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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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2
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Abdul Halim MF, Hanson EH, Costa KC. Methanococcus maripaludis. Trends Microbiol 2024:S0966-842X(24)00092-1. [PMID: 38702257 DOI: 10.1016/j.tim.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Affiliation(s)
| | - Emily H Hanson
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA.
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Kleikamp HBC, Palacios PA, Kofoed MVW, Papacharalampos G, Bentien A, Nielsen JL. The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6637-6646. [PMID: 38580315 PMCID: PMC11025550 DOI: 10.1021/acs.est.3c07725] [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: 09/21/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
Methanogenesis is a critical process in the carbon cycle that is applied industrially in anaerobic digestion and biogas production. While naturally occurring in diverse environments, methanogenesis requires anaerobic and reduced conditions, although varying degrees of oxygen tolerance have been described. Microaeration is suggested as the next step to increase methane production and improve hydrolysis in digestion processes; therefore, a deeper understanding of the methanogenic response to oxygen stress is needed. To explore the drivers of oxygen tolerance in methanogenesis, two parallel enrichments were performed under the addition of H2/CO2 in an environment without reducing agents and in a redox-buffered environment by adding redox mediator 9,10-anthraquinone-2,7-disulfonate disodium. The cellular response to oxidative conditions is mapped using proteomic analysis. The resulting community showed remarkable tolerance to high-redox environments and was unperturbed in its methane production. Next to the expression of pathways to mitigate reactive oxygen species, the higher redox potential environment showed an increased presence of selenocysteine and selenium-associated pathways. By including sulfur-to-selenium mass shifts in a proteomic database search, we provide the first evidence of the dynamic and large-scale incorporation of selenocysteine as a response to oxidative stress in hydrogenotrophic methanogenesis and the presence of a dynamic selenoproteome.
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Affiliation(s)
- Hugo B. C. Kleikamp
- Department
of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Paola A. Palacios
- Department
of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Michael V. W. Kofoed
- Department
of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Georgios Papacharalampos
- Department
of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Anders Bentien
- Department
of Biological and Chemical Engineering, Aarhus University, Åbogade 40, 8200 Aarhus, Denmark
| | - Jeppe L. Nielsen
- Department
of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
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4
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Wright DE, O’Donoghue P. Biosynthesis, Engineering, and Delivery of Selenoproteins. Int J Mol Sci 2023; 25:223. [PMID: 38203392 PMCID: PMC10778597 DOI: 10.3390/ijms25010223] [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: 11/15/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.
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Affiliation(s)
- David E. Wright
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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6
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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7
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Peiter N, Rother M. In vivo probing of SECIS-dependent selenocysteine translation in Archaea. Life Sci Alliance 2023; 6:6/1/e202201676. [PMID: 36316034 PMCID: PMC9622424 DOI: 10.26508/lsa.202201676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.
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Affiliation(s)
- Nils Peiter
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
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8
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Li J, Akinyemi TS, Shao N, Chen C, Dong X, Liu Y, Whitman WB. Genetic and Metabolic Engineering of Methanococcus spp. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Manta B, Makarova NE, Mariotti M. The selenophosphate synthetase family: A review. Free Radic Biol Med 2022; 192:63-76. [PMID: 36122644 DOI: 10.1016/j.freeradbiomed.2022.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022]
Abstract
Selenophosphate synthetases use selenium and ATP to synthesize selenophosphate. This is required for biological utilization of selenium, most notably for the synthesis of the non-canonical amino acid selenocysteine (Sec). Therefore, selenophosphate synthetases underlie all functions of selenoproteins, which include redox homeostasis, protein quality control, hormone regulation, metabolism, and many others. This protein family comprises two groups, SelD/SPS2 and SPS1. The SelD/SPS2 group represent true selenophosphate synthetases, enzymes central to selenium metabolism which are present in all Sec-utilizing organisms across the tree of life. Notably, many SelD/SPS2 proteins contain Sec as catalytic residue in their N-terminal flexible selenium-binding loop, while others replace it with cysteine (Cys). The SPS1 group comprises proteins originated through gene duplications of SelD/SPS2 in metazoa in which the Sec/Cys-dependent catalysis was disrupted. SPS1 proteins do not synthesize selenophosphate and are not required for Sec synthesis. They have essential regulatory functions related to redox homeostasis and pyridoxal phosphate, which affect signaling pathways for growth and differentiation. In this review, we summarize the knowledge about the selenophosphate synthetase family acquired through decades of research, encompassing their structure, mechanism, function, and evolution.
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Affiliation(s)
- Bruno Manta
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Uruguay, Cátedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Uruguay
| | - Nadezhda E Makarova
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Avinguda Diagonal 643, Barcelona, 08028, Catalonia, Spain
| | - Marco Mariotti
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Avinguda Diagonal 643, Barcelona, 08028, Catalonia, Spain.
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10
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Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Front Microbiol 2022; 13:1007832. [PMID: 36160229 PMCID: PMC9499178 DOI: 10.3389/fmicb.2022.1007832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.
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Affiliation(s)
- Kexin Meng
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Natalie Krahn,
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11
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Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective. Biomolecules 2022; 12:biom12070917. [PMID: 35883471 PMCID: PMC9312934 DOI: 10.3390/biom12070917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 01/25/2023] Open
Abstract
Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.
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12
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Expressing recombinant selenoproteins using redefinition of a single UAG codon in an RF1-depleted E. coli host strain. Methods Enzymol 2022; 662:95-118. [PMID: 35101220 DOI: 10.1016/bs.mie.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selenoproteins containing the rare amino acid selenocysteine (Sec), typically being enzymes utilizing the selenium atom of Sec for promoted catalysis of redox reactions, are challenging to obtain at high amounts in pure form. The technical challenges limiting selenoprotein supply derive from intricacies in their translation, necessitating the recoding of a UGA stop codon to a sense codon for Sec. This, in turn, involves the interactions of a Sec-dedicated elongation factor, either directly or indirectly, with a structure in the selenoprotein-encoding mRNA called a SECIS element (Selenocysteine Insertion Sequence), a dedicated tRNA species for Sec with an anticodon for the UGA, and several accessory enzymes and proteins involved in the selenoprotein synthesis. Here, we describe an alternative method for recombinant selenoprotein production using UAG as the Sec codon in a specific strain of E. coli lacking other UAG codons and lacking the release factor RF1 that normally terminates translation at UAG. We also describe how such recombinant selenoproteins can be purified and further analyzed for final Sec contents. The methodology can be used for production of natural selenoproteins in recombinant form as well as for production of synthetic selenoproteins that may be designed to use the unique biophysical properties of Sec for diverse biotechnological applications.
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Yang H, Yang X, Ning Z, Kwon SY, Li ML, Tack FMG, Kwon EE, Rinklebe J, Yin R. The beneficial and hazardous effects of selenium on the health of the soil-plant-human system: An overview. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126876. [PMID: 34416699 DOI: 10.1016/j.jhazmat.2021.126876] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/25/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Selenium (Se), which can be both hazardous and beneficial to plants, animals and humans, plays a pivotal role in regulating soil-plant-human ecosystem functions. The biogeochemical behavior of Se and its environmental impact on the soil-plant-human system has received broad attention in the last decades. This review provides a comprehensive understanding of Se biogeochemistry in the soil-plant-human system. The speciation, transformation, bioavailability as well as the beneficial and hazardous effects of Se in the soil-plant-human system are summarized. Several important aspects in Se in the soil-plant-human system are detailed mentioned, including (1) strategies for biofortification in Se-deficient areas and phytoremediation of soil Se in seleniferous areas; (2) factors affecting Se uptake and transport by plants; (3) metabolic pathways of Se in the human body; (4) the interactions between Se and other trace elements in plant and animals, in particular, the detoxification of heavy metals by Se. Important research hotspots of Se biogeochemistry are outlined, including (1) the coupling of soil microbial activity and the Se biogeochemical cycle; (2) the molecular mechanism of Se metabolic in plants and animals; and (3) the application of Se isotopes as a biogeochemical tracer in research. This review provides up-to-date knowledge and guidelines on Se biogeochemistry research.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; Guizhou Academy of Tobacco Science, 550081 Guiyang, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuefeng Yang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Sae Yun Kwon
- Division of Environmental Science & Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam Gu, Pohang 37673, South Korea
| | - Mi-Ling Li
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716 USA
| | - Filip M G Tack
- Ghent University, Department of Green Chemistry and Technology, Ghent, Belgium
| | - Eilhann E Kwon
- Department of Environment, Energy and Geoinformatics, Sejong University, 98 Gunja-Dong, Guangjin-Gu, Seoul, Republic of Korea
| | - Jörg Rinklebe
- Department of Environment, Energy and Geoinformatics, Sejong University, 98 Gunja-Dong, Guangjin-Gu, Seoul, Republic of Korea; University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Runsheng Yin
- State Key Laboratory of Ore Deposit Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
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Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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15
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Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME COMMUNICATIONS 2021; 1:30. [PMID: 36739331 PMCID: PMC9723677 DOI: 10.1038/s43705-021-00032-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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Affiliation(s)
- Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Gagen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
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16
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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17
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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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18
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Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo. Molecules 2021; 26:molecules26071861. [PMID: 33806142 PMCID: PMC8037382 DOI: 10.3390/molecules26071861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed "recoding". In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for -1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed -1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed.
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19
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Santesmasses D, Mariotti M, Gladyshev VN. Bioinformatics of Selenoproteins. Antioxid Redox Signal 2020; 33:525-536. [PMID: 32031018 PMCID: PMC7409585 DOI: 10.1089/ars.2020.8044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Significance: Bioinformatics has brought important insights into the field of selenium research. The progress made in the development of computational tools in the last two decades, coordinated with growing genome resources, provided new opportunities to study selenoproteins. The present review discusses existing tools for selenoprotein gene finding and other bioinformatic approaches to study the biology of selenium. Recent Advances: The availability of complete selenoproteomes allowed assessing a global distribution of the use of selenocysteine (Sec) across the tree of life, as well as studying the evolution of selenoproteins and their biosynthetic pathway. Beyond gene identification and characterization, human genetic variants in selenoprotein genes were used to examine adaptations to selenium levels in diverse human populations and to estimate selective constraints against gene loss. Critical Issues: The synthesis of selenoproteins is essential for development in mice. In humans, several mutations in selenoprotein genes have been linked to rare congenital disorders. And yet, the mechanism of Sec insertion and the regulation of selenoprotein synthesis in mammalian cells are not completely understood. Future Directions: Omics technologies offer new possibilities to study selenoproteins and mechanisms of Sec incorporation in cells, tissues, and organisms.
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Affiliation(s)
- Didac Santesmasses
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
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20
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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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 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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21
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Kamal A, Nazari V M, Yaseen M, Iqbal MA, Ahamed MBK, Majid ASA, Bhatti HN. Green synthesis of selenium-N-heterocyclic carbene compounds: Evaluation of antimicrobial and anticancer potential. Bioorg Chem 2019; 90:103042. [PMID: 31226469 DOI: 10.1016/j.bioorg.2019.103042] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/22/2019] [Accepted: 06/03/2019] [Indexed: 12/11/2022]
Abstract
Three benzimidazolium salts (III-V) and respective selenium adducts (VI-VIII) were designed, synthesized and characterized by various analytical techniques (FT-IR and NMR 1H, 13C). Selected salts and respective selenium N-Heterocyclic carbenes (selenium-NHC) adducts were tested in vitro against Cervical Cancer Cell line (Hela), Breast Adenocarcinoma cell line (MCF-7), Retinal Ganglion Cell line (RGC-5) and Mouse Melanoma Cell line (B16F10) using MTT assay and the results were compared with standard drug 5-Fluorouracil. Se-NHC compounds and azolium salts showed significant anticancer potential. Molecular docking studies of compounds (VI, VII and VIII) showed strong binding energies and ligand affinity toward following angiogenic factors: VEGF-A (vascular endothelial growth factor A), EGF (human epidermal growth factor), HIF (Hypoxia-inducible factor) and COX-1 (Cyclooxygenase-1) suggesting that the anticancer activity of adducts (VI, VII and VIII) may be due to their strong anti-angiogenic effect. In addition, compounds III-VIII were screened for their antibacterial and antifungal potential. Adduct VI was found to be potent anti-fungal agent against A. Niger with zone of inhibition (ZI) value 27.01 ± 0.251 mm which is better than standard drug Clotrimazole tested in parallel.
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Affiliation(s)
- Amna Kamal
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Mansoureh Nazari V
- Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, 11800 Pulau Penang, Malaysia
| | - Muhammad Yaseen
- Department of Chemistry, University of Education (Lahore), Faisalabad Campus, Faisalabad, Pakistan
| | - Muhammad Adnan Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan; Organometallic and Coordination Chemistry Laboratory, Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Mohamed B Khadeer Ahamed
- EMAN Biodiscoveries Sdn. Bhd., A1-4, Lot 5, Persiaran 2/1, Kedah Halal Park, Kawasan Perindustrian Sungai Petani, 08000 Sungai Petani, Kedah, Malaysia
| | | | - Haq Nawaz Bhatti
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan.
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22
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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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23
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Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion. Emerg Top Life Sci 2018; 2:607-618. [PMID: 33525836 DOI: 10.1042/etls20180094] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022]
Abstract
The 22nd amino acid discovered to be directly encoded, pyrrolysine, is specified by UAG. Until recently, pyrrolysine was only known to be present in archaea from a methanogenic lineage (Methanosarcinales), where it is important in enzymes catalysing anoxic methylamines metabolism, and a few anaerobic bacteria. Relatively new discoveries have revealed wider presence in archaea, deepened functional understanding, shown remarkable carbon source-dependent expression of expanded decoding and extended exploitation of the pyrrolysine machinery for synthetic code expansion. At the same time, other studies have shown the presence of pyrrolysine-containing archaea in the human gut and this has prompted health considerations. The article reviews our knowledge of this fascinating exception to the 'standard' genetic code.
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