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Swindell J, Dos Santos PC. Interactions with sulfur acceptors modulate the reactivity of cysteine desulfurases and define their physiological functions. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119794. [PMID: 39033933 DOI: 10.1016/j.bbamcr.2024.119794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/21/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Sulfur-containing biomolecules such as [FeS] clusters, thiamin, biotin, molybdenum cofactor, and sulfur-containing tRNA nucleosides are essential for various biochemical reactions. The amino acid l-cysteine serves as the major sulfur source for the biosynthetic pathways of these sulfur-containing cofactors in prokaryotic and eukaryotic systems. The first reaction in the sulfur mobilization involves a class of pyridoxal-5'-phosphate (PLP) dependent enzymes catalyzing a Cys:sulfur acceptor sulfurtransferase reaction. The first half of the catalytic reaction involves a PLP-dependent CS bond cleavage, resulting in a persulfide enzyme intermediate. The second half of the reaction involves the subsequent transfer of the thiol group to a specific acceptor molecule, which is responsible for the physiological role of the enzyme. Structural and biochemical analysis of these Cys sulfurtransferase enzymes shows that specific protein-protein interactions with sulfur acceptors modulate their catalytic reactivity and restrict their biochemical functions.
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Affiliation(s)
- Jimmy Swindell
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, United States of America
| | - Patricia C Dos Santos
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, United States of America.
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Jamontas R, Laurynėnas A, Povilaitytė D, Meškys R, Aučynaitė A. RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification. Nucleic Acids Res 2024; 52:10543-10562. [PMID: 39166491 PMCID: PMC11417400 DOI: 10.1093/nar/gkae716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
In this study, we present an extensive analysis of a widespread group of bacterial tRNA de-modifying enzymes, dubbed RudS, which consist of a TudS desulfidase fused to a Domain of Unknown Function 1722 (DUF1722). RudS enzymes exhibit specific de-modification activity towards the 4-thiouridine modification (s4U) in tRNA molecules, as indicated by our experimental findings. The heterologous overexpression of RudS genes in Escherichia coli significantly reduces the tRNA 4-thiouridine content and diminishes UVA-induced growth delay, indicating the enzyme's role in regulating photosensitive tRNA s4U modification. Through a combination of protein modeling, docking studies, and molecular dynamics simulations, we have identified amino acid residues involved in catalysis and tRNA binding. Experimental validation through targeted mutagenesis confirms the TudS domain as the catalytic core of RudS, with the DUF1722 domain facilitating tRNA binding in the anticodon region. Our results suggest that RudS tRNA modification eraser proteins may play a role in regulating tRNA during prokaryotic stress responses.
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Affiliation(s)
- Rapolas Jamontas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Deimantė Povilaitytė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
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Martin Říhová J, Gupta S, Darby AC, Nováková E, Hypša V. Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance. mSystems 2023; 8:e0070623. [PMID: 37750682 PMCID: PMC10654098 DOI: 10.1128/msystems.00706-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Insects that live exclusively on vertebrate blood utilize symbiotic bacteria as a source of essential compounds, e.g., B vitamins. In louse flies, the most frequent symbiont originated in genus Arsenophonus, known from a wide range of insects. Here, we analyze genomic traits, phylogenetic origins, and metabolic capacities of 11 Arsenophonus strains associated with louse flies. We show that in louse flies, Arsenophonus established symbiosis in at least four independent events, reaching different stages of symbiogenesis. This allowed for comparative genomic analysis, including convergence of metabolic capacities. The significance of the results is twofold. First, based on a comparison of independently originated Arsenophonus symbioses, it determines the importance of individual B vitamins for the insect host. This expands our theoretical insight into insect-bacteria symbiosis. The second outcome is of methodological significance. We show that the comparative approach reveals artifacts that would be difficult to identify based on a single-genome analysis.
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Affiliation(s)
- Jana Martin Říhová
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Shruti Gupta
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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He N, Zhou J, Bimai O, Oltmanns J, Ravanat JL, Velours C, Schünemann V, Fontecave M, Golinelli-Pimpaneau B. A subclass of archaeal U8-tRNA sulfurases requires a [4Fe-4S] cluster for catalysis. Nucleic Acids Res 2022; 50:12969-12978. [PMID: 36533440 PMCID: PMC9825150 DOI: 10.1093/nar/gkac1156] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/22/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
Sulfuration of uridine 8, in bacterial and archaeal tRNAs, is catalyzed by enzymes formerly known as ThiI, but renamed here TtuI. Two different classes of TtuI proteins, which possess a PP-loop-containing pyrophosphatase domain that includes a conserved cysteine important for catalysis, have been identified. The first class, as exemplified by the prototypic Escherichia coli enzyme, possesses an additional C-terminal rhodanese domain harboring a second cysteine, which serves to form a catalytic persulfide. Among the second class of TtuI proteins that do not possess the rhodanese domain, some archaeal proteins display a conserved CXXC + C motif. We report here spectroscopic and enzymatic studies showing that TtuI from Methanococcus maripaludis and Pyrococcus furiosus can assemble a [4Fe-4S] cluster that is essential for tRNA sulfuration activity. Moreover, structural modeling studies, together with previously reported mutagenesis experiments of M. maripaludis TtuI, indicate that the [4Fe-4S] cluster is coordinated by the three cysteines of the CXXC + C motif. Altogether, our results raise a novel mechanism for U8-tRNA sulfuration, in which the cluster is proposed to catalyze the transfer of sulfur atoms to the activated tRNA substrate.
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Affiliation(s)
| | | | - Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Jonathan Oltmanns
- Technische Universität Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES UMR 5819, F-38000 Grenoble, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France,Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Volker Schünemann
- Technische Universität Kaiserslautern, Fachbereich Physik, Erwin-Schrödinger-Str. 46, D-67663 Kaiserslautern, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
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Ran M, Li Q, Xin Y, Ma S, Zhao R, Wang M, Xun L, Xia Y. Rhodaneses minimize the accumulation of cellular sulfane sulfur to avoid disulfide stress during sulfide oxidation in bacteria. Redox Biol 2022; 53:102345. [PMID: 35653932 PMCID: PMC9163753 DOI: 10.1016/j.redox.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 10/27/2022] Open
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Glutaredoxin-like protein (GLP)-a novel bacteria sulfurtransferase that protects cells against cyanide and oxidative stresses. Appl Microbiol Biotechnol 2020; 104:5477-5492. [PMID: 32307572 DOI: 10.1007/s00253-020-10491-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 02/01/2023]
Abstract
The pathogen Xylella fastidiosa belongs to the Xanthomonadaceae family, a large group of Gram-negative bacteria that cause diseases in many economically important crops. A predicted gene, annotated as glutaredoxin-like protein (glp), was found to be highly conserved among the genomes of different genera within this family and highly expressed in X. fastidiosa. Analysis of the GLP protein sequences revealed three protein domains: one similar to monothiol glutaredoxins (Grx), an Fe-S cluster and a thiosulfate sulfurtransferase/rhodanese domain (Tst/Rho), which is generally involved in sulfur metabolism and cyanide detoxification. To characterize the biochemical properties of GLP, we expressed and purified the X. fastidiosa recombinant GLP enzyme. Grx activity and Fe-S cluster formation were not observed, while an evaluation of Tst/Rho enzymatic activity revealed that GLP can detoxify cyanide and transfer inorganic sulfur to acceptor molecules in vitro. The biological activity of GLP relies on the cysteine residues in the Grx and Tst/Rho domains (Cys33 and Cys266, respectively), and structural analysis showed that GLP and GLPC266S were able to form high molecular weight oligomers (> 600 kDa), while replacement of Cys33 with Ser destabilized the quaternary structure. In vivo heterologous enzyme expression experiments in Escherichia coli revealed that GLP can protect bacteria against high concentrations of cyanide and hydrogen peroxide. Finally, phylogenetic analysis showed that homologous glp genes are distributed across Gram-negative bacterial families with conservation of the N- to C-domain order. However, no eukaryotic organism contains this enzyme. Altogether, these results suggest that GLP is an important enzyme with cyanide-decomposing and sulfurtransferase functions in bacteria, whose presence in eukaryotes we could not observe, representing a promising biological target for new pharmaceuticals.
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Senior NJ, Sasidharan K, Saint RJ, Scott AE, Sarkar-Tyson M, Ireland PM, Bullifent HL, Rong Yang Z, Moore K, Oyston PCF, Atkins TP, Atkins HS, Soyer OS, Titball RW. An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions. BMC Microbiol 2017; 17:163. [PMID: 28732479 PMCID: PMC5521123 DOI: 10.1186/s12866-017-1073-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/17/2017] [Indexed: 01/07/2023] Open
Abstract
Background The World Health Organization has categorized plague as a re-emerging disease and the potential for Yersinia pestis to also be used as a bioweapon makes the identification of new drug targets against this pathogen a priority. Environmental temperature is a key signal which regulates virulence of the bacterium. The bacterium normally grows outside the human host at 28 °C. Therefore, understanding the mechanisms that the bacterium used to adapt to a mammalian host at 37 °C is central to the development of vaccines or drugs for the prevention or treatment of human disease. Results Using a library of over 1 million Y. pestis CO92 random mutants and transposon-directed insertion site sequencing, we identified 530 essential genes when the bacteria were cultured at 28 °C. When the library of mutants was subsequently cultured at 37 °C we identified 19 genes that were essential at 37 °C but not at 28 °C, including genes which encode proteins that play a role in enabling functioning of the type III secretion and in DNA replication and maintenance. Using genome-scale metabolic network reconstruction we showed that growth conditions profoundly influence the physiology of the bacterium, and by combining computational and experimental approaches we were able to identify 54 genes that are essential under a broad range of conditions. Conclusions Using an integrated computational-experimental approach we identify genes which are required for growth at 37 °C and under a broad range of environments may be the best targets for the development of new interventions to prevent or treat plague in humans. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1073-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicola J Senior
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK
| | - Kalesh Sasidharan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard J Saint
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Andrew E Scott
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Mitali Sarkar-Tyson
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK.,Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, 6009, Australia
| | - Philip M Ireland
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Helen L Bullifent
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Z Rong Yang
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK
| | - Karen Moore
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK
| | - Petra C F Oyston
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Timothy P Atkins
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK.,Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Helen S Atkins
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK.,Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 OJQ, UK
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard W Titball
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4SB, UK.
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Hepowit NL, de Vera IMS, Cao S, Fu X, Wu Y, Uthandi S, Chavarria NE, Englert M, Su D, Sӧll D, Kojetin DJ, Maupin-Furlow JA. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J 2017; 283:3567-3586. [PMID: 27459543 DOI: 10.1111/febs.13819] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/17/2016] [Accepted: 07/22/2016] [Indexed: 01/01/2023]
Abstract
Here we provide the first detailed biochemical study of a noncanonical E1-like enzyme with broad specificity for cognate ubiquitin-like (Ubl) proteins that mediates Ubl protein modification and sulfur mobilization to form molybdopterin and thiolated tRNA. Isothermal titration calorimetry and in vivo analyses proved useful in discovering that environmental conditions, ATP binding, and Ubl type controlled the mechanism of association of the Ubl protein with its cognate E1-like enzyme (SAMP and UbaA of the archaeon Haloferax volcanii, respectively). Further analysis revealed that ATP hydrolysis triggered the formation of thioester and peptide bonds within the Ubl:E1-like complex. Importantly, the thioester was an apparent precursor to Ubl protein modification but not sulfur mobilization. Comparative modeling to MoeB/ThiF guided the discovery of key residues within the adenylation domain of UbaA that were needed to bind ATP as well as residues that were specifically needed to catalyze the downstream reactions of sulfur mobilization and/or Ubl protein modification. UbaA was also found to be Ubl-automodified at lysine residues required for early (ATP binding) and late (sulfur mobilization) stages of enzyme activity revealing multiple layers of autoregulation. Cysteine residues, distinct from the canonical E1 'active site' cysteine, were found important in UbaA function supporting a model that this noncanonical E1 is structurally flexible in its active site to allow Ubl~adenylate, Ubl~E1-like thioester and cysteine persulfide(s) intermediates to form.
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Affiliation(s)
- Nathaniel L Hepowit
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Ian Mitchelle S de Vera
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Shiyun Cao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Xian Fu
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Yifei Wu
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sivakumar Uthandi
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Sӧll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA. .,Genetics Institute, University of Florida, Gainesville, FL, USA.
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11
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Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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12
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Veerareddygari GR, Klusman TC, Mueller EG. Characterization of the catalytic disulfide bond in E. coli 4-thiouridine synthetase to elucidate its functional quaternary structure. Protein Sci 2016; 25:1737-43. [PMID: 27293139 DOI: 10.1002/pro.2965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022]
Abstract
4-Thiouridine at position 8 in prokaryotic tRNA serves as a photosensor for near-UV light, and the posttranscriptional conversion of uridine to 4-thiouridine is catalyzed by the 4-thiouridine synthetases (s(4) US, also named ThiI), which fall into two classes that differ in the presence of a C-terminal rhodanese homology domain. A cysteine residue in this domain first bears a persulfide group and then forms a disulfide bond with a cysteine residue that is conserved in both classes of s(4) US. Recent crystal structures suggest that s(4) US dimerizes in the presence of RNA substrate with domains from each subunit contributing to the binding and reaction of one RNA molecule, which raises the question of whether the catalytic disulfide bond in the longer class of s(4) US is formed within or between subunits. The E. coli enzyme is the best-characterized member of the longer class of s(4) US, and it was examined after quantitative installation of the disulfide bond during a single catalytic turnover. Gel electrophoresis and proteolysis/MALDI-MS results strongly imply that the disulfide bond forms within a single subunit, which provides a vital constraint for the structural modeling of the class of s(4) US with an appended rhodanese homology domain and the design and interpretation of experiments to probe the dynamics of the domains during catalysis.
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Affiliation(s)
| | - Thomas C Klusman
- Department of Chemistry, University of Louisville, Louisville, Kentucky, 40205
| | - Eugene G Mueller
- Department of Chemistry, University of Louisville, Louisville, Kentucky, 40205
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13
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Kenyon LJ, Meulia T, Sabree ZL. Habitat visualization and genomic analysis of "Candidatus Pantoea carbekii," the primary symbiont of the brown marmorated stink bug. Genome Biol Evol 2015; 7:620-35. [PMID: 25587021 PMCID: PMC4350177 DOI: 10.1093/gbe/evv006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phytophagous pentatomid insects can negatively impact agricultural productivity and the brown marmorated stink bug (Halyomorpha halys) is an emerging invasive pest responsible for damage to many fruit crops and ornamental plants in North America. Many phytophagous stink bugs, including H. halys, harbor gammaproteobacterial symbionts that likely contribute to host development, and characterization of symbiont transmission/acquisition and their contribution to host fitness may offer alternative strategies for managing pest species. “Candidatus Pantoea carbekii” is the primary occupant of gastric ceca lumina flanking the distal midgut of H. halys insects and it is acquired each generation when nymphs feed on maternal extrachorion secretions following hatching. Insects prevented from symbiont uptake exhibit developmental delays and aberrant behaviors. To infer contributions of Ca. P. carbekii to H. halys, the complete genome was sequenced and annotated from a North American H. halys population. Overall, the Ca. P. carbekii genome is nearly one-fourth (1.2 Mb) that of free-living congenerics, and retains genes encoding many functions that are potentially host-supportive. Gene content reflects patterns of gene loss/retention typical of intracellular mutualists of plant-feeding insects. Electron and fluorescence in situ microscopic imaging of H. halys egg surfaces revealed that maternal extrachorion secretions were populated with Ca. P. carbekii cells. The reported findings detail a transgenerational mode of symbiont transmission distinct from that observed for intracellular insect mutualists and illustrate the potential additive functions contributed by the bacterial symbiont to this important agricultural pest.
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Affiliation(s)
- Laura J Kenyon
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
| | - Tea Meulia
- Molecular and Cellular Imaging Center, Ohio Agricultural Research and Development Center and the Department of Plant Pathology, The Ohio State University
| | - Zakee L Sabree
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University
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Lim S, Baek W, Lee SC. Identification and functional roles of CaDIN1 in abscisic acid signaling and drought sensitivity. PLANT MOLECULAR BIOLOGY 2014; 86:513-25. [PMID: 25149469 DOI: 10.1007/s11103-014-0242-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/19/2014] [Indexed: 06/03/2023]
Abstract
Plants frequently face challenges caused by various abiotic stresses, including drought, and have evolved defense mechanisms to counteract the deleterious effects of these stresses. The phytohormone abscisic acid (ABA) is involved in signal transduction pathways that mediate defense responses of plants to abiotic stress. Here, we report a new function of the CaDIN1 protein in defense responses to abiotic stress. The CaDIN1 gene was strongly induced in pepper leaves exposed to ABA, NaCl, and drought stresses. CaDIN1 proteins share high sequence homology with other known DIN1 proteins and are localized in chloroplasts. We generated CaDIN1-silenced peppers and overexpressing transgenic Arabidopsis plants and evaluated their response to ABA and drought stress. Virus-induced gene silencing of CaDIN1 in pepper plants conferred enhanced tolerance to drought stress, which was accompanied by low levels of lipid peroxidation in dehydrated leaves. CaDIN1-overexpressing transgenic plants exhibited reduced sensitivity to ABA during seed germination and seedling stages. Transgenic plants were more vulnerable to drought than that by the wild-type plants because of decreased expression of ABA responsive stress-related genes and reduced stomatal closure in response to ABA. Together, these results suggest that CaDIN1 modulates drought sensitivity through ABA-mediated cell signaling.
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Affiliation(s)
- Sohee Lim
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, 156-756, Republic of Korea
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15
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Shared-intermediates in the biosynthesis of thio-cofactors: Mechanism and functions of cysteine desulfurases and sulfur acceptors. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1470-80. [PMID: 25447671 DOI: 10.1016/j.bbamcr.2014.10.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/07/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
Abstract
Cysteine desulfurases utilize a PLP-dependent mechanism to catalyze the first step of sulfur mobilization in the biosynthesis of sulfur-containing cofactors. Sulfur activation and integration into thiocofactors involve complex mechanisms and intricate biosynthetic schemes. Cysteine desulfurases catalyze sulfur-transfer reactions from l-cysteine to sulfur acceptor molecules participating in the biosynthesis of thio-cofactors, including Fe-S clusters, thionucleosides, thiamin, biotin, and molybdenum cofactor. The proposed mechanism of cysteine desulfurases involves the PLP-dependent cleavage of the C-S bond from l-cysteine via the formation of a persulfide enzyme intermediate, which is considered the hallmark step in sulfur mobilization. The subsequent sulfur transfer reaction varies with the class of cysteine desulfurase and sulfur acceptor. IscS serves as a mecca for sulfur incorporation into a network of intertwined pathways for the biosynthesis of thio-cofactors. The involvement of a single enzyme interacting with multiple acceptors, the recruitment of shared-intermediates partaking roles in multiple pathways, and the participation of Fe-S enzymes denote the interconnectivity of pathways involving sulfur trafficking. In Bacillus subtilis, the occurrence of multiple cysteine desulfurases partnering with dedicated sulfur acceptors partially deconvolutes the routes of sulfur trafficking and assigns specific roles for these enzymes. Understanding the roles of promiscuous vs. dedicated cysteine desulfurases and their partnership with shared-intermediates in the biosynthesis of thio-cofactors will help to map sulfur transfer events across interconnected pathways and to provide insight into the hierarchy of sulfur incorporation into biomolecules. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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16
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The cysteine desulfhydrase CdsH is conditionally required for sulfur mobilization to the thiamine thiazole in Salmonella enterica. J Bacteriol 2014; 196:3964-70. [PMID: 25182497 DOI: 10.1128/jb.02159-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Thiamine pyrophosphate is a required coenzyme that contains a mechanistically important sulfur atom. In Salmonella enterica, sulfur is trafficked to both thiamine biosynthesis and 4-thiouridine biosynthesis by the enzyme ThiI using persulfide (R-S-S-H) chemistry. It was previously reported that a thiI mutant strain could grow independent of exogenous thiamine in the presence of cysteine, suggesting there was a second mechanism for sulfur mobilization. Data reported here show that oxidation products of cysteine rescue the growth of a thiI mutant strain by a mechanism that requires the transporter YdjN and the cysteine desulfhydrase CdsH. The data are consistent with a model in which sulfide produced by CdsH reacts with cystine (Cys-S-S-Cys), S-sulfocysteine (Cys-S-SO3 (-)), or another disulfide to form a small-molecule persulfide (R-S-S-H). We suggest that this persulfide replaced ThiI by donating sulfur to the thiamine sulfur carrier protein ThiS. This model describes a potential mechanism used for sulfur trafficking in organisms that lack ThiI but are capable of thiamine biosynthesis.
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17
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Liu Y, Zhu X, Nakamura A, Orlando R, Söll D, Whitman WB. Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis. J Biol Chem 2012; 287:36683-92. [PMID: 22904325 DOI: 10.1074/jbc.m112.405688] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
4-Thiouridine (s(4)U) is a conserved modified nucleotide at position 8 of bacterial and archaeal tRNAs and plays a role in protecting cells from near-UV killing. Escherichia coli employs the following two enzymes for its synthesis: the cysteine desulfurase IscS, which forms a Cys persulfide enzyme adduct from free Cys; and ThiI, which adenylates U8 and transfers sulfur from IscS to form s(4)U. The C-terminal rhodanese-like domain (RLD) of ThiI is responsible for the sulfurtransferase activity. The mechanism of s(4)U biosynthesis in archaea is not known as many archaea lack cysteine desulfurase and an RLD of the putative ThiI. Using the methanogenic archaeon Methanococcus maripaludis, we show that deletion of ThiI (MMP1354) abolished the biosynthesis of s(4)U but not of thiamine. MMP1354 complements an Escherichia coli ΔthiI mutant for s(4)U formation, indicating that MMP1354 is sufficient for sulfur incorporation into s(4)U. In the absence of an RLD, MMP1354 uses Cys(265) and Cys(268) located in the PP-loop pyrophosphatase domain to generate persulfide and disulfide intermediates for sulfur transfer. In vitro assays suggest that S(2-) is a physiologically relevant sulfur donor for s(4)U formation catalyzed by MMP1354 (K(m) for Na(2)S is ∼1 mm). Thus, methanogenic archaea developed a strategy for sulfur incorporation into s(4)U that differs from bacteria; this may be an adaptation to life in sulfide-rich environments.
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Affiliation(s)
- Yuchen Liu
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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18
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The tsetse fly obligate mutualist Wigglesworthia morsitans alters gene expression and population density via exogenous nutrient provisioning. Appl Environ Microbiol 2012; 78:7792-7. [PMID: 22904061 DOI: 10.1128/aem.02052-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate mutualist Wigglesworthia morsitans provisions nutrients to tsetse flies. The symbiont's response to thiamine (B(1)) supplementation of blood meals, specifically towards the regulation of thiamine biosynthesis and population density, is described. Despite an ancient symbiosis and associated genome tailoring, Wigglesworthia responds to nutrient availability, potentially accommodating a decreased need.
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19
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Functional Analysis of Bacillus subtilis Genes Involved in the Biosynthesis of 4-Thiouridine in tRNA. J Bacteriol 2012; 194:4933-40. [PMID: 22773787 DOI: 10.1128/jb.00842-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ThiI has been identified as an essential enzyme involved in the biosynthesis of thiamine and the tRNA thionucleoside modification, 4-thiouridine. In Escherichia coli and Salmonella enterica, ThiI acts as a sulfurtransferase, receiving the sulfur donated from the cysteine desulfurase IscS and transferring it to the target molecule or additional sulfur carrier proteins. However, in Bacillus subtilis and most species from the Firmicutes phylum, ThiI lacks the rhodanese domain that contains the site responsible for the sulfurtransferase activity. The lack of the gene encoding for a canonical IscS cysteine desulfurase and the presence of a short sequence of ThiI in these bacteria pointed to mechanistic differences involving sulfur trafficking reactions in both biosynthetic pathways. Here, we have carried out functional analysis of B. subtilis thiI and the adjacent gene, nifZ, encoding for a cysteine desulfurase. Gene inactivation experiments in B. subtilis indicate the requirement of ThiI and NifZ for the biosynthesis of 4-thiouridine, but not thiamine. In vitro synthesis of 4-thiouridine by ThiI and NifZ, along with labeling experiments, suggests the occurrence of an alternate transient site for sulfur transfer, thus obviating the need for a rhodanese domain. In vivo complementation studies in E. coli IscS- or ThiI-deficient strains provide further support for specific interactions between NifZ and ThiI. These results are compatible with the proposal that B. subtilis NifZ and ThiI utilize mechanistically distinct and mutually specific sulfur transfer reactions.
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20
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Begley TP, Ealick SE, McLafferty FW. Thiamin biosynthesis: still yielding fascinating biological chemistry. Biochem Soc Trans 2012; 40:555-60. [PMID: 22616866 PMCID: PMC3771315 DOI: 10.1042/bst20120084] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present paper describes the biosynthesis of the thiamin thiazole in Bacillus subtilis and Saccharomyces cerevisiae. The two pathways are quite different: in B. subtilis, the thiazole is formed by an oxidative condensation of glycine, deoxy-D-xylulose 5-phosphate and a protein thiocarboxylate, whereas, in S. cerevisiae, the thiazole is assembled from glycine, NAD and Cys205 of the thiazole synthase.
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Affiliation(s)
- Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, U.S.A.
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21
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The danger of annotation by analogy: most "thiI" genes play no role in thiamine biosynthesis. J Bacteriol 2011; 193:4574-5. [PMID: 21742874 DOI: 10.1128/jb.05666-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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