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Kekez M, Zanki V, Kekez I, Baranasic J, Hodnik V, Duchêne A, Anderluh G, Gruic‐Sovulj I, Matković‐Čalogović D, Weygand‐Durasevic I, Rokov‐Plavec J. Arabidopsis
seryl‐
tRNA
synthetase: the first crystal structure and novel protein interactor of plant aminoacyl‐
tRNA
synthetase. FEBS J 2019; 286:536-554. [DOI: 10.1111/febs.14735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/01/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Mario Kekez
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Vladimir Zanki
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Ivana Kekez
- Division of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Jurica Baranasic
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Vesna Hodnik
- National Institute of Chemistry Ljubljana Slovenia
- Biotechnical faculty University of Ljubljana Slovenia
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes CNRS, Université de Strasbourg Strasbourg Cedex France
| | | | - Ita Gruic‐Sovulj
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Dubravka Matković‐Čalogović
- Division of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Ivana Weygand‐Durasevic
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Jasmina Rokov‐Plavec
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
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Fujishiro T, Ataka K, Ermler U, Shima S. Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs. FEBS J 2015; 282:3412-23. [PMID: 26094576 DOI: 10.1111/febs.13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED [Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4MPT(+)). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4MPT(+) compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. DATABASE Structural data are available in the Protein Data Bank under the accession numbers 4YT8; 4YT2; 4YT4 and 4YT5.
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Affiliation(s)
- Takashi Fujishiro
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany.,PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
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3
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Aminoacyl-tRNA synthetase complexes in evolution. Int J Mol Sci 2015; 16:6571-94. [PMID: 25807264 PMCID: PMC4394549 DOI: 10.3390/ijms16036571] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/17/2015] [Accepted: 03/11/2015] [Indexed: 11/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases are essential enzymes for interpreting the genetic code. They are responsible for the proper pairing of codons on mRNA with amino acids. In addition to this canonical, translational function, they are also involved in the control of many cellular pathways essential for the maintenance of cellular homeostasis. Association of several of these enzymes within supramolecular assemblies is a key feature of organization of the translation apparatus in eukaryotes. It could be a means to control their oscillation between translational functions, when associated within a multi-aminoacyl-tRNA synthetase complex (MARS), and nontranslational functions, after dissociation from the MARS and association with other partners. In this review, we summarize the composition of the different MARS described from archaea to mammals, the mode of assembly of these complexes, and their roles in maintenance of cellular homeostasis.
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Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 2014; 5:634. [PMID: 25520705 PMCID: PMC4253957 DOI: 10.3389/fmicb.2014.00634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/05/2014] [Indexed: 11/21/2022] Open
Abstract
Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).
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Affiliation(s)
- Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Jane Lomax
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Hinxton, UK
| | - João C Setubal
- Department of Biochemistry, Universidade de São Paulo São Paulo, Brazil ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Center for Genome Research and Biocomputing, Oregon State University Corvallis, OR, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Department of Biological Sciences, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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Laporte D, Huot JL, Bader G, Enkler L, Senger B, Becker HD. Exploring the evolutionary diversity and assembly modes of multi-aminoacyl-tRNA synthetase complexes: lessons from unicellular organisms. FEBS Lett 2014; 588:4268-78. [PMID: 25315413 DOI: 10.1016/j.febslet.2014.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/03/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and ancient enzymes, mostly known for their essential role in generating aminoacylated tRNAs. During the last two decades, many aaRSs have been found to perform additional and equally crucial tasks outside translation. In metazoans, aaRSs have been shown to assemble, together with non-enzymatic assembly proteins called aaRSs-interacting multifunctional proteins (AIMPs), into so-called multi-synthetase complexes (MSCs). Metazoan MSCs are dynamic particles able to specifically release some of their constituents in response to a given stimulus. Upon their release from MSCs, aaRSs can reach other subcellular compartments, where they often participate to cellular processes that do not exploit their primary function of synthesizing aminoacyl-tRNAs. The dynamics of MSCs and the expansion of the aaRSs functional repertoire are features that are so far thought to be restricted to higher and multicellular eukaryotes. However, much can be learnt about how MSCs are assembled and function from apparently 'simple' organisms. Here we provide an overview on the diversity of these MSCs, their composition, mode of assembly and the functions that their constituents, namely aaRSs and AIMPs, exert in unicellular organisms.
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Affiliation(s)
- Daphné Laporte
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Jonathan L Huot
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Gaétan Bader
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Ludovic Enkler
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Bruno Senger
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France
| | - Hubert Dominique Becker
- UMR 'Génétique Moléculaire, Génomique, Microbiologie', CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg Cedex, France.
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Random mutagenesis identifies factors involved in formate-dependent growth of the methanogenic archaeon Methanococcus maripaludis. Mol Genet Genomics 2013; 288:413-24. [PMID: 23801407 DOI: 10.1007/s00438-013-0756-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/31/2013] [Indexed: 01/25/2023]
Abstract
Methane is a key intermediate in the carbon cycle and biologically produced by methanogenic archaea. Most methanogens are able to conserve energy by reducing CO2 to methane using molecular hydrogen as electron donor (hydrogenotrophic methanogenesis), but several hydrogenotrophic methanogens can also use formate as electron donor for methanogenesis. Formate dehydrogenase (Fdh) oxidizes formate to CO2 and is involved in funneling reducing equivalents into the methanogenic pathway, but details on other factors relevant for formate-dependent physiology of methanogens are not available. To learn more about the factors involved in formate-dependent growth of Methanococcus maripaludis strain JJ, we used a recently developed system for random in vitro mutagenesis, which is based on a modified insect transposable element to create 2,865 chromosomal transposon mutants and screened them for impaired growth on formate. Of 12 M. maripaludis transposon-induced mutants exhibiting this phenotype, the transposon insertion sites in the chromosome were mapped. Among the genes, apparently affecting formate-dependent growth were those encoding archaeal transcription factor S, a regulator of ion transport, and carbon monoxide dehydrogenase/acetyl-CoA synthase. Interestingly, in seven of the mutants, transposons were localized in a 10.2 kb region where Fdh1, one of two Fdh isoforms in the organism, is encoded. Two transcription start sites within the 10.2 kb region could be mapped, and quantification of transcripts revealed that transposon insertion in this region diminished fdhA1 expression due to polar effects.
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Raina M, Elgamal S, Santangelo TJ, Ibba M. Association of a multi-synthetase complex with translating ribosomes in the archaeon Thermococcus kodakarensis. FEBS Lett 2012; 586:2232-8. [PMID: 22683511 DOI: 10.1016/j.febslet.2012.05.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/12/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
Abstract
In archaea and eukaryotes aminoacyl-tRNA synthetases (aaRSs) associate in multi-synthetase complexes (MSCs), however the role of such MSCs in translation is unknown. MSC function was investigated in vivo in the archaeon Thermococcus kodakarensis, wherein six aaRSs were affinity co-purified together with several other factors involved in protein synthesis, suggesting that MSCs may interact directly with translating ribosomes. In support of this hypothesis, the aminoacyl-tRNA synthetase (aaRS) activities of the MSC were enriched in isolated T. kodakarensis polysome fractions. These data indicate that components of the archaeal protein synthesis machinery associate into macromolecular assemblies in vivo and provide the potential to increase translation efficiency by limiting substrate diffusion away from the ribosome, thus facilitating rapid recycling of tRNAs.
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Affiliation(s)
- Medha Raina
- Ohio State Biochemistry Program, Ohio State University, Columbus, OH 43210, USA
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