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Ling J, O'Donoghue P, Söll D. Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology. Nat Rev Microbiol 2015; 13:707-721. [PMID: 26411296 DOI: 10.1038/nrmicro3568] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The genetic code, initially thought to be universal and immutable, is now known to contain many variations, including biased codon usage, codon reassignment, ambiguous decoding and recoding. As a result of recent advances in the areas of genome sequencing, biochemistry, bioinformatics and structural biology, our understanding of genetic code flexibility has advanced substantially in the past decade. In this Review, we highlight the prevalence, evolution and mechanistic basis of genetic code variations in microorganisms, and we discuss how this flexibility of the genetic code affects microbial physiology.
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Affiliation(s)
- Jiqiang Ling
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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Fonknechten N, Chaussonnerie S, Tricot S, Lajus A, Andreesen JR, Perchat N, Pelletier E, Gouyvenoux M, Barbe V, Salanoubat M, Le Paslier D, Weissenbach J, Cohen GN, Kreimeyer A. Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence. BMC Genomics 2010; 11:555. [PMID: 20937090 PMCID: PMC3091704 DOI: 10.1186/1471-2164-11-555] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed. RESULTS C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms. CONCLUSIONS Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.
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Affiliation(s)
- Nuria Fonknechten
- Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, F-91057 Evry, France
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Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol 2009; 11:1038-55. [PMID: 19187283 PMCID: PMC2702500 DOI: 10.1111/j.1462-2920.2008.01825.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 10/25/2008] [Indexed: 01/23/2023]
Abstract
Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
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Affiliation(s)
- Axel W Strittmatter
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Heiko Liesegang
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Ralf Rabus
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University OldenburgCarl-von-Ossietzky Str. 9-11, D-26111 Oldenburg, Germany
| | - Iwona Decker
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Judith Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Sönke Andres
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Anke Henne
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Wolfgang Florian Fricke
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rosa Martinez-Arias
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Daniela Bartels
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Lutz Krause
- Center for Biotechnology (CeBiTec), Bielefeld UniversityUniversitätsstr. 37, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität BielefeldD-33594 Bielefeld, Germany
| | - Hans-Peter Klenk
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHInhoffenstraße 7 B, D-38124 Braunschweig, Germany
| | - Michael Richter
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Margarete Schüler
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | | | - Anke Meyerdierks
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Georg-August-UniversityGrisebachstr. 8, D-37077 Göttingen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstr. 1, D-28359 Bremen, Germany
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Factors and selenocysteine insertion sequence requirements for the synthesis of selenoproteins from a gram-positive anaerobe in Escherichia coli. Appl Environ Microbiol 2007; 74:1385-93. [PMID: 18165360 DOI: 10.1128/aem.02238-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selenoprotein synthesis in Escherichia coli strictly depends on the presence of a specific selenocysteine insertion sequence (SECIS) following the selenocysteine-encoding UGA codon of the respective mRNA. It is recognized by the selenocysteine-specific elongation factor SelB, leading to cotranslational insertion of selenocysteine into the nascent polypeptide chain. The synthesis of three different selenoproteins from the gram-positive anaerobe Eubacterium acidaminophilum in E. coli was studied. Incorporation of (75)Se into glycine reductase protein B (GrdB1), the peroxiredoxin PrxU, and selenophosphate synthetase (SelD1) was negligible in an E. coli wild-type strain and was fully absent in an E. coli SelB mutant. Selenoprotein synthesis, however, was strongly increased if selB and selC (tRNA(Sec)) from E. acidaminophilum were coexpressed. Putative secondary structures downstream of the UGA codons did not show any sequence similarity to each other or to the E. coli SECIS element. However, mutations in these structures strongly reduced the amount of (75)Se-labeled protein, indicating that they indeed act as SECIS elements. UGA readthrough mediated by the three different SECIS elements was further analyzed using gst-lacZ translational fusions. In the presence of selB and selC from E. acidaminophilum, UGA readthrough was 36 to 64% compared to the respective cysteine-encoding UGC variant. UGA readthrough of SECIS elements present in Desulfomicrobium baculatum (hydV), Treponema denticola (selD), and Campylobacter jejuni (selW-like gene) was also considerably enhanced in the presence of E. acidaminophilum selB and selC. This indicates recognition of these SECIS elements and might open new perspectives for heterologous selenoprotein synthesis in E. coli.
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