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Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. Front Microbiol 2024; 15:1369018. [PMID: 38544857 PMCID: PMC10965804 DOI: 10.3389/fmicb.2024.1369018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens-Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana. Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. Bartonella quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
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Affiliation(s)
- Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Virginie Marchand
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Yuri Motorin
- Université de Lorraine, UAR2008/US40 IBSLor, EpiRNA-Seq Core Facility and UMR7365 IMoPA, CNRS-Inserm, Biopôle UL, Nancy, France
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
- Genetic Institute, University of Florida, Gainesville, FL, United States
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2
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Quaiyum S, Sun J, Marchand V, Sun G, Reed CJ, Motorin Y, Dedon PC, Minnick MF, de Crécy-Lagard V. Mapping the tRNA Modification Landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574729. [PMID: 38260440 PMCID: PMC10802484 DOI: 10.1101/2024.01.08.574729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens- Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana . Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. B. quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
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3
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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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Yuanyuan N, Xiaobo Y, Shang W, Yutong Y, Hongrui Z, Chenyu L, Bin X, Xi Z, Chen Z, Zhiqiang S, Jingfeng W, Yun L, Pingfeng Y, Zhigang Q. Isolation and characterization of two homolog phages infecting Pseudomonas aeruginosa. Front Microbiol 2022; 13:946251. [PMID: 35935197 PMCID: PMC9348578 DOI: 10.3389/fmicb.2022.946251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteriophages (phages) are capable of infecting specific bacteria, and therefore can be used as a biological control agent to control bacteria-induced animal, plant, and human diseases. In this study, two homolog phages (named PPAY and PPAT) that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. The results of the phage plaque assay showed that PPAT plaques were transparent dots, while the PPAY plaques were translucent dots with a halo. Transmission electron microscopy results showed that PPAT (65 nm) and PPAY (60 nm) strains are similar in size and have an icosahedral head and a short tail. Therefore, these belong to the short-tailed phage family Podoviridae. One-step growth curves revealed the latent period of 20 min and burst time of 30 min for PPAT and PPAY. The burst size of PPAT (953 PFUs/infected cell) was higher than that of PPAY (457 PFUs/infected cell). Also, the adsorption rate constant of PPAT (5.97 × 10−7 ml/min) was higher than that of PPAY (1.32 × 10−7 ml/min) at 5 min. Whole-genome sequencing of phages was carried out using the Illumina HiSeq platform. The genomes of PPAT and PPAY have 54,888 and 50,154 bp, respectively. Only 17 of the 352 predicted ORFs of PPAT could be matched to homologous genes of known function. Likewise, among the 351 predicted ORFs of PPAY, only 18 ORFs could be matched to genes of established functions. Homology and evolutionary analysis indicated that PPAT and PPAY are closely related to PA11. The presence of tail fiber proteins in PPAY but not in PPAT may have contributed to the halo effect of its plaque spots. In all, PPAT and PPAY, newly discovered P. aeruginosa phages, showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
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Affiliation(s)
- Niu Yuanyuan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Xiaobo
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Shang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Yutong
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhou Hongrui
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Li Chenyu
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xue Bin
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhang Xi
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhao Chen
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shen Zhiqiang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Jingfeng
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ling Yun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- *Correspondence: Ling Yun,
| | - Yu Pingfeng
- College of Environment and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qiu Zhigang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
- Qiu Zhigang,
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5
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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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6
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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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7
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Spirescu VA, Chircov C, Grumezescu AM, Andronescu E. Polymeric Nanoparticles for Antimicrobial Therapies: An Up-To-Date Overview. Polymers (Basel) 2021; 13:724. [PMID: 33673451 PMCID: PMC7956825 DOI: 10.3390/polym13050724] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the many advancements in the pharmaceutical and medical fields and the development of numerous antimicrobial drugs aimed to suppress and destroy pathogenic microorganisms, infectious diseases still represent a major health threat affecting millions of lives daily. In addition to the limitations of antimicrobial drugs associated with low transportation rate, water solubility, oral bioavailability and stability, inefficient drug targeting, considerable toxicity, and limited patient compliance, the major cause for their inefficiency is the antimicrobial resistance of microorganisms. In this context, the risk of a pre-antibiotic era is a real possibility. For this reason, the research focus has shifted toward the discovery and development of novel and alternative antimicrobial agents that could overcome the challenges associated with conventional drugs. Nanotechnology is a possible alternative, as there is significant evidence of the broad-spectrum antimicrobial activity of nanomaterials and nanoparticles in particular. Moreover, owing to their considerable advantages regarding their efficient cargo dissolving, entrapment, encapsulation, or surface attachment, the possibility of forming antimicrobial groups for specific targeting and destruction, biocompatibility and biodegradability, low toxicity, and synergistic therapy, polymeric nanoparticles have received considerable attention as potential antimicrobial drug delivery agents. In this context, the aim of this paper is to provide an up-to-date overview of the most recent studies investigating polymeric nanoparticles designed for antimicrobial therapies, describing both their targeting strategies and their effects.
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Affiliation(s)
- Vera Alexandra Spirescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (V.A.S.); (C.C.); (E.A.)
| | - Cristina Chircov
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (V.A.S.); (C.C.); (E.A.)
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (V.A.S.); (C.C.); (E.A.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
| | - Ecaterina Andronescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (V.A.S.); (C.C.); (E.A.)
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Myllykallio H, Becker HF, Aleksandrov A. Mechanism of Naphthoquinone Selectivity of Thymidylate Synthase ThyX. Biophys J 2020; 119:2508-2516. [PMID: 33217379 DOI: 10.1016/j.bpj.2020.10.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022] Open
Abstract
Naphthoquinones (NQs) are natural and synthetic compounds with a wide range of biological activities commonly attributed to their redox activity and/or chemical reactivity. However, genetic and biochemical experiments have recently demonstrated that 2-hydroxy-NQs (2-OH-NQs) act as highly specific noncovalent inhibitors of the essential bacterial thymidylate synthase ThyX in a cellular context. We used biochemical experiments and molecular dynamics simulations to elucidate the selective inhibition mechanism of NQ inhibitors of ThyX from Mycobacterium tuberculosis (Mtb). Free energy simulations rationalized how ThyX recognizes the natural substrate dUMP in the N3-ionized form using an arginine, Arg199, in Mtb. The results further demonstrated that 2-OH-NQ, similar to dUMP, binds to ThyX in the ionized form, and the strong and selective binding of 2-OH-NQ to ThyX is also explained by electrostatic interactions with Arg199. The stronger binding of the close analog 5F-dUMP to ThyX and its inhibitory properties compared with dUMP were explained by the stronger acidity of the uracil N3 atom. Our results, therefore, revealed that the ionization of 2-OH-NQs drives their biological activities by mimicking the interactions with the natural substrate. Our observations encourage the rational design of optimized ThyX inhibitors that ultimately may serve as antibiotics.
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Affiliation(s)
- Hannu Myllykallio
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.
| | - Hubert F Becker
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France; Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
| | - Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.
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9
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Sirand-Pugnet P, Brégeon D, Béven L, Goyenvalle C, Blanchard A, Rose S, Grosjean H, Douthwaite S, Hamdane D, de Crécy-Lagard V. Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes. Biomolecules 2020; 10:E587. [PMID: 32290235 PMCID: PMC7226160 DOI: 10.3390/biom10040587] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 01/17/2023] Open
Abstract
The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Here, we investigate the evolution of 5-methyluracil synthase families in Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor. Cases of duplication and subsequent shift of function are also described. For example, most members of the Spiroplasma subgroup use the ancestral tetrahydrofolate-dependent TrmFO enzyme to catalyze the formation of m5U54 in tRNA, while a TrmFO paralog (termed RlmFO) is responsible for m5U1939 formation in 23S rRNA. RlmFO has replaced the S-adenosyl-L-methionine (SAM)-enzyme RlmD that adds the same modification in the ancestor and which is still present in mollicutes from the Hominis subgroup. Another paralog of this family, the TrmFO-like protein, has a yet unidentified function that differs from the TrmFO and RlmFO homologs. Despite having evolved towards minimal genomes, the mollicutes possess a repertoire of m5U-modifying enzymes that is highly dynamic and has undergone horizontal transfer.
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Affiliation(s)
- Pascal Sirand-Pugnet
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 quai Saint Bernard, CEDEX 05, F-75252 Paris, France; (D.B.); (C.G.)
| | - Laure Béven
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Catherine Goyenvalle
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 quai Saint Bernard, CEDEX 05, F-75252 Paris, France; (D.B.); (C.G.)
| | - Alain Blanchard
- INRAE, UMR BFP, University Bordeaux, 33882 Bordeaux Villenave D’Ornon, France; (L.B.); (A.B.)
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (S.R.); (S.D.)
| | - Henri Grosjean
- Institute for Integrative Biology of the Cell (I2BC), French Atomic Energy and Energy Commission Alternatives, CNRS, Paris-Sud University, Paris-Saclay University, Gif-sur-Yvette CEDEX, 91198 Paris, France;
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (S.R.); (S.D.)
| | - Djemel Hamdane
- Laboratory of Biological Process Chemistry, CNRS-UMR 8229, College De France, Sorbonne University, 11 Place Marcelin Berthelot, CEDEX 05, 75231 Paris, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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10
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Dozova N, Lacombat F, Bou-Nader C, Hamdane D, Plaza P. Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO. Phys Chem Chem Phys 2019; 21:8743-8756. [PMID: 30968076 DOI: 10.1039/c8cp06072j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis. Sci Rep 2019; 9:13617. [PMID: 31541138 PMCID: PMC6754364 DOI: 10.1038/s41598-019-48940-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022] Open
Abstract
Thymidylate synthase A (ThyA) is the key enzyme involved in the folate pathway in Mycobacterium tuberculosis. Mutation of key residues of ThyA enzyme which are involved in interaction with substrate 2′-deoxyuridine-5′-monophosphate (dUMP), cofactor 5,10-methylenetetrahydrofolate (MTHF), and catalytic site have caused para-aminosalicylic acid (PAS) resistance in TB patients. Focusing on R127L, L143P, C146R, L172P, A182P, and V261G mutations, including wild-type, we performed long molecular dynamics (MD) simulations in explicit solvent to investigate the molecular principles underlying PAS resistance due to missense mutations. We found that these mutations lead to (i) extensive changes in the dUMP and MTHF binding sites, (ii) weak interaction of ThyA enzyme with dUMP and MTHF by inducing conformational changes in the structure, (iii) loss of the hydrogen bond and other atomic interactions and (iv) enhanced movement of protein atoms indicated by principal component analysis (PCA). In this study, MD simulations framework has provided considerable insight into mutation induced conformational changes in the ThyA enzyme of Mycobacterium.
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