1
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Aktürk Dizman Y. Codon usage bias analysis of the gene encoding NAD +-dependent DNA ligase protein of Invertebrate iridescent virus 6. Arch Microbiol 2023; 205:352. [PMID: 37812231 DOI: 10.1007/s00203-023-03688-5] [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: 08/05/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
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2
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Bhattacharya S. Episomal and chromosomal DNA replication and recombination in Entamoeba histolytica. Front Mol Biosci 2023; 10:1212082. [PMID: 37363402 PMCID: PMC10285105 DOI: 10.3389/fmolb.2023.1212082] [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: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Entamoeba histolytica is the causative agent of amoebiasis. DNA replication studies in E. histolytica first started with the ribosomal RNA genes located on episomal circles. Unlike most plasmids, Entamoeba histolytica rDNA circles lacked a fixed origin. Replication initiated from multiple sites on the episome, and these were preferentially used under different growth conditions. In synchronized cells the early origins mapped within the rDNA transcription unit, while at later times an origin in the promoter-proximal upstream intergenic spacer was activated. This is reminiscent of eukaryotic chromosomal replication where multiple potential origins are used. Biochemical studies on replication and recombination proteins in Entamoeba histolytica picked up momentum once the genome sequence was available. Sequence search revealed homologs of DNA replication and recombination proteins, including meiotic genes. The replicative DNA polymerases identified included the α, δ, ε of polymerase family B; lesion repair polymerases Rev1 and Rev3; a translesion repair polymerase of family A, and five families of polymerases related to family B2. Biochemical analysis of EhDNApolA confirmed its polymerase activity with expected kinetic constants. It could perform strand displacement, and translesion synthesis. The purified EhDNApolB2 had polymerase and exonuclease activities, and could efficiently bypass some types of DNA lesions. The single DNA ligase (EhDNAligI) was similar to eukaryotic DNA ligase I. It was a high-fidelity DNA ligase, likely involved in both replication and repair. Its interaction with EhPCNA was also demonstrated. The recombination-related proteins biochemically characterized were EhRad51 and EhDmc1. Both shared the canonical properties of a recombinase and could catalyse strand exchange over long DNA stretches. Presence of Dmc1 indicates the likelihood of meiosis in this parasite. Direct evidence of recombination in Entamoeba histolytica was provided by use of inverted repeat sequences located on plasmids or chromosomes. In response to a variety of stress conditions, and during encystation in Entamoeba invadens, recombination-related genes were upregulated and homologous recombination was enhanced. These data suggest that homologous recombination could have critical roles in trophozoite growth and stage conversion. Availability of biochemically characterized replication and recombination proteins is an important resource for exploration of novel anti-amoebic drug targets.
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3
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Luo J, Chen H, An R, Liang X. Efficient preparation of AppDNA/AppRNA by T4 DNA ligase aided by a DNA involving mismatched mini-hairpin structure at its 3′ side. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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4
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Tesfahun AN, Alexeeva M, Tomkuvienė M, Arshad A, Guragain P, Klungland A, Klimašauskas S, Ruoff P, Bjelland S. Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein. Front Microbiol 2021; 12:608839. [PMID: 34276575 PMCID: PMC8278400 DOI: 10.3389/fmicb.2021.608839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/20/2021] [Indexed: 11/18/2022] Open
Abstract
DNA polymerase III mis-insertion may, where not corrected by its 3′→ 5′ exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in Escherichia coli, and its repair mechanism remains elusive. We present here in vitro evidence that C⋅C mismatch can be processed by base excision repair initiated by the E. coli formamidopyrimidine-DNA glycosylase (Fpg) protein. The kcat for C⋅C is, however, 2.5 to 10 times lower than for its primary substrate 8-oxoguanine (oxo8G)⋅C, but approaches those for 5,6-dihydrothymine (dHT)⋅C and thymine glycol (Tg)⋅C. The KM values are all in the same range, which indicates efficient recognition of C⋅C mismatches in DNA. Fpg activity was also exhibited for the thymine (T)⋅T mismatch and for N4- and/or 5-methylated C opposite C or T, Fpg activity being enabled on a broad spectrum of DNA lesions and mismatches by the flexibility of the active site loop. We hypothesize that Fpg plays a role in resolving C⋅C in particular, but also other pyrimidine⋅pyrimidine mismatches, which increases survival at the cost of some mutagenesis.
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Affiliation(s)
- Almaz Nigatu Tesfahun
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Aysha Arshad
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Prashanna Guragain
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Molecular Medicine, Life Sciences Center, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Peter Ruoff
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway.,Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
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5
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Kimoto M, Soh SHG, Tan HP, Okamoto I, Hirao I. Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase. Biopolymers 2020; 112:e23407. [PMID: 33156531 PMCID: PMC7900958 DOI: 10.1002/bip.23407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022]
Abstract
We present cognate base pair selectivity in template-dependent ligation by T4 DNA ligase using a hydrophobic unnatural base pair (UBP), Ds-Pa. T4 DNA ligase efficiently recognizes the Ds-Pa pairing at the conjugation position, and Ds excludes the noncognate pairings with the natural bases. Our results indicate that the hydrophobic base pairing is allowed in enzymatic ligation with higher cognate base-pair selectivity, relative to the hydrogen-bond interactions between pairing bases. The efficient ligation using Ds-Pa can be employed in recombinant DNA technology using genetic alphabet expansion, toward the creation of semi-synthetic organisms containing UBPs.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore.,Raffles Institution, Singapore, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Itaru Okamoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
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6
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Breiner B, Johnson K, Stolarek M, Silva AL, Negrea A, Bell NM, Isaac TH, Dethlefsen M, Chana J, Ibbotson LA, Palmer RN, Bush J, Dunning AJ, Love DM, Pachoumi O, Kelly DJ, Shibahara A, Wu M, Sosna M, Dear PH, Tolle F, Petrini E, Amasio M, Shelford LR, Saavedra MS, Sheridan E, Kuleshova J, Podd GJ, Balmforth BW, Frayling CA. Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets. Nucleic Acids Res 2019; 47:e101. [PMID: 31318971 PMCID: PMC6753480 DOI: 10.1093/nar/gkz611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/10/2019] [Accepted: 07/03/2019] [Indexed: 11/12/2022] Open
Abstract
A new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.
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Affiliation(s)
- Boris Breiner
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Kerr Johnson
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Magdalena Stolarek
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Ana-Luisa Silva
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aurel Negrea
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Neil M Bell
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Tom H Isaac
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mark Dethlefsen
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jasmin Chana
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Lindsey A Ibbotson
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Rebecca N Palmer
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - James Bush
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Alexander J Dunning
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - David M Love
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Olympia Pachoumi
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Douglas J Kelly
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aya Shibahara
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mei Wu
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Maciej Sosna
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Paul H Dear
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Fabian Tolle
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Edoardo Petrini
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Michele Amasio
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Leigh R Shelford
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Monica S Saavedra
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Eoin Sheridan
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jekaterina Kuleshova
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Gareth J Podd
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Barnaby W Balmforth
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Cameron A Frayling
- Base4 Innovation Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, UK
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7
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Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS. Two-tiered enforcement of high-fidelity DNA ligation. Nat Commun 2019; 10:5431. [PMID: 31780661 PMCID: PMC6882888 DOI: 10.1038/s41467-019-13478-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/05/2019] [Indexed: 01/07/2023] Open
Abstract
DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3'-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg2+-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg2+, and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.
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Affiliation(s)
- Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Thomas J Jurkiw
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA
| | - Matthew J Schellenberg
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Patrick J O'Brien
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA.
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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8
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Uson ML, Carl A, Goldgur Y, Shuman S. Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities. Nucleic Acids Res 2019; 46:4164-4175. [PMID: 29635474 PMCID: PMC5934675 DOI: 10.1093/nar/gky238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/21/2018] [Indexed: 02/02/2023] Open
Abstract
Mycobacterium smegmatis FenA is a nucleic acid phosphodiesterase with flap endonuclease and 5' exonuclease activities. The 1.8 Å crystal structure of FenA reported here highlights as its closest homologs bacterial FEN-family enzymes ExoIX, the Pol1 exonuclease domain and phage T5 Fen. Mycobacterial FenA assimilates three active site manganese ions (M1, M2, M3) that are coordinated, directly and via waters, to a constellation of eight carboxylate side chains. We find via mutagenesis that the carboxylate contacts to all three manganese ions are essential for FenA's activities. Structures of nuclease-dead FenA mutants D125N, D148N and D208N reveal how they fail to bind one of the three active site Mn2+ ions, in a distinctive fashion for each Asn change. The structure of FenA D208N with a phosphate anion engaged by M1 and M2 in a state mimetic of a product complex suggests a mechanism for metal-catalyzed phosphodiester hydrolysis similar to that proposed for human Exo1. A distinctive feature of FenA is that it does not have the helical arch module found in many other FEN/FEN-like enzymes. Instead, this segment of FenA adopts a unique structure comprising a short 310 helix and surface β-loop that coordinates a fourth manganese ion (M4).
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Affiliation(s)
- Maria Loressa Uson
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Ayala Carl
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Yehuda Goldgur
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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9
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Potapov V, Ong JL, Langhorst BW, Bilotti K, Cahoon D, Canton B, Knight TF, Evans TC, Lohman GJS. A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining. Nucleic Acids Res 2019; 46:e79. [PMID: 29741723 PMCID: PMC6061786 DOI: 10.1093/nar/gky303] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA ligases are key enzymes in molecular and synthetic biology that catalyze the joining of breaks in duplex DNA and the end-joining of DNA fragments. Ligation fidelity (discrimination against the ligation of substrates containing mismatched base pairs) and bias (preferential ligation of particular sequences over others) have been well-studied in the context of nick ligation. However, almost no data exist for fidelity and bias in end-joining ligation contexts. In this study, we applied Pacific Biosciences Single-Molecule Real-Time sequencing technology to directly sequence the products of a highly multiplexed ligation reaction. This method has been used to profile the ligation of all three-base 5′-overhangs by T4 DNA ligase under typical ligation conditions in a single experiment. We report the relative frequency of all ligation products with or without mismatches, the position-dependent frequency of each mismatch, and the surprising observation that 5′-TNA overhangs ligate extremely inefficiently compared to all other Watson–Crick pairings. The method can easily be extended to profile other ligases, end-types (e.g. blunt ends and overhangs of different lengths), and the effect of adjacent sequence on the ligation results. Further, the method has the potential to provide new insights into the thermodynamics of annealing and the kinetics of end-joining reactions.
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Affiliation(s)
- Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Jennifer L Ong
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Bradley W Langhorst
- Applications and Product Development, New England Biolabs, Ipswich, MA 01938, USA
| | | | | | | | | | - Thomas C Evans
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
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10
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Azuara-Liceaga E, Betanzos A, Cardona-Felix CS, Castañeda-Ortiz EJ, Cárdenas H, Cárdenas-Guerra RE, Pastor-Palacios G, García-Rivera G, Hernández-Álvarez D, Trasviña-Arenas CH, Diaz-Quezada C, Orozco E, Brieba LG. The Sole DNA Ligase in Entamoeba histolytica Is a High-Fidelity DNA Ligase Involved in DNA Damage Repair. Front Cell Infect Microbiol 2018; 8:214. [PMID: 30050869 PMCID: PMC6052137 DOI: 10.3389/fcimb.2018.00214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/07/2018] [Indexed: 01/03/2023] Open
Abstract
The protozoan parasite Entamoeba histolytica is exposed to reactive oxygen and nitric oxide species that have the potential to damage its genome. E. histolytica harbors enzymes involved in DNA repair pathways like Base and Nucleotide Excision Repair. The majority of DNA repairs pathways converge in their final step in which a DNA ligase seals the DNA nicks. In contrast to other eukaryotes, the genome of E. histolytica encodes only one DNA ligase (EhDNAligI), suggesting that this ligase is involved in both DNA replication and DNA repair. Therefore, the aim of this work was to characterize EhDNAligI, its ligation fidelity and its ability to ligate opposite DNA mismatches and oxidative DNA lesions, and to study its expression changes and localization during and after recovery from UV and H2O2 treatment. We found that EhDNAligI is a high-fidelity DNA ligase on canonical substrates and is able to discriminate erroneous base-pairing opposite DNA lesions. EhDNAligI expression decreases after DNA damage induced by UV and H2O2 treatments, but it was upregulated during recovery time. Upon oxidative DNA damage, EhDNAligI relocates into the nucleus where it co-localizes with EhPCNA and the 8-oxoG adduct. The appearance and disappearance of 8-oxoG during and after both treatments suggest that DNA damaged was efficiently repaired because the mainly NER and BER components are expressed in this parasite and some of them were modulated after DNA insults. All these data disclose the relevance of EhDNAligI as a specialized and unique ligase in E. histolytica that may be involved in DNA repair of the 8-oxoG lesions.
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Affiliation(s)
- Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico,*Correspondence: Elisa Azuara-Liceaga
| | - Abigail Betanzos
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Cesar S. Cardona-Felix
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | | | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Rosa E. Cárdenas-Guerra
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Guillermo Pastor-Palacios
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - David Hernández-Álvarez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Carlos H. Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Corina Diaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico,Luis G. Brieba
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11
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Alexeeva M, Guragain P, Tesfahun AN, Tomkuvienė M, Arshad A, Gerasimaitė R, Rukšėnaitė A, Urbanavičiūtė G, Bjørås M, Laerdahl JK, Klungland A, Klimašauskas S, Bjelland S. Excision of the doubly methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170337. [PMID: 29685966 PMCID: PMC5915725 DOI: 10.1098/rstb.2017.0337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
Cytosine (C) in DNA is often modified to 5-methylcytosine (m5C) to execute important cellular functions. Despite the significance of m5C for epigenetic regulation in mammals, damage to m5C has received little attention. For instance, almost no studies exist on erroneous methylation of m5C by alkylating agents to doubly or triply methylated bases. Owing to chemical evidence, and because many prokaryotes express methyltransferases able to convert m5C into N4,5-dimethylcytosine (m N4,5C) in DNA, m N4,5C is probably present in vivo We screened a series of glycosylases from prokaryotic to human and found significant DNA incision activity of the Escherichia coli Nei and Fpg proteins at m N4,5C residues in vitro The activity of Nei was highest opposite cognate guanine followed by adenine, thymine (T) and C. Fpg-complemented Nei by exhibiting the highest activity opposite C followed by lower activity opposite T. To our knowledge, this is the first description of a repair enzyme activity at a further methylated m5C in DNA, as well as the first alkylated base allocated as a Nei or Fpg substrate. Based on our observed high sensitivity to nuclease S1 digestion, we suggest that m N4,5C occurs as a disturbing lesion in DNA and that Nei may serve as a major DNA glycosylase in E. coli to initiate its repair.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Prashanna Guragain
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Almaz N Tesfahun
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Aysha Arshad
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
| | - Rūta Gerasimaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Audronė Rukšėnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Giedrė Urbanavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Magnar Bjørås
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Jon K Laerdahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology-Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, PO Box 8600 Forus, 4021 Stavanger, Norway
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Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proc Natl Acad Sci U S A 2017; 114:9164-9169. [PMID: 28794281 DOI: 10.1073/pnas.1707466114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Downstream metabolic events can contribute to the lethality of drugs or agents that interact with a primary cellular target. In bacteria, the production of reactive oxygen species (ROS) has been associated with the lethal effects of a variety of stresses including bactericidal antibiotics, but the relative contribution of this oxidative component to cell death depends on a variety of factors. Experimental evidence has suggested that unresolvable DNA problems caused by incorporation of oxidized nucleotides into nascent DNA followed by incomplete base excision repair contribute to the ROS-dependent component of antibiotic lethality. Expression of the chimeric periplasmic-cytoplasmic MalE-LacZ72-47 protein is an historically important lethal stress originally identified during seminal genetic experiments that defined the SecY-dependent protein translocation system. Multiple, independent lines of evidence presented here indicate that the predominant mechanism for MalE-LacZ lethality shares attributes with the ROS-dependent component of antibiotic lethality. MalE-LacZ lethality requires molecular oxygen, and its expression induces ROS production. The increased susceptibility of mutants sensitive to oxidative stress to MalE-LacZ lethality indicates that ROS contribute causally to cell death rather than simply being produced by dying cells. Observations that support the proposed mechanism of cell death include MalE-LacZ expression being bacteriostatic rather than bactericidal in cells that overexpress MutT, a nucleotide sanitizer that hydrolyzes 8-oxo-dGTP to the monophosphate, or that lack MutM and MutY, DNA glycosylases that process base pairs involving 8-oxo-dGTP. Our studies suggest stress-induced physiological changes that favor this mode of ROS-dependent death.
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The DNA Repair Repertoire of Mycobacterium smegmatis FenA Includes the Incision of DNA 5' Flaps and the Removal of 5' Adenylylated Products of Aborted Nick Ligation. J Bacteriol 2017. [PMID: 28630124 DOI: 10.1128/jb.00304-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We characterize Mycobacterium smegmatis FenA as a manganese-dependent 5'-flap endonuclease homologous to the 5'-exonuclease of DNA polymerase I. FenA incises a nicked 5' flap between the first and second nucleotides of the duplex segment to yield a 1-nucleotide gapped DNA, which is then further resected in dinucleotide steps. Initial FenA cleavage at a Y-flap or nick occurs between the first and second nucleotides of the duplex. However, when the template 3' single strand is eliminated to create a 5'-tailed duplex, FenA incision shifts to between the second and third nucleotides. A double-flap substrate with a mobile junction (mimicking limited strand displacement synthesis during gap repair) is preferentially incised as the 1-nucleotide 3'-flap isomer, with the scissile phosphodiester shifted by one nucleotide versus a static double flap. FenA efficiently removes the 5' App(dN) terminus of an aborted nick ligation reaction intermediate, thereby highlighting FenA as an agent of repair of such lesions, which are formed under a variety of circumstances by bacterial NAD+-dependent DNA ligases and especially by mycobacterial DNA ligases D and C.IMPORTANCE Structure-specific DNA endonucleases are implicated in bacterial DNA replication, repair, and recombination, yet there is scant knowledge of the roster and catalytic repertoire of such nucleases in Mycobacteria This study identifies M. smegmatis FenA as a stand-alone endonuclease homologous to the 5'-exonuclease domain of mycobacterial DNA polymerase 1. FenA incises 5' flaps, 5' nicks, and 5' App(dN) intermediates of aborted nick ligation. The isolated N-terminal domain of M. smegmatis Pol1 is also shown to be a flap endonuclease.
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14
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Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD +-dependent polynucleotide ligases. Proc Natl Acad Sci U S A 2017; 114:2592-2597. [PMID: 28223499 DOI: 10.1073/pnas.1619220114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Polynucleotide ligases comprise a ubiquitous superfamily of nucleic acid repair enzymes that join 3'-OH and 5'-PO4 DNA or RNA ends. Ligases react with ATP or NAD+ and a divalent cation cofactor to form a covalent enzyme-(lysine-Nζ)-adenylate intermediate. Here, we report crystal structures of the founding members of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD+-dependent DNA ligase family (Escherichia coli LigA), captured as their respective Michaelis complexes, which illuminate distinctive catalytic mechanisms of the lysine adenylylation reaction. The 2.2-Å Rnl1•ATP•(Mg2+)2 structure highlights a two-metal mechanism, whereby: a ligase-bound "catalytic" Mg2+(H2O)5 coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; a second octahedral Mg2+ coordination complex bridges the β and γ phosphates; and protein elements unique to Rnl1 engage the γ phosphate and associated metal complex and orient the pyrophosphate leaving group for in-line catalysis. By contrast, the 1.55-Å LigA•NAD+•Mg2+ structure reveals a one-metal mechanism in which a ligase-bound Mg2+(H2O)5 complex lowers the lysine pKa and engages the NAD+ α phosphate, but the β phosphate and the nicotinamide nucleoside of the nicotinamide mononucleotide (NMN) leaving group are oriented solely via atomic interactions with protein elements that are unique to the LigA clade. The two-metal versus one-metal dichotomy demarcates a branchpoint in ligase evolution and favors LigA as an antibacterial drug target.
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15
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Bauer RJ, Jurkiw TJ, Evans TC, Lohman GJS. Rapid Time Scale Analysis of T4 DNA Ligase-DNA Binding. Biochemistry 2017; 56:1117-1129. [PMID: 28165732 DOI: 10.1021/acs.biochem.6b01261] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA ligases, essential to both in vivo genome integrity and in vitro molecular biology, catalyze phosphodiester bond formation between adjacent 3'-OH and 5'-phosphorylated termini in dsDNA. This reaction requires enzyme self-adenylylation, using ATP or NAD+ as a cofactor, and AMP release concomitant with phosphodiester bond formation. In this study, we present the first fast time scale binding kinetics of T4 DNA ligase to both nicked substrate DNA (nDNA) and product-equivalent non-nicked dsDNA, as well as binding and release kinetics of AMP. The described assays utilized a fluorescein-dT labeled DNA substrate as a reporter for ligase·DNA interactions via stopped-flow fluorescence spectroscopy. The analysis revealed that binding to nDNA by the active adenylylated ligase occurs in two steps, an initial rapid association equilibrium followed by a transition to a second bound state prior to catalysis. Furthermore, the ligase binds and dissociates from nicked and nonsubstrate dsDNA rapidly with initial association affinities on the order of 100 nM regardless of enzyme adenylylation state. DNA binding occurs through a two-step mechanism in all cases, confirming prior proposals of transient binding followed by a transition to a productive ligase·nDNA (Lig·nDNA) conformation but suggesting that weaker nonproductive "closed" complexes are formed as well. These observations demonstrate the mechanistic underpinnings of competitive inhibition by rapid binding of nonsubstrate DNA, and of substrate inhibition by blocking of the self-adenylylation reaction through nick binding by deadenylylated ligase. Our analysis further reveals that product release is not the rate-determining step in turnover.
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Affiliation(s)
- Robert J Bauer
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Thomas J Jurkiw
- University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - Thomas C Evans
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
| | - Gregory J S Lohman
- DNA Enzymes Division, New England BioLabs, Inc. , Ipswich, Massachusetts 01938-2723, United States
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16
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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