1
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Delaye L. The Unfinished Reconstructed Nature of the Last Universal Common Ancestor. J Mol Evol 2024:10.1007/s00239-024-10187-8. [PMID: 39026043 DOI: 10.1007/s00239-024-10187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
The ultimate consequence of Darwin's theory of common descent implies that all life on earth descends ultimately from a common ancestor. Biochemistry and molecular biology now provide sufficient evidence of shared ancestry of all extant life forms. However, the nature of the Last Universal Common Ancestor (LUCA) has been a topic of much debate over the years. This review offers a historical perspective on different attempts to infer LUCA's nature, exploring the debate surrounding its complexity. We further examine how different methodologies identify sets of ancient protein that exhibit only partial overlap. For example, different bioinformatic approaches have identified distinct protein subunits from the ATP synthetase identified as potentially inherited from LUCA. Additionally, we discuss how detailed molecular evolutionary analysis of reverse gyrase has modified previous inferences about an hyperthermophilic LUCA based mainly on automatic bioinformatic pipelines. We conclude by emphasizing the importance of developing a database dedicated to studying genes and proteins traceable back to LUCA and earlier stages of cellular evolution. Such a database would house the most ancient genes on earth.
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Affiliation(s)
- Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León CP. 36824, Irapuato, Gto., Mexico.
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2
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Yutin N, Tolstoy I, Mutz P, Wolf YI, Krupovic M, Koonin EV. Jumping DNA polymerases in bacteriophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591309. [PMID: 38903090 PMCID: PMC11188092 DOI: 10.1101/2024.04.26.591309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families. Here we identify four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage replication. We hypothesize that DNAP swapping is driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
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3
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Jacobs RQ, Schneider DA. Transcription elongation mechanisms of RNA polymerases I, II, and III and their therapeutic implications. J Biol Chem 2024; 300:105737. [PMID: 38336292 PMCID: PMC10907179 DOI: 10.1016/j.jbc.2024.105737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Transcription is a tightly regulated, complex, and essential cellular process in all living organisms. Transcription is comprised of three steps, transcription initiation, elongation, and termination. The distinct transcription initiation and termination mechanisms of eukaryotic RNA polymerases I, II, and III (Pols I, II, and III) have long been appreciated. Recent methodological advances have empowered high-resolution investigations of the Pols' transcription elongation mechanisms. Here, we review the kinetic similarities and differences in the individual steps of Pol I-, II-, and III-catalyzed transcription elongation, including NTP binding, bond formation, pyrophosphate release, and translocation. This review serves as an important summation of Saccharomyces cerevisiae (yeast) Pol I, II, and III kinetic investigations which reveal that transcription elongation by the Pols is governed by distinct mechanisms. Further, these studies illustrate how basic, biochemical investigations of the Pols can empower the development of chemotherapeutic compounds.
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Affiliation(s)
- Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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4
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Chaban A, Minakhin L, Goldobina E, Bae B, Hao Y, Borukhov S, Putzeys L, Boon M, Kabinger F, Lavigne R, Makarova KS, Koonin EV, Nair SK, Tagami S, Severinov K, Sokolova ML. Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nat Commun 2024; 15:317. [PMID: 38182597 PMCID: PMC10770324 DOI: 10.1038/s41467-023-44630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
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Affiliation(s)
- Anastasiia Chaban
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, 19107, USA
| | - Ekaterina Goldobina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Brain Bae
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yue Hao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA
| | - Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Institute of Molecular Genetics National Kurchatov Center, Moscow, 123182, Russia.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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5
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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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6
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Cui R, Li H, Zhao J, Li X, Gan J, Ma J. Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1. Nucleic Acids Res 2022; 50:10169-10186. [PMID: 36039765 PMCID: PMC9508822 DOI: 10.1093/nar/gkac727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/27/2022] [Indexed: 11/19/2022] Open
Abstract
Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1ΔN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position –7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.
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Affiliation(s)
- Ruixue Cui
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jin Zhao
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuhang Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinbiao Ma
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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7
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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8
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Yagi S, Padhi AK, Vucinic J, Barbe S, Schiex T, Nakagawa R, Simoncini D, Zhang KYJ, Tagami S. Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. J Am Chem Soc 2021; 143:15998-16006. [PMID: 34559526 DOI: 10.1021/jacs.1c05367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extant complex proteins must have evolved from ancient short and simple ancestors. The double-ψ β-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.
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Affiliation(s)
- Sota Yagi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Aditya K Padhi
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jelena Vucinic
- Université Fédérale de Toulouse, ANITI, INRAE-UR 875, 31000 Toulouse, France.,TBI, Université Fédérale de Toulouse, CNRS, INRAE, INSA, ANITI, 31000 Toulouse, France.,Université Fédérale de Toulouse, ANITI, IRIT-UMR 5505, 31000 Toulouse, France
| | - Sophie Barbe
- TBI, Université Fédérale de Toulouse, CNRS, INRAE, INSA, ANITI, 31000 Toulouse, France
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE-UR 875, 31000 Toulouse, France
| | - Reiko Nakagawa
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - David Simoncini
- Université Fédérale de Toulouse, ANITI, IRIT-UMR 5505, 31000 Toulouse, France
| | - Kam Y J Zhang
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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9
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Abstract
Diverse models have been advanced for the evolution of the genetic code. Here, models for tRNA, aminoacyl-tRNA synthetase (aaRS) and genetic code evolution were combined with an understanding of EF-Tu suppression of tRNA 3rd anticodon position wobbling. The result is a highly detailed scheme that describes the placements of all amino acids in the standard genetic code. The model describes evolution of 6-, 4-, 3-, 2- and 1-codon sectors. Innovation in column 3 of the code is explained. Wobbling and code degeneracy are explained. Separate distribution of serine sectors between columns 2 and 4 of the code is described. We conclude that very little chaos contributed to evolution of the genetic code and that the pattern of evolution of aaRS enzymes describes a history of the evolution of the code. A model is proposed to describe the biological selection for the earliest evolution of the code and for protocell evolution.
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Affiliation(s)
- Lei Lei
- Department of Biology, University of New England, Biddeford, ME, USA
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, USA
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10
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Lei L, Burton ZF. Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria. Front Mol Biosci 2021; 8:651134. [PMID: 34026831 PMCID: PMC8131849 DOI: 10.3389/fmolb.2021.651134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
DNA template-dependent multi-subunit RNA polymerases (RNAPs) found in all three domains of life and some viruses are of the two-double-Ψ-β-barrel (DPBB) type. The 2-DPBB protein format is also found in some RNA template-dependent RNAPs and a major replicative DNA template-dependent DNA polymerase (DNAP) from Archaea (PolD). The 2-DPBB family of RNAPs and DNAPs probably evolved prior to the last universal common cellular ancestor (LUCA). Archaeal Transcription Factor B (TFB) and bacterial σ factors include homologous strings of helix-turn-helix units. The consequences of TFB-σ homology are discussed in terms of the evolution of archaeal and bacterial core promoters. Domain-specific DPBB loop inserts functionally connect general transcription factors to the RNAP active site. Archaea appear to be more similar to LUCA than Bacteria. Evolution of bacterial σ factors from TFB appears to have driven divergence of Bacteria from Archaea, splitting the prokaryotic domains.
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Affiliation(s)
- Lei Lei
- Department of Biology, University of New England, Biddeford, ME, United States
| | - Zachary F Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, United States
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11
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Di Giulio M. The late appearance of DNA, the nature of the LUCA and ancestors of the domains of life. Biosystems 2020; 202:104330. [PMID: 33352234 DOI: 10.1016/j.biosystems.2020.104330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 01/27/2023]
Abstract
It has been firmly observed that replicative DNA polymerases of bacteria, archaea and eukaryotes are not homologous proteins. This lack of homology in the replication apparatus among the domains of life is not only compatible with but would seem to imply the view that the emergence of DNA occurred in the fundamental cellular lineages. In consequence, this diversity of DNA polymerase would go back to the level of ancestors of the domains of life and to the evolutionary time in which the DNA emerged. Therefore, the presumed evolutionary stage linked to the RNA- > DNA transition would have occurred only at the level of ancestors of the main lineages of the tree of life. Thus, the high noise associated with this major evolutionary transition and the impossibility for a cellular stage to generate different fundamental genetically profound traits - such as the different replication apparatuses of bacteria, archaea and eukaryotes - would imply not only that the last universal common ancestor (LUCA) was a progenote but that the ancestors of the domains of life were also at this evolutionary stage. So, I criticize the hypotheses which want, instead, that completely different cells - such as, bacteria and archaea - could have originated from a cellular LUCA.
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Affiliation(s)
- Massimo Di Giulio
- The Ionian School, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena (L'Aquila), Italy; Institute of Biosciences and Bioresources, National Research Council, Via P. Castellino, 111, 80131, Naples, Italy.
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12
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Zatopek KM, Alpaslan E, Evans T, Sauguet L, Gardner A. Novel ribonucleotide discrimination in the RNA polymerase-like two-barrel catalytic core of Family D DNA polymerases. Nucleic Acids Res 2020; 48:12204-12218. [PMID: 33137176 PMCID: PMC7708050 DOI: 10.1093/nar/gkaa986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Family D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). While PolD has an ancestral RNA polymerase catalytic core, its active site has evolved the ability to discriminate against ribonucleotides. Until now, the mechanism evolved by PolD to prevent ribonucleotide incorporation was unknown. In all other DNA polymerase families, an active site steric gate residue prevents ribonucleotide incorporation. In this work, we identify two consensus active site acidic (a) and basic (b) motifs shared across the entire two-barrel nucleotide polymerase superfamily, and a nucleotide selectivity (s) motif specific to PolD versus RNAPs. A novel steric gate histidine residue (H931 in Thermococcus sp. 9°N PolD) in the PolD s-motif both prevents ribonucleotide incorporation and promotes efficient dNTP incorporation. Further, a PolD H931A steric gate mutant abolishes ribonucleotide discrimination and readily incorporates a variety of 2' modified nucleotides. Taken together, we construct the first putative nucleotide bound PolD active site model and provide structural and functional evidence for the emergence of DNA replication through the evolution of an ancestral RNAP two-barrel catalytic core.
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Affiliation(s)
| | - Ece Alpaslan
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Thomas C Evans
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France
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13
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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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14
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Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č. Diversity and evolution of B-family DNA polymerases. Nucleic Acids Res 2020; 48:10142-10156. [PMID: 32976577 PMCID: PMC7544198 DOI: 10.1093/nar/gkaa760] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Julien Guglielmini
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Patrick Forterre
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
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15
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Abstract
Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales mimic RNA synthesis of their eukaryotic counterparts by utilizing multifunctional RNA polymerases to replicate entire viral genomes and transcribe viral mRNAs from individual viral genes as well as synthesize 5′ methylated cap and 3′ poly(A) tail of the transcribed viral mRNAs. The catalytic subunit large protein (L) and cofactor phosphoprotein (P) constitute the Mononegavirales polymerases. In this review, we discuss the shared and unique features of RNA synthesis, the monomeric multifunctional enzyme L, and the oligomeric multimodular adapter P of Mononegavirales. We outline the structural analyses of the Mononegavirales polymerases since the first structure of the vesicular stomatitis virus (VSV) L protein determined in 2015 and highlight multiple high-resolution cryo-electron microscopy (cryo-EM) structures of the polymerases of Mononegavirales, namely, VSV, RABV, HRSV, human metapneumovirus (HMPV), and human parainfluenza virus (HPIV), that have been reported in recent months (2019 to 2020). We compare the structures of those polymerases grouped by virus family, illustrate the similarities and differences among those polymerases, and reveal the potential RNA synthesis mechanisms and models of highly conserved Mononegavirales. We conclude by the discussion of remaining questions, evolutionary perspectives, and future directions.
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16
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A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase. Nat Commun 2020; 11:4506. [PMID: 32908149 PMCID: PMC7481178 DOI: 10.1038/s41467-020-18281-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/14/2020] [Indexed: 01/27/2023] Open
Abstract
Bacteriophages play critical roles in the biosphere, but their vast genomic diversity has obscured their evolutionary origins, and phylogenetic analyses have traditionally been hindered by their lack of universal phylogenetic marker genes. In this study we mine metagenomic data and identify a clade of Caudovirales that encodes the β and β' subunits of multi-subunit RNA polymerase (RNAP), a high-resolution phylogenetic marker which enables detailed evolutionary analyses. Our RNAP phylogeny revealed that the Caudovirales RNAP forms a clade distinct from cellular homologs, suggesting an ancient acquisition of this enzyme. Within these multimeric RNAP-encoding Caudovirales (mReC), we find that the similarity of major capsid proteins and terminase large subunits further suggests they form a distinct clade with common evolutionary origin. Our study characterizes a clade of RNAP-encoding Caudovirales and suggests the ancient origin of this enzyme in this group, underscoring the important role of viruses in the early evolution of life on Earth.
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17
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Abstract
The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.
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18
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Koonin EV, Krupovic M, Ishino S, Ishino Y. The replication machinery of LUCA: common origin of DNA replication and transcription. BMC Biol 2020; 18:61. [PMID: 32517760 PMCID: PMC7281927 DOI: 10.1186/s12915-020-00800-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. The replicative DNAP of the Last Universal Cellular Ancestor (LUCA) would be the ancestor of the archaeal PolD.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015, Paris, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
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19
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Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun 2020; 11:1591. [PMID: 32221299 PMCID: PMC7101311 DOI: 10.1038/s41467-020-15392-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/05/2020] [Indexed: 11/09/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi at 3.77 Å. Using an integrative structural biology approach — combining cryo-EM, X-ray crystallography, protein–protein interaction measurements, and activity assays — we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication. Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. Here, the authors present a cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi to reveal the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA.
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Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Ghislaine Henneke
- CNRS, Ifremer, Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.,Sorbonne Université, École Doctorale Complexité du Vivant (ED515), Paris, France
| | - Inès Hugonneau-Beaufet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | | | - Patrick England
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.
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20
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Ebright RH, Werner F, Zhang X. RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes. J Mol Biol 2019; 431:3945-3946. [PMID: 31356803 DOI: 10.1016/j.jmb.2019.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
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