1
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Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya. Nat Commun 2023; 14:838. [PMID: 36792581 PMCID: PMC9931769 DOI: 10.1038/s41467-023-36487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.
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2
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Dozova N, Lacombat F, Lombard M, Hamdane D, Plaza P. Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX. Phys Chem Chem Phys 2021; 23:22692-22702. [PMID: 34605505 DOI: 10.1039/d1cp03379d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH-) as prosthetic group and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH- in ThyX is only mildly more constrained than that of free FADH- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH- photophysics to the constraints exerted by its immediate surroundings.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Pascal Plaza
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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3
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Bou-Nader C, Stull FW, Pecqueur L, Simon P, Guérineau V, Royant A, Fontecave M, Lombard M, Palfey BA, Hamdane D. An enzymatic activation of formaldehyde for nucleotide methylation. Nat Commun 2021; 12:4542. [PMID: 34315871 PMCID: PMC8316439 DOI: 10.1038/s41467-021-24756-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH2O-shunt may be relevant in several other important folate-dependent reactions.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Frederick W Stull
- Programs in Chemical Biology and the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Philippe Simon
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Vincent Guérineau
- CNRS, Institut de Chimie des Substances Naturelles UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Antoine Royant
- CEA, CNRS, Institut de Biologie Structurale (IBS), Université Grenoble Alpes, Grenoble, France.,European Synchrotron Radiation Facility, Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France
| | - Bruce A Palfey
- Programs in Chemical Biology and the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France.
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4
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Myllykallio H, Sournia P, Heliou A, Liebl U. Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information. Front Microbiol 2018; 9:918. [PMID: 29867829 PMCID: PMC5954106 DOI: 10.3389/fmicb.2018.00918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence.
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Affiliation(s)
- Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Pierre Sournia
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Alice Heliou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France.,Laboratoire d'Informatique de l'École Polytechnique, Ecole Polytechnique, Centre National de la Recherche Scientifique, Université Paris-Saclay, Palaiseau, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
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5
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Karunaratne K, Luedtke N, Quinn DM, Kohen A. Flavin-dependent thymidylate synthase: N5 of flavin as a Methylene carrier. Arch Biochem Biophys 2017; 632:11-19. [PMID: 28821425 DOI: 10.1016/j.abb.2017.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/09/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
Abstract
Thymidylate is synthesized de novo in all living organisms for replication of genomes. The chemical transformation is reductive methylation of deoxyuridylate at C5 to form deoxythymidylate. All eukaryotes including humans complete this well-understood transformation with thymidylate synthase utilizing 6R-N5-N10-methylene-5,6,7,8-tetrahydrofolate as both a source of methylene and a reducing hydride. In 2002, flavin-dependent thymidylate synthase was discovered as a new pathway for de novo thymidylate synthesis. The flavin-dependent catalytic mechanism is different than thymidylate synthase because it requires flavin as a reducing agent and methylene transporter. This catalytic mechanism is not well-understood, but since it is known to be very different from thymidylate synthase, there is potential for mechanism-based inhibitors that can selectively inhibit the flavin-dependent enzyme to target many human pathogens with low host toxicity.
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Affiliation(s)
| | - Nicholas Luedtke
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Daniel M Quinn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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6
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Discovery of a new Mycobacterium tuberculosis thymidylate synthase X inhibitor with a unique inhibition profile. Biochem Pharmacol 2017; 135:69-78. [PMID: 28359706 DOI: 10.1016/j.bcp.2017.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/24/2017] [Indexed: 01/24/2023]
Abstract
Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), is an infection that is responsible for roughly 1.5 million deaths per year. The situation is further complicated by the wide-spread resistance to the existing first- and second-line drugs. As a result of this, it is urgent to develop new drugs to combat the resistant bacteria as well as have lower side effects, which can promote adherence to the treatment regimens. Targeting the de novo synthesis of thymidylate (dTMP) is an important pathway to develop drugs for TB. Although Mtb carries genes for two families of thymidylate synthases (TS), ThyA and ThyX, only ThyX is essential for its normal growth. Both enzymes catalyze the conversion of uridylate (dUMP) to dTMP but employ a different catalytic approach and have different structures. Also, ThyA is the only TS found in humans. This is the rationale for identifying selective inhibitors against ThyX. We exploited the NADPH oxidation to NADP+ step, catalyzed by ThyX, to develop a spectrophotometric biochemical assay. Success of the assay was demonstrated by its effectiveness (average Z'=0.77) and identification of selective ThyX inhibitors. The most potent compound is a tight-binding inhibitor with an IC50 of 710nM. Its mechanism of inhibition is analyzed in relation to the latest findings of ThyX mechanism and substrate and cofactor binding order.
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7
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Krumova S, Todinova S, Tileva M, Bouzhir-Sima L, Vos MH, Liebl U, Taneva SG. Thermal stability and binding energetics of thymidylate synthase ThyX. Int J Biol Macromol 2016; 91:560-7. [PMID: 27268384 DOI: 10.1016/j.ijbiomac.2016.05.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
The bacterial thymidylate synthase ThyX is a multisubstrate flavoenzyme that takes part in the de novo synthesis of thymidylate in a variety of microorganisms. Herein we study the effect of FAD and dUMP binding on the thermal stability of wild type (WT) ThyX from the mesophilic Paramecium bursaria chlorella virus-1 (PBCV-1) and from the thermophilic bacterium Thermotoga maritima (TmThyX), and from two variants of TmThyX, Y91F and S88W, using differential scanning calorimetry. The energetics underlying these processes was characterized by isothermal titration calorimetry. The PBCV-1 protein is significantly less stable against the thermal challenge than the TmThyX WT. FAD exerted stabilizing effect greater for PBCV-1 than for TmThyX and for both mutants, whereas binding of dUMP to FAD-loaded proteins stabilized further only TmThyX. Different thermodynamic signatures describe the FAD binding to the WT ThyX proteins. While TmThyX binds FAD with a low μM binding affinity in a process characterized by a favorable entropy change, the assembly of PBCV-1 with FAD is governed by a large enthalpy change opposed by an unfavorable entropy change resulting in a relatively strong nM binding. An enthalpy-driven formation of a high affinity ternary ThyX/FAD/dUMP complex was observed only for TmThyX.
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Affiliation(s)
- Sashka Krumova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | - Svetla Todinova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | - Milena Tileva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria
| | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, 91128 Palaiseau Cedex, France
| | - Stefka G Taneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 21, 1113 Sofia, Bulgaria.
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8
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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9
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Skouloubris S, Djaout K, Lamarre I, Lambry JC, Anger K, Briffotaux J, Liebl U, de Reuse H, Myllykallio H. Targeting of Helicobacter pylori thymidylate synthase ThyX by non-mitotoxic hydroxy-naphthoquinones. Open Biol 2016; 5:150015. [PMID: 26040760 PMCID: PMC4632503 DOI: 10.1098/rsob.150015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the functionally analogous human enzyme, thus providing means for selective inhibition of bacterial growth. To identify novel compounds with anti-bacterial activity against the human pathogenic bacterium Helicobacter pylori, based on our earlier biochemical and structural analyses, we designed a series of eighteen 2-hydroxy-1,4-naphthoquinones (2-OH-1,4-NQs) that target HpThyX. Our lead-like molecules markedly inhibited the NADPH oxidation and 2′-deoxythymidine-5′-monophosphate-forming activities of HpThyX enzyme in vitro, with inhibitory constants in the low nanomolar range. The identification of non-cytotoxic and non-mitotoxic 2-OH-1,4-NQ inhibitors permitted testing their in vivo efficacy in a mouse model for H. pylori infections. Despite the widely assumed toxicity of naphthoquinones (NQs), we identified tight-binding ThyX inhibitors that were tolerated in mice and can be associated with a modest effect in reducing the number of colonizing bacteria. Our results thus provide proof-of-concept that targeting ThyX enzymes is a highly feasible strategy for the development of therapies against H. pylori and a high number of other ThyX-dependent pathogenic bacteria. We also demonstrate that chemical reactivity of NQs does not prevent their exploitation as anti-microbial compounds, particularly when mitotoxicity screening is used to prioritize these compounds for further experimentation.
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Affiliation(s)
- Stéphane Skouloubris
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France Department of Biology, Université Paris-Sud, Orsay 91405, France
| | - Kamel Djaout
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Karine Anger
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Hilde de Reuse
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
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10
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Conrad JA, Ortiz-Maldonado M, Hoppe SW, Palfey BA. Detection of intermediates in the oxidative half-reaction of the FAD-dependent thymidylate synthase from Thermotoga maritima: carbon transfer without covalent pyrimidine activation. Biochemistry 2014; 53:5199-207. [PMID: 25068636 PMCID: PMC4139161 DOI: 10.1021/bi500648n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Thymidylate, a vital DNA precursor, is synthesized by thymidylate synthases (TSs). A second class of TSs, encoded by the thyX gene, is found in bacteria and a few other microbes and is especially widespread in anaerobes. TS encoded by thyX requires a flavin adenine dinucleotide prosthetic group for activity. In the oxidative half-reaction, the reduced flavin is oxidized by 2'-deoxyuridine 5'-monophosphate (dUMP) and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF), synthesizing 2'-deoxythymidine 5'-monophosphate (dTMP). dTMP synthesis is a complex process, requiring the enzyme to promote carbon transfer, probably by increasing the nucleophilicity of dUMP and the electrophilicity of CH2THF, and reduction of the transferred carbon. The mechanism of the oxidative half-reaction was investigated by transient kinetics. Two intermediates were detected, the first by a change in the flavin absorbance spectrum in stopped-flow experiments and the second by the transient disappearance of deoxynucleotide in acid quenching experiments. The effects of substrate analogues and the behavior of mutated enzymes on these reactions lead to the conclusion that activation of dUMP does not occur through a Michael-like addition, the mechanism for the activation analogous with that of the flavin-independent TS. Rather, we propose that the nucleophilicity of dUMP is enhanced by electrostatic polarization upon binding to the active site. This conclusion rationalizes many of our observations, for instance, the markedly slower reactions when two arginine residues that hydrogen bond with the uracil moiety of dUMP were mutated to alanine. The activation of dUMP by polarization is consistent with the majority of the published data on ThyX and provides a testable mechanistic hypothesis.
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Affiliation(s)
- John A Conrad
- Department of Biological Chemistry and ‡Chemical Biology Doctoral Program, University of Michigan Medical School , 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, United States
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11
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Mishanina TV, Corcoran JM, Kohen A. Substrate activation in flavin-dependent thymidylate synthase. J Am Chem Soc 2014; 136:10597-600. [PMID: 25025487 PMCID: PMC4121000 DOI: 10.1021/ja506108b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Thymidylate is a critical DNA nucleotide
that has to be synthesized
in cells de novo by all organisms. Flavin-dependent
thymidylate synthase (FDTS) catalyzes the final step in this de novo production of thymidylate in many human pathogens,
but it is absent from humans. The FDTS reaction proceeds via a chemical
route that is different from its human enzyme analogue, making FDTS
a potential antimicrobial target. The chemical mechanism of FDTS is
still not understood, and the two most recently proposed mechanisms
involve reaction intermediates that are unusual in pyrimidine biosynthesis
and biology in general. These mechanisms differ in the relative timing
of the reaction of the flavin with the substrate. The consequence
of this difference is significant: the intermediates are cationic
in one case and neutral in the other, an important consideration in
the construction of mechanism-based enzyme inhibitors. Here we test
these mechanisms via chemical trapping of reaction intermediates,
stopped-flow, and substrate hydrogen isotope exchange techniques.
Our findings suggest that an initial activation of the pyrimidine
substrate by reduced flavin is required for catalysis, and a revised
mechanism is proposed on the basis of previous and new data. These
findings and the newly proposed mechanism add an important piece to
the puzzle of the mechanism of FDTS and suggest a new class of intermediates
that, in the future, may serve as targets for mechanism-based design
of FDTS-specific inhibitors.
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Affiliation(s)
- Tatiana V Mishanina
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242-1727, United States
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12
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Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA. Pathogenomic inference of virulence-associated genes in Leptospira interrogans. PLoS Negl Trop Dis 2013; 7:e2468. [PMID: 24098822 PMCID: PMC3789758 DOI: 10.1371/journal.pntd.0002468] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
Leptospirosis is a globally important, neglected zoonotic infection caused by spirochetes of the genus Leptospira. Since genetic transformation remains technically limited for pathogenic Leptospira, a systems biology pathogenomic approach was used to infer leptospiral virulence genes by whole genome comparison of culture-attenuated Leptospira interrogans serovar Lai with its virulent, isogenic parent. Among the 11 pathogen-specific protein-coding genes in which non-synonymous mutations were found, a putative soluble adenylate cyclase with host cell cAMP-elevating activity, and two members of a previously unstudied ∼15 member paralogous gene family of unknown function were identified. This gene family was also uniquely found in the alpha-proteobacteria Bartonella bacilliformis and Bartonella australis that are geographically restricted to the Andes and Australia, respectively. How the pathogenic Leptospira and these two Bartonella species came to share this expanded gene family remains an evolutionary mystery. In vivo expression analyses demonstrated up-regulation of 10/11 Leptospira genes identified in the attenuation screen, and profound in vivo, tissue-specific up-regulation by members of the paralogous gene family, suggesting a direct role in virulence and host-pathogen interactions. The pathogenomic experimental design here is generalizable as a functional systems biology approach to studying bacterial pathogenesis and virulence and should encourage similar experimental studies of other pathogens.
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Affiliation(s)
- Jason S Lehmann
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
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13
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Basta T, Boum Y, Briffotaux J, Becker HF, Lamarre-Jouenne I, Lambry JC, Skouloubris S, Liebl U, Graille M, van Tilbeurgh H, Myllykallio H. Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biol 2013; 2:120120. [PMID: 23155486 PMCID: PMC3498832 DOI: 10.1098/rsob.120120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/11/2012] [Indexed: 11/12/2022] Open
Abstract
Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.
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Affiliation(s)
- Tamara Basta
- Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France
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14
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Parchina A, Froeyen M, Margamuljana L, Rozenski J, De Jonghe S, Briers Y, Lavigne R, Herdewijn P, Lescrinier E. Discovery of an acyclic nucleoside phosphonate that inhibits Mycobacterium tuberculosis ThyX based on the binding mode of a 5-alkynyl substrate analogue. ChemMedChem 2013; 8:1373-83. [PMID: 23836539 DOI: 10.1002/cmdc.201300146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 11/10/2022]
Abstract
The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5-triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the "classic" TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5-(3-octanamidoprop-1yn-1yl)-2'-deoxyuridine-5'-monophosphate (1) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the "5-alkynyl tail") extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH3 group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5-alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6-(5-(3-octanamidoprop-1-yn-1-yl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)hexyl)phosphonate (3 e) exhibited 43 % of inhibitory effect on ThyX at 50 μM. While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.
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Affiliation(s)
- Anastasia Parchina
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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15
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Laptenok SP, Bouzhir-Sima L, Lambry JC, Myllykallio H, Liebl U, Vos MH. Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX. Proc Natl Acad Sci U S A 2013; 110:8924-9. [PMID: 23671075 PMCID: PMC3670337 DOI: 10.1073/pnas.1218729110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.
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Affiliation(s)
- Sergey P. Laptenok
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Hannu Myllykallio
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Marten H. Vos
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
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16
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Mathews II. Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design. ACTA ACUST UNITED AC 2013; Suppl 12:004. [PMID: 24563811 DOI: 10.4172/2157-2526.s12-004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The identification of flavin-dependent thymidylate synthase (FDTS) as an essential enzyme and its occurrence in several pathogenic microbes opens opportunities for using FDTS enzyme as an excellent target for new antimicrobial drug discovery. In contrast to the human thymidylate synthase enzyme that utilizes methylene-tetrahydrofolate (CH2H4 folate) for the conversion of dUMP to dTMP, the microbial enzymes utilize an additional non-covalently bound FAD molecule for the hydride transfer from NAD(P)H. The structural and mechanistic differences between the human and microbial enzymes present an attractive opportunity for the design of antimicrobial compounds specific for the pathogens. We have determined the crystal structure of FDTS enzyme in complex with the methyl donor, CH2H4 folate. We describe here the structure of a FDTS mutant and compare it with other FDTS complex structures, including a FDTS-CH2H4 folate complex. We identified a conformational change essential for substrate binding and propose a strategy for the design of FDTS specific inhibitors.
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Affiliation(s)
- Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
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17
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Abstract
The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH(2)H(4)folate). Most organisms, including humans, rely on the thyA- or TYMS-encoded classic thymidylate synthase, whereas, certain microorganisms, including all Rickettsia and other pathogens, use an alternative thyX-encoded flavin-dependent thymidylate synthase (FDTS). Although several crystal structures of FDTSs have been reported, the absence of a structure with folates limits understanding of the molecular mechanism and the scope of drug design for these enzymes. Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate further elucidation of FDTSs' mechanism and the design of structure-based inhibitors as potential leads to new antimicrobial drugs.
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18
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Mishanina TV, Koehn EM, Kohen A. Mechanisms and inhibition of uracil methylating enzymes. Bioorg Chem 2012; 43:37-43. [PMID: 22172597 PMCID: PMC3315608 DOI: 10.1016/j.bioorg.2011.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
Abstract
Uracil methylation is essential for survival of organisms and passage of information from generation to generation with high fidelity. Two alternative uridyl methylation enzymes, flavin-dependent thymidylate synthase and folate/FAD-dependent RNA methyltransferase, have joined the long-known classical enzymes, thymidylate synthase and SAM-dependent RNA methyltransferase. These alternative enzymes differ significantly from their classical counterparts in structure, cofactor requirements and chemical mechanism. This review covers the available structural and mechanistic knowledge of the classical and alternative enzymes in biological uracil methylation, and offers a possibility of using inhibitors specifically aiming at microbial thymidylate production as antimicrobial drugs.
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Affiliation(s)
- Tatiana V. Mishanina
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
| | - Eric M. Koehn
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, E274 Chemistry Building, Iowa City, IA 52245, USA
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19
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Mishanina TV, Koehn EM, Conrad JA, Palfey BA, Lesley SA, Kohen A. Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase. J Am Chem Soc 2012; 134:4442-8. [PMID: 22295882 DOI: 10.1021/ja2120822] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. It has recently been shown that FDTS catalysis does not rely on an enzymatic nucleophile and that the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and it has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist efforts directed toward the rational design of inhibitors as leads for future antibiotics.
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20
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Hamdane D, Argentini M, Cornu D, Myllykallio H, Skouloubris S, Hui-Bon-Hoa G, Golinelli-Pimpaneau B. Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis. J Biol Chem 2011; 286:36268-80. [PMID: 21846722 DOI: 10.1074/jbc.m111.256966] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavoprotein TrmFO methylates specifically the C5 carbon of the highly conserved uridine 54 in tRNAs. Contrary to most methyltransferases, the 1-carbon unit transferred by TrmFO derives from 5,10-methylenetetrahydrofolate and not from S-adenosyl-L-methionine. The enzyme also employs the FAD hydroquinone as a reducing agent of the C5 methylene U54-tRNA intermediate in vitro. By analogy with the catalytic mechanism of thymidylate synthase ThyA, a conserved cysteine located near the FAD isoalloxazine ring was proposed to act as a nucleophile during catalysis. Here, we mutated this residue (Cys-53 in Bacillus subtilis TrmFO) to alanine and investigated its functional role. Biophysical characterization of this variant demonstrated the major structural role of Cys-53 in maintaining both the integrity and plasticity of the flavin binding site. Unexpectedly, gel mobility shift assays showed that, like the wild-type enzyme, the inactive C53A variant was capable of forming a covalent complex with a 5-fluorouridine-containing mini-RNA. This result confirms the existence of a covalent intermediate during catalysis but rules out a nucleophilic role for Cys-53. To identify the actual nucleophile, two other strictly conserved cysteines (Cys-192 and Cys-226) that are relatively far from the active site were replaced with alanine, and a double mutant C53A/C226A was generated. Interestingly, only mutations that target Cys-226 impeded TrmFO from forming a covalent complex and methylating tRNA. Altogether, we propose a revised mechanism for the m(5)U54 modification catalyzed by TrmFO, where Cys-226 attacks the C6 atom of the uridine, and Cys-53 plays the role of the general base abstracting the C5 proton.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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21
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Wang K, Wang Q, Chen J, Chen L, Jiang H, Shen X. Crystal structure and enzymatic characterization of thymidylate synthase X from Helicobacter pylori strain SS1. Protein Sci 2011; 20:1398-410. [PMID: 21633987 PMCID: PMC3189525 DOI: 10.1002/pro.668] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 05/23/2011] [Accepted: 05/23/2011] [Indexed: 11/09/2022]
Abstract
Thymidylate synthase X (ThyX) catalyzes the methylation of dUMP to form dTMP in bacterial life cycle and is regarded as a promising target for antibiotics discovery. Helicobacter pylori is a human pathogen associated with a number of human diseases. Here, we cloned and purified the ThyX enzyme from H. pylori SS1 strain (HpThyX). The recombinant HpThyX was discovered to exhibit the maximum activity at pH 8.5, and K(m) values of the two substrates dUMP and CH(2) H(4) folate were determined to be 15.3 ± 1.25 μM and 0.35 ± 0.18 mM, respectively. The analyzed crystal structure of HpThyX with the cofactor FAD and the substrate dUMP (at 2.31 Å) revealed that the enzyme was a tetramer bound to four dUMP and four FAD molecules. Different from the catalytic feature of the classical thymidylate synthase (ThyA), N5 atom of the FAD functioned as a nucleophile in the catalytic reaction instead of Ser84 and Ser85 residues. Our current work is expected to help better understand the structural and enzymatic features of HpThyX thus further providing valuable information for anti-H. pylori inhibitor discovery.
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Affiliation(s)
| | | | - Jing Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
| | | | | | - Xu Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghai 201203, China
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22
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Biochemical characterization of two thymidylate synthases in Corynebacterium glutamicum NCHU 87078. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1751-9. [PMID: 20595007 DOI: 10.1016/j.bbapap.2010.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 05/06/2010] [Accepted: 05/17/2010] [Indexed: 11/23/2022]
Abstract
The genome of Corynebacterium glutamicum NCHU 87078 contains two putative thymidylate synthase genes, designated CgthyA and CgthyX. These two genes were expressed in Escherichia coli NovaBlue and the expressed His(6)-tagged enzymes were purified by nickel-chelate chromatography. The purified CgThyA had a specific activity of 414 mU mg(-)(1) protein, whereas thymidylate synthase activity for CgThyX could not be detected in a functional complementation assay using a 10-day incubation period. Gel filtration chromatography and chemical cross-linking experiments showed that CgThyX may exist as a dimer in solution, unlike a typical ThyX protein with homotetrameric structure for catalytic activity. Spectroscopic analysis indicated that purified CgThyX lacked the cofactor FAD. The 2.3A resolution crystal structure of CgThyX-FAD demonstrated a loose tetramer, in which FAD is chelated between the subunits via a manner distinct from that of other flavin-dependent thymidylate synthases. Structure-based mutational studies have identified a non-conserved segment (residues 70-73) of CgThyX protein with crucial role in binding to FAD. Taken together, our biochemical and structural analyses highlight unique features of the C. glutamicum ThyX that distinguish this enzyme from ThyX proteins from other organisms. Our results also suggest that thymidylate synthesis in C. glutamicum requires ThyA but not ThyX.
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23
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Koehn EM, Kohen A. Flavin-dependent thymidylate synthase: a novel pathway towards thymine. Arch Biochem Biophys 2009; 493:96-102. [PMID: 19643076 DOI: 10.1016/j.abb.2009.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/21/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
Abstract
For several decades only one chemical pathway was known for the de novo biosynthesis of the essential DNA nucleotide, thymidylate. This reaction catalyzed by thyA or TYMS encoded thymidylate synthases is the last committed step in the biosynthesis of thymidylate and proceeds via the reductive methylation of uridylate. However, many microorganisms have recently been shown to produce a novel, flavin-dependent thymidylate synthase encoded by the thyX gene. Preliminary structural and mechanistic studies have shown substantial differences between these deoxyuridylate-methylating enzymes. Recently, both the chemical and kinetic mechanisms of FDTS have provided further insight into the distinctions between thyA and thyX encoded thymidylate synthases. Since FDTSs are found in several severe human pathogens their unusual mechanism offers a promising future for the development of antibiotic and antiviral drugs with little effect on human thymidylate biosynthesis.
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Affiliation(s)
- Eric M Koehn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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24
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25
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An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature 2009; 458:919-23. [PMID: 19370033 PMCID: PMC2759699 DOI: 10.1038/nature07973] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 02/26/2009] [Indexed: 11/15/2022]
Abstract
Biosynthesis of the DNA base thymine depends on activity of the enzyme
thymidylate synthase (TS) to catalyze the methylation of the uracil moiety of
2’-deoxyuridine-5’-monophosphate (dUMP). All known thymidylate
synthases (TSs) rely on an active site residue of the enzyme to activate
dUMP1, 2. This functionality has been demonstrated for classical TSs,
including human TS, and is instrumental in mechanism-based inhibition of these
enzymes. Here we report the first example of thymidylate biosynthesis that
occurs without an enzymatic nucleophile. This unusual biosynthetic pathway
occurs in organisms containing the thyX gene, which codes for a
flavin-dependent thymidylate synthase (FDTS), and is present in several human
pathogens3–5. Our findings indicate that the putative
active site nucleophile is not required for FDTS catalysis, and no alternative
nucleophilic residues capable of serving this function can be identified.
Instead, our findings suggest that a hydride equivalent (i.e. a proton and two
electrons) is transferred from the reduced flavin cofactor directly to the
uracil ring, followed by an isomerization of the intermediate to form the
product, 2’-deoxythymidine-5’-monophosphate (dTMP). These
observations indicate a very different chemical cascade than that of classical
TSs or any other known biological methylation. The findings and chemical
mechanism proposed here, together with available structural data, suggest that
selective inhibition of FDTSs, with little effect on human thymine biosynthesis,
should be feasible. Since several human pathogens depend on FDTS for DNA
biosynthesis, its unique mechanism makes it an attractive target for antibiotic
drugs.
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26
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Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc Natl Acad Sci U S A 2009; 106:8180-5. [PMID: 19416846 DOI: 10.1073/pnas.0901330106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
tRNAs from all 3 phylogenetic domains have a 5-methyluridine at position 54 (T54) in the T-loop. The methyl group is transferred from S-adenosylmethionine by TrmA methyltransferase in most Gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (MTHF) by TrmFO, a folate/FAD-dependent methyltransferase, in most Gram-positive bacteria and some Gram-negative bacteria. However, the catalytic mechanism remains unclear, because the crystal structure of TrmFO has not been solved. Here, we report the crystal structures of Thermus thermophilus TrmFO in its free form, tetrahydrofolate (THF)-bound form, and glutathione-bound form at 2.1-, 1.6-, and 1.05-A resolutions, respectively. TrmFO consists of an FAD-binding domain and an insertion domain, which both share structural similarity with those of GidA, an enzyme involved in the 5-carboxymethylaminomethylation of U34 of some tRNAs. However, the overall structures of TrmFO and GidA are basically different because of their distinct domain orientations, which are consistent with their respective functional specificities. In the THF complex, the pteridin ring of THF is sandwiched between the flavin ring of FAD and the imidazole ring of a His residue. This structure provides a snapshot of the folate/FAD-dependent methyl transfer, suggesting that the transferring methylene group of MTHF is located close to the redox-active N5 atom of FAD. Furthermore, we established an in vitro system to measure the methylation activity. Our TrmFO-tRNA docking model, in combination with mutational analyses, suggests a catalytic mechanism, in which the methylene of MTHF is directly transferred onto U54, and then the exocyclic methylene of U54 is reduced by FADH(2).
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27
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Flavin-dependent thymidylate synthase X limits chromosomal DNA replication. Proc Natl Acad Sci U S A 2008; 105:9948-52. [PMID: 18621705 DOI: 10.1073/pnas.0801356105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have investigated the hitherto unexplored possibility that differences in the catalytic efficiencies of thymidylate synthases ThyX and ThyA, enzymes that produce the essential DNA precursor dTMP, have influenced prokaryotic genome evolution. We demonstrate that DNA replication speed in bacteria and archaea that contain the low-activity ThyX enzyme is up to 10-fold decreased compared with species that contain the catalytically more efficient ThyA. Our statistical studies of >400 genomes indicated that ThyA proteins are preferred for the replication of large genomes, providing further evidence that the thymidylate metabolism is limiting expansion of prokaryotic genomes. Because both ThyX and ThyA participate in frequent reciprocal gene replacement events, our observations indicate that the bacterial metabolism continues to modulate the size and composition of prokaryotic genomes. We also propose that the increased kinetic efficiency of thymidylate synthesis has contributed to extending the prokaryotic evolutionary potential.
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Hunter JH, Gujjar R, Pang CKT, Rathod PK. Kinetics and ligand-binding preferences of Mycobacterium tuberculosis thymidylate synthases, ThyA and ThyX. PLoS One 2008; 3:e2237. [PMID: 18493582 PMCID: PMC2386288 DOI: 10.1371/journal.pone.0002237] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 04/14/2008] [Indexed: 11/19/2022] Open
Abstract
Background Mycobacterium tuberculosis kills approximately 2 million people each year and presents an urgent need to identify new targets and new antitubercular drugs. Thymidylate synthase (TS) enzymes from other species offer good targets for drug development and the M. tuberculosis genome contains two putative TS enzymes, a conventional ThyA and a flavin-based ThyX. In M. tuberculosis, both TS enzymes have been implicated as essential for growth, either based on drug-resistance studies or genome-wide mutagenesis screens. To facilitate future small molecule inhibitors against these proteins, a detailed enzymatic characterization was necessary. Methodology/Principal Findings After cloning, overexpression, and purification, the thymidylate-synthesizing ability of ThyA and ThyX gene products were directly confirmed by HPLC analysis of reaction products and substrate saturation kinetics were established. 5-Fluoro-2′-deoxyuridine 5′-monophosphate (FdUMP) was a potent inhibitor of both ThyA and ThyX, offering important clues to double-targeting strategies. In contrast, the folate-based 1843U89 was a potent inhibitor of ThyA but not ThyX suggesting that it should be possible to find ThyX-specific antifolates. A turnover-dependent kinetic assay, combined with the active-site titration approach of Ackermann and Potter, revealed that both M. tuberculosis enzymes had very low kcat values. One possible explanation for the low catalytic activity of M. tuberculosis ThyX is that its true biological substrates remain to be identified. Alternatively, this slow-growing pathogen, with low demands for TMP, may have evolved to down-regulate TS activities by altering the turnover rate of individual enzyme molecules, perhaps to preserve total protein quantities for other purposes. In many organisms, TS is often used as a part of larger complexes of macromolecules that control replication and DNA repair. Conclusions/Significance Thus, the present enzymatic characterization of ThyA and ThyX from M. tuberculosis provides a framework for future development of cell-active inhibitors and the biological roles of these TS enzymes in M. tuberculosis.
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Affiliation(s)
- Joshua H. Hunter
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Ramesh Gujjar
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Cullen K. T. Pang
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Ferrari S, Losasso V, Costi M. Sequence-Based Identification of Specific Drug Target Regions in the Thymidylate Synthase Enzyme Family. ChemMedChem 2008; 3:392-401. [DOI: 10.1002/cmdc.200700215] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Functional analysis of the Mycobacterium tuberculosis FAD-dependent thymidylate synthase, ThyX, reveals new amino acid residues contributing to an extended ThyX motif. J Bacteriol 2008; 190:2056-64. [PMID: 18192395 DOI: 10.1128/jb.01094-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel FAD-dependent thymidylate synthase, ThyX, is present in a variety of eubacteria and archaea, including the mycobacteria. A short motif found in all thyX genes, RHRX(7-8)S, has been identified. The three-dimensional structure of the Mycobacterium tuberculosis ThyX enzyme has been solved. Building upon this information, we used directed mutagenesis to produce 67 mutants of the M. tuberculosis thyX gene. Each enzyme was assayed to determine its ability to complement the defect in thymidine biosynthesis in a delta thyA strain of Escherichia coli. Enzymes from selected strains were then tested in vitro for their ability to catalyze the oxidation of NADPH and the release of a proton from position 5 of the pyrimidine ring of dUMP. The results defined an extended motif of amino acids essential to enzyme activity in M. tuberculosis (Y44X(24)H69X(25)R95HRX(7)S105XRYX(90)R199 [with the underlined histidine acting as the catalytic residue and the underlined serine as the nucleophile]) and provided insight into the ThyX reaction mechanism. ThyX is found in a variety of bacterial pathogens but is absent in humans, which depend upon an unrelated thymidylate synthase, ThyA. Therefore, ThyX is a potential target for development of antibacterial drugs.
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31
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Chernyshev A, Fleischmann T, Koehn E, Lesley SA, Kohen A. The relationships between oxidase and synthase activities of flavin dependent thymidylate synthase (FDTS). Chem Commun (Camb) 2007:2861-3. [PMID: 17609801 PMCID: PMC4341948 DOI: 10.1039/b700977a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New findings lead to a revised understanding of the substrates' binding order, the role of the substrate as an activator, and the observed lag phase in the FDTS catalyzed reaction.
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Affiliation(s)
| | - Todd Fleischmann
- Department of Chemistry, The University of Iowa, Iowa City, IA, USA
| | - Eric Koehn
- Department of Chemistry, The University of Iowa, Iowa City, IA, USA
| | - Scott A. Lesley
- The Joint Center for Structural Genomics at The Genomics Institute of Novartis Research Foundation, 10675 JohnJay Hopkins Drive, San Diego, California 92121, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA, USA
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32
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Chernyshev A, Fleischmann T, Kohen A. Thymidyl biosynthesis enzymes as antibiotic targets. Appl Microbiol Biotechnol 2007; 74:282-9. [PMID: 17216455 DOI: 10.1007/s00253-006-0763-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/13/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
The two long-known "classical" enzymes of uridyl-5-methylation, thymidylate synthase and ribothymidyl synthase, have been joined by two alternative methylation enzymes, flavin-dependent thymidylate synthase and folate-dependent ribothymidyl synthase. These two newly discovered enzymes have much in common: both contain flavin cofactors, utilize methylenetetrahydrofolate as a source of methyl group, and perform thymidylate synthesis via chemical pathways distinct from those of their classic counterparts. Several severe human pathogens (e.g., typhus, anthrax, tuberculosis, and more) depend on these "alternative" enzymes for reproduction. These and other distinctive properties make the alternative enzymes and their corresponding genes appealing targets for new antibiotics.
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Affiliation(s)
- Anatoly Chernyshev
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
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33
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Kim E, Simpson AGB, Graham LE. Evolutionary Relationships of Apusomonads Inferred from Taxon-Rich Analyses of 6 Nuclear Encoded Genes. Mol Biol Evol 2006; 23:2455-66. [PMID: 16982820 DOI: 10.1093/molbev/msl120] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The phylogenetic relationships of the biflagellate protist group Apusomonadidae have been unclear despite the availability of some molecular data. We analyzed sequences from 6 nuclear encoded genes-small-subunit rRNA, large-subunit rRNA, alpha-tubulin, beta-tubulin, actin, and heat shock protein 90-to infer the phylogenetic position of Apusomonas proboscidea Aléxéieff 1924. To increase the taxon richness of the study, we also obtained new sequences from representatives of several other major eukaryotic groups: Chrysochromulina sp. National Institute for Environmental Studies 1333 (Haptophyta), Cyanophora paradoxa (Glaucophyta), Goniomonas truncata (Cryptophyceae), Leucocryptos marina (Kathablepharidae), Mesostigma viride (Streptophyta, Viridiplantae), Peridinium limbatum (Alveolata), Pterosperma cristatum (Prasinophytae, Viridiplantae), Synura sphagnicola (Stramenopiles), and Thaumatomonas sp. (Rhizaria). In most individual gene phylogenies, Apusomonas branched close to either of the 2 related taxa-Opisthokonta (including animals, fungi, and choanoflagellates) or Amoebozoa. Combined analyses of all 4 protein-coding genes or all 6 studied genes strongly supported the hypothesis that Apusomonadidae is closely related to Opisthokonta (or to all other eukaryotic groups except Opisthokonta, depending on the position of the eukaryotic root). Alternative hypotheses were rejected in approximately unbiased tests at the 5% level. However, the strong phylogenetic signal supporting a specific affiliation between Apusomonadidae and Opisthokonta largely originated from the alpha-tubulin data. If alpha-tubulin is not considered, topologies in which Apusomonadidae is sister to Opisthokonta or is sister to Amoebozoa were more or less equally supported. One current model for deep eukaryotic evolution holds that eukaryotes are divided into primary "unikont" and "bikont" clades and are descended from a "uniflagellate" common ancestor. Together with other information, our data suggest instead that unikonts (=Opisthokonta and Amoebozoa) are not strictly monophyletic and are descended from biflagellate ancestors.
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Affiliation(s)
- Eunsoo Kim
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
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34
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Andreeva A, Murzin AG. Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 2006; 16:399-408. [PMID: 16650981 DOI: 10.1016/j.sbi.2006.04.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 03/28/2006] [Accepted: 04/21/2006] [Indexed: 11/24/2022]
Abstract
The functional requirement to form and maintain the active site structure probably exerts a strong selective pressure on a protein to adopt just one stable and evolutionarily conserved fold. Nonetheless, new evidence suggests the likelihood of protein fold being neither physically nor biologically invariant. Alternative folds discovered in several proteins are composed of constant and variable parts. The latter display context-dependent conformations and a tendency to form new oligomeric interfaces. In turn, oligomerisation mediates fold evolution without loss of protein function. Gene duplication breaks down homo-oligomeric symmetry and relieves the pressure to maintain the local architecture of redundant active sites; this can lead to further structural changes.
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Affiliation(s)
- Antonina Andreeva
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK
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35
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Graziani S, Bernauer J, Skouloubris S, Graille M, Zhou CZ, Marchand C, Decottignies P, van Tilbeurgh H, Myllykallio H, Liebl U. Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J Biol Chem 2006; 281:24048-57. [PMID: 16707489 DOI: 10.1074/jbc.m600745200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By using biochemical and structural analyses, we have investigated the catalytic mechanism of the recently discovered flavin-dependent thymidylate synthase ThyX from Paramecium bursaria chlorella virus-1 (PBCV-1). Site-directed mutagenesis experiments have identified several residues implicated in either NADPH oxidation or deprotonation activity of PBCV-1 ThyX. Chemical modification by diethyl pyrocarbonate and mass spectroscopic analyses identified a histidine residue (His53) crucial for NADPH oxidation and located in the vicinity of the redox active N-5 atom of the FAD ring system. Moreover, we observed that the conformation of active site key residues of PBCV-1 ThyX differs from earlier reported ThyX structures, suggesting structural changes during catalysis. Steady-state kinetic analyses support a reaction mechanism where ThyX catalysis proceeds via formation of distinct ternary complexes without formation of a methyl enzyme intermediate.
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Affiliation(s)
- Sébastien Graziani
- CNRS, UMR 7645, Laboratory of Optics and Biosciences, Ecole Polytechnique, 91128 Palaiseau, France
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36
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Zhong J, Skouloubris S, Dai Q, Myllykallio H, Barbour AG. Function and evolution of plasmid-borne genes for pyrimidine biosynthesis in Borrelia spp. J Bacteriol 2006; 188:909-18. [PMID: 16428394 PMCID: PMC1347342 DOI: 10.1128/jb.188.3.909-918.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The thyX gene for thymidylate synthase of the Lyme borreliosis (LB) agent Borrelia burgdorferi is located in a 54-kb linear plasmid. In the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (RF) agent Borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. The functions of the B. hermsii and B. burgdorferi thyX gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient Escherichia coli mutant, and in vitro, by testing their activities after purification. The B. hermsii thyX gene complemented the thyA mutation in E. coli, and purified B. hermsii ThyX protein catalyzed the conversion of dTMP from dUMP. In contrast, the B. burgdorferi ThyX protein had only weakly detectable activity in vitro, and the B. burgdorferi thyX gene did not provide complementation in vivo. The lack of activity of B. burgdorferi's ThyX protein was associated with the substitution of a cysteine for a highly conserved arginine at position 91. The B. hermsii thyX locus was further distinguished by the downstream presence in the plasmid of orthologues of nrdI, nrdE, and nrdF, which encode the subunits of ribonucleoside diphosphate reductase and which are not present in the LB agents B. burgdorferi and Borrelia garinii. Phylogenetic analysis suggested that the nrdIEF cluster of B. hermsii was acquired by horizontal gene transfer. These findings indicate that Borrelia spp. causing RF have a greater capability for de novo pyrimidine synthesis than those causing LB, thus providing a basis for some of the biological differences between the two groups of pathogens.
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Affiliation(s)
- Jianmin Zhong
- Departments of Microbiology and of Molecular Genetics and Medicine, University of California Irvine, Irvine, CA 92697-4028, USA
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37
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Kanai A, Sato A, Imoto J, Tomita M. Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. Biochem J 2006; 393:373-9. [PMID: 16176183 PMCID: PMC1383696 DOI: 10.1042/bj20050608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using a stem-loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and found that a flavin-dependent thymidylate synthase, Pf-Thy1 (Pyrococcus furiosus thymidylate synthase 1), possessed RNA-binding activity. Recombinant Pf-Thy1 was able to bind to the stem-loop structure at a high temperature (75 degrees C) with an apparent dissociation constant of 0.6 microM. A similar stem-loop RNA structure was located around the translation start AUG codon of Pf-Thy1 RNA, and gel-shift analysis revealed that Pf-Thy1 could also bind to this stem-loop structure. In vitro translation analysis using chimaeric constructs containing the stem-loop sequence in their Pf-Thy1 RNA and a luciferase reporter gene indicated that the stem-loop structure acted as an inhibitory regulator of translation by preventing the binding of its Shine-Dalgarno-like sequence by positioning it in the stem region. Addition of Pf-Thy1 into the in vitro translation system also inhibited translation. These results suggested that this class of thymidylate synthases may autoregulate their own translation in a manner analogous to that of the well characterized thymidylate synthase A proteins, although there is no significant amino acid sequence similarity between them.
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Affiliation(s)
- Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
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38
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Sampathkumar P, Turley S, Ulmer JE, Rhie HG, Sibley CH, Hol WGJ. Structure of the Mycobacterium tuberculosis flavin dependent thymidylate synthase (MtbThyX) at 2.0A resolution. J Mol Biol 2005; 352:1091-104. [PMID: 16139296 DOI: 10.1016/j.jmb.2005.07.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 07/26/2005] [Accepted: 07/28/2005] [Indexed: 11/30/2022]
Abstract
A novel flavin-dependent thymidylate synthase was identified recently as an essential gene in many archaebacteria and some pathogenic eubacteria. This enzyme, ThyX, is a potential antibacterial drug target, since humans and most eukaryotes lack the thyX gene and depend upon the conventional thymidylate synthase (TS) for their dTMP requirements. We have cloned and overexpressed the thyX gene (Rv2754c) from Mycobacterium tuberculosis in Escherichia coli. The M.tuberculosis ThyX (MtbThyX) enzyme complements the E.coli chi2913 strain that lacks its conventional TS activity. The crystal structure of the homotetrameric MtbThyX was determined in the presence of the cofactor FAD and the substrate analog, 5-bromo-2'-deoxyuridine-5'-monophosphate (BrdUMP). In the active site, which is formed by three monomers, FAD is bound in an extended conformation with the adenosine ring in a deep pocket and BrdUMP in a closed conformation near the isoalloxazine ring. Structure-based mutational studies have revealed a critical role played by residues Lys165 and Arg168 in ThyX activity, possibly by governing access to the carbon atom to be methylated of a totally buried substrate dUMP.
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39
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Chanama M, Chitnumsub P, Yuthavong Y. Subunit complementation of thymidylate synthase in Plasmodium falciparum bifunctional dihydrofolate reductase-thymidylate synthase. Mol Biochem Parasitol 2005; 139:83-90. [PMID: 15610822 DOI: 10.1016/j.molbiopara.2004.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 08/30/2004] [Accepted: 09/23/2004] [Indexed: 10/26/2022]
Abstract
Thymidylate synthase of Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) functions as a dimeric enzyme with extensive contact between the two TS domains. Structural data of PfDHFR-TS shows that the formation of the two TS active sites involves contribution of the amino acid residues from both TS domains. Arg-470 donated from the adjoining domain is shown to hydrogen-bond to dUMP, while Cys-490 is a key nucleophile for TS catalysis by attacking C-6 of dUMP. However, mutants of the two series could complement one another, giving rise to active enzyme. By means of subunit complementation assay using Arg-470 and Cys-490 mutants, it is shown that co-transformants of both TS-inactive Arg-470 and Cys-490 mutants can complement the growth of thymidine auxotroph chi2913RecA(DE3) by formation of a functional TS heterodimer contributing from both Arg-470 and Cys-490 mutant subunits. 6-[3H]-FdUMP thymidylate synthase activity assay further elaborate the essence of restoration of TS activity. The TS k(cat) value of the R470D+C490A heterodimer is decreased by half from that of the wild-type PfDHFR-TS. However, the Km values for dUMP and CH2H4folate of the R470D+C490A heterodimer are similar to those of wild-type enzyme, indicating that the catalytic efficiency of the functional TS from the R470D+C490A heterodimer is similar to the wild-type TS enzyme in P. falciparum DHFR-TS.
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Affiliation(s)
- Manee Chanama
- Department of Microbiology, Faculty of Public Health, Mahidol University, Rajvithi Road, Bangkok 10400, Thailand
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40
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Urbonavičius J, Skouloubris S, Myllykallio H, Grosjean H. Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications. Nucleic Acids Res 2005; 33:3955-64. [PMID: 16027442 PMCID: PMC1178002 DOI: 10.1093/nar/gki703] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA:m5U-54 MTase). In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N5, N10-methylenetetrahydrofolate (CH2H4folate). We have identified the gene for Bacillus subtilis tRNA:m5U-54 MTase. The encoded recombinant protein contains tightly bound flavin and is active in Escherichia coli mutant lacking m5U-54 in tRNAs and in vitro using T7 tRNA transcript as substrate. This gene is currently annotated gid in Genome Data Banks and it is here renamed trmFO. TrmFO (Gid) orthologs have also been identified in many other bacterial genomes and comparison of their amino acid sequences reveals that they are phylogenetically distinct from either ThyA or ThyX class of thymidylate synthases, which catalyze folate-dependent formation of deoxyribothymine monophosphate, the universal DNA precursor.
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Affiliation(s)
| | - Stéphane Skouloubris
- INSERM Avenir group, Institute of Genetics and Microbiology, CNRS, University Paris XIOrsay, F-91405, France
| | - Hannu Myllykallio
- INSERM Avenir group, Institute of Genetics and Microbiology, CNRS, University Paris XIOrsay, F-91405, France
| | - Henri Grosjean
- To whom correspondence should be addressed. Tel: +33 1 69823468; Fax: +33 1 69823129;
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Griffin J, Roshick C, Iliffe-Lee E, McClarty G. Catalytic mechanism of Chlamydia trachomatis flavin-dependent thymidylate synthase. J Biol Chem 2004; 280:5456-67. [PMID: 15591067 DOI: 10.1074/jbc.m412415200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we report on a Chlamydia trachomatis gene that complements the growth defect of a thymidylate synthase-deficient strain of Escherichia coli. The complementing gene encodes a 60.9-kDa protein that shows low level primary sequence homology to a new class of thymidylate-synthesizing enzymes, termed flavin-dependent thymidylate synthases (FDTS). Purified recombinant chlamydial FDTS (CTThyX) contains bound flavin. Results with site-directed mutants indicate that highly conserved arginine residues are required for flavin binding. Kinetic characterization indicates that CTThyX is active as a tetramer with NADPH, methylenetetrahydrofolate, and dUMP required as substrates, serving as source of reducing equivalents, methyl donor, and methyl acceptor, respectively. dTMP and H(4)folate are products of the reaction. Production of H(4)folate rather than H(2)folate, as in the classical thymidylate synthase reaction, eliminates the need for dihydrofolate reductase, explaining the trimethoprim-resistant phenotype displayed by thyA(-) E. coli-expressing CTThyX. In contrast to the extensively characterized thyA-encoded thymidylate synthases, which form a ternary complex with substrates dUMP and CH(2)H(4)folate and follow an ordered sequential mechanism, CTThyX follows a ping-pong kinetic mechanism involving a methyl enzyme intermediate. Mass spectrometry was used to localize the methyl group to a highly conserved arginine, and site-directed mutagenesis showed this arginine to be critical for thymidylate synthesizing activity. These differentiating characteristics clearly distinguish FDTS from ThyA, making this class of enzymes attractive targets for rational drug design.
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Affiliation(s)
- Jonathon Griffin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St., Winnipeg, Manitoba R3E 3R2, Canada
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42
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Graziani S, Xia Y, Gurnon JR, Van Etten JL, Leduc D, Skouloubris S, Myllykallio H, Liebl U. Functional analysis of FAD-dependent thymidylate synthase ThyX from Paramecium bursaria Chlorella virus-1. J Biol Chem 2004; 279:54340-7. [PMID: 15471872 DOI: 10.1074/jbc.m409121200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sequence analysis of the 330-kb double-stranded DNA genome of Paramecium bursaria chlorella virus-1 revealed an open reading frame A674R that encodes a protein with up to 53% amino acid identity to a recently discovered new class of thymidylate synthases, called ThyX. Unlike the traditional thymidylate synthase, ThyA, that uses methylenetetrahydrofolate (CH(2)H(4)folate) as both a source of the methylene group and the reductant, CH(2)H(4)folate only supplies the methylene group in ThyX-catalyzed reactions. Furthermore, ThyX only catalyzes thymidylate (dTMP) formation in the presence of reduced pyridine nucleotides and oxidized FAD. The distribution and transcription patterns of the a674r gene in Chlorella viruses were examined. The a674r gene was cloned, and the protein was expressed in Escherichia coli. Biochemical characterization of the P. bursaria chlorella virus-1 recombinant ThyX protein indicates that it is more efficient at converting dUMP to dTMP than previously studied ThyX enzymes, thus allowing more detailed mechanistic studies of the enzyme. The ThyX-dUMP complexes with bound FAD function as efficient NAD(P)H oxidases, indicating that dUMP binds to the enzyme prior to NAD(P)H. This oxidation activity is directly linked to FAD reduction. Our results indicate that ThyX-specific inhibitors can be designed that do not affect ThyA enzymes. Finally, a model is proposed for the early stages of ThyX catalysis.
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Affiliation(s)
- Sébastien Graziani
- Laboratory of Optics and Biosciences, INSERM U451-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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43
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Liu XQ, Yang J. Bacterial thymidylate synthase with intein, group II Intron, and distinctive ThyX motifs. J Bacteriol 2004; 186:6316-9. [PMID: 15342603 PMCID: PMC515151 DOI: 10.1128/jb.186.18.6316-6319.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ThyX class of thymidylate synthases was previously characterized by a common ThyX motif, RHRX7S. We report bacterial ThyX sequences having distinctive ThyX motifs, suggesting a more general ThyX motif, R/THRX7-8S. One ThyX sequence has an intein in its ThyX motif that was shown to do protein splicing and a group II intron in its gene, suggesting a hot spot for these self-splicing mobile elements.
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Affiliation(s)
- Xiang-Qin Liu
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
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