1
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Reichelt R, Rothmeier T, Grünberger F, Willkomm S, Bruckmann A, Hausner W, Grohmann D. The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biol Chem 2023; 404:1085-1100. [PMID: 37709673 DOI: 10.1515/hsz-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Posttranscriptional processes in Bacteria include the association of small regulatory RNAs (sRNA) with a target mRNA. The sRNA/mRNA annealing process is often mediated by an RNA chaperone called Hfq. The functional role of bacterial and eukaryotic Lsm proteins is partially understood, whereas knowledge about archaeal Lsm proteins is scarce. Here, we used the genetically tractable archaeal hyperthermophile Pyrococcus furiosus to identify the protein interaction partners of the archaeal Sm-like proteins (PfuSmAP1) using mass spectrometry and performed a transcriptome-wide binding site analysis of PfuSmAP1. Most of the protein interaction partners we found are part of the RNA homoeostasis network in Archaea including ribosomal proteins, the exosome, RNA-modifying enzymes, but also RNA polymerase subunits, and transcription factors. We show that PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs recognizing a gapped poly(U) sequence with high affinity. Furthermore, we found that SmAP1 co-transcriptionally associates with target RNAs. Our study reveals that in contrast to bacterial Hfq, PfuSmAP1 does not affect the transcriptional activity or the pausing behaviour of archaeal RNA polymerases. We propose that PfuSmAP1 recruits antisense RNAs to target mRNAs and thereby executes its putative regulatory function on the posttranscriptional level.
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Affiliation(s)
- Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Tamara Rothmeier
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Sarah Willkomm
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology (Biochemistry I), Protein Mass Spectrometry Laboratory, University of Regensburg, D-93053 Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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2
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Abstract
RNA structural conformation and dynamics govern the functional properties of all RNA/RNP. Accordingly, defining changes of RNA structure and dynamics in various conditions may provide detailed insight into how RNA structural properties regulate the function of RNA/RNP. Traditional chemical footprinting analysis using chemical modifiers allows to sample the dynamics and conformation landscape of diverse RNA/RNP. However, many chemical modifiers are limited in their capacity to provide unbiased information reflecting the in vivo RNA/RNP structural landscape. In the recent years, the development of selective-2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology that uses powerful new chemical modifiers has significantly improved in vitro and in vivo structural probing of secondary and tertiary interactions of diverse RNA species at the single nucleotide level.Although the original discovery of Archaea as an independent domain of life is intimately linked to the technological development of RNA analysis, our understanding of in vivo RNA structural conformation and dynamics in this domain of life remains scarce.This protocol describes the in vivo use of SHAPE chemistry in two evolutionary divergent model Archaea, Sulfolobus acidocaldarius and Haloferax volcanii.
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Affiliation(s)
- Robert Knüppel
- Department of Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Martin Fenk
- Department of Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Michael Jüttner
- Department of Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Department of Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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3
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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4
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Abstract
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
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MESH Headings
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/metabolism
- Base Pairing
- Base Sequence
- Clostridiales/classification
- Clostridiales/genetics
- Clostridiales/metabolism
- Firmicutes/classification
- Firmicutes/genetics
- Firmicutes/metabolism
- Genome, Archaeal
- Genome, Bacterial
- Halobacteriales/classification
- Halobacteriales/genetics
- Halobacteriales/metabolism
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Thermoanaerobacterium/classification
- Thermoanaerobacterium/genetics
- Thermoanaerobacterium/metabolism
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Affiliation(s)
- Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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5
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Phung DK, Etienne C, Batista M, Langendijk-Genevaux P, Moalic Y, Laurent S, Liuu S, Morales V, Jebbar M, Fichant G, Bouvier M, Flament D, Clouet-d’Orval B. RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery. Nucleic Acids Res 2020; 48:3832-3847. [PMID: 32030412 PMCID: PMC7144898 DOI: 10.1093/nar/gkaa052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.
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Affiliation(s)
- Duy Khanh Phung
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Clarisse Etienne
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Petra Langendijk-Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Yann Moalic
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sophie Liuu
- Micalis Institute, PAPPSO, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Violette Morales
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Mohamed Jebbar
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Béatrice Clouet-d’Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France
- To whom correspondence should be addressed. Tel: +33 561 335 875; Fax: +33 561 335 886;
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6
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Majumder M, Mukhopadhyay S, Kharel P, Gupta R. The presence of the ACA box in archaeal H/ACA guide RNAs promotes atypical pseudouridylation. RNA 2020; 26:396-418. [PMID: 31919243 PMCID: PMC7075261 DOI: 10.1261/rna.073734.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
Archaea and eukaryotes, in addition to protein-only enzymes, also possess ribonucleoproteins containing an H/ACA guide RNA plus four proteins that produce pseudouridine (Ψ). Although typical conditions for these RNA-guided reactions are known, certain variant conditions allow pseudouridylation. We used mutants of the two stem-loops of the Haloferax volcanii sR-h45 RNA that guides three pseudouridylations in 23S rRNA and their target RNAs to characterize modifications under various atypical conditions. The 5' stem-loop produces Ψ2605 and the 3' stem-loop produces Ψ1940 and Ψ1942. The latter two modifications require unpaired "UVUN" (V = A, C, or G) in the target and ACA box in the guide. Ψ1942 modification requires the presence of U1940 (or Ψ1940). Ψ1940 is not produced in the Ψ1942-containing substrate, suggesting a sequential modification of the two residues. The ACA box of a single stem-loop guide is not required when typically unpaired "UN" is up to 17 bases from its position in the guide, but is needed when the distance increases to 19 bases or the N is paired. However, ANA of the H box of the double stem-loop guide is needed even for the 5' typical pseudouridylation. The most 5' unpaired U in a string of U's is converted to Ψ, and in the absence of an unpaired U, a paired U can also be modified. Certain mutants of the Cbf5 protein affect pseudouridylation by the two stem-loops of sR-h45 differently. This study will help elucidate the conditions for production of nonconstitutive Ψ's, determine functions for orphan H/ACA RNAs and in target designing.
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Affiliation(s)
- Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Parinati Kharel
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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7
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Evguenieva-Hackenberg E, Gauernack AS, Hou L, Klug G. Enzymatic Analysis of Reconstituted Archaeal Exosomes. Methods Mol Biol 2020; 2062:63-79. [PMID: 31768972 DOI: 10.1007/978-1-4939-9822-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The archaeal exosome is a protein complex with phosphorolytic activity. It is built of a catalytically active hexameric ring containing the archaeal Rrp41 and Rrp42 proteins, and a heteromeric RNA-binding platform. The platform contains a heterotrimer of the archaeal Rrp4 and Csl4 proteins (which harbor S1 and KH or Zn-ribbon RNA binding domains), and comprises additional archaea-specific subunits. The latter are represented by the archaeal DnaG protein, which harbors a novel RNA-binding domain and tightly interacts with the majority of the exosome isoforms, and Nop5, known as a part of an rRNA methylating complex and found to associate with the archaeal exosome at late stationary phase. Although in the cell the archaeal exosome exists in different isoforms with heterotrimeric Rrp4-Csl4-caps, in vitro it is possible to reconstitute complexes with defined, homotrimeric caps and to study the impact of each RNA-binding subunit on exoribonucleolytic degradation and on polynucleotidylation of RNA. Here we describe procedures for reconstitution of isoforms of the Sulfolobus solfataricus exosome and for set-up of RNA degradation and polyadenylation assays.
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Affiliation(s)
| | - A Susann Gauernack
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Linlin Hou
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Gabriele Klug
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany.
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8
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Li J, Zhang B, Zhou L, Qi L, Yue L, Zhang W, Cheng H, Whitman WB, Dong X. The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis. PLoS Genet 2019; 15:e1008328. [PMID: 31404065 PMCID: PMC6705878 DOI: 10.1371/journal.pgen.1008328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/22/2019] [Accepted: 07/22/2019] [Indexed: 11/27/2022] Open
Abstract
TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Bo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Liguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Huicai Cheng
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang, China
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
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9
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Bassani F, Zink IA, Pribasnig T, Wolfinger MT, Romagnoli A, Resch A, Schleper C, Bläsi U, La Teana A. Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus. RNA Biol 2019; 16:675-685. [PMID: 30777488 PMCID: PMC6546411 DOI: 10.1080/15476286.2019.1582953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
Translation factor a/eIF5A is highly conserved in Eukarya and Archaea. The eukaryal eIF5A protein is required for transit of ribosomes across consecutive proline codons, whereas the function of the archaeal orthologue remains unknown. Here, we provide a first hint for an involvement of Sulfolobus solfataricus (Sso) aIF5A in translation. CRISPR-mediated knock down of the aif5A gene resulted in strong growth retardation, underlining a pivotal function. Moreover, in vitro studies revealed that Sso aIF5A is endowed with endoribonucleolytic activity. Thus, aIF5A appears to be a moonlighting protein that might be involved in protein synthesis as well as in RNA metabolism.
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Affiliation(s)
- Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Isabelle Anna Zink
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Pribasnig
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | | | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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10
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Huang L, Ashraf S, Lilley DMJ. The role of RNA structure in translational regulation by L7Ae protein in archaea. RNA 2019; 25:60-69. [PMID: 30327333 PMCID: PMC6298567 DOI: 10.1261/rna.068510.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/07/2018] [Indexed: 05/03/2023]
Abstract
A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
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11
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Tomkuvienė M, Ličytė J, Olendraitė I, Liutkevičiūtė Z, Clouet-d'Orval B, Klimašauskas S. Archaeal fibrillarin-Nop5 heterodimer 2'- O-methylates RNA independently of the C/D guide RNP particle. RNA 2017; 23:1329-1337. [PMID: 28576826 PMCID: PMC5558902 DOI: 10.1261/rna.059832.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/19/2017] [Indexed: 06/01/2023]
Abstract
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'-O-methylated positions in the 16S rRNA of P. abyssi, positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.
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MESH Headings
- Archaea/genetics
- Archaea/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Methylation
- Nucleic Acid Conformation
- Protein Binding
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/metabolism
- Substrate Specificity
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Affiliation(s)
- Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Ingrida Olendraitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Zita Liutkevičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et Génétique Moléculaires UMR 5100, CNRS, Université de Toulouse, F-31062 Toulouse, France
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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12
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Morten MJ, Gamsjaeger R, Cubeddu L, Kariawasam R, Peregrina J, Penedo JC, White MF. High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein. Extremophiles 2017; 21:369-379. [PMID: 28074284 PMCID: PMC5346138 DOI: 10.1007/s00792-016-0910-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may represent an adaptation to a hyperthermophilic lifestyle, where DNA and RNA damage is a more frequent event.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jose Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
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13
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Babski J, Haas KA, Näther-Schindler D, Pfeiffer F, Förstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A, Soppa J. Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). BMC Genomics 2016; 17:629. [PMID: 27519343 PMCID: PMC4983044 DOI: 10.1186/s12864-016-2920-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/07/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii. RESULTS Three independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5'-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 % of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 %) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 %) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 % of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs). CONCLUSION This study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated.
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Affiliation(s)
- Julia Babski
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | | | - Daniela Näther-Schindler
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, MaxPlanckInstitute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Konrad U. Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany
| | - Matthias Hammelmann
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
| | - Rolf Hilker
- Bioinformatik und Systembiologie, University of Gießen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Anke Becker
- LOEWE-Center for Synthetic Microbiology, Hans-Meerwein-Str., 35032 Marburg, Germany
| | - Cynthia M. Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany
| | | | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, Biocentre, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany
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14
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Toffano-Nioche C, Gautheret D, Leclerc F. Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea. Nucleic Acids Res 2015; 43:7744-61. [PMID: 26240384 PMCID: PMC4652768 DOI: 10.1093/nar/gkv756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/22/2023] Open
Abstract
A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.
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Affiliation(s)
- Claire Toffano-Nioche
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Daniel Gautheret
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Fabrice Leclerc
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
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15
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Tillault AS, Fourmann JB, Loegler C, Wieden HJ, Kothe U, Charpentier B. Contribution of two conserved histidines to the dual activity of archaeal RNA guide-dependent and -independent pseudouridine synthase Cbf5. RNA 2015; 21:1233-1239. [PMID: 25990001 PMCID: PMC4478342 DOI: 10.1261/rna.051425.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/09/2015] [Indexed: 06/01/2023]
Abstract
In all organisms, several distinct stand-alone pseudouridine synthase (PUS) family enzymes are expressed to isomerize uridine into pseudouridine (Ψ) by specific recognition of RNAs. In addition, Ψs are generated in Archaea and Eukaryotes by PUS enzymes which are organized as ribonucleoprotein particles (RNP)--the box H/ACA s/snoRNPs. For this modification system, a unique TruB-like catalytic PUS subunit is associated with various RNA guides which specifically target and secure substrate RNAs by base-pairing. The archaeal Cbf5 PUS displays the special feature of exhibiting both RNA guide-dependent and -independent activities. Structures of substrate-bound TruB and H/ACA sRNP revealed the importance of histidines in positioning the target uridine in the active site. To analyze the respective role of H60 and H77, we have generated variants carrying alanine substitutions at these positions. The impact of the mutations was analyzed for unguided modifications U(55) in tRNA and U2603 in 23S rRNA, and for activity of the box H/ACA Pab91 sRNP enzyme. H77 (H43 in TruB), but not H60, appeared to be crucial for the RNA guide-independent activity. In contrast to earlier suggestions, H60 was found to be noncritical for the activity of the H/ACA sRNP, but contributes together with H77 to the full activity of H/ACA sRNPs. The data suggest that a similar catalytic process was conserved in the two divergent pseudouridylation systems.
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Affiliation(s)
- Anne-Sophie Tillault
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 54505 Vandœuvre-lès-Nancy, France
| | - Jean-Baptiste Fourmann
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 54505 Vandœuvre-lès-Nancy, France
| | - Christine Loegler
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 54505 Vandœuvre-lès-Nancy, France
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Bruno Charpentier
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 54505 Vandœuvre-lès-Nancy, France
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16
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Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CVC, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. RNA 2015; 21:1147-58. [PMID: 25904135 PMCID: PMC4436667 DOI: 10.1261/rna.049130.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5' ends (8-nt repeat-derived 5' tag sequences) but heterogeneous 3' ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3' end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
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Affiliation(s)
- Sonali Majumdar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Neil T Pfister
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Mark Compton
- Department of Poultry Science, University of Georgia, Athens, Georgia 30602, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Claiborne V C Glover
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA Department of Genetics, University of Georgia, Athens, Georgia 30602, USA Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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17
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Abstract
Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.
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MESH Headings
- Archaea/genetics
- Base Sequence
- Evolution, Molecular
- Gene Expression Regulation, Archaeal
- Genome, Archaeal/genetics
- Hot Temperature
- Models, Genetic
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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18
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Peng W, Feng M, Feng X, Liang YX, She Q. An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference. Nucleic Acids Res 2015; 43:406-17. [PMID: 25505143 PMCID: PMC4288192 DOI: 10.1093/nar/gku1302] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/30/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide a small RNA-based mechanism to defend against invasive genetic elements in archaea and bacteria. To investigate the in vivo mechanism of RNA interference by two type III-B systems (Cmr-α and Cmr-β) in Sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-CRISPR (AC) locus with a single spacer. After pAC plasmids were introduced into different strains, Northern analyses confirmed that mature crRNAs were produced from the plasmid-borne CRISPR loci, which then guided gene silencing to target gene expression. Spacer mutagenesis identified a trinucleotide sequence in the 3'-region of crRNA that was crucial for RNA interference. Studying mutants lacking Cmr-α or Cmr-β system showed that each Cmr complex exhibited RNA interference. Strikingly, these analyses further revealed that the two Cmr systems displayed distinctive interference features. Whereas Cmr-β complexes targeted transcripts and could be recycled in RNA cleavage, Cmr-α complexes probably targeted nascent RNA transcripts and remained associated with the substrate. Moreover, Cmr-β exhibited much stronger RNA cleavage activity than Cmr-α. Since we previously showed that S. islandicus Cmr-α mediated transcription-dependent DNA interference, the Cmr-α constitutes the first CRISPR system exhibiting dual targeting of RNA and DNA.
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Affiliation(s)
- Wenfang Peng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xu Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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19
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Chavarria NE, Hwang S, Cao S, Fu X, Holman M, Elbanna D, Rodriguez S, Arrington D, Englert M, Uthandi S, Söll D, Maupin-Furlow JA. Archaeal Tuc1/Ncs6 homolog required for wobble uridine tRNA thiolation is associated with ubiquitin-proteasome, translation, and RNA processing system homologs. PLoS One 2014; 9:e99104. [PMID: 24906001 PMCID: PMC4048286 DOI: 10.1371/journal.pone.0099104] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/11/2014] [Indexed: 11/29/2022] Open
Abstract
While cytoplasmic tRNA 2-thiolation protein 1 (Tuc1/Ncs6) and ubiquitin-related modifier-1 (Urm1) are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at wobble uridines of tRNAs in eukaryotes, the biocatalytic roles and properties of Ncs6/Tuc1 and its homologs are poorly understood. Here we present the first report of an Ncs6 homolog of archaea (NcsA of Haloferax volcanii) that is essential for maintaining cellular pools of thiolated tRNALysUUU and for growth at high temperature. When purified from Hfx. volcanii, NcsA was found to be modified at Lys204 by isopeptide linkage to polymeric chains of the ubiquitin-fold protein SAMP2. The ubiquitin-activating E1 enzyme homolog of archaea (UbaA) was required for this covalent modification. Non-covalent protein partners that specifically associated with NcsA were also identified including UbaA, SAMP2, proteasome activating nucleotidase (PAN)-A/1, translation elongation factor aEF-1α and a β-CASP ribonuclease homolog of the archaeal cleavage and polyadenylation specificity factor 1 family (aCPSF1). Together, our study reveals that NcsA is essential for growth at high temperature, required for formation of thiolated tRNALysUUU and intimately linked to homologs of ubiquitin-proteasome, translation and RNA processing systems.
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Affiliation(s)
- Nikita E. Chavarria
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Shiyun Cao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Xian Fu
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mary Holman
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Dina Elbanna
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Suzanne Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Deanna Arrington
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Sivakumar Uthandi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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20
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Mandal D, Köhrer C, Su D, Babu IR, Chan CT, Liu Y, Söll D, Blum P, Kuwahara M, Dedon PC, RajBhandary UL. Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA 2014; 20:177-88. [PMID: 24344322 PMCID: PMC3895270 DOI: 10.1261/rna.042358.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.
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MESH Headings
- Anticodon/genetics
- Base Pairing
- Base Sequence
- Codon/genetics
- Escherichia coli/genetics
- Haloarcula marismortui/genetics
- Haloferax/genetics
- Molecular Structure
- Point Mutation
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/genetics
- RNA, Fungal/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Ile/metabolism
- Ribosomes/chemistry
- Saccharomyces cerevisiae/genetics
- Sulfolobus/genetics
- Transfer RNA Aminoacylation
- Uridine/analogs & derivatives
- Uridine/chemistry
- Uridine/genetics
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Affiliation(s)
- Debabrata Mandal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - I. Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clement T.Y. Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yuchen Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska 68508, USA
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Corresponding authorE-mail
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21
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Lapinaite A, Simon B, Skjaerven L, Rakwalska-Bange M, Gabel F, Carlomagno T. The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature 2013; 502:519-23. [PMID: 24121435 DOI: 10.1038/nature12581] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022]
Abstract
Post-transcriptional modifications are essential to the cell life cycle, as they affect both pre-ribosomal RNA processing and ribosome assembly. The box C/D ribonucleoprotein enzyme that methylates ribosomal RNA at the 2'-O-ribose uses a multitude of guide RNAs as templates for the recognition of rRNA target sites. Two methylation guide sequences are combined on each guide RNA, the significance of which has remained unclear. Here we use a powerful combination of NMR spectroscopy and small-angle neutron scattering to solve the structure of the 390 kDa archaeal RNP enzyme bound to substrate RNA. We show that the two methylation guide sequences are located in different environments in the complex and that the methylation of physiological substrates targeted by the same guide RNA occurs sequentially. This structure provides a means for differential control of methylation levels at the two sites and at the same time offers an unexpected regulatory mechanism for rRNA folding.
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MESH Headings
- Apoproteins/chemistry
- Apoproteins/metabolism
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Biocatalysis
- Chromosomal Proteins, Non-Histone/metabolism
- Methylation
- Models, Molecular
- Multiprotein Complexes/chemistry
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Pyrococcus furiosus/enzymology
- Pyrococcus furiosus/genetics
- RNA Folding
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/metabolism
- RNA, Small Untranslated
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Affiliation(s)
- Audrone Lapinaite
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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22
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Märtens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Bläsi U. Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2. PLoS One 2013; 8:e76569. [PMID: 24116119 PMCID: PMC3792030 DOI: 10.1371/journal.pone.0076569] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/24/2013] [Indexed: 11/24/2022] Open
Abstract
Recent studies identified a 5´ to 3´ exoribonuclease termed Sso-RNase J in the crenarchaeon Sulfolobus solfataricus (Sso), which has been reclassified to the aCPSF2 (archaeal cleavage and polyadenylation specificity factor 2) group of β-CASP proteins. In this study, the Sso-aCPSF2 orthologue of Sulfolobus acidocaldarius (Saci-aCPSF2) was functionally characterized. Like Sso-aCPSF2, Saci-aCPSF2 degrades RNA with 5´ to 3´ directionality in vitro. To address the biological significance of Saci-aCPSF2, a deletion mutant was constructed, and the influence of Saci-aCPSF2 on the transcriptome profile was assessed employing high throughput RNA sequencing. This analysis revealed 560 genes with differential transcript abundance, suggesting a considerable role of this enzyme in RNA metabolism. In addition, bioinformatic analyses revealed several transcripts that are preferentially degraded at the 5´ end. This was exemplarily verified for two transcripts by Northern-blot analyses, showing for the first time that aCPSF2 proteins play a role in 5' to 3' directional mRNA decay in the crenarchaeal clade of Archaea.
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Affiliation(s)
- Birgit Märtens
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University Vienna, Vienna, Austria
- Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Salim Manoharadas
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Lukas Zeichen
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Alvaro Orell
- Molecular Biology of Archaea, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University Vienna, Vienna, Austria
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
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23
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An D, Caffrey SM, Soh J, Agrawal A, Brown D, Budwill K, Dong X, Dunfield P, Foght J, Gieg LM, Hallam SJ, Hanson NW, He Z, Jack TR, Klassen J, Konwar KM, Kuatsjah E, Li C, Larter S, Leopatra V, Nesbø CL, Oldenburg T, Pagé A, Ramos-Padron E, Rochman FF, Saidi-Mehrabad A, Sensen CW, Sipahimalani P, Song YC, Wilson S, Wolbring G, Wong ML, Voordouw G. Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol 2013; 47:10708-17. [PMID: 23889694 PMCID: PMC3864245 DOI: 10.1021/es4020184] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 05/29/2023]
Abstract
Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential. Although anaerobic communities were common, cores from oil sands and coal beds had unexpectedly high proportions of aerobic hydrocarbon-degrading bacteria. Likewise, most metagenomes had high proportions of genes for enzymes involved in aerobic hydrocarbon metabolism. Hence, although HREs may have been strictly anaerobic and typically methanogenic for much of their history, this may not hold today for coal beds and for the Alberta oil sands, one of the largest remaining oil reservoirs in the world. This finding may influence strategies to recover energy or chemicals from these HREs by in situ microbial processes.
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Affiliation(s)
- Dongshan An
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Sean M. Caffrey
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Jung Soh
- Visual Genomics Centre, Faculty
of Medicine, University of Calgary, Calgary,
Alberta, T2N 1N4, Canada
| | - Akhil Agrawal
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Damon Brown
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Karen Budwill
- Environment and Carbon Management Division, Alberta Innovates−Technology Futures, Edmonton,
Alberta, T6N 1E4, Canada
| | - Xiaoli Dong
- Visual Genomics Centre, Faculty
of Medicine, University of Calgary, Calgary,
Alberta, T2N 1N4, Canada
| | - Peter
F. Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, P6G 2M7,
Canada
| | - Lisa M. Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Steven J. Hallam
- Department of Microbiology &
Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British
Columbia, V6T 1Z4, Canada
- Michael
Smith Genome Sciences Centre,
Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Niels W. Hanson
- Genome Sciences and Technology
Training Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Zhiguo He
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Thomas R. Jack
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Jonathan Klassen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, P6G 2M7,
Canada
| | - Kishori M. Konwar
- Department of Microbiology &
Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Eugene Kuatsjah
- Genome Sciences and Technology
Training Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, P6G 2M7,
Canada
| | - Steve Larter
- Department
of Geosciences, University of Calgary,
Calgary, Alberta, T2N 1N4, Canada
| | - Verlyn Leopatra
- Department of Community Health
Sciences, University of Calgary, Alberta,
T2N 1N4, Canada
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, P6G 2M7,
Canada
- Department of Biology, University of Oslo, 0313 Oslo, Norway
| | - Thomas Oldenburg
- Department
of Geosciences, University of Calgary,
Calgary, Alberta, T2N 1N4, Canada
| | - Antoine
P. Pagé
- Department of Microbiology &
Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Esther Ramos-Padron
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Fauziah F. Rochman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | | | - Christoph W. Sensen
- Visual Genomics Centre, Faculty
of Medicine, University of Calgary, Calgary,
Alberta, T2N 1N4, Canada
| | - Payal Sipahimalani
- Michael
Smith Genome Sciences Centre,
Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Young C. Song
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British
Columbia, V6T 1Z4, Canada
| | - Sandra Wilson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Gregor Wolbring
- Department of Community Health
Sciences, University of Calgary, Alberta,
T2N 1N4, Canada
| | - Man-Ling Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Gerrit Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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24
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Xiang L, Moncivais K, Jiang F, Willams B, Alfonta L, Zhang ZJ. Crucial optimization of translational components towards efficient incorporation of unnatural amino acids into proteins in mammalian cells. PLoS One 2013; 8:e67333. [PMID: 23874413 PMCID: PMC3709914 DOI: 10.1371/journal.pone.0067333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
The ability to site-specifically incorporate unnatural amino acids (UAAs) into proteins is a powerful tool in protein engineering. While dozens of UAAs have been successfully introduced into proteins expressed by Escherichia coli cells, it has been much more challenging to create tRNA and tRNA-Synthetase pairs that enable UAAs incorporation, for use in mammalian systems. By altering the orthogonality properties of existing unnatural pairs, previously evolved pairs for use in E. coli could be used in mammalian cells. This would bypass the cumbersome step of having to evolve mutant synthetases and would allow for the rapid development of new mammalian pairs. A major limitation to the amount of UAA-containing proteins that can be expressed in the cell is the availability of UAA-charged orthogonal suppressor tRNA. By using a natural mammalian tRNA promoter, the amount of functional suppressor tRNA can be greatly increased. Furthermore, increasing recognition of the suppressor tRNA by the mutant synthetase will ultimately lead to the appearance of more UAA-charged tRNA.
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Affiliation(s)
- Liang Xiang
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
- Biomedical Engineering Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Kathryn Moncivais
- Biomedical Engineering Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Faqin Jiang
- School of Pharmacy, Shanghai Jiaotong University, Shanghai, China
| | - Blake Willams
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
| | - Lital Alfonta
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (LF); (ZJZ)
| | - Zhiwen J. Zhang
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
- * E-mail: (LF); (ZJZ)
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25
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Su AAH, Tripp V, Randau L. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 2013; 41:6250-8. [PMID: 23620296 PMCID: PMC3695527 DOI: 10.1093/nar/gkt317] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/03/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022] Open
Abstract
The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.
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MESH Headings
- Euryarchaeota/genetics
- Euryarchaeota/metabolism
- High-Throughput Nucleotide Sequencing
- Hot Temperature
- Inverted Repeat Sequences
- RNA Editing
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- Andreas A. H. Su
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Max Planck Research Group: Prokaryotic Small RNA Biology, Karl-von-Frisch Strasse 10, 35037 Marburg, Germany and LOEWE Center for Synthetic Microbiology (Synmikro), 35037 Marburg, Germany
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26
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Nguyen TN, You DJ, Matsumoto H, Kanaya E, Koga Y, Kanaya S. Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid. J Struct Biol 2013; 182:144-54. [PMID: 23500886 DOI: 10.1016/j.jsb.2013.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/26/2013] [Accepted: 02/28/2013] [Indexed: 12/11/2022]
Abstract
LC11-RNase H1 is a Sulfolobus tokodaii RNase H1 (Sto-RNase H1) homologue isolated by metagenomic approach. In this study, the crystal structure of LC11-RNase H1 in complex with an RNA/DNA substrate was determined. Unlike Bacillus halodurans RNase H1 without hybrid binding domain (HBD) (Bh-RNase HC) and human RNase H1 without HBD (Hs-RNase HC), LC11-RNase H1 interacts with four non-consecutive 2'-OH groups of the RNA strand. The lack of interactions with four consecutive 2'-OH groups leads to a dramatic decrease in the ability of LC11-RNase H1 to cleave the DNA-RNA-DNA/DNA substrate containing four ribonucleotides as compared to those to cleave the substrates containing five and six ribonucleotides. The interaction of LC11-RNase H1 with the DNA strand is also different from those of Bh-RNase HC and Hs-RNase HC. Beside the common phosphate-binding pocket, LC11-RNase H1 has a unique DNA-binding channel. Furthermore, the active-site residues of LC11-RNase H1 are located farther away from the scissile phosphate group than those of Bh-RNase HC and Hs-RNase HC. Modeling of Sto-RNase H1 in complex with the 14bp RNA/DNA substrate, together with the structure-based mutational analyses, suggest that the ability of Sto-RNase H1 to cleave double-stranded RNA is dependent on the local conformation of the basic residues located at the DNA binding site.
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Affiliation(s)
- Tri-Nhan Nguyen
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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27
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Mukherjee A, Wheaton GH, Blum PH, Kelly RM. Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species. Proc Natl Acad Sci U S A 2012; 109:16702-7. [PMID: 23010932 PMCID: PMC3478614 DOI: 10.1073/pnas.1210904109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermoacidophilic archaea are found in heavy metal-rich environments, and, in some cases, these microorganisms are causative agents of metal mobilization through cellular processes related to their bioenergetics. Given the nature of their habitats, these microorganisms must deal with the potentially toxic effect of heavy metals. Here, we show that two thermoacidophilic Metallosphaera species with nearly identical (99.99%) genomes differed significantly in their sensitivity and reactivity to uranium (U). Metallosphaera prunae, isolated from a smoldering heap on a uranium mine in Thüringen, Germany, could be viewed as a "spontaneous mutant" of Metallosphaera sedula, an isolate from Pisciarelli Solfatara near Naples. Metallosphaera prunae tolerated triuranium octaoxide (U(3)O(8)) and soluble uranium [U(VI)] to a much greater extent than M. sedula. Within 15 min following exposure to "U(VI) shock," M. sedula, and not M. prunae, exhibited transcriptomic features associated with severe stress response. Furthermore, within 15 min post-U(VI) shock, M. prunae, and not M. sedula, showed evidence of substantial degradation of cellular RNA, suggesting that transcriptional and translational processes were aborted as a dynamic mechanism for resisting U toxicity; by 60 min post-U(VI) shock, RNA integrity in M. prunae recovered, and known modes for heavy metal resistance were activated. In addition, M. sedula rapidly oxidized solid U(3)O(8) to soluble U(VI) for bioenergetic purposes, a chemolithoautotrophic feature not previously reported. M. prunae, however, did not solubilize solid U(3)O(8) to any significant extent, thereby not exacerbating U(VI) toxicity. These results point to uranium extremophily as an adaptive, rather than intrinsic, feature for Metallosphaera species, driven by environmental factors.
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Affiliation(s)
- Arpan Mukherjee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Garrett H. Wheaton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Paul H. Blum
- Beadle Center for Genetics, University of Nebraska-Lincoln, Lincoln, NE 68588-0666
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
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28
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Naor A, Thiaville PC, Altman-Price N, Cohen-Or I, Allers T, de Crécy-Lagard V, Gophna U. A genetic investigation of the KEOPS complex in halophilic Archaea. PLoS One 2012; 7:e43013. [PMID: 22927945 PMCID: PMC3426518 DOI: 10.1371/journal.pone.0043013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/17/2012] [Indexed: 12/01/2022] Open
Abstract
KEOPS is an important cellular complex conserved in Eukarya, with some subunits conserved in Archaea and Bacteria. This complex was recently found to play an essential role in formation of the tRNA modification threonylcarbamoyladenosine (t6A), and was previously associated with telomere length maintenance and transcription. KEOPS subunits are conserved in Archaea, especially in the Euryarchaea, where they had been studied in vitro. Here we attempted to delete the genes encoding the four conserved subunits of the KEOPS complex in the euryarchaeote Haloferax volcanii and study their phenotypes in vivo. The fused kae1-bud32 gene was shown to be essential as was cgi121, which is dispensable in yeast. In contrast, pcc1 (encoding the putative dimerizing unit of KEOPS) was not essential in H. volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t6A modification, and elevated levels of intra-cellular glycation products.
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Affiliation(s)
- Adit Naor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Patrick C. Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Neta Altman-Price
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Cohen-Or
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Thorsten Allers
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (VdC); (UG)
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (VdC); (UG)
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29
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Bower-Phipps KR, Taylor DW, Wang HW, Baserga SJ. The box C/D sRNP dimeric architecture is conserved across domain Archaea. RNA 2012; 18:1527-1540. [PMID: 22753779 PMCID: PMC3404373 DOI: 10.1261/rna.033134.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/26/2012] [Indexed: 06/01/2023]
Abstract
Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.
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Affiliation(s)
| | | | | | - Susan J. Baserga
- Department of Molecular Biophysics and Biochemistry
- Department of Genetics
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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30
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Abstract
BACKGROUND The methanogenic Archaea Methanosphaera stadtmanae has been detected in the human gut microbiota by both culture and culture-independent methods. Its growth reaches an exponential phase after 5 to 7-day culture in medium 322 (10% vol). Our recent successful isolation of Methanomassiliicoccus luminyensis, a tungstate-selenite-requiring Archaea sharing similar metabolism characteristics with M. stadtmanae prompted us to study the effects of tungsten and selenium on M. stadtmanae growth. FINDINGS Addition of 0.2 mg/L sodium tungstate to medium 322 yielded, 48 hours after inoculation, a growth rate equivalent to that obtained after 6 days with control culture as measured by methane monitoring and optical density measurement. Addition of 50 μg/mL sodium selenate had no effect on M. stadtmanae growth. Quantitative real-time PCRs targeting the M. stadtmanae 16S rRNA confirmed these data. CONCLUSIONS These data provide new information regarding the poorly known nutritional requirements of the human gut colonizing organismsM. stadtmanae. Adding sodium tungstate to basal medium may facilitate phenotypic characterization of this organism and additionally aid the isolation of new Archaea from complex host microbiota.
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Affiliation(s)
- Bédis Dridi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IDR 198, IFR48, Institut Méditerranée Infection, Aix-Marseille-Université, Marseille, France
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IDR 198, IFR48, Institut Méditerranée Infection, Aix-Marseille-Université, Marseille, France
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, UMR D180, Microbiologie et Biotechnologie des Environnements Chauds, Aix-Marseille-Université, ESIL, Marseille, France
| | - Bernard Ollivier
- Laboratoire de Microbiologie IRD, UMR D180, Microbiologie et Biotechnologie des Environnements Chauds, Aix-Marseille-Université, ESIL, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IDR 198, IFR48, Institut Méditerranée Infection, Aix-Marseille-Université, Marseille, France
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31
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Abstract
Aeropyrum pernix contains one homolog of ribonuclease H (RNase H), A. pernix RNase HII (Ape-RNase HII). Activity characterization showed that Ape-RNase HII exhibited the highest activity in the presence of 5 mM Mn(2+), 1 mM Co(2+), or 10 mM Mg(2+), respectively; however, its cleavage efficiencies at different cleavage sites for Mn(2+) and Mg(2+) were different. Ape-RNase HII cleaved 12-bp RNA/DNA substrates at multiple sites and the optimum pH value was 11.0. Moreover, 16-bp DNA-r4-DNA/DNA and 13-bp DNA-r1-DNA/DNA chimeric substrates were cleaved at DNA-RNA junction. Ape-RNase HII was thermostable and the stabilization was enhanced with increased salt concentration. This work is believed to be the first in vitro functional study of Ape-RNase HII and the results should contribute to the analysis of RNase H of other archaeal species.
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Affiliation(s)
- Jingli Hou
- Instrumental Analysis Center of Shanghai Jiaotong University, Shanghai, China
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32
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Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V. The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA 2012; 18:421-33. [PMID: 22274953 PMCID: PMC3285931 DOI: 10.1261/rna.030841.111] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The methylation of pseudouridine (Ψ) at position 54 of tRNA, producing m(1)Ψ, is a hallmark of many archaeal species, but the specific methylase involved in the formation of this modification had yet to be characterized. A comparative genomics analysis had previously identified COG1901 (DUF358), part of the SPOUT superfamily, as a candidate for this missing methylase family. To test this prediction, the COG1901 encoding gene, HVO_1989, was deleted from the Haloferax volcanii genome. Analyses of modified base contents indicated that while m(1)Ψ was present in tRNA extracted from the wild-type strain, it was absent from tRNA extracted from the mutant strain. Expression of the gene encoding COG1901 from Halobacterium sp. NRC-1, VNG1980C, complemented the m(1)Ψ minus phenotype of the ΔHVO_1989 strain. This in vivo validation was extended with in vitro tests. Using the COG1901 recombinant enzyme from Methanocaldococcus jannaschii (Mj1640), purified enzyme Pus10 from M. jannaschii and full-size tRNA transcripts or TΨ-arm (17-mer) fragments as substrates, the sequential pathway of m(1)Ψ54 formation in Archaea was reconstituted. The methylation reaction is AdoMet dependent. The efficiency of the methylase reaction depended on the identity of the residue at position 55 of the TΨ-loop. The presence of Ψ55 allowed the efficient conversion of Ψ54 to m(1)Ψ54, whereas in the presence of C55, the reaction was rather inefficient and no methylation reaction occurred if a purine was present at this position. These results led to renaming the Archaeal COG1901 members as TrmY proteins.
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Affiliation(s)
- Kunal Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Ian K. Blaby
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Patrick C. Thiaville
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Henri Grosjean
- Université Paris11, IGM, CNRS, UMR 8621, Orsay, F 91405, France
| | - Y. Adam Yuan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117543
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
- Corresponding authors.E-mail .E-mail .
| | - Valérie de Crécy-Lagard
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
- Corresponding authors.E-mail .E-mail .
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33
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Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crécy-Lagard V, Gupta R. Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. RNA 2011; 17:1367-80. [PMID: 21628430 PMCID: PMC3138572 DOI: 10.1261/rna.2712811] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Pseudouridine (Ψ), the isomer of uridine, is commonly found at various positions of noncoding RNAs of all organisms. Ψ residues are formed by a number of single- or multisite specific Ψ synthases, which generally act as stand-alone proteins. In addition, in Eukarya and Archaea, specific ribonucleoprotein complexes, each containing a distinct box H/ACA guide RNA and four core proteins, can produce Ψ at many sites of different cellular RNAs. Cbf5 is the core Ψ synthase in these complexes. Using Haloferax volcanii as an archaeal model organism, we show that, contrary to eukaryotes, the Cbf5 homolog (HVO_2493) is not essential in this archaeon. The Cbf5-deleted strain of H. volcanii completely lacks Ψ at positions 1940, 1942, 2605, and 2591 (Escherichia coli positions 1915, 1917, 2572, and 2586) of its 23S rRNA, and contains reduced steady-state levels of some box H/ACA RNAs. Archaeal Cbf5 is known to have tRNA Ψ55 synthase activity in vitro but we could not confirm this activity in vivo in H. volcanii. Conversely, the Pus10 (previously PsuX) homolog (HVO_1979), which can produce tRNA Ψ55, as well as Ψ54 in vitro, is shown here to be essential in H. volcanii, whereas the corresponding tRNA Ψ55 synthases, Pus4 and TruB, are not essential in yeast and E. coli, respectively. Finally, we demonstrate that HVO_1852, the TruA/Pus3 homolog, is responsible for the pseudouridylation of position 39 in H. volcanii tRNAs and that the corresponding gene is not essential.
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Affiliation(s)
- Ian K. Blaby
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Kunal Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Sujata Jana
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Henri Grosjean
- Université Paris 11, IGM, CNRS, UMR 8621, Orsay, F 91405, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
- Corresponding authors.E-mail .E-mail .
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
- Corresponding authors.E-mail .E-mail .
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34
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Lintner NG, Kerou M, Brumfield SK, Graham S, Liu H, Naismith JH, Sdano M, Peng N, She Q, Copié V, Young MJ, White MF, Lawrence CM. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J Biol Chem 2011; 286:21643-56. [PMID: 21507944 PMCID: PMC3122221 DOI: 10.1074/jbc.m111.238485] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 04/08/2011] [Indexed: 12/26/2022] Open
Abstract
In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.
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Affiliation(s)
| | - Melina Kerou
- the Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom, and
| | - Susan K. Brumfield
- From the Thermal Biology Institute
- Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Shirley Graham
- the Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom, and
| | - Huanting Liu
- the Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom, and
| | - James H. Naismith
- the Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom, and
| | - Matthew Sdano
- From the Thermal Biology Institute
- Departments of Chemistry and Biochemistry and
| | - Nan Peng
- the Department of Biology, Archaea Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Qunxin She
- the Department of Biology, Archaea Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Valérie Copié
- From the Thermal Biology Institute
- Departments of Chemistry and Biochemistry and
| | - Mark J. Young
- From the Thermal Biology Institute
- Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Malcolm F. White
- the Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom, and
| | - C. Martin Lawrence
- From the Thermal Biology Institute
- Departments of Chemistry and Biochemistry and
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35
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Qu G, van Nues RW, Watkins NJ, Maxwell ES. The spatial-functional coupling of box C/D and C'/D' RNPs is an evolutionarily conserved feature of the eukaryotic box C/D snoRNP nucleotide modification complex. Mol Cell Biol 2011; 31:365-74. [PMID: 21041475 PMCID: PMC3019978 DOI: 10.1128/mcb.00918-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 09/10/2010] [Accepted: 10/26/2010] [Indexed: 11/20/2022] Open
Abstract
Box C/D ribonucleoprotein particles guide the 2'-O-ribose methylation of target nucleotides in both archaeal and eukaryotic RNAs. These complexes contain two functional centers, assembled around the C/D and C'/D' motifs in the box C/D RNA. The C/D and C'/D' RNPs of the archaeal snoRNA-like RNP (sRNP) are spatially and functionally coupled. Here, we show that similar coupling also occurs in eukaryotic box C/D snoRNPs. The C/D RNP guided 2'-O-methylation when the C'/D' motif was either mutated or ablated. In contrast, the C'/D' RNP was inactive as an independent complex. Additional experiments demonstrated that the internal C'/D' RNP is spatially coupled to the terminal box C/D complex. Pulldown experiments also indicated that all four core proteins are independently recruited to the box C/D and C'/D' motifs. Therefore, the spatial-functional coupling of box C/D and C'/D' RNPs is an evolutionarily conserved feature of both archaeal and eukaryotic box C/D RNP complexes.
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Affiliation(s)
- Guosheng Qu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA.
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36
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Ghalei H, Hsiao HH, Urlaub H, Wahl MC, Watkins NJ. A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation. RNA 2010; 16:2341-8. [PMID: 20962039 PMCID: PMC2995396 DOI: 10.1261/rna.2380410] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 09/16/2010] [Indexed: 05/30/2023]
Abstract
Archaeal and eukaryotic box C/D RNPs catalyze the 2'-O-methylation of ribosomal RNA, a modification that is essential for the correct folding and function of the ribosome. Each archaeal RNP contains three core proteins--L7Ae, Nop5, and fibrillarin (methyltransferase)--and a box C/D sRNA. Base-pairing between the sRNA guide region and the rRNA directs target site selection with the C/D and related C'/D' motifs functioning as protein binding sites. Recent structural analysis of in vitro assembled archaeal complexes has produced two divergent models of box C/D sRNP structure. In one model, the complex is proposed to be monomeric, while the other suggests a dimeric sRNP. The position of the RNA in the RNP is significantly different in each model. We have used UV-cross-linking to characterize protein-RNA contacts in the in vitro assembled Pyrococcus furiosus box C/D sRNP. The P. furiosus sRNP components assemble into complexes that are the expected size of di-sRNPs. Analysis of UV-induced protein-RNA cross-links revealed a novel interaction between the ALFR motif, in the Nop domain of Nop5, and the guide/spacer regions of the sRNA. We show that the ALFR motif and the spacer sequence adjacent to box C or C' are important for box C/D sRNP assembly in vitro. These data therefore reveal new RNA-protein contacts in the box C/D sRNP and suggest a role for Nop5 in substrate binding and/or release.
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Affiliation(s)
- Homa Ghalei
- Abteilung Zelluläre Biochemie, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
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37
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Jia B, Lee S, Pham BP, Cho YS, Yang JK, Byeon HS, Kim JC, Cheong GW. An archaeal NADH oxidase causes damage to both proteins and nucleic acids under oxidative stress. Mol Cells 2010; 29:363-71. [PMID: 20213313 DOI: 10.1007/s10059-010-0045-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 12/18/2009] [Accepted: 12/23/2009] [Indexed: 10/19/2022] Open
Abstract
NADH oxidases (NOXs) catalyze the two-electron reduction of oxygen to H2O2 or four-electron reduction of oxygen to H2O. In this report, we show that an NADH oxidase from Thermococcus profundus (NOXtp) displays two forms: a native dimeric protein under physiological conditions and an oxidized hexameric form under oxidative stress. Native NOXtp displays high NADH oxidase activity, and oxidized NOXtp can accelerate the aggregation of partially unfolded proteins. The aggregates formed by NOXtp have characteristics similar to beta-amyloid and Lewy bodies in neurodegenerative diseases, including an increase of beta-sheet content. Oxidized NOXtp can also bind nucleic acids and cause their degradation by oxidizing NADH to produce H2O2. Furthermore, Escherichia coli cells expressing NOXtp are less viable than cells not expressing NOXtp after treatment with H2O2. As NOXtp shares similar features with eukaryotic cell death isozymes and life may have originated from hyperthermophiles, we suggest that NOXtp may be an ancestor of cell death proteins.
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MESH Headings
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Archaeal Proteins/ultrastructure
- Blotting, Western
- DNA Damage
- DNA, Archaeal/genetics
- DNA, Archaeal/metabolism
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Hydrogen Peroxide/metabolism
- Hydrogen Peroxide/pharmacology
- Microbial Viability/genetics
- Microscopy, Electron
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/ultrastructure
- NADH, NADPH Oxidoreductases/chemistry
- NADH, NADPH Oxidoreductases/metabolism
- NADH, NADPH Oxidoreductases/ultrastructure
- Oxidation-Reduction
- Oxidative Stress
- Protein Conformation/drug effects
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- Temperature
- Thermococcus/enzymology
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Affiliation(s)
- Baolei Jia
- Division of Applied Life Sciences (Brain Korea 21 Program), Gyeongsang National University, Jinju, 660-701, Korea
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38
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Sun FJ, Caetano-Anollés G. The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 2010; 11:153. [PMID: 20334683 PMCID: PMC2858038 DOI: 10.1186/1471-2105-11-153] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 03/24/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ribonuclease P is an ancient endonuclease that cleaves precursor tRNA and generally consists of a catalytic RNA subunit (RPR) and one or more proteins (RPPs). It represents an important macromolecular complex and model system that is universally distributed in life. Its putative origins have inspired fundamental hypotheses, including the proposal of an ancient RNA world. RESULTS To study the evolution of this complex, we constructed rooted phylogenetic trees of RPR molecules and substructures and estimated RPP age using a cladistic method that embeds structure directly into phylogenetic analysis. The general approach was used previously to study the evolution of tRNA, SINE RNA and 5S rRNA, the origins of metabolism, and the evolution and complexity of the protein world, and revealed here remarkable evolutionary patterns. Trees of molecules uncovered the tripartite nature of life and the early origin of archaeal RPRs. Trees of substructures showed molecules originated in stem P12 and were accessorized with a catalytic P1-P4 core structure before the first substructure was lost in Archaea. This core currently interacts with RPPs and ancient segments of the tRNA molecule. Finally, a census of protein domain structure in hundreds of genomes established RPPs appeared after the rise of metabolic enzymes at the onset of the protein world. CONCLUSIONS The study provides a detailed account of the history and early diversification of a fundamental ribonucleoprotein and offers further evidence in support of the existence of a tripartite organismal world that originated by the segregation of archaeal lineages from an ancient community of primordial organisms.
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Affiliation(s)
- Feng-Jie Sun
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Laboratory of Molecular Epigenetics of the Ministry of Education, School of Life Sciences, Northeast Normal University, Changchun 130024, Jilin Province, PR China
- W.M. Keck Center for Comparative and Functional Genomics, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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39
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Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One 2010; 5:e8739. [PMID: 20090900 PMCID: PMC2806925 DOI: 10.1371/journal.pone.0008739] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 12/18/2009] [Indexed: 11/18/2022] Open
Abstract
Background The exosome complex is an essential RNA 3′-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. Methodology/Principal Findings Here we report an asymmetric 2.9 Å Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. Conclusion/Significance This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.
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Affiliation(s)
- Changrui Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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40
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Gagnon KT, Zhang X, Qu G, Biswas S, Suryadi J, Brown BA, Maxwell ES. Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. RNA 2010; 16:79-90. [PMID: 19926724 PMCID: PMC2802039 DOI: 10.1261/rna.1692310] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 09/29/2009] [Indexed: 05/28/2023]
Abstract
The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C'/D' RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C'/D' RNP despite its inability to bind the K-loop, thus indicating the importance of protein-protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs.
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Affiliation(s)
- Keith T Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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41
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Evguenieva-Hackenberg E. The archaeal exosome. Adv Exp Med Biol 2010; 702:29-38. [PMID: 21618872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The archaeal exosome is aprotein complex with structural similarities to the eukaryotic exosome and bacterial PNPase. Its catalytic core is formed by alternating Rrp41 and Rrp42 polypeptides, arranged in a hexameric ring. A flexible RNA binding cap composed of the evolutionarily conserved proteins Rrp4 and/or Cs14 is bound at the top of the ring and seems to be involved in recruitment of specific substrates and their unwinding. Additionally, the protein complex contains an archaea-specific subunit annotated as DnaG, the function of which is still unknown. The archaeal exosome degrades RNA phosphorolytically in 3' to 5' direction. In a reverse reaction, it synthesizes heteropolymeric RNA tails using nucleoside diphosphates. The functional similarity between the archaeal exosome and PNPase shows that important processes of RNA degradation and posttranscriptional modification in Archaea are similar to the processes in Bacteria and organelles.
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Hasenöhrl D, Fabbretti A, Londei P, Gualerzi CO, Bläsi U. Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus. RNA 2009; 15:2288-2298. [PMID: 19861425 PMCID: PMC2779686 DOI: 10.1261/rna.1662609] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
The function of initiation factors in and the sequence of events during translation initiation have been intensively studied in Bacteria and Eukaryotes, whereas in Archaea knowledge on these functions/processes is limited. By employing chemical probing, we show that translation initiation factor aIF1 of the model crenarchaeon Sulfolobus solfataricus binds to the same area on the ribosome as the bacterial and eukaryal orthologs. Fluorescence energy transfer assays (FRET) showed that aIF1, like its eukaryotic and bacterial orthologs, has a fidelity function in translation initiation complex formation, and that both aIF1 and aIF1A exert a synergistic effect in stimulating ribosomal association of the Met-tRNAi(Met) binding factor a/eIF2. However, as in Eukaryotes their effect on a/eIF2 binding appears to be indirect. Moreover, FRET was used to analyze for the first time the sequence of events toward translation initiation complex formation in an archaeal model system. These studies suggested that a/eIF2-GTP binds first to the ribosome and then recruits Met-tRNAi(Met), which appears to comply with the operational mode of bacterial IF2, and deviates from the shuttle function of the eukaryotic counterpart eIF2. Thus, despite the resemblance of eIF2 and a/eIF2, recruitment of initiator tRNA to the ribosome is mechanistically different in Pro- and Eukaryotes.
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Affiliation(s)
- David Hasenöhrl
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, 1030 Vienna, Austria.
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43
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Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 2009; 139:945-56. [PMID: 19945378 PMCID: PMC2951265 DOI: 10.1016/j.cell.2009.07.040] [Citation(s) in RCA: 763] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 04/13/2009] [Accepted: 07/17/2009] [Indexed: 12/19/2022]
Abstract
Compelling evidence indicates that the CRISPR-Cas system protects prokaryotes from viruses and other potential genome invaders. This adaptive prokaryotic immune system arises from the clustered regularly interspaced short palindromic repeats (CRISPRs) found in prokaryotic genomes, which harbor short invader-derived sequences, and the CRISPR-associated (Cas) protein-coding genes. Here, we have identified a CRISPR-Cas effector complex that is comprised of small invader-targeting RNAs from the CRISPR loci (termed prokaryotic silencing (psi)RNAs) and the RAMP module (or Cmr) Cas proteins. The psiRNA-Cmr protein complexes cleave complementary target RNAs at a fixed distance from the 3' end of the integral psiRNAs. In Pyrococcus furiosus, psiRNAs occur in two size forms that share a common 5' sequence tag but have distinct 3' ends that direct cleavage of a given target RNA at two distinct sites. Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs.
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Affiliation(s)
- Caryn R. Hale
- Department of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Sara Olson
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, 263 armington Avenue, Farmington, CT 06030-3301, USA
| | - Michael O. Duff
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, 263 armington Avenue, Farmington, CT 06030-3301, USA
| | - Brenton R. Graveley
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, 263 armington Avenue, Farmington, CT 06030-3301, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rebecca M. Terns
- Department of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Michael P. Terns
- Department of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
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Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions. J Mol Biol 2009; 393:1043-55. [PMID: 19733182 DOI: 10.1016/j.jmb.2009.08.068] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/28/2009] [Accepted: 08/30/2009] [Indexed: 01/05/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) enzyme that catalyzes the Mg(2+)-dependent 5' maturation of precursor tRNAs. In all domains of life, it is a ribozyme: the RNase P RNA (RPR) component has been demonstrated to be responsible for catalysis. However, the number of RNase P protein subunits (RPPs) varies from 1 in bacteria to 9 or 10 in eukarya. The archaeal RPR is associated with at least 4 RPPs, which function in pairs (RPP21-RPP29 and RPP30-POP5). We used solution NMR spectroscopy to determine the three-dimensional structure of the protein-protein complex comprising Pyrococcus furiosus RPP21 and RPP29. We found that the protein-protein interaction is characterized by coupled folding of secondary structural elements that participate in interface formation. In addition to detailing the intermolecular contacts that stabilize this 30-kDa binary complex, the structure identifies surfaces rich in conserved basic residues likely vital for recognition of the RPR and/or precursor tRNA. Furthermore, enzymatic footprinting experiments allowed us to localize the RPP21-RPP29 complex to the specificity domain of the RPR. These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme.
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Affiliation(s)
- Yiren Xu
- Ohio State Biochemistry Program, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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45
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Hardin JW, Reyes FE, Batey RT. Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. J Biol Chem 2009; 284:15317-24. [PMID: 19336398 PMCID: PMC2685712 DOI: 10.1074/jbc.m901368200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 11/06/2022] Open
Abstract
In archaea and eukarya, box C/D ribonucleoprotein (RNP) complexes are responsible for 2'-O-methylation of tRNAs and rRNAs. The archaeal box C/D small RNP complex requires a small RNA component (sRNA) possessing Watson-Crick complementarity to the target RNA along with three proteins: L7Ae, Nop5p, and fibrillarin. Transfer of a methyl group from S-adenosylmethionine to the target RNA is performed by fibrillarin, which by itself has no affinity for the sRNA-target duplex. Instead, it is targeted to the site of methylation through association with Nop5p, which in turn binds to the L7Ae-sRNA complex. To understand how Nop5p serves as a bridge between the targeting and catalytic functions of the box C/D small RNP complex, we have employed alanine scanning to evaluate the interaction between the Pyrococcus horikoshii Nop5p domain and an L7Ae box C/D RNA complex. From these data, we were able to construct an isolated RNA-binding domain (Nop-RBD) that folds correctly as demonstrated by x-ray crystallography and binds to the L7Ae box C/D RNA complex with near wild type affinity. These data demonstrate that the Nop-RBD is an autonomously folding and functional module important for protein assembly in a number of complexes centered on the L7Ae-kinkturn RNP.
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Affiliation(s)
- John W Hardin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
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Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NGA. Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PLoS Biol 2009; 7:e1000102. [PMID: 19419240 PMCID: PMC2675907 DOI: 10.1371/journal.pbio.1000102] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 03/19/2009] [Indexed: 11/19/2022] Open
Abstract
The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.
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Affiliation(s)
- Yakov Korkhin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Ulug M Unligil
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Otis Littlefield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Pamlea J Nelson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - David I Stuart
- Division of Structural Biology and the Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paul B Sigler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, United States of America
| | - Stephen D Bell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nicola G. A Abrescia
- Division of Structural Biology and the Oxford Protein Production Facility, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- * To whom correspondence should be addressed. E-mail:
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Abstract
All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.
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MESH Headings
- Amino Acid Motifs
- Catalytic Domain
- Crystallography, X-Ray
- Cytidine Deaminase/chemistry
- Cytidine Deaminase/metabolism
- Deamination
- Euryarchaeota/enzymology
- Euryarchaeota/genetics
- Euryarchaeota/metabolism
- Genes, Archaeal
- Models, Chemical
- Models, Molecular
- Nucleic Acid Conformation
- Protein Multimerization
- Protein Structure, Tertiary
- RNA Editing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Lennart Randau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Bradford J. Stanley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Sarah Mechta
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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Muller S, Urban A, Hecker A, Leclerc F, Branlant C, Motorin Y. Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery. Nucleic Acids Res 2009; 37:1308-22. [PMID: 19139072 PMCID: PMC2651775 DOI: 10.1093/nar/gkn1037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Revised: 12/11/2008] [Accepted: 12/12/2008] [Indexed: 11/21/2022] Open
Abstract
Up to now, Psi formation in tRNAs was found to be catalysed by stand-alone enzymes. By computational analysis of archaeal genomes we detected putative H/ACA sRNAs, in four Sulfolobales species and in Aeropyrum pernix, that might guide Psi 35 formation in pre-tRNA(Tyr)(GUA). This modification is achieved by Pus7p in eukarya. The validity of the computational predictions was verified by in vitro reconstitution of H/ACA sRNPs using the identified Sulfolobus solfataricus H/ACA sRNA. Comparison of Pus7-like enzymes encoded by archaeal genomes revealed amino acid substitutions in motifs IIIa and II in Sulfolobales and A. pernix Pus7-like enzymes. These conserved RNA:Psi-synthase- motifs are essential for catalysis. As expected, the recombinant Pyrococcus abyssi aPus7 was fully active and acted at positions 35 and 13 and other positions in tRNAs, while the recombinant S. solfataricus aPus7 was only found to have a poor activity at position 13. We showed that the presence of an A residue 3' to the target U residue is required for P. abyssi aPus7 activity, and that this is not the case for the reconstituted S. solfataricus H/ACA sRNP. In agreement with the possible formation of Psi 35 in tRNA(Tyr)(GUA) by aPus7 in P. abyssi and by an H/ACA sRNP in S. solfataricus, the A36G mutation in the P. abyssi tRNA(Tyr)(GUA) abolished Psi 35 formation when using P. abyssi extract, whereas the A36G substitution in the S. solfataricus pre-tRNA(Tyr) did not affect Psi 35 formation in this RNA when using an S. solfataricus extract.
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Affiliation(s)
- Sébastien Muller
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
| | - Alan Urban
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
| | - Arnaud Hecker
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
| | - Fabrice Leclerc
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
| | - Christiane Branlant
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
| | - Yuri Motorin
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy Université, BP 239, 54506 Vandoeuvre-les-Nancy Cedex and Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
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Parker JS, Parizotto EA, Wang M, Roe SM, Barford D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell 2009; 33:204-14. [PMID: 19187762 PMCID: PMC2642989 DOI: 10.1016/j.molcel.2008.12.012] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 10/20/2008] [Accepted: 12/04/2008] [Indexed: 12/03/2022]
Abstract
Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. Over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. Enhancement is achieved through a reduced entropy penalty for the interaction. In contrast, interactions 3' of the seed are inhibited. We quantified mismatched target recognition inside and outside the seed, revealing amplified discrimination at the third position in the seed mediated by the PIWI/MID domain. Thus, association of the guide strand with the PIWI/MID domain generates an enhanced affinity anchor site over the seed that can promote fidelity in target recognition and stabilize and guide the assembly of the active silencing complex.
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Affiliation(s)
- James S. Parker
- Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Eneida A. Parizotto
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Muhan Wang
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - S. Mark Roe
- Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - David Barford
- Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
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50
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Rao KN, Burley SK, Swaminathan S. UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function. PLoS One 2008; 3:e3903. [PMID: 19079550 PMCID: PMC2596488 DOI: 10.1371/journal.pone.0003903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 11/16/2008] [Indexed: 11/18/2022] Open
Abstract
We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10–40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel β-sheet and five α-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.
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Affiliation(s)
- Krishnamurthy N. Rao
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Stephen K. Burley
- Eli Lilly and Company, San Diego, California, United States of America
| | - Subramanyam Swaminathan
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America
- * E-mail:
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