981-10-6955-0_13] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Bell SD. Initiation of DNA Replication in the Archaea. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:99-115. [PMID: 29357055 DOI: 10.1007/978-981-10-6955-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. While some archaea possess a bacterial-like mode of DNA replication with single origins of replication per chromosome, the majority of species characterized to date possess chromosomes with multiple replication origins. Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. Recent work has begun to shed light on the mechanisms of replication initiation in these organisms.
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Affiliation(s)
- Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Department of Biology, Indiana University, Bloomington, IN, USA.
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Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
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Affiliation(s)
- Phillip J. Brumm
- C5-6 Technologies LLCFitchburg, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Frank T. Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of MarylandBaltimore, MD, USA
| | - David A. Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
- Varigen Biosciences CorporationMadison, WI, USA
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Xu Y, Gristwood T, Hodgson B, Trinidad JC, Albers SV, Bell SD. Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM. Proc Natl Acad Sci U S A 2016; 113:13390-13395. [PMID: 27821767 PMCID: PMC5127375 DOI: 10.1073/pnas.1613825113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.
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Affiliation(s)
- Yuli Xu
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
- Biology Department, Indiana University, Bloomington, IN 47405
| | - Tamzin Gristwood
- Sir William Dunn School of Pathology, Oxford OX13RE, United Kingdom
| | - Ben Hodgson
- Sir William Dunn School of Pathology, Oxford OX13RE, United Kingdom
| | | | - Sonja-Verena Albers
- Max Planck Institute für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Stephen D Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405;
- Biology Department, Indiana University, Bloomington, IN 47405
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Archaeal DNA Polymerase-B as a DNA Template Guardian: Links between Polymerases and Base/Alternative Excision Repair Enzymes in Handling the Deaminated Bases Uracil and Hypoxanthine. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1510938. [PMID: 27721668 PMCID: PMC5045986 DOI: 10.1155/2016/1510938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 02/03/2023]
Abstract
In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine. Here it is demonstrated that binding of Pol-D to primer-templates containing deaminated bases inhibits the activity of UDG, EndoV, and EndoQ. Similarly Pol-B almost completely turns off EndoQ, extending earlier work that demonstrated that Pol-B reduces catalysis by UDG and EndoV. Pol-B was observed to be a more potent inhibitor of the enzymes compared to Pol-D. Although Pol-D is directly inhibited by template strand uracil, the presence of Pol-B further suppresses any residual activity of Pol-D, to near-zero levels. The results are compatible with Pol-D acting as the replicative polymerase and Pol-B functioning primarily as a guardian preventing deaminated base-induced DNA mutations.
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Fundamental Characteristics of AAA+ Protein Family Structure and Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:9294307. [PMID: 27703410 PMCID: PMC5039278 DOI: 10.1155/2016/9294307] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022]
Abstract
Many complex cellular events depend on multiprotein complexes known as molecular machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to the generation of mechanical force. Members of the AAA+ ATPase superfamily (ATPases Associated with various cellular Activities) are critical components of many molecular machines. AAA+ proteins are defined by conserved modules that precisely position the active site elements of two adjacent subunits to catalyze ATP hydrolysis. In many cases, AAA+ proteins form a ring structure that translocates a polymeric substrate through the central channel using specialized loops that project into the central channel. We discuss the major features of AAA+ protein structure and function with an emphasis on pivotal aspects elucidated with archaeal proteins.
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Abstract
DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.
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Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Superieure (IBENS), Ecole Normale Superieure, PSL Research University, Paris, France
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40
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Abellón-Ruiz J, Waldron KJ, Connolly BA. Archaeoglobus Fulgidus DNA Polymerase D: A Zinc-Binding Protein Inhibited by Hypoxanthine and Uracil. J Mol Biol 2016; 428:2805-13. [PMID: 27320386 PMCID: PMC4942837 DOI: 10.1016/j.jmb.2016.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/28/2016] [Accepted: 06/13/2016] [Indexed: 02/03/2023]
Abstract
Archaeal family-D DNA polymerases (Pol-D) comprise a small (DP1) proofreading subunit and a large (DP2) polymerase subunit. Pol-D is one of the least studied polymerase families, and this publication investigates the enzyme from Archaeoglobus fulgidus (Afu Pol-D). The C-terminal region of DP2 contains two conserved cysteine clusters, and their roles are investigated using site-directed mutagenesis. The cluster nearest the C terminus is essential for polymerase activity, and the cysteines are shown to serve as ligands for a single, critical Zn(2+) ion. The cysteines farthest from the C terminal were not required for activity, and a role for these amino acids has yet to be defined. Additionally, it is shown that Afu Pol-D activity is slowed by the template strand hypoxanthine, extending previous results that demonstrated inhibition by uracil. Hypoxanthine was a weaker inhibitor than uracil. Investigations with isolated DP2, which has a measurable polymerase activity, localised the deaminated base binding site to this subunit. Uracil and hypoxanthine slowed Afu Pol-D "in trans", that is, a copied DNA strand could be inhibited by a deaminated base in the alternate strand of a replication fork. The error rate of Afu Pol-D, measured in vitro, was 0.24×10(-5), typical for a polymerase that has been proposed to carry out genome replication in the Archaea. Deleting the 3'-5' proofreading exonuclease activity reduced fidelity twofold. The results presented in this publication considerably increase our knowledge of Pol-D.
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Affiliation(s)
- Javier Abellón-Ruiz
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin J Waldron
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Bernard A Connolly
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
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Altieri AS, Ladner JE, Li Z, Robinson H, Sallman ZF, Marino JP, Kelman Z. A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic Acids Res 2016; 44:6232-41. [PMID: 27141962 PMCID: PMC5181682 DOI: 10.1093/nar/gkw351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/19/2016] [Indexed: 12/18/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.
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Affiliation(s)
- Amanda S Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Jane E Ladner
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zhuo Li
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen, Fujian 361005, China
| | - Howard Robinson
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Zahur F Sallman
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Marques CA, Tiengwe C, Lemgruber L, Damasceno JD, Scott A, Paape D, Marcello L, McCulloch R. Diverged composition and regulation of the Trypanosoma brucei origin recognition complex that mediates DNA replication initiation. Nucleic Acids Res 2016; 44:4763-84. [PMID: 26951375 PMCID: PMC4889932 DOI: 10.1093/nar/gkw147] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/01/2016] [Indexed: 01/14/2023] Open
Abstract
Initiation of DNA replication depends upon recognition of genomic sites, termed origins, by AAA+ ATPases. In prokaryotes a single factor binds each origin, whereas in eukaryotes this role is played by a six-protein origin recognition complex (ORC). Why eukaryotes evolved a multisubunit initiator, and the roles of each component, remains unclear. In Trypanosoma brucei, an ancient unicellular eukaryote, only one ORC-related initiator, TbORC1/CDC6, has been identified by sequence homology. Here we show that three TbORC1/CDC6-interacting factors also act in T. brucei nuclear DNA replication and demonstrate that TbORC1/CDC6 interacts in a high molecular complex in which a diverged Orc4 homologue and one replicative helicase subunit can also be found. Analysing the subcellular localization of four TbORC1/CDC6-interacting factors during the cell cycle reveals that one factor, TbORC1B, is not a static constituent of ORC but displays S-phase restricted nuclear localization and expression, suggesting it positively regulates replication. This work shows that ORC architecture and regulation are diverged features of DNA replication initiation in T. brucei, providing new insight into this key stage of eukaryotic genome copying.
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Affiliation(s)
- Catarina A Marques
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Calvin Tiengwe
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Leandro Lemgruber
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Jeziel D Damasceno
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Alan Scott
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Daniel Paape
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Lucio Marcello
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
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Abstract
The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some "gears" of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the "replisome" machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus.
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Affiliation(s)
- Nina Y Yao
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and
| | - Mike E O'Donnell
- a DNA Replication Laboratory, The Rockefeller University , New York , NY , USA and.,b Howard Hughes Medical Institute, The Rockefeller University , New York , NY , USA
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44
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Xia Y, Niu Y, Cui J, Fu Y, Chen XS, Lou H, Cao Q. The Helicase Activity of Hyperthermophilic Archaeal MCM is Enhanced at High Temperatures by Lysine Methylation. Front Microbiol 2015; 6:1247. [PMID: 26617586 PMCID: PMC4639711 DOI: 10.3389/fmicb.2015.01247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022] Open
Abstract
Lysine methylation and methyltransferases are widespread in the third domain of life, archaea. Nevertheless, the effects of methylation on archaeal proteins wait to be defined. Here, we report that recombinant sisMCM, an archaeal homolog of Mcm2-7 eukaryotic replicative helicase, is methylated by aKMT4 in vitro. Mono-methylation of these lysine residues occurs coincidently in the endogenous sisMCM protein purified from the hyperthermophilic Sulfolobus islandicus cells as indicated by mass spectra. The helicase activity of mini-chromosome maintenance (MCM) is stimulated by methylation, particularly at temperatures over 70°C. The methylated MCM shows optimal DNA unwinding activity after heat-treatment between 76 and 82°C, which correlates well with the typical growth temperatures of hyperthermophilic Sulfolobus. After methylation, the half life of MCM helicase is dramatically extended at 80°C. The methylated sites are located on the accessible protein surface, which might modulate the intra- and inter- molecular interactions through changing the hydrophobicity and surface charge. Furthermore, the methylation-mimic mutants of MCM show heat resistance helicase activity comparable to the methylated MCM. These data provide the biochemical evidence that posttranslational modifications such as methylation may enhance kinetic stability of proteins under the elevated growth temperatures of hyperthermophilic archaea.
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Affiliation(s)
- Yisui Xia
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Yanling Niu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Jiamin Cui
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Yang Fu
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles CA, USA ; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles CA, USA ; Department of Chemistry, University of Southern California, Los Angeles CA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles CA, USA ; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles CA, USA ; Department of Chemistry, University of Southern California, Los Angeles CA, USA
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University Beijing, China
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45
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Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:942605. [PMID: 26146487 PMCID: PMC4471258 DOI: 10.1155/2015/942605] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/21/2015] [Indexed: 11/17/2022]
Abstract
Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.
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46
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Greenough L, Kelman Z, Gardner AF. The roles of family B and D DNA polymerases in Thermococcus species 9°N Okazaki fragment maturation. J Biol Chem 2015; 290:12514-22. [PMID: 25814667 PMCID: PMC4432273 DOI: 10.1074/jbc.m115.638130] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 01/03/2023] Open
Abstract
During replication, Okazaki fragment maturation is a fundamental process that joins discontinuously synthesized DNA fragments into a contiguous lagging strand. Efficient maturation prevents repeat sequence expansions, small duplications, and generation of double-stranded DNA breaks. To address the components required for the process in Thermococcus, Okazaki fragment maturation was reconstituted in vitro using purified proteins from Thermococcus species 9°N or cell extracts. A dual color fluorescence assay was developed to monitor reaction substrates, intermediates, and products. DNA polymerase D (polD) was proposed to function as the replicative polymerase in Thermococcus replicating both the leading and the lagging strands. It is shown here, however, that it stops before the previous Okazaki fragments, failing to rapidly process them. Instead, Family B DNA polymerase (polB) was observed to rapidly fill the gaps left by polD and displaces the downstream Okazaki fragment to create a flap structure. This flap structure was cleaved by flap endonuclease 1 (Fen1) and the resultant nick was ligated by DNA ligase to form a mature lagging strand. The similarities to both bacterial and eukaryotic systems and evolutionary implications of archaeal Okazaki fragment maturation are discussed.
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Affiliation(s)
- Lucia Greenough
- From New England Biolabs, Inc., Ipswich, Massachusetts 01938 and
| | - Zvi Kelman
- the National Institute of Standards and Technology, Rockville, Maryland 20850
| | - Andrew F Gardner
- From New England Biolabs, Inc., Ipswich, Massachusetts 01938 and
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