1
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Johnstone MA, Self WT. Clostridioides difficile exploits xanthine and uric acid as nutrients by utilizing a selenium-dependent catabolic pathway. Microbiol Spectr 2024:e0084424. [PMID: 39166854 DOI: 10.1128/spectrum.00844-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/21/2024] [Indexed: 08/23/2024] Open
Abstract
Selenium is a trace element that plays critical roles in redox biology; it is typically incorporated into "selenoproteins" as the 21st amino acid selenocysteine. Additionally, selenium exists as a labile non-selenocysteine cofactor in a small subset of selenoproteins known as selenium-dependent molybdenum hydroxylases (SDMHs). In purinolytic clostridia, SDMHs are implicated in the degradation of hypoxanthine, xanthine, and uric acid for carbon and nitrogen. While SDMHs have been biochemically analyzed, the genes responsible for the insertion and maturation of the selenium cofactor lack characterization. In this study, we utilized the nosocomial pathogen Clostridioides difficile as a genetic model to begin characterizing this poorly understood selenium utilization pathway and its role in the catabolism of host-derived purines. We first observed that C. difficile could utilize hypoxanthine, xanthine, or uric acid to overcome a growth defect in a minimal medium devoid of glycine and threonine. However, strains lacking selenophosphate synthetase (selD mutants) still grew poorly in the presence of xanthine and uric acid, suggesting a selenium-dependent purinolytic process. Previous computational studies have identified yqeB and yqeC as potential candidates for cofactor maturation, so we subsequently deleted each gene using CRISPR-Cas9 technology. We surprisingly found that the growth of the ΔyqeB mutant in response to each purine was similar to the behavior of the selD mutants, while the ΔyqeC mutant exhibited no obvious phenotype. Our results suggest an important role for YqeB in selenium-dependent purine catabolism and also showcase C. difficile as an appropriate model organism to study the biological use of selenium.IMPORTANCEThe apparent modification of bacterial molybdenum hydroxylases with a catalytically essential selenium cofactor is the least understood mechanism of selenium incorporation. Selenium-dependent molybdenum hydroxylases play an important role in scavenging carbon and nitrogen from purines for purinolytic clostridia. Here, we used Clostridioides difficile as a genetic platform to begin dissecting the selenium cofactor trait and found genetic evidence for a selenium-dependent purinolytic pathway. The absence of selD or yqeB-a predicted genetic marker for the selenium cofactor trait-resulted in impaired growth on xanthine and uric acid, known substrates for selenium-dependent molybdenum hydroxylases. Our findings provide a genetic foundation for future research of this pathway and suggest a novel metabolic strategy for C. difficile to scavenge host-derived purines from the gut.
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Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - William T Self
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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2
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Kayrouz CM, Seyedsayamdost MR. Enzymatic strategies for selenium incorporation into biological molecules. Curr Opin Chem Biol 2024; 81:102495. [PMID: 38954947 DOI: 10.1016/j.cbpa.2024.102495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/09/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
The trace element selenium (Se) is essential to the physiology of most organisms on the planet. The most well documented of Se's biological forms are selenoproteins, where selenocysteine often serves as the catalytic center for crucial redox processes. Se is also found in several other classes of biological molecules, including nucleic acids, sugars, and modified amino acids, although its role in the function of these metabolites is less understood. Despite its prevalence, only a small number of Se-specific biosynthetic pathways have been discovered. Around half of these were first characterized in the past three years, suggesting that the selenometabolome may be more diverse than previously appreciated. Here, we review the recent advances in our understanding of this intriguing biochemical space, and discuss prospects for future discovery efforts.
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Affiliation(s)
- Chase M Kayrouz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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3
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Funkner K, Poehlein A, Jehmlich N, Egelkamp R, Daniel R, von Bergen M, Rother M. Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis. mSystems 2024; 9:e0133823. [PMID: 38591896 PMCID: PMC11097638 DOI: 10.1128/msystems.01338-23] [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: 12/11/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Methanococcus maripaludis utilizes selenocysteine- (Sec-) containing proteins (selenoproteins), mostly active in the organism's primary energy metabolism, methanogenesis. During selenium depletion, M. maripaludis employs a set of enzymes containing cysteine (Cys) instead of Sec. The genes coding for these Sec-/Cys-containing isoforms were the only genes known of which expression is influenced by the selenium status of the cell. Using proteomics and transcriptomics, approx. 7% and 12%, respectively, of all genes/proteins were found differentially expressed/synthesized in response to the selenium supply. Some of the genes identified involve methanogenesis, nitrogenase functions, and putative transporters. An increase of transcript abundance for putative transporters under selenium depletion indicated the organism's effort to tap into alternative sources of selenium. M. maripaludis is known to utilize selenite and dimethylselenide as selenium sources. To expand this list, a selenium-responsive reporter strain was assessed with nine other, environmentally relevant selenium species. While the effect of some was very similar to that of selenite, others were effectively utilized at lower concentrations. Conversely, selenate and seleno-amino acids were only utilized at unphysiologically high concentrations and two compounds were not utilized at all. To address the role of the selenium-regulated putative transporters, M. maripaludis mutant strains lacking one or two of the putative transporters were tested for the capability to utilize the different selenium species. Of the five putative transporters analyzed by loss-of-function mutagenesis, none appeared to be absolutely required for utilizing any of the selenium species tested, indicating they have redundant and/or overlapping specificities or are not dedicated selenium transporters. IMPORTANCE While selenium metabolism in microorganisms has been studied intensively in the past, global gene expression approaches have not been employed so far. Furthermore, the use of different selenium sources, widely environmentally interconvertible via biotic and abiotic processes, was also not extensively studied before. Methanococcus maripaludis JJ is ideally suited for such analyses, thanks to its known selenium usage and available genetic tools. Thus, an overall view on the selenium regulon of M. maripaludis was obtained via transcriptomic and proteomic analyses, which inspired further experimentation. This led to demonstrating the use of selenium sources M. maripaludis was previously not known to employ. Also, an attempt-although so far unsuccessful-was made to pinpoint potential selenium transporter genes, in order to deepen our understanding of trace element utilization in this important model organism.
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Affiliation(s)
- Katrina Funkner
- Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH–UFZ, Leipzig, Germany
| | - Richard Egelkamp
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH–UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | - Michael Rother
- Faculty of Biology, Technische Universität Dresden, Dresden, Germany
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4
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Huang B, Xiao Y, Zhang Y. Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery. THE ISME JOURNAL 2024; 18:wrae111. [PMID: 38896033 PMCID: PMC11227280 DOI: 10.1093/ismejo/wrae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024]
Abstract
Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed >400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.
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Affiliation(s)
- Biyan Huang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, Guangdong Province, P. R. China
| | - Yao Xiao
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, Guangdong Province, P. R. China
| | - Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, Guangdong Province, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, Guangdong Province, P. R. China
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5
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Sonego JM, de Diego SI, Szajnman SH, Gallo-Rodriguez C, Rodriguez JB. Organoselenium Compounds: Chemistry and Applications in Organic Synthesis. Chemistry 2023; 29:e202300030. [PMID: 37378970 DOI: 10.1002/chem.202300030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 06/29/2023]
Abstract
Selenium, originally described as a toxin, turns out to be a crucial trace element for life that appears as selenocysteine and its dimer, selenocystine. From the point of view of drug developments, selenium-containing drugs are isosteres of sulfur and oxygen with the advantage that the presence of the selenium atom confers antioxidant properties and high lipophilicity, which would increase cell membrane permeation leading to better oral bioavailability. In this article, we have focused on the relevant features of the selenium atom, above all, the corresponding synthetic approaches to access a variety of organoselenium molecules along with the proposed reaction mechanisms. The preparation and biological properties of selenosugars, including selenoglycosides, selenonucleosides, selenopeptides, and other selenium-containing compounds will be treated. We have attempted to condense the most important aspects and interesting examples of the chemistry of selenium into a single article.
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Affiliation(s)
- Juan M Sonego
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Sheila I de Diego
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Sergio H Szajnman
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Carola Gallo-Rodriguez
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), C1428EHA, Buenos Aires, Argentina
| | - Juan B Rodriguez
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
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6
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Yu Q, Ran M, Xin Y, Liu H, Liu H, Xia Y, Xun L. The Rhodanese PspE Converts Thiosulfate to Cellular Sulfane Sulfur in Escherichia coli. Antioxidants (Basel) 2023; 12:antiox12051127. [PMID: 37237993 DOI: 10.3390/antiox12051127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Hydrogen sulfide (H2S) and its oxidation product zero-valent sulfur (S0) play important roles in animals, plants, and bacteria. Inside cells, S0 exists in various forms, including polysulfide and persulfide, which are collectively referred to as sulfane sulfur. Due to the known health benefits, the donors of H2S and sulfane sulfur have been developed and tested. Among them, thiosulfate is a known H2S and sulfane sulfur donor. We have previously reported that thiosulfate is an effective sulfane sulfur donor in Escherichia coli; however, it is unclear how it converts thiosulfate to cellular sulfane sulfur. In this study, we showed that one of the various rhodaneses, PspE, in E. coli was responsible for the conversion. After the thiosulfate addition, the ΔpspE mutant did not increase cellular sulfane sulfur, but the wild type and the complemented strain ΔpspE::pspE increased cellular sulfane sulfur from about 92 μM to 220 μM and 355 μM, respectively. LC-MS analysis revealed a significant increase in glutathione persulfide (GSSH) in the wild type and the ΔpspE::pspE strain. The kinetic analysis supported that PspE was the most effective rhodanese in E. coli in converting thiosulfate to glutathione persulfide. The increased cellular sulfane sulfur alleviated the toxicity of hydrogen peroxide during E. coli growth. Although cellular thiols might reduce the increased cellular sulfane sulfur to H2S, increased H2S was not detected in the wild type. The finding that rhodanese is required to convert thiosulfate to cellular sulfane sulfur in E. coli may guide the use of thiosulfate as the donor of H2S and sulfane sulfur in human and animal tests.
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Affiliation(s)
- Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Mingxue Ran
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Yuping Xin
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Honglei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- School of Molecular Biosciences, Washington State University, Pullman, WA 991647520, USA
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7
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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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8
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Kayrouz CM, Huang J, Hauser N, Seyedsayamdost MR. Biosynthesis of selenium-containing small molecules in diverse microorganisms. Nature 2022; 610:199-204. [PMID: 36071162 DOI: 10.1038/s41586-022-05174-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/02/2022] [Indexed: 01/02/2023]
Abstract
Selenium is an essential micronutrient in diverse organisms. Two routes are known for its insertion into proteins and nucleic acids, via selenocysteine and 2-selenouridine, respectively1. However, despite its importance, pathways for specific incorporation of selenium into small molecules have remained elusive. Here we use a genome-mining strategy in various microorganisms to uncover a widespread three-gene cluster that encodes a dedicated pathway for producing selenoneine, the selenium analogue of the multifunctional molecule ergothioneine2,3. We elucidate the reactions of all three proteins and uncover two novel selenium-carbon bond-forming enzymes and the biosynthetic pathway for production of a selenosugar, which is an unexpected intermediate en route to the final product. Our findings expand the scope of biological selenium utilization, suggest that the selenometabolome is more diverse than previously thought, and set the stage for the discovery of other selenium-containing natural products.
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Affiliation(s)
- Chase M Kayrouz
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Jonathan Huang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Nicole Hauser
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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9
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Buonvino S, Arciero I, Melino S. Thiosulfate-Cyanide Sulfurtransferase a Mitochondrial Essential Enzyme: From Cell Metabolism to the Biotechnological Applications. Int J Mol Sci 2022; 23:ijms23158452. [PMID: 35955583 PMCID: PMC9369223 DOI: 10.3390/ijms23158452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Thiosulfate: cyanide sulfurtransferase (TST), also named rhodanese, is an enzyme widely distributed in both prokaryotes and eukaryotes, where it plays a relevant role in mitochondrial function. TST enzyme is involved in several biochemical processes such as: cyanide detoxification, the transport of sulfur and selenium in biologically available forms, the restoration of iron–sulfur clusters, redox system maintenance and the mitochondrial import of 5S rRNA. Recently, the relevance of TST in metabolic diseases, such as diabetes, has been highlighted, opening the way for research on important aspects of sulfur metabolism in diabetes. This review underlines the structural and functional characteristics of TST, describing the physiological role and biomedical and biotechnological applications of this essential enzyme.
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10
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Kulik K, Sadowska K, Wielgus E, Pacholczyk-Sienicka B, Sochacka E, Nawrot B. 2-Selenouridine, a Modified Nucleoside of Bacterial tRNAs, Its Reactivity in the Presence of Oxidizing and Reducing Reagents. Int J Mol Sci 2022; 23:ijms23147973. [PMID: 35887319 PMCID: PMC9325004 DOI: 10.3390/ijms23147973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023] Open
Abstract
The 5-substituted 2-selenouridines are natural components of the bacterial tRNA epitranscriptome. Because selenium-containing biomolecules are redox-active entities, the oxidation susceptibility of 2-selenouridine (Se2U) was studied in the presence of hydrogen peroxide under various conditions and compared with previously reported data for 2-thiouridine (S2U). It was found that Se2U is more susceptible to oxidation and converted in the first step to the corresponding diselenide (Se2U)2, an unstable intermediate that decomposes to uridine and selenium. The reversibility of the oxidized state of Se2U was demonstrated by the efficient reduction of (Se2U)2 to Se2U in the presence of common reducing agents. Thus, the 2-selenouridine component of tRNA may have antioxidant potential in cells because of its ability to react with both cellular ROS components and reducing agents. Interestingly, in the course of the reactions studied, we found that (Se2U)2 reacts with Se2U to form new ‘oligomeric nucleosides′ as linear and cyclic byproducts.
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Affiliation(s)
- Katarzyna Kulik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (E.W.); (B.N.)
- Correspondence: ; Tel.: +48-(42)-68-03-215
| | - Klaudia Sadowska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.S.); (B.P.-S.); (E.S.)
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (E.W.); (B.N.)
| | - Barbara Pacholczyk-Sienicka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.S.); (B.P.-S.); (E.S.)
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.S.); (B.P.-S.); (E.S.)
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (E.W.); (B.N.)
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11
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Haruehanroengra P, Zheng YY, Ma G, Lan TH, Hassan AEA, Zhou Y, Sheng J. Probing the Substrate Requirements of the in vitro Geranylation Activity of Selenouridine Synthase (SelU). Chembiochem 2022; 23:e202200089. [DOI: 10.1002/cbic.202200089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/31/2022] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ya Ying Zheng
- University at Albany Chemistry 1400 Washington Ave.Life Science 2033B 12222 Albany UNITED STATES
| | - Guolin Ma
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | - Tien-Hung Lan
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | | | - Yubin Zhou
- Texas A&M University System Health Science Center College of Medicine: Texas A&M University College of Medicine Bioscience and Technology UNITED STATES
| | - Jia Sheng
- University at Albany State University of New York Chemistry 1400 Washington Ave.LSRB 2033B 12222 Albany UNITED STATES
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12
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Szczupak P, Sierant M, Wielgus E, Radzikowska-Cieciura E, Kulik K, Krakowiak A, Kuwerska P, Leszczynska G, Nawrot B. Escherichia coli tRNA 2-Selenouridine Synthase (SelU): Elucidation of Substrate Specificity to Understand the Role of S-Geranyl-tRNA in the Conversion of 2-Thio- into 2-Selenouridines in Bacterial tRNA. Cells 2022; 11:cells11091522. [PMID: 35563829 PMCID: PMC9105526 DOI: 10.3390/cells11091522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
The bacterial enzyme tRNA 2-selenouridine synthase (SelU) is responsible for the conversion of 5-substituted 2-thiouridine (R5S2U), present in the anticodon of some bacterial tRNAs, into 5-substituted 2-selenouridine (R5Se2U). We have already demonstrated using synthetic RNAs that transformation S2U→Se2U is a two-step process, in which the S2U-RNA is geranylated and the resulting geS2U-RNA is selenated. Currently, the question is how SelU recognizes its substrates and what the cellular pathway of R5S2U→R5Se2U conversion is in natural tRNA. In the study presented here, we characterized the SelU substrate requirements, identified SelU-associated tRNAs and their specific modifications in the wobble position. Finally, we explained the sequence of steps in the selenation of tRNA. The S2U position within the RNA chain, the flanking sequence of the modification, and the length of the RNA substrate, all have a key influence on the recognition by SelU. MST data on the affinity of SelU to individual RNAs confirmed the presumed process. SelU binds the R5S2U-tRNA and then catalyzes its geranylation to the R5geS2U-tRNA, which remains bound to the enzyme and is selenated in the next step of the transformation. Finally, the R5Se2U-tRNA leaves the enzyme and participates in the translation process. The enzyme does not directly catalyze the R5S2U-tRNA selenation and the R5geS2U-tRNA is the intermediate product in the linear sequence of reactions.
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Affiliation(s)
- Patrycja Szczupak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
| | - Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
- Correspondence: ; Tel.: +48-(42)-680-32-72
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
| | - Katarzyna Kulik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
| | - Paulina Kuwerska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (P.K.); (G.L.)
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (P.K.); (G.L.)
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (P.S.); (E.W.); (E.R.-C.); (K.K.); (A.K.); (B.N.)
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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: 6] [Impact Index Per Article: 3.0] [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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14
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Szczupak P, Radzikowska-Cieciura E, Kulik K, Madaj R, Sierant M, Krakowiak A, Nawrot B. Escherichia coli tRNA 2-selenouridine synthase SelU selects its prenyl substrate to accomplish its enzymatic function. Bioorg Chem 2022; 122:105739. [DOI: 10.1016/j.bioorg.2022.105739] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/09/2022] [Indexed: 12/15/2022]
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15
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Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. RSC Chem Biol 2021; 2:990-1003. [PMID: 34458821 PMCID: PMC8341892 DOI: 10.1039/d1cb00038a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification location and cellular function, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobases with an emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating sulfur modifications is to aid the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapies. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Ying Wu
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- Department of Biological Science, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
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Wells M, Basu P, Stolz JF. The physiology and evolution of microbial selenium metabolism. Metallomics 2021; 13:6261189. [PMID: 33930157 DOI: 10.1093/mtomcs/mfab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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Wu W, Li D, Feng X, Zhao F, Li C, Zheng S, Lyu J. A pan-cancer study of selenoprotein genes as promising targets for cancer therapy. BMC Med Genomics 2021; 14:78. [PMID: 33706760 PMCID: PMC7948377 DOI: 10.1186/s12920-021-00930-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/26/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The most important health benefit of selenium (Se) is in the prevention and control of cancer. Glutathione peroxidases (GPXs) and thioredoxin reductases (TXNRDs) are selenoenzymes that are thought to play a role in oxidative stress. The differential expression of genes of the TXNRD and GPX families is closely related to carcinogenesis and the occurrence of cancer. This study comprehensively analyzed the expression profiles of seven genes in the TXNRD and GPX families, in terms of their correlations with patient survival and immune-cell subtypes, tumor microenvironment, and drug sensitivity. RESULTS The expression profiles of genes in the TXNRD and GPX families differ between different types of cancer, and also between and within individual cancer cases. The expression levels of the seven analyzed genes are related to the overall survival of patients. The TXNRD1 and TXNRD3 genes are mainly related to poor prognoses, while other genes are related to good or poor prognoses depending on the type of cancer. All of the genes were found to be correlated to varying degrees with immune-cell subtypes, level of mechanistic cell infiltration, and tumor cell stemness. The TXNRD1, GPX1, and GPX2 genes may exert dual effects in tumor mutagenesis and development, while the TXNRD1, GPX1, GPX2, and GPX3 genes were found to be related to drug sensitivity or the formation of drug resistance. CONCLUSIONS The results will greatly help in identifying the association between genes and tumorigenesis, especially in the immune response, tumor microenvironment, and drug resistance, and very important when attempting to identify new therapeutic targets.
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Affiliation(s)
- Wentao Wu
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Daning Li
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiaojie Feng
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Fanfan Zhao
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Chengzhuo Li
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Shuai Zheng
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China
| | - Jun Lyu
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of Clinical Research, The First Affiliated Hospital of Jinan University, 613 Whampoa Avenue, Tianhe District, Guangzhou, China.
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China.
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18
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Johnstone MA, Nelson SJ, O'Leary C, Self WT. Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase. Biochimie 2021; 182:166-176. [PMID: 33444662 DOI: 10.1016/j.biochi.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/15/2022]
Abstract
Selenium is a vital micronutrient in many organisms. While traces are required for microbial utilization, excess amounts are toxic; thus, selenium can be regarded as a biological double-edged sword. Selenium is chemically similar to the essential element sulfur, but curiously, evolution has selected the former over the latter for a subset of oxidoreductases. Enzymes involved in sulfur metabolism are less discriminate in terms of preventing selenium incorporation; however, its specific incorporation into selenoproteins reveals a highly discriminate process that is not completely understood. We have identified SclA, a NifS-like protein in the nosocomial pathogen, Enterococcus faecalis, and characterized its enzymatic activity and specificity for l-selenocysteine over l-cysteine. It is known that Asp-146 is required for selenocysteine specificity in the human selenocysteine lyase. Thus, using computational biology, we compared the bacterial and mammalian enzymes and identified His-100, an Asp-146 ortholog in SclA, and generated site-directed mutants in order to study the residue's potential role in the l-selenocysteine discrimination mechanism. The proteins were overexpressed, purified, and characterized for their biochemical properties. All mutants exhibited varying Michaelis-Menten behavior towards l-selenocysteine, but His-100 was not found to be essential for this activity. Additionally, l-cysteine acted as a competitive inhibitor of all enzymes with higher affinity than l-selenocysteine. Finally, we discovered that SclA exhibited low activity with l-cysteine as a poor substrate regardless of mutations. We conclude that His-100 is not required for l-selenocysteine specificity, underscoring the inherent differences in discriminatory mechanisms between bacterial NifS-like proteins and mammalian selenocysteine lyases.
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Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Samantha J Nelson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Christine O'Leary
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - William T Self
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA.
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Wells M, Stolz JF. Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology. FEMS Microbiol Ecol 2020; 96:5921172. [DOI: 10.1093/femsec/fiaa209] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
ABSTRACTSelenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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20
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Wang Y, Ehsan M, Huang J, Aimulajiang K, Yan R, Song X, Xu L, Li X. Characterization of a rhodanese homologue from Haemonchus contortus and its immune-modulatory effects on goat immune cells in vitro. Parasit Vectors 2020; 13:454. [PMID: 32894178 PMCID: PMC7487571 DOI: 10.1186/s13071-020-04333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Modulation of the host immune response by nematode parasites has been widely reported. Rhodaneses (thiosulfate: cyanide sulfurtransferases) are present in a wide range of organisms, such as archaea, bacteria, fungi, plants and animals. Previously, it was reported that a rhodanese homologue could be bound by goat peripheral blood mononuclear cells (PBMCs) in vivo. METHODS In the present study, we cloned and produced a recombinant rhodanese protein originating from Haemonchus contortus (rHCRD), a parasitic nematode of small ruminants. rHCRD was co-incubated with goat PBMCs to assess its immunomodulatory effects on proliferation, apoptosis and cytokine secretion. RESULTS We verified that the natural HCRD protein localized predominantly to the bowel wall and body surface of the parasite. We further demonstrated that serum produced by goats artificially infected with H. contortus successfully recognized rHCRD, which bound to goat PBMCs. rHCRD suppressed proliferation of goat PBMCs stimulated by concanavalin A but did not induce apoptosis in goat PBMCs. The production of TNF-α and IFN-γ decreased significantly, whereas secretion of IL-10 and TGF-β1 increased, in goat PBMCs after exposure to rHCRD. rHCRD also inhibited phagocytosis by goat monocytes. Moreover, rHCRD downregulated the expression of major histocompatibility complex (MHC)-II on goat monocytes in a dose-dependent manner, but did not alter MHC-I expression. CONCLUSIONS These results propose a possible immunomodulatory target that may help illuminate the interactions between parasites and their hosts at the molecular level and reveal innovative protein species as candidate drug and vaccine targets.
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Affiliation(s)
- Yujian Wang
- School of Life Science, Huizhou University, Huizhou, 516007, People's Republic of China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Muhammad Ehsan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jianmei Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kalibixiati Aimulajiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - RuoFeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - XiaoKai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - LiXin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - XiangRui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons. Int J Mol Sci 2020; 21:ijms21082882. [PMID: 32326096 PMCID: PMC7216251 DOI: 10.3390/ijms21082882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022] Open
Abstract
5-Substituted 2-selenouridines (R5Se2U) are post-transcriptional modifications present in the first anticodon position of transfer RNA. Their functional role in the regulation of gene expression is elusive. Here, we present efficient syntheses of 5-methylaminomethyl-2-selenouridine (1, mnm5Se2U), 5-carboxymethylaminomethyl-2-selenouridine (2, cmnm5Se2U), and Se2U (3) alongside the crystal structure of the latter nucleoside. By using pH-dependent potentiometric titration, pKa values for the N3H groups of 1–3 were assessed to be significantly lower compared to their 2-thio- and 2-oxo-congeners. At physiological conditions (pH 7.4), Se2-uridines 1 and 2 preferentially adopted the zwitterionic form (ZI, ca. 90%), with the positive charge located at the amino alkyl side chain and the negative charge at the Se2-N3-O4 edge. As shown by density functional theory (DFT) calculations, this ZI form efficiently bound to guanine, forming the so-called “new wobble base pair”, which was accepted by the ribosome architecture. These data suggest that the tRNA anticodons with wobble R5Se2Us may preferentially read the 5′-NNG-3′ synonymous codons, unlike their 2-thio- and 2-oxo-precursors, which preferentially read the 5′-NNA-3′ codons. Thus, the interplay between the levels of U-, S2U- and Se2U-tRNA may have a dominant role in the epitranscriptomic regulation of gene expression via reading of the synonymous 3′-A- and 3′-G-ending codons.
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Farukh M. Comparative genomic analysis of selenium utilization traits in different marine environments. J Microbiol 2020; 58:113-122. [PMID: 31993987 DOI: 10.1007/s12275-020-9250-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/02/2019] [Accepted: 10/31/2019] [Indexed: 11/25/2022]
Abstract
Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.
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Affiliation(s)
- Muhammad Farukh
- Department of Biotechnology, School of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Hongshan District, Wuhan, 430074, P. R. China.
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, P. R. China.
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Abstract
Antibiotic persistence, the noninherited tolerance of a subpopulation of bacteria to high levels of antibiotics, is a bet-hedging phenomenon with broad clinical implications. Indeed, the isolation of bacteria with substantially increased persistence rates from chronic infections suggests that evolution of hyperpersistence is a significant factor in clinical therapy resistance. However, the pathways that lead to hyperpersistence and the underlying cellular states have yet to be systematically studied. Here, we show that laboratory evolution can lead to increase in persistence rates by orders of magnitude for multiple independently evolved populations of Escherichia coli and that the driving mutations are highly enriched in translation-related genes. Furthermore, two distinct adaptive mutations converge on concordant transcriptional changes, including increased population heterogeneity in the expression of several genes. Cells with extreme expression of these genes showed dramatic differences in persistence rates, enabling isolation of subpopulations in which a substantial fraction of cells are persisters. Expression analysis reveals coherent regulation of specific pathways that may be critical to establishing the hyperpersistence state. Hyperpersister mutants can thus enable the systematic molecular characterization of this unique physiological state, a critical prerequisite for developing antipersistence strategies.IMPORTANCE Bacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates remain largely unknown. Here, we utilized experimental evolution to select for Escherichia coli mutants that have more than a thousandfold increase in persistence rates. We discovered that a variety of individual mutations to translation-related processes are causally involved. Furthermore, we found that these mutations lead to population heterogeneity in the expression of specific genes. We show that this can be used to isolate populations in which the majority of bacteria are persisters, thereby enabling systems-level characterization of this fascinating and clinically significant microbial phenomenon.
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Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability. Nat Commun 2019; 10:2858. [PMID: 31253794 PMCID: PMC6599085 DOI: 10.1038/s41467-019-10750-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 05/30/2019] [Indexed: 11/09/2022] Open
Abstract
In bacterial tRNAs, 5-carboxymethoxyuridine (cmo5U) and its derivatives at the first position of the anticodon facilitate non-Watson-Crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expanding decoding capabilities. However, their biogenesis and physiological roles remained to be investigated. Using reverse genetics and comparative genomics, we identify two factors responsible for 5-hydroxyuridine (ho5U) formation, which is the first step of the cmo5U synthesis: TrhP (formerly known as YegQ), a peptidase U32 family protein, is involved in prephenate-dependent ho5U formation; and TrhO (formerly known as YceA), a rhodanese family protein, catalyzes oxygen-dependent ho5U formation and bypasses cmo5U biogenesis in a subset of tRNAs under aerobic conditions. E. coli strains lacking both trhP and trhO exhibit a temperature-sensitive phenotype, and decode codons ending in G (GCG and UCG) less efficiently than the wild-type strain. These findings confirm that tRNA hydroxylation ensures efficient decoding during protein synthesis.
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25
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Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10. J Bacteriol 2019; 201:JB.00614-18. [PMID: 30642986 DOI: 10.1128/jb.00614-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/03/2019] [Indexed: 11/20/2022] Open
Abstract
The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 μM, a V max of 23 ± 2.5 μM min-1, and a k cat of 23 ± 2.68 s-1 These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.
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26
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Zhang Y, Ying H, Xu Y. Comparative genomics and metagenomics of the metallomes. Metallomics 2019; 11:1026-1043. [DOI: 10.1039/c9mt00023b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent achievements and advances in comparative genomic and metagenomic analyses of trace metals were reviewed and discussed.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
| | - Huimin Ying
- Department of Endocrinology
- Hangzhou Xixi Hospital
- Hangzhou
- P. R. China
| | - Yinzhen Xu
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
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27
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Na J, Jung J, Bang J, Lu Q, Carlson BA, Guo X, Gladyshev VN, Kim J, Hatfield DL, Lee BJ. Selenophosphate synthetase 1 and its role in redox homeostasis, defense and proliferation. Free Radic Biol Med 2018; 127:190-197. [PMID: 29715549 DOI: 10.1016/j.freeradbiomed.2018.04.577] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
Selenophosphate synthetase (SEPHS) synthesizes selenophosphate, the active selenium donor, using ATP and selenide as substrates. SEPHS was initially identified and isolated from bacteria and has been characterized in many eukaryotes and archaea. Two SEPHS paralogues, SEPHS1 and SEPHS2, occur in various eukaryotes, while prokaryotes and archaea have only one form of SEPHS. Between the two isoforms in eukaryotes, only SEPHS2 shows catalytic activity during selenophosphate synthesis. Although SEPHS1 does not contain any significant selenophosphate synthesis activity, it has been reported to play an essential role in regulating cellular physiology. Prokaryotic SEPHS contains a cysteine or selenocysteine (Sec) at the catalytic domain. However, in eukaryotes, SEPHS1 contains other amino acids such as Thr, Arg, Gly, or Leu at the catalytic domain, and SEPHS2 contains only a Sec. Sequence comparisons, crystal structure analyses, and ATP hydrolysis assays suggest that selenophosphate synthesis occurs in two steps. In the first step, ATP is hydrolyzed to produce ADP and gamma-phosphate. In the second step, ADP is further hydrolyzed and selenophosphate is produced using gamma-phosphate and selenide. Both SEPHS1 and SEPHS2 have ATP hydrolyzing activities, but Cys or Sec is required in the catalytic domain for the second step of reaction. The gene encoding SEPHS1 is divided by introns, and five different splice variants are produced by alternative splicing in humans. SEPHS1 mRNA is abundant in rapidly proliferating cells such as embryonic and cancer cells and its expression is induced by various stresses including oxidative stress and salinity stress. The disruption of the SEPHS1 gene in mice or Drosophila leads to the inhibition of cell proliferation, embryonic lethality, and morphological changes in the embryos. Targeted removal of SEPHS1 mRNA in insect, mouse, and human cells also leads to common phenotypic changes similar to those observed by in vivo gene knockout: the inhibition of cell growth/proliferation, the accumulation of hydrogen peroxide in mammals and an unidentified reactive oxygen species (ROS) in Drosophila, and the activation of a defense system. Hydrogen peroxide accumulation in SEPHS1-deficient cells is mainly caused by the down-regulation of genes involved in ROS scavenging, and leads to the inhibition of cell proliferation and survival. However, the mechanisms underlying SEPHS1 regulation of redox homeostasis are still not understood.
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Affiliation(s)
- Jiwoon Na
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jisu Jung
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeyoung Bang
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Qiao Lu
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bradley A Carlson
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiong Guo
- School of Public Health, Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jinhong Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dolph L Hatfield
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Byeong Jae Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Rother M, Quitzke V. Selenoprotein synthesis and regulation in Archaea. Biochim Biophys Acta Gen Subj 2018; 1862:2451-2462. [DOI: 10.1016/j.bbagen.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023]
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29
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Sierant M, Leszczynska G, Sadowska K, Komar P, Radzikowska-Cieciura E, Sochacka E, Nawrot B. Escherichia coli
tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via
S-geranylated-intermediate. FEBS Lett 2018; 592:2248-2258. [DOI: 10.1002/1873-3468.13124] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
| | | | - Klaudia Sadowska
- Institute of Organic Chemistry; Lodz University of Technology; Poland
| | - Patrycja Komar
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
| | | | - Elzbieta Sochacka
- Institute of Organic Chemistry; Lodz University of Technology; Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies; Polish Academy of Sciences; Lodz Poland
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30
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Cambridge JM, Blinkova AL, Salvador Rocha EI, Bode Hernández A, Moreno M, Ginés-Candelaria E, Goetz BM, Hunicke-Smith S, Satterwhite E, Tucker HO, Walker JR. Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages. PLoS One 2018; 13:e0189673. [PMID: 29293521 PMCID: PMC5749712 DOI: 10.1371/journal.pone.0189673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/30/2017] [Indexed: 01/21/2023] Open
Abstract
Clostridium taeniosporum, a non-pathogenic anaerobe closely related to the C. botulinum Group II members, was isolated from Crimean lake silt about 60 years ago. Its endospores are surrounded by an encasement layer which forms a trunk at one spore pole to which about 12–14 large, ribbon-like appendages are attached. The genome consists of one 3,264,813 bp, circular chromosome (with 26.6% GC) and three plasmids. The chromosome contains 2,892 potential protein coding sequences: 2,124 have specific functions, 147 have general functions, 228 are conserved but without known function and 393 are hypothetical based on the fact that no statistically significant orthologs were found. The chromosome also contains 101 genes for stable RNAs, including 7 rRNA clusters. Over 84% of the protein coding sequences and 96% of the stable RNA coding regions are oriented in the same direction as replication. The three known appendage genes are located within a single cluster with five other genes, the protein products of which are closely related, in terms of sequence, to the known appendage proteins. The relatedness of the deduced protein products suggests that all or some of the closely related genes might code for minor appendage proteins or assembly factors. The appendage genes might be unique among the known clostridia; no statistically significant orthologs were found within other clostridial genomes for which sequence data are available. The C. taeniosporum chromosome contains two functional prophages, one Siphoviridae and one Myoviridae, and one defective prophage. Three plasmids of 5.9, 69.7 and 163.1 Kbp are present. These data are expected to contribute to future studies of developmental, structural and evolutionary biology and to potential industrial applications of this organism.
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Affiliation(s)
- Joshua M. Cambridge
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Alexandra L. Blinkova
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Erick I. Salvador Rocha
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Addys Bode Hernández
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Maday Moreno
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Edwin Ginés-Candelaria
- Department of Natural Sciences, Health & Wellness, Miami Dade College-Wolfson Campus, Miami, FL, United States of America
| | - Benjamin M. Goetz
- Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX, United States of America
| | - Scott Hunicke-Smith
- Genomic Sequencing and Analysis Facility, Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Ed Satterwhite
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - Haley O. Tucker
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
| | - James R. Walker
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas, Austin, TX, United States of America
- * E-mail:
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31
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Miller WG, Yee E, Lopes BS, Chapman MH, Huynh S, Bono JL, Parker CT, Strachan NJC, Forbes KJ. Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism. Genome Biol Evol 2017; 9:1843-1858. [PMID: 28854596 PMCID: PMC5570042 DOI: 10.1093/gbe/evx093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.
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Affiliation(s)
- William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Bruno S Lopes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - James L Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA
| | - Norval J C Strachan
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, United Kingdom
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32
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Tang T, Ji C, Yang Z, Liu F, Xie S. Involvement of the Macrobrachium nipponense rhodanese homologue 2, MnRDH2 in innate immunity and antioxidant defense. FISH & SHELLFISH IMMUNOLOGY 2017; 70:327-334. [PMID: 28882803 DOI: 10.1016/j.fsi.2017.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/27/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
In Macrobrachium nipponense, the rhodanese homologue 2 (MnRDH2) gene codes for a single rhodanese domain protein. Considering the lack of information on the biological role of the ubiquitous rhodaneses in invertebrate, we examined the functions of MnRDH2 using both in silico and in vitro approaches. Quantitative PCR analysis of different tissues indicated that expression of MnRDH2 was enriched in hepatopancreas, in which bacterial challenge by Aeromonas hydrophila induced MnRDH2 expression. Knocking down MnRDH2 by RNA interference caused significant accumulations of reactive oxygen species and malondialdehyde (MDA). Using Escherichia coli (DE3), we expressed MnRDH2 and the mutant MnRDH2C78A, in which the predicted catalytic cysteine was mutated to alanine, and found significant rodanese activity of the recombinant MnRDH2 in vitro, but not for the mutant rMnRDH2C78A. We observed that rMnRDH2 was able to significantly increase tolerance of the host bacteria to oxidative stressor phenazine methosulfate. These results suggest that MnRDH2 might have the potential to buffer general levels of oxidants via regulation of redox reactions. In conclusion, our study begins to hint a possible biological functionality of MnRDH2 as a redox switch to activate defensive activities against oxidative damage, which helps host in maintaining the cellular redox balance. These characteristics will facilitate future investigations into the physiological functions for invertebrate rhodanese family genes.
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Affiliation(s)
- Ting Tang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Congcong Ji
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zilan Yang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Fengsong Liu
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
| | - Song Xie
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
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Haruehanroengra P, Vangaveti S, Ranganathan SV, Wang R, Chen A, Sheng J. Nature's Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity. ACS Chem Biol 2017; 12:1504-1513. [PMID: 28418649 DOI: 10.1021/acschembio.7b00108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recently discovered geranyl modification on the 2-thio position of wobble U34 residues in tRNAGlu, tRNALys, and tRNAGln in several bacteria has been found to enhance the U:G pairing specificity and reduce the frameshifting error during translation. It is a fundamentally interesting question why nature chose a C10 terpene group in tRNA systems. In this study, we explore the significance of the terpene length on base-paring stability and specificity using a series of 2-thiouridine analogues containing different lengths of carbon chains, namely, methyl- (C1), dimethylallyl- (C5), and farnesyl-modified (C15) 2-thiothymidines in a DNA duplex. Our thermal denaturation studies indicate that the relatively long chain length of ≥ C10 is required to maintain the base-pairing discrimination of thymidine between G and A. The results from our molecular dynamics simulations show that in the T:G-pair-containing duplex, the geranyl and farnesyl groups fit into the minor groove and stabilize the overall duplex stability. This effect cannot be achieved by the shorter carbon chains such as methyl and dimethylallyl groups. For a duplex containing a T:A pair, the terpene groups disrupt both hydrogen bonding and stacking interactions by pushing the opposite A out of the helical structure. Overall, as the terpene chain length increases, the xT:G pair stabilizes the duplex, whereas the xT:A pair causes destabilization, indicating the evolutionary significance of the long terpene group on base-pairing specificity and codon recognition.
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Affiliation(s)
- Phensinee Haruehanroengra
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Sweta Vangaveti
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Srivathsan V. Ranganathan
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Rui Wang
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alan Chen
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Jia Sheng
- Department
of Chemistry and ‡The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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34
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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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35
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Wang R, Haruehanroengra P, Sheng J. Synthesis of Geranyl‐2‐Thiouridine‐Modified RNA. ACTA ACUST UNITED AC 2017; 68:4.72.1-4.72.13. [DOI: 10.1002/cpnc.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rui Wang
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York Albany New York
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York Albany New York
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York Albany New York
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36
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Payne NC, Geissler A, Button A, Sasuclark AR, Schroll AL, Ruggles EL, Gladyshev VN, Hondal RJ. Comparison of the redox chemistry of sulfur- and selenium-containing analogs of uracil. Free Radic Biol Med 2017; 104:249-261. [PMID: 28108278 PMCID: PMC5328918 DOI: 10.1016/j.freeradbiomed.2017.01.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/16/2022]
Abstract
Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNAGlu, tRNAGln and tRNALys. It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen. Both selenocysteine and 2-selenouridine have widespread analogs, cysteine and thiouridine, where sulfur is used instead. To examine the role of selenium in 2-selenouridine, we comparatively analyzed the oxidation reactions of sulfur-containing 2-thiouracil-5-carboxylic acid (s2c5Ura) and its selenium analog 2-selenouracil-5-carboxylic acid (se2c5Ura) using 1H-NMR spectroscopy, 77Se-NMR spectroscopy, and liquid chromatography-mass spectrometry. Treatment of s2c5Ura with hydrogen peroxide led to oxidized intermediates, followed by irreversible desulfurization to form uracil-5-carboxylic acid (c5Ura). In contrast, se2c5Ura oxidation resulted in a diselenide intermediate, followed by conversion to the seleninic acid, both of which could be readily reduced by ascorbate and glutathione. Glutathione and ascorbate only minimally prevented desulfurization of s2c5Ura, whereas very little deselenization of se2c5Ura occurred in the presence of the same antioxidants. In addition, se2c5Ura but not s2c5Ura showed glutathione peroxidase activity, further suggesting that oxidation of se2c5Ura is readily reversible, while oxidation of s2c5Ura is not. The results of the study of these model nucleobases suggest that the use of 2-selenouridine is related to resistance to oxidative inactivation that otherwise characterizes 2-thiouridine. As the use of selenocysteine in proteins also confers resistance to oxidation, our findings suggest a common mechanism for the use of selenium in biology.
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Affiliation(s)
- N Connor Payne
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Andrew Geissler
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Aileen Button
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Alexandru R Sasuclark
- Department of Chemistry, St. Michael's College, 1 Winooski Park, Colchester, VT 05439, United States
| | - Alayne L Schroll
- Department of Chemistry, St. Michael's College, 1 Winooski Park, Colchester, VT 05439, United States
| | - Erik L Ruggles
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Robert J Hondal
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States.
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Sierant M, Leszczynska G, Sadowska K, Dziergowska A, Rozanski M, Sochacka E, Nawrot B. S-Geranyl-2-thiouridine wobble nucleosides of bacterial tRNAs; chemical and enzymatic synthesis of S-geranylated-RNAs and their physicochemical characterization. Nucleic Acids Res 2016; 44:10986-10998. [PMID: 27566149 PMCID: PMC5159532 DOI: 10.1093/nar/gkw727] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 07/30/2016] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Recently, highly lipophilic S-geranylated derivatives of 5-methylaminomethyl-2-thiouridine (mnm5geS2U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm5geS2U) were found at the first (wobble) anticodon position in bacterial tRNAs specific for Lys, Glu and Gln. The function and cellular biogenesis of these unique tRNAs remain poorly understood. Here, we present one direct and two post-synthetic chemical routes for preparing model geS2U-RNAs. Our experimental data demonstrate that geS2U-RNAs are more lipophilic than their parent S2U-RNAs as well as non-modified U-RNAs. Thermodynamic studies revealed that the S-geranyl-2-thiouridine-containing RNA has higher affinity toward complementary RNA strand with G opposite the modified unit than with A. Recombinant tRNA selenouridine synthase (SelU) exhibits sulfur-specific geranylation activity toward model S2U-RNA, which is composed of the anticodon-stem-loop (ASL) from the human tRNALys3 sequence. In addition, the presence of magnesium ions is required to achieve appreciable geranylation efficiencies.
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Affiliation(s)
- Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Klaudia Sadowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Agnieszka Dziergowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Michal Rozanski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland
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38
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Wang R, Ranganathan SV, Basanta-Sanchez M, Shen F, Chen A, Sheng J. Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine. Chem Commun (Camb) 2016; 51:16369-72. [PMID: 26405057 DOI: 10.1039/c5cc07479g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The synthesis and base pairing of DNA duplexes containing the geranylated 2-thiothymidine have been investigated. This naturally existing hydrophobic modification could grant better base pairing stability to the T-G pair over normal T-A and other mismatched pairs in the duplex context. This study provides a potential explanation for the different codon recognition preferences of the geranylated tRNAs.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA. and The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
| | - Srivathsan V Ranganathan
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
| | - Maria Basanta-Sanchez
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
| | - Fusheng Shen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA. and The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
| | - Alan Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA. and The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA. and The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave. Albany, NY 12222, USA
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Wang R, Vangaveti S, Ranganathan SV, Basanta-Sanchez M, Haruehanroengra P, Chen A, Sheng J. Synthesis, base pairing and structure studies of geranylated RNA. Nucleic Acids Res 2016; 44:6036-45. [PMID: 27307604 PMCID: PMC5291276 DOI: 10.1093/nar/gkw544] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/02/2016] [Indexed: 02/07/2023] Open
Abstract
Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium. The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNAGluUUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon–anticodon interaction during ribosome binding.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Maria Basanta-Sanchez
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Phensinee Haruehanroengra
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alan Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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Jäger G, Chen P, Björk GR. Transfer RNA Bound to MnmH Protein Is Enriched with Geranylated tRNA--A Possible Intermediate in Its Selenation? PLoS One 2016; 11:e0153488. [PMID: 27073879 PMCID: PMC4830565 DOI: 10.1371/journal.pone.0153488] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/30/2016] [Indexed: 01/17/2023] Open
Abstract
The wobble nucleoside 5-methylaminomethyl-2-thio-uridine (mnm5s2U) is present in bacterial tRNAs specific for Lys and Glu and 5-carboxymethylaminomethyl-2-thio-uridine (cmnm5s2U) in tRNA specific for Gln. The sulfur of (c)mnm5s2U may be exchanged by selenium (Se)-a reaction catalyzed by the selenophosphate-dependent tRNA 2-selenouridine synthase encoded by the mnmH (ybbB, selU, sufY) gene. The MnmH protein has a rhodanese domain containing one catalytic Cys (C97) and a P-loop domain containing a Walker A motif, which is a potential nucleotide binding site. We have earlier isolated a mutant of Salmonella enterica, serovar Typhimurium with an alteration in the rhodanese domain of the MnmH protein (G67E) mediating the formation of modified nucleosides having a geranyl (ge)-group (C10H17-fragment) attached to the s2 group of mnm5s2U and of cmnm5s2U in tRNA. To further characterize the structural requirements to increase the geranylation activity, we here report the analysis of 39 independently isolated mutants catalyzing the formation of mnm5ges2U. All these mutants have amino acid substitutions in the rhodanese domain demonstrating that this domain is pivotal to increase the geranylation activity. The wild type form of MnmH+ also possesses geranyltransferase activity in vitro although only a small amount of the geranyl derivatives of (c)mnm5s2U is detected in vivo. The selenation activity in vivo has an absolute requirement for the catalytic Cys97 in the rhodanese domain whereas the geranylation activity does not. Clearly, MnmH has two distinct enzymatic activities for which the rhodanese domain is pivotal. An intact Walker motif in the P-loop domain is required for the geranylation activity implying that it is the binding site for geranylpyrophosphate (GePP), which is the donor molecule in vitro in the geranyltransfer reaction. Purified MnmH from wild type and from the MnmH(G67E) mutant have bound tRNA, which is enriched with geranylated tRNA. This in conjunction with earlier published data, suggests that this bound geranylated tRNA may be an intermediate in the selenation of the tRNA.
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Affiliation(s)
- Gunilla Jäger
- Department of Molecular Biology, Umeå university, 901 87, Umeå, Sweden
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Glenn R Björk
- Department of Molecular Biology, Umeå university, 901 87, Umeå, Sweden
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Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria. ISME JOURNAL 2016; 10:2048-59. [PMID: 26800233 PMCID: PMC5029168 DOI: 10.1038/ismej.2015.246] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/28/2015] [Accepted: 11/27/2015] [Indexed: 12/15/2022]
Abstract
Selenium (Se) is an important micronutrient for many organisms, which is required for the biosynthesis of selenocysteine, selenouridine and Se-containing cofactor. Several key genes involved in different Se utilization traits have been characterized; however, systematic studies on the evolution and ecological niches of Se utilization are very limited. Here, we analyzed more than 5200 sequenced organisms to examine the occurrence patterns of all Se traits in bacteria. A global species map of all Se utilization pathways has been generated, which demonstrates the most detailed understanding of Se utilization in bacteria so far. In addition, the selenophosphate synthetase gene, which is used to define the overall Se utilization, was also detected in some organisms that do not have any of the known Se traits, implying the presence of a novel Se form in this domain. Phylogenetic analyses of components of different Se utilization traits revealed new horizontal gene transfer events for each of them. Moreover, by characterizing the selenoproteomes of all organisms, we found a new selenoprotein-rich phylum and additional selenoprotein-rich species. Finally, the relationship between ecological environments and Se utilization was investigated and further verified by metagenomic analysis of environmental samples, which indicates new macroevolutionary trends of each Se utilization trait in bacteria. Our data provide insights into the general features of Se utilization in bacteria and should be useful for a further understanding of the evolutionary dynamics of Se utilization in nature.
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Cravedi P, Mori G, Fischer F, Percudani R. Evolution of the Selenoproteome in Helicobacter pylori and Epsilonproteobacteria. Genome Biol Evol 2015; 7:2692-704. [PMID: 26342139 PMCID: PMC4607533 DOI: 10.1093/gbe/evv177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2015] [Indexed: 12/14/2022] Open
Abstract
By competing for the acquisition of essential nutrients, Helicobacter pylori has the unique ability to persist in the human stomach, also causing nutritional insufficiencies in the host. Although the H. pylori genome apparently encodes selenocysteine synthase (SelA, HP1513), a key pyridoxal phosphate (PLP)-dependent enzyme for the incorporation of selenium into bacterial proteins, nothing is known about the use of this essential element in protein synthesis by this pathogen. We analyzed the evolution of the complete machinery for incorporation of selenium into proteins and the selenoproteome of several H. pylori strains and related Epsilonproteobacteria. Our searches identified the presence of selenoproteins-including the previously unknown DUF466 family-in various Epsilonproteobacteria, but not in H. pylori. We found that a complete system for selenocysteine incorporation was present in the Helicobacteriaceae ancestor and has been recently lost before the split of Helicobacter acinonychis and H. pylori. Our results indicate that H. pylori, at variance with other gastric and enterohepatic Helicobacter, does not use selenocysteine in protein synthesis and does not use selenium for tRNA wobble base modification. However, selA has survived as a functional gene, having lost the domain for the binding of selenocysteine tRNA, but maintaining the ability to bind the PLP cofactor. The evolutionary modifications described for the SelA protein of H. pylori find parallels in other bacterial and archaeal species, suggesting that an alternative enzymatic function is hidden in many proteins annotated as selenocysteinyl-tRNA synthase.
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Affiliation(s)
| | - Giulia Mori
- Department of Life Sciences, University of Parma, Italy
| | - Frédéric Fischer
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, Institut Pasteur, ERL CNRS 3526, Paris, France
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44
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Lin J, Peng T, Jiang L, Ni JZ, Liu Q, Chen L, Zhang Y. Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Genome Biol Evol 2015; 7:664-76. [PMID: 25638258 PMCID: PMC5322559 DOI: 10.1093/gbe/evv022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Selenium (Se) is an important micronutrient that mainly occurs in proteins in the form of selenocysteine and in tRNAs in the form of selenouridine. In the past 20 years, several genes involved in Se utilization have been characterized in both prokaryotes and eukaryotes. However, Se homeostasis and the associated regulatory network are not fully understood. In this study, we conducted comparative genomics and phylogenetic analyses to examine the occurrence of all known Se utilization traits in prokaryotes. Our results revealed a highly mosaic pattern of species that use Se (in different forms) in spite that most organisms do not use this element. Further investigation of genomic context of known Se-related genes in different organisms suggested novel candidate genes that may participate in Se metabolism in bacteria and/or archaea. Among them, a membrane protein, YedE, which contains ten transmembrane domains and shows distant similarity to a sulfur transporter, is exclusively found in Se-utilizing organisms, suggesting that it may be involved in Se transport. A LysR-like transcription factor subfamily might be important for the regulation of Sec biosynthesis and/or other Se-related genes. In addition, a small protein family DUF3343 is widespread in Se-utilizing organisms, which probably serves as an important chaperone for Se trafficking within the cells. Finally, we proposed a simple model of Se homeostasis based on our findings. Our study reveals new candidate genes involved in Se metabolism in prokaryotes and should be useful for a further understanding of the complex metabolism and the roles of Se in biology.
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Affiliation(s)
- Jie Lin
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ting Peng
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Liang Jiang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences, Shenzhen University, Guangdong Province, China
| | - Jia-Zuan Ni
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences, Shenzhen University, Guangdong Province, China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences, Shenzhen University, Guangdong Province, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet 2014; 10:e1004553. [PMID: 25144653 PMCID: PMC4140641 DOI: 10.1371/journal.pgen.1004553] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022] Open
Abstract
Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell. Elongation factor P (EF-P) is a well-conserved bacterial protein. Although it can enhance protein synthesis in vitro, it is generally regarded as an ancillary factor required for robust translation of transcripts with stretches of consecutive prolines. In this work we performed ribosome profiling to better understand the role of EF-P during translation. Our data confirmed that translational effects due to lack of EF-P are mainly confined to PPX–encoding genes. Wide variations in EF-P dependent translation of these PPXs led us to investigate the effect of sequences upstream of diproline-containing motifs. We found that amino acids encoded upstream of PPX play a key role in EF-P-dependent translation. Finally, comparison of ribosome profiling data to existing proteomic data indicates that although many PPX-containing patterns have increased ribosome occupancies, this does not necessarily lead to altered protein levels. Taken together these data show a direct role for EF-P during synthesis of PPX motifs, and indirect effects on other post-transcriptional regulators of gene expression.
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Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway. Bioorg Chem 2014; 56:49-53. [PMID: 24971911 DOI: 10.1016/j.bioorg.2014.05.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 01/23/2023]
Abstract
The newly discovered S-geranylated 2-thiouridines (geS2U) (Dumelin et al., 2012) and 2-selenouridines (Se2U) were recently shown to be synthesized by a single enzyme (selenouridine synthase, SelU) through two distinct pathways using the same 2-thiouridine substrate (S2U); however, no clear catalytic mechanism was proposed. We suggest that S-geranyl-2-thiouridine is an intermediate of the SelU-catalyzed conversion of S2U to Se2U. The successful chemical transformation of S2U→geS2U→Se2U is demonstrated here as an initial approximation of the intracellular pathway. The structure of Se2U was confirmed by spectroscopic methods, which included, for the first time, (77)Se NMR data (δ 354ppm).
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47
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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48
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Transcriptional Response of Selenopolypeptide Genes and Selenocysteine Biosynthesis Machinery Genes in Escherichia coli during Selenite Reduction. Int J Microbiol 2014; 2014:394835. [PMID: 24839442 PMCID: PMC4009273 DOI: 10.1155/2014/394835] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 02/28/2014] [Accepted: 03/16/2014] [Indexed: 01/05/2023] Open
Abstract
Bacteria can reduce toxic selenite into less toxic, elemental selenium (Se0), but the mechanism on how bacterial cells reduce selenite at molecular level is still not clear. We used Escherichia coli strain K12, a common bacterial strain, as a model to study its growth response to sodium selenite (Na2SeO3) treatment and then used quantitative real-time PCR (qRT-PCR) to quantify transcript levels of three E. coli selenopolypeptide genes and a set of machinery genes for selenocysteine (SeCys) biosynthesis and incorporation into polypeptides, whose involvements in the selenite reduction are largely unknown. We determined that 5 mM Na2SeO3 treatment inhibited growth by ∼50% while 0.001 to 0.01 mM treatments stimulated cell growth by ∼30%. Under 50% inhibitory or 30% stimulatory Na2SeO3 concentration, selenopolypeptide genes (fdnG, fdoG, and fdhF) whose products require SeCys but not SeCys biosynthesis machinery genes were found to be induced ≥2-fold. In addition, one sulfur (S) metabolic gene iscS and two previously reported selenite-responsive genes sodA and gutS were also induced ≥2-fold under 50% inhibitory concentration. Our findings provide insight about the detoxification of selenite in E. coli via induction of these genes involved in the selenite reduction process.
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49
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Kaur M, Rob A, Caton-Williams J, Huang Z. Biochemistry of Nucleic Acids Functionalized with Sulfur, Selenium, and Tellurium: Roles of the Single-Atom Substitution. ACTA ACUST UNITED AC 2013. [DOI: 10.1021/bk-2013-1152.ch005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Manindar Kaur
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Abdur Rob
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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50
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Branco R, Morais PV. Identification and characterization of the transcriptional regulator ChrB in the chromate resistance determinant of Ochrobactrum tritici 5bvl1. PLoS One 2013; 8:e77987. [PMID: 24223748 PMCID: PMC3817168 DOI: 10.1371/journal.pone.0077987] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/06/2013] [Indexed: 12/30/2022] Open
Abstract
Ochrobactrum tritici 5bvl1 is able to resist to high concentrations of chromate through the expression of an inducible chromate-resistant determinant, found in a mobile element (TnOtChr), which carries the genes, chrB, chrA, chrC and chrF. The regulation of chr operon present in TnOtChr, which is controlled by a transcriptional regulator, ChrB, was characterized in the current work. Fusions of chr promoter, or chr promoter and chrB gene, upstream of a gfp reporter gene, identified the most probable promoter sequence within the tnpR-chrB intergenic region. This region contains an AT-rich imperfect inverted repeat sequence, which overlaps a part of the −10 sequence. The results of the in vitro DNA-binding assays with purified ChrB (His- or no-tagged) showed that the protein binds directly to the chr promoter region. In order to identify the ChrB functional domain for sensing chromate stress and for DNA-binding, site-directed mutagenesis of ChrB was performed. Among several single amino acid mutants, three mutants (R180; R187 and H229) prevented chromate induction without any modification to the protein’s stability. Interestingly, two ChrB mutants (R18 and R23) were constitutively active, regardless of chromate stress conditions, indicating that the residues most probably belong to the protein-DNA binding site. As such, the ChrB was classified as a transcriptional regulator that recognizes a specific DNA sequence, regulating the expression of a chromate resistance determinant.
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Affiliation(s)
- Rita Branco
- IMAR-CMA-Marine and Environmental Research Centre, Coimbra, Portugal
- Interdisciplinary Research Institute, University of Coimbra, Coimbra, Portugal
| | - Paula V. Morais
- IMAR-CMA-Marine and Environmental Research Centre, Coimbra, Portugal
- Department of Life Sciences, FCTUC, University of Coimbra, Coimbra, Portugal
- * E-mail:
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