1
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Jedrzejewski M, Belza B, Lewandowska I, Sadlej M, Perlinska AP, Augustyniak R, Christian T, Hou YM, Kalek M, Sulkowska JI. Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study. Comput Struct Biotechnol J 2023; 21:3999-4008. [PMID: 37649713 PMCID: PMC10462857 DOI: 10.1016/j.csbj.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023] Open
Abstract
The Nep1 protein is essential for the formation of eukaryotic and archaeal small ribosomal subunits, and it catalyzes the site-directed SAM-dependent methylation of pseudouridine (Ψ) during pre-rRNA processing. It possesses a non-trivial topology, namely, a 31 knot in the active site. Here, we address the issue of seemingly unfeasible deprotonation of Ψ in Nep1 active site by a distant aspartate residue (D101 in S. cerevisiae), using a combination of bioinformatics, computational, and experimental methods. We identified a conserved hydroxyl-containing amino acid (S233 in S. cerevisiae, T198 in A. fulgidus) that may act as a proton-transfer mediator. Molecular dynamics simulations, based on the crystal structure of S. cerevisiae, and on a complex generated by molecular docking in A. fulgidus, confirmed that this amino acid can shuttle protons, however, a water molecule in the active site may also serve this role. Quantum-chemical calculations based on density functional theory and the cluster approach showed that the water-mediated pathway is the most favorable for catalysis. Experimental kinetic and mutational studies reinforce the requirement for the aspartate D101, but not S233. These findings provide insight into the catalytic mechanisms underlying proton transfer over extended distances and comprehensively elucidate the mode of action of Nep1.
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Affiliation(s)
- Mateusz Jedrzejewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Barbara Belza
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Iwona Lewandowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Marta Sadlej
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Agata P. Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Rafal Augustyniak
- Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Marcin Kalek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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2
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Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022; 298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022] Open
Abstract
The SpoU-TrmD (SPOUT) methyltransferase superfamily was designated when structural similarity was identified between the transfer RNA-modifying enzymes TrmH (SpoU) and TrmD. SPOUT methyltransferases are found in all domains of life and predominantly modify transfer RNA or ribosomal RNA substrates, though one instance of an enzyme with a protein substrate has been reported. Modifications placed by SPOUT methyltransferases play diverse roles in regulating cellular processes such as ensuring translational fidelity, altering RNA stability, and conferring bacterial resistance to antibiotics. This large collection of S-adenosyl-L-methionine-dependent methyltransferases is defined by a unique α/β fold with a deep trefoil knot in their catalytic (SPOUT) domain. Herein, we describe current knowledge of SPOUT enzyme structure, domain architecture, and key elements of catalytic function, including S-adenosyl-L-methionine co-substrate binding, beginning with a new sequence alignment that divides the SPOUT methyltransferase superfamily into four major clades. Finally, a major focus of this review will be on our growing understanding of how these diverse enzymes accomplish the molecular feat of specific substrate recognition and modification, as highlighted by recent advances in our knowledge of protein-RNA complex structures and the discovery of the dependence of one SPOUT methyltransferase on metal ion binding for catalysis. Considering the broad biological roles of RNA modifications, developing a deeper understanding of the process of substrate recognition by the SPOUT enzymes will be critical for defining many facets of fundamental RNA biology with implications for human disease.
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Affiliation(s)
- Sarah E Strassler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA.
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA.
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3
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Li X, Li K, Guo W, Wen Y, Meng C, Wu B. Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK. Front Microbiol 2022; 13:926099. [PMID: 35783380 PMCID: PMC9247573 DOI: 10.3389/fmicb.2022.926099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5′-phosphate (ΨMP) and further hydrolyzing 5′-ΨMP to produce uracil and ribose 5′-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Ψ or N1-methyl-pseudouridine (m1Ψ). The structure of EcPsuK showed a homodimer conformation assembled by its β-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of EcPsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover.
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Affiliation(s)
- Xiaojia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kangjie Li
- Department of Biopharmaceutical Technology, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Wenting Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunyan Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Baixing Wu,
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4
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Abstract
Cellular RNAs in all three kingdoms of life are modified with diverse chemical modifications. These chemical modifications expand the topological repertoire of RNAs, and fine-tune their functions. Ribosomal RNA in yeast contains more than 100 chemically modified residues in the functionally crucial and evolutionary conserved regions. The chemical modifications in the rRNA are of three types-methylation of the ribose sugars at the C2-positionAbstract (Nm), isomerization of uridines to pseudouridines (Ψ), and base modifications such as (methylation (mN), acetylation (acN), and aminocarboxypropylation (acpN)). The modifications profile of the yeast rRNA has been recently completed, providing an excellent platform to analyze the function of these modifications in RNA metabolism and in cellular physiology. Remarkably, majority of the rRNA modifications and the enzymatic machineries discovered in yeast are highly conserved in eukaryotes including humans. Mutations in factors involved in rRNA modification are linked to several rare severe human diseases (e.g., X-linked Dyskeratosis congenita, the Bowen-Conradi syndrome and the William-Beuren disease). In this chapter, we summarize all rRNA modifications and the corresponding enzymatic machineries of the budding yeast.
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Affiliation(s)
- Sunny Sharma
- Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ, USA.
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, J.W. Goethe University, Frankfurt/M., Germany.
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5
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Meyer B, Immer C, Kaiser S, Sharma S, Yang J, Watzinger P, Weiß L, Kotter A, Helm M, Seitz HM, Kötter P, Kellner S, Entian KD, Wöhnert J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res 2020; 48:1435-1450. [PMID: 31863583 PMCID: PMC7026641 DOI: 10.1093/nar/gkz1191] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
tRNAs from all domains of life contain modified nucleotides. However, even for the experimentally most thoroughly characterized model organism Escherichia coli not all tRNA modification enzymes are known. In particular, no enzyme has been found yet for introducing the acp3U modification at position 47 in the variable loop of eight E. coli tRNAs. Here we identify the so far functionally uncharacterized YfiP protein as the SAM-dependent 3-amino-3-carboxypropyl transferase catalyzing this modification and thereby extend the list of known tRNA modification enzymes in E. coli. Similar to the Tsr3 enzymes that introduce acp modifications at U or m1Ψ nucleotides in rRNAs this protein contains a DTW domain suggesting that acp transfer reactions to RNA nucleotides are a general function of DTW domain containing proteins. The introduction of the acp3U-47 modification in E. coli tRNAs is promoted by the presence of the m7G-46 modification as well as by growth in rich medium. However, a deletion of the enzymes responsible for the modifications at position 46 and 47 in the variable loop of E. coli tRNAs did not lead to a clearly discernible phenotype suggesting that these two modifications play only a minor role in ensuring the proper function of tRNAs in E. coli.
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Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Steffen Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Sunny Sharma
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Peter Watzinger
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Lena Weiß
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Hans-Michael Seitz
- Institute for Geosciences, Research Unit Mineralogy, and Frankfurt Isotope and Element Research Center (FIERCE), Goethe-Universität Frankfurt, Altenhöferallee 1, 60438 Frankfurt/M., Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
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6
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Kaiser M, Hacker C, Duchardt-Ferner E, Wöhnert J. 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:309-314. [PMID: 31069720 DOI: 10.1007/s12104-019-09897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The protein dimethyladenosine transferase 1 (Dim1) is a highly conserved protein occurring in organisms ranging from bacteria such as E. coli where it is named KsgA to humans. Since Dim1 is involved in the biogenesis of the small ribosomal subunit it is an essential protein. During ribosome biogenesis Dim1 acts as an rRNA modification enzyme and dimethylates two adjacent adenosine residues of the small ribosomal subunit rRNA. In eukaryotes it is also required to ensure the proper endonucleolytic processing of the small ribosomal subunit rRNA precursor. Recently, a third function was proposed for eukaryotic Dim1. Karbstein and coworkers suggested that Dim1 interacts with the essential ribosome assembly factor Fap7 and that Fap7 is responsible for the dissociation of Dim1 from the nascent small ribosomal subunit. Here, we report the backbone 1H, 13C and 15N NMR resonance assignments for the 30.9 kDa Dim1 homologue from the hyperthermophilic archaeon Pyrococcus horikoshii (PhDim1) as a prerequisite for a detailed structural investigation of the PhDim1/PhFap7 interaction.
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Affiliation(s)
- Marco Kaiser
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Carolin Hacker
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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7
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Krishnamohan A, Jackman JE. A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily. Biochemistry 2018; 58:336-345. [PMID: 30457841 DOI: 10.1021/acs.biochem.8b01047] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The SPOUT family of enzymes makes up the second largest of seven structurally distinct groups of methyltransferases and is named after two evolutionarily related RNA methyltransferases, SpoU and TrmD. A deep trefoil knotted domain in the tertiary structures of member enzymes defines the SPOUT family. For many years, formation of a homodimeric quaternary structure was thought to be a strict requirement for all SPOUT enzymes, critical for substrate binding and formation of the active site. However, recent structural characterization of two SPOUT members, Trm10 and Sfm1, revealed that they function as monomers without the requirement of this critical dimerization. This unusual monomeric form implies that these enzymes must exhibit a nontraditional substrate binding mode and active site architecture and may represent a new division in the SPOUT family with distinct properties removed from the dimeric enzymes. Here we discuss the mechanistic features of SPOUT enzymes with an emphasis on the monomeric members and implications of this "novel" monomeric structure on cofactor and substrate binding.
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Affiliation(s)
- Aiswarya Krishnamohan
- The Ohio State Biochemistry Program, Center for RNA Biology, and Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Jane E Jackman
- The Ohio State Biochemistry Program, Center for RNA Biology, and Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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8
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Krüger DM, Neubacher S, Grossmann TN. Protein-RNA interactions: structural characteristics and hotspot amino acids. RNA (NEW YORK, N.Y.) 2018; 24:1457-1465. [PMID: 30093489 PMCID: PMC6191724 DOI: 10.1261/rna.066464.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/06/2018] [Indexed: 06/01/2023]
Abstract
Structural information about protein-RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important. In contrast to protein-protein interactions, in silico approaches for protein-RNA interactions lag behind in their development. Herein, we report an analysis of available protein-RNA structures. We assembled a data set of 322 crystal and NMR structures and analyzed them regarding interface properties. In addition, we describe a computational alanine-scanning approach which provides interaction scores for interface amino acids, allowing the identification of potential hotspots in protein-RNA interfaces. We have made the computational approach available as an online tool, which allows interaction scores to be calculated for any structure of a protein-RNA complex by uploading atomic coordinates to the PRI HotScore web server (https://pri-hotscore.labs.vu.nl).
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Affiliation(s)
- Dennis M Krüger
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
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9
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Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U. The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. Nucleic Acids Res 2017; 45:7938-7949. [PMID: 28520934 PMCID: PMC5570065 DOI: 10.1093/nar/gkx437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 05/03/2017] [Indexed: 01/26/2023] Open
Abstract
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Linlin Hou
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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10
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Warda AS, Freytag B, Haag S, Sloan KE, Görlich D, Bohnsack MT. Effects of the Bowen-Conradi syndrome mutation in EMG1 on its nuclear import, stability and nucleolar recruitment. Hum Mol Genet 2017; 25:5353-5364. [PMID: 27798105 PMCID: PMC5418833 DOI: 10.1093/hmg/ddw351] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/11/2016] [Indexed: 12/14/2022] Open
Abstract
Bowen-Conradi syndrome (BCS) is a severe genetic disorder that is characterised by various developmental abnormalities, bone marrow failure and early infant death. This disease is caused by a single mutation leading to the aspartate 86 to glycine (D86G) exchange in the essential nucleolar RNA methyltransferase EMG1. EMG1 is required for the synthesis of the small ribosomal subunit and is involved in modification of the 18S ribosomal RNA. Here, we identify the pre-ribosomal factors NOP14, NOC4L and UTP14A as members of a nucleolar subcomplex that contains EMG1 and is required for its recruitment to nucleoli. The BCS mutation in EMG1 leads to reduced nucleolar localisation, accumulation of EMG1D86G in nuclear foci and its proteasome-dependent degradation. We further show that EMG1 can be imported into the nucleus by the importins (Imp) Impα/β or Impβ/7. Interestingly, in addition to its role in nuclear import, binding of the Impβ/7 heterodimer can prevent unspecific aggregation of both EMG1 and EMG1D86G on RNAs in vitro, indicating that the importins act as chaperones by binding to basic regions of the RNA methyltransferase. Our findings further indicate that in BCS, nuclear disassembly of the import complex and release of EMG1D86G lead to its nuclear aggregation and degradation, resulting in the reduced nucleolar recruitment of the RNA methyltransferase and defects in the biogenesis of the small ribosomal subunit.
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Affiliation(s)
- Ahmed S Warda
- Institute for Molecular Biology, Georg-August University, Göttingen, Germany
| | - Bernard Freytag
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sara Haag
- Institute for Molecular Biology, Georg-August University, Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, Georg-August University, Göttingen, Germany
| | - Dirk Görlich
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, Georg-August University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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11
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Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Sci Rep 2017; 7:969. [PMID: 28428565 PMCID: PMC5430550 DOI: 10.1038/s41598-017-01186-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/23/2017] [Indexed: 11/24/2022] Open
Abstract
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.
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12
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Zhang Y, Agrebi R, Bellows LE, Collet JF, Kaever V, Gründling A. Evolutionary Adaptation of the Essential tRNA Methyltransferase TrmD to the Signaling Molecule 3',5'-cAMP in Bacteria. J Biol Chem 2017; 292:313-327. [PMID: 27881678 PMCID: PMC5217690 DOI: 10.1074/jbc.m116.758896] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide signaling molecule 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) plays important physiological roles, ranging from carbon catabolite repression in bacteria to mediating the action of hormones in higher eukaryotes, including human. However, it remains unclear whether 3',5'-cAMP is universally present in the Firmicutes group of bacteria. We hypothesized that searching for proteins that bind 3',5'-cAMP might provide new insight into this question. Accordingly, we performed a genome-wide screen and identified the essential Staphylococcus aureus tRNA m1G37 methyltransferase enzyme TrmD, which is conserved in all three domains of life as a tight 3',5'-cAMP-binding protein. TrmD enzymes are known to use S-adenosyl-l-methionine (AdoMet) as substrate; we have shown that 3',5'-cAMP binds competitively with AdoMet to the S. aureus TrmD protein, indicating an overlapping binding site. However, the physiological relevance of this discovery remained unclear, as we were unable to identify a functional adenylate cyclase in S. aureus and only detected 2',3'-cAMP but not 3',5'-cAMP in cellular extracts. Interestingly, TrmD proteins from Escherichia coli and Mycobacterium tuberculosis, organisms known to synthesize 3',5'-cAMP, did not bind this signaling nucleotide. Comparative bioinformatics, mutagenesis, and biochemical analyses revealed that the highly conserved Tyr-86 residue in E. coli TrmD is essential to discriminate between 3',5'-cAMP and the native substrate AdoMet. Combined with a phylogenetic analysis, these results suggest that amino acids in the substrate binding pocket of TrmD underwent an adaptive evolution to accommodate the emergence of adenylate cyclases and thus the signaling molecule 3',5'-cAMP. Altogether this further indicates that S. aureus does not produce 3',5'-cAMP, which would otherwise competitively inhibit an essential enzyme.
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Affiliation(s)
- Yong Zhang
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Lauren E Bellows
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium, and
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Angelika Gründling
- From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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13
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Sloan KE, Warda AS, Sharma S, Entian KD, Lafontaine DLJ, Bohnsack MT. Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol 2016; 14:1138-1152. [PMID: 27911188 PMCID: PMC5699541 DOI: 10.1080/15476286.2016.1259781] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
rRNAs are extensively modified during their transcription and subsequent maturation in the nucleolus, nucleus and cytoplasm. RNA modifications, which are installed either by snoRNA-guided or by stand-alone enzymes, generally stabilize the structure of the ribosome. However, they also cluster at functionally important sites of the ribosome, such as the peptidyltransferase center and the decoding site, where they facilitate efficient and accurate protein synthesis. The recent identification of sites of substoichiometric 2'-O-methylation and pseudouridylation has overturned the notion that all rRNA modifications are constitutively present on ribosomes, highlighting nucleotide modifications as an important source of ribosomal heterogeneity. While the mechanisms regulating partial modification and the functions of specialized ribosomes are largely unknown, changes in the rRNA modification pattern have been observed in response to environmental changes, during development, and in disease. This suggests that rRNA modifications may contribute to the translational control of gene expression.
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Affiliation(s)
- Katherine E Sloan
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Ahmed S Warda
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Sunny Sharma
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Karl-Dieter Entian
- c Institute for Molecular Biosciences, Goethe University , Frankfurt am Main , Germany
| | - Denis L J Lafontaine
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Markus T Bohnsack
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany.,d Göttingen Centre for Molecular Biosciences, Georg-August-University , Göttingen , Germany
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14
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Meyer B, Wurm JP, Sharma S, Immer C, Pogoryelov D, Kötter P, Lafontaine DLJ, Wöhnert J, Entian KD. Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans. Nucleic Acids Res 2016; 44:4304-16. [PMID: 27084949 PMCID: PMC4872110 DOI: 10.1093/nar/gkw244] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/28/2016] [Indexed: 12/15/2022] Open
Abstract
The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m(1)acp(3)Ψ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive. Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells. In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation. The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.
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Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany
| | - Jan Philip Wurm
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt/M, Germany
| | - Sunny Sharma
- RNA Molecular Biology & Center for Microscopy and Molecular Imaging, Fonds National de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB)
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt/M, Germany
| | - Denys Pogoryelov
- Institute of Biochemistry, Goethe University, Frankfurt/M, Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany
| | - Denis L J Lafontaine
- RNA Molecular Biology & Center for Microscopy and Molecular Imaging, Fonds National de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles (ULB)
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt/M, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany
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15
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Sharma S, Lafontaine DLJ. 'View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification. Trends Biochem Sci 2016; 40:560-575. [PMID: 26410597 DOI: 10.1016/j.tibs.2015.07.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/23/2023]
Abstract
Eukaryotic rRNA are modified frequently, although the diversity of modifications is low: in yeast rRNA, there are only 12 different types out of a possible natural repertoire exceeding 112. All nine rRNA base methyltransferases (MTases) and one acetyltransferase have recently been identified in budding yeast, and several instances of crosstalk between rRNA, tRNA, and mRNA modifications are emerging. Although the machinery has largely been identified, the functions of most rRNA modifications remain to be established. Remarkably, a eukaryote-specific bridge, comprising a single ribosomal protein (RP) from the large subunit (LSU), contacts four rRNA base modifications across the ribosomal subunit interface, potentially probing for their presence. We hypothesize in this article that long-range allosteric communication involving rRNA modifications is taking place between the two subunits during translation or, perhaps, the late stages of ribosome assembly.
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Affiliation(s)
- Sunny Sharma
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium; Center for Microscopy and Molecular Imaging, BioPark campus, B-6041 Charleroi-Gosselies, Belgium.
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16
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Myers CL, Kuiper EG, Grant PC, Hernandez J, Conn GL, Honek JF. Functional roles in S-adenosyl-L-methionine binding and catalysis for active site residues of the thiostrepton resistance methyltransferase. FEBS Lett 2015; 589:3263-70. [PMID: 26450779 DOI: 10.1016/j.febslet.2015.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/28/2015] [Accepted: 09/28/2015] [Indexed: 11/17/2022]
Abstract
Resistance to the antibiotic thiostrepton, in producing Streptomycetes, is conferred by the S-adenosyl-L-methionine (SAM)-dependent SPOUT methyltransferase Tsr. For this and related enzymes, the roles of active site amino acids have been inadequately described. Herein, we have probed SAM interactions in the Tsr active site by investigating the catalytic activity and the thermodynamics of SAM binding by site-directed Tsr mutants. Two arginine residues were demonstrated to be critical for binding, one of which appears to participate in the catalytic reaction. Additionally, evidence consistent with the involvement of an asparagine in the structural organization of the SAM binding site is presented.
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Affiliation(s)
- Cullen L Myers
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pei C Grant
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jennifer Hernandez
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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17
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Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Proc Natl Acad Sci U S A 2015; 112:E4197-205. [PMID: 26183229 DOI: 10.1073/pnas.1422981112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N(1)-methylguanosine (m(1)G) modification at position 37 in transfer RNAs (tRNAs) with the (36)GG(37) sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m(1)G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m(1)G37-tRNA.
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18
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Wurm JP, Lioutikov A, Kötter P, Entian KD, Wöhnert J. Backbone and side chain NMR assignments for the ribosome assembly factor Nop6 from Saccharomyces cerevisiae. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:345-348. [PMID: 23921755 DOI: 10.1007/s12104-013-9514-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
The Saccharomyces cerevisiae Nop6 protein is involved in the maturation of the small ribosomal subunit. It contains a central RNA binding domain and a predicted C-terminal coiled-coil domain. Here we report the almost complete (>90%) (1)H,(13)C,(15)N backbone and side chain NMR assignment of a 15 kDa Nop6 construct comprising the RNA binding and coiled-coil domains.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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19
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Sharma S, Yang J, Düttmann S, Watzinger P, Kötter P, Entian KD. Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res 2013; 42:3246-60. [PMID: 24335083 PMCID: PMC3950682 DOI: 10.1093/nar/gkt1281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RNA contains various chemical modifications that expand its otherwise limited repertoire to mediate complex processes like translation and gene regulation. 25S rRNA of the large subunit of ribosome contains eight base methylations. Except for the methylation of uridine residues, methyltransferases for all other known base methylations have been recently identified. Here we report the identification of BMT5 (YIL096C) and BMT6 (YLR063W), two previously uncharacterized genes, to be responsible for m3U2634 and m3U2843 methylation of the 25S rRNA, respectively. These genes were identified by RP-HPLC screening of all deletion mutants of putative RNA methyltransferases and were confirmed by gene complementation and phenotypic characterization. Both proteins belong to Rossmann-fold–like methyltransferases and the point mutations in the S-adenosyl-l-methionine binding pocket abolish the methylation reaction. Bmt5 localizes in the nucleolus, whereas Bmt6 is localized predominantly in the cytoplasm. Furthermore, we showed that 25S rRNA of yeast does not contain any m5U residues as previously predicted. With Bmt5 and Bmt6, all base methyltransferases of the 25S rRNA have been identified. This will facilitate the analyses of the significance of these modifications in ribosome function and cellular physiology.
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Affiliation(s)
- Sunny Sharma
- Department of Molecular Genetics and Cellular Microbiology, Institute of Molecular Biosciences, Goethe University, Frankfurt, Max-von-Laue Strasse 9, Frankfurt/M 60438, Germany
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20
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Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA-protein interactions during small ribosomal subunit biogenesis. Proc Natl Acad Sci U S A 2013; 110:15253-8. [PMID: 24003121 DOI: 10.1073/pnas.1306389110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Factor activating Pos9 (Fap7) is an essential ribosome biogenesis factor important for the assembly of the small ribosomal subunit with an uncommon dual ATPase and adenylate kinase activity. Depletion of Fap7 or mutations in its ATPase motifs lead to defects in small ribosomal subunit rRNA maturation, the absence of ribosomal protein Rps14 from the assembled subunit, and retention of the nascent small subunit in a quality control complex with the large ribosomal subunit. The molecular basis for the role of Fap7 in ribosome biogenesis is, however, not yet understood. Here we show that Fap7 regulates multiple interactions between the precursor rRNA, ribosomal proteins, and ribosome assembly factors in a hierarchical manner. Fap7 binds to Rps14 with a very high affinity. Fap7 binding blocks both rRNA-binding elements of Rps14, suggesting that Fap7 inhibits premature interactions of Rps14 with RNA. The Fap7/Rps14 interaction is modulated by nucleotide binding to Fap7. Rps14 strongly activates the ATPase activity but not the adenylate kinase activity of Fap7, identifying Rps14 as an example of a ribosomal protein functioning as an ATPase-activating factor. In addition, Fap7 inhibits the RNA cleavage activity of Nob1, the endonuclease responsible for the final maturation step of the small subunit rRNA, in a nucleotide independent manner. Thus, Fap7 may regulate small subunit biogenesis at multiple stages.
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21
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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22
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Genetic interactions of yeast NEP1 (EMG1), encoding an essential factor in ribosome biogenesis. Yeast 2012; 29:167-83. [DOI: 10.1002/yea.2898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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23
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Veith T, Martin R, Wurm JP, Weis BL, Duchardt-Ferner E, Safferthal C, Hennig R, Mirus O, Bohnsack MT, Wöhnert J, Schleiff E. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res 2012; 40:3259-74. [PMID: 22156373 PMCID: PMC3326319 DOI: 10.1093/nar/gkr1186] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/11/2011] [Accepted: 11/14/2011] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.
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Affiliation(s)
- Thomas Veith
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Roman Martin
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jan P. Wurm
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Benjamin L. Weis
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Charlotta Safferthal
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Raoul Hennig
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Oliver Mirus
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Markus T. Bohnsack
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Center of Biomolecular Magnetic Resonance (BMRZ), Cluster of Excellence Frankfurt: Macromolecular Complexes and Centre of Membrane Proteomics, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany
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24
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Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wöhnert J. Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. RNA (NEW YORK, N.Y.) 2012; 18:412-420. [PMID: 22274954 PMCID: PMC3285930 DOI: 10.1261/rna.028498.111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 11/23/2011] [Indexed: 05/31/2023]
Abstract
tRNAs from all three kingdoms of life contain a variety of modified nucleotides required for their stability, proper folding, and accurate decoding. One prominent example is the eponymous ribothymidine (rT) modification at position 54 in the T-arm of eukaryotic and bacterial tRNAs. In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine. While the enzyme catalyzing pseudouridine formation at this position is known, the pseudouridine N1-specific methyltransferase responsible for this modification has not yet been experimentally identified. Here, we present biochemical and genetic evidence that the two homologous proteins, Mja_1640 (COG 1901, Pfam DUF358) and Hvo_1989 (Pfam DUF358) from Methanocaldococcus jannaschii and Haloferax volcanii, respectively, are representatives of the methyltransferase responsible for this modification. However, the in-frame deletion of the pseudouridine N1-methyltransferase gene in H. volcanii did not result in a discernable phenotype in line with similar observations for knockouts of other T-arm methylating enzymes.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Marco Griese
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Ute Bahr
- Institut für Pharmazeutische Chemie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Martin Held
- Institut für Pharmazeutische Chemie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Institut für Organische Chemie und Chemische Biologie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Alexander Heckel
- Institut für Pharmazeutische Chemie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Institut für Organische Chemie und Chemische Biologie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Cluster of Excellence “Macromolecular complexes,” Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Michael Karas
- Institut für Pharmazeutische Chemie, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Cluster of Excellence “Macromolecular complexes,” Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Jörg Soppa
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Cluster of Excellence “Macromolecular complexes,” Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
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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 (NEW YORK, N.Y.) 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] [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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26
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Chen HY, Yuan YA. Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. J Mol Cell Biol 2011; 2:366-74. [PMID: 21098051 DOI: 10.1093/jmcb/mjq034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The proteins in DUF358 family are all bacterial proteins, which are ∼200 amino acids long with unknown function. Bioinformatics analysis suggests that these proteins contain several conserved arginines and aspartates that might adopt SPOUT-class fold. Here we report crystal structure of Methanocaldococcus jannaschii DUF358/Mj1640 in complex with S-adenosyl-L-methionine (SAM) at 1.4 Å resolution. The structure reveals a single domain structure consisting of eight-stranded β-sheets sandwiched by six α-helices at both sides. Similar to other SPOUT-class members, Mj1640 contains a typical deep trefoil knot at its C-terminus to accommodate the SAM cofactor. However, Mj1640 has limited structural extension at its N-terminus, which is unique to this family member. Mj1640 forms a dimer, which is mediated by two parallel pairs of α-helices oriented almost perpendicular to each other. Although Mj1640 shares close structural similarity with Nep1, the significant differences in N-terminal extension domain and the overall surface charge distribution strongly suggest that Mj1640 might target a different RNA sequence. Detailed structural analysis of the SAM-binding pocket reveals that Asp157 or Glu183 from its own monomer or Ser43 from the associate monomer probably plays the catalytic role for RNA methylation.
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Affiliation(s)
- Hong-Ying Chen
- Mechanobiology Institute, National University of Singapore, T-lab Building, 5A Engineering Drive 1, Singapore 117411, Singapore
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27
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Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA. Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res 2010; 39:2445-57. [PMID: 21087996 PMCID: PMC3064781 DOI: 10.1093/nar/gkq1131] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen–Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.
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Affiliation(s)
- Seth R Thomas
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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28
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Meyer B, Wurm JP, Kötter P, Leisegang MS, Schilling V, Buchhaupt M, Held M, Bahr U, Karas M, Heckel A, Bohnsack MT, Wöhnert J, Entian KD. The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA. Nucleic Acids Res 2010; 39:1526-37. [PMID: 20972225 PMCID: PMC3045603 DOI: 10.1093/nar/gkq931] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Nep1 (Emg1) SPOUT-class methyltransferase is an essential ribosome assembly factor and the human Bowen–Conradi syndrome (BCS) is caused by a specific Nep1D86G mutation. We recently showed in vitro that Methanocaldococcus jannaschii Nep1 is a sequence-specific pseudouridine-N1-methyltransferase. Here, we show that in yeast the in vivo target site for Nep1-catalyzed methylation is located within loop 35 of the 18S rRNA that contains the unique hypermodification of U1191 to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouri-dine (m1acp3Ψ). Specific 14C-methionine labelling of 18S rRNA in yeast mutants showed that Nep1 is not required for acp-modification but suggested a function in Ψ1191 methylation. ESI MS analysis of acp-modified Ψ-nucleosides in a Δnep1-mutant showed that Nep1 catalyzes the Ψ1191 methylation in vivo. Remarkably, the restored growth of a nep1-1ts mutant upon addition of S-adenosylmethionine was even observed after preventing U1191 methylation in a Δsnr35 mutant. This strongly suggests a dual Nep1 function, as Ψ1191-methyltransferase and ribosome assembly factor. Interestingly, the Nep1 methyltransferase activity is not affected upon introduction of the BCS mutation. Instead, the mutated protein shows enhanced dimerization propensity and increased affinity for its RNA-target in vitro. Furthermore, the BCS mutation prevents nucleolar accumulation of Nep1, which could be the reason for reduced growth in yeast and the Bowen-Conradi syndrome.
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Affiliation(s)
- Britta Meyer
- Cluster of Excellence Frankfurt: Macromolecular Complexes, Max-von-Laue Str. 9, D-60438 Frankfurt/M., Germany
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Wu X, Sandhu S, Patel N, Triggs-Raine B, Ding H. EMG1 is essential for mouse pre-implantation embryo development. BMC DEVELOPMENTAL BIOLOGY 2010; 10:99. [PMID: 20858271 PMCID: PMC2954994 DOI: 10.1186/1471-213x-10-99] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 09/21/2010] [Indexed: 12/12/2022]
Abstract
Background Essential for mitotic growth 1 (EMG1) is a highly conserved nucleolar protein identified in yeast to have a critical function in ribosome biogenesis. A mutation in the human EMG1 homolog causes Bowen-Conradi syndrome (BCS), a developmental disorder characterized by severe growth failure and psychomotor retardation leading to death in early childhood. To begin to understand the role of EMG1 in mammalian development, and how its deficiency could lead to Bowen-Conradi syndrome, we have used mouse as a model. The expression of Emg1 during mouse development was examined and mice carrying a null mutation for Emg1 were generated and characterized. Results Our studies indicated that Emg1 is broadly expressed during early mouse embryonic development. However, in late embryonic stages and during postnatal development, Emg1 exhibited specific expression patterns. To assess a developmental role for EMG1 in vivo, we exploited a mouse gene-targeting approach. Loss of EMG1 function in mice arrested embryonic development prior to the blastocyst stage. The arrested Emg1-/- embryos exhibited defects in early cell lineage-specification as well as in nucleologenesis. Further, loss of p53, which has been shown to rescue some phenotypes resulting from defects in ribosome biogenesis, failed to rescue the Emg1-/- pre-implantation lethality. Conclusion Our data demonstrate that Emg1 is highly expressed during mouse embryonic development, and essential for mouse pre-implantation development. The absolute requirement for EMG1 in early embryonic development is consistent with its essential role in yeast. Further, our findings also lend support to the previous study that showed Bowen-Conradi syndrome results from a partial EMG1 deficiency. A complete deficiency would not be expected to be compatible with a live birth.
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Affiliation(s)
- Xiaoli Wu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada
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30
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Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kötter P, Engels JW, Heckel A, Karas M, Entian KD, Wöhnert J. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res 2010; 38:2387-98. [PMID: 20047967 PMCID: PMC2853112 DOI: 10.1093/nar/gkp1189] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen-Conradi syndrome-a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910-921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
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31
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Wurm JP, Duchardt E, Meyer B, Leal BZ, Kötter P, Entian KD, Wöhnert J. Backbone resonance assignments of the 48 kDa dimeric putative 18S rRNA-methyltransferase Nep1 from Methanocaldococcus jannaschii. BIOMOLECULAR NMR ASSIGNMENTS 2009; 3:251-254. [PMID: 19779849 DOI: 10.1007/s12104-009-9187-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 09/05/2009] [Indexed: 05/28/2023]
Abstract
Nep1 from Methanocaldococcus jannaschii is a 48 kDa dimeric protein belonging to the SPOUT-class of S-adenosylmethionine dependent RNA-methyltransferases and acting as a ribosome assembly factor. Mutations in the human homolog are the cause of Bowen-Conradi syndrome. We report here 1H, 15N and 13C chemical shift assignments for the backbone of the protein in its apo state.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität Frankfurt/M., Frankfurt, Germany
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32
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Abstract
Methylation of DNA, protein, and even RNA species are integral processes in epigenesis. Enzymes that catalyze these reactions using the donor S-adenosylmethionine fall into several structurally distinct classes. The members in each class share sequence similarity that can be used to identify additional methyltransferases. Here, we characterize these classes and in silico approaches to infer protein function. Computational methods such as hidden Markov model profiling and the Multiple Motif Scanning program can be used to analyze known methyltransferases and relay information into the prediction of new ones. In some cases, the substrate of methylation can be inferred from hidden Markov model sequence similarity networks. Functional identification of these candidate species is much more difficult; we discuss one biochemical approach.
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Affiliation(s)
- Tanya Petrossian
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1570
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33
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Dunstan MS, Hang PC, Zelinskaya NV, Honek JF, Conn GL. Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA. J Biol Chem 2009; 284:17013-17020. [PMID: 19369248 PMCID: PMC2719339 DOI: 10.1074/jbc.m901618200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 03/31/2009] [Indexed: 12/03/2022] Open
Abstract
The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr).S-adenosyl-L-methionine (AdoMet) complex was determined at 2.45-A resolution. Tsr is definitively confirmed as a Class IV methyltransferase of the SpoU family with an N-terminal "L30-like" putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr.rRNA binding is dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.
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MESH Headings
- Base Sequence
- Catalytic Domain
- Crystallography, X-Ray
- Dimerization
- Drug Resistance, Bacterial
- Macromolecular Substances
- Methyltransferases/chemistry
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- S-Adenosylmethionine/chemistry
- S-Adenosylmethionine/metabolism
- Staphylococcus aureus/drug effects
- Staphylococcus aureus/enzymology
- Staphylococcus aureus/genetics
- Static Electricity
- Thiostrepton/pharmacology
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Affiliation(s)
- Mark S Dunstan
- From the Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Pei C Hang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Natalia V Zelinskaya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.
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34
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Armistead J, Khatkar S, Meyer B, Mark BL, Patel N, Coghlan G, Lamont RE, Liu S, Wiechert J, Cattini PA, Koetter P, Wrogemann K, Greenberg CR, Entian KD, Zelinski T, Triggs-Raine B. Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome. Am J Hum Genet 2009; 84:728-39. [PMID: 19463982 DOI: 10.1016/j.ajhg.2009.04.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 04/15/2009] [Accepted: 04/27/2009] [Indexed: 11/27/2022] Open
Abstract
Bowen-Conradi syndrome (BCS) is an autosomal-recessive disorder characterized by severely impaired prenatal and postnatal growth, profound psychomotor retardation, and death in early childhood. Nearly all reported BCS cases have been among Hutterites, with an estimated birth prevalence of 1/355. We previously localized the BCS gene to a 1.9 Mbp interval on human chromosome 12p13.3. The 59 genes in this interval were ranked as candidates for BCS, and 35 of these, including all of the best candidates, were sequenced. We identified variant NM_006331.6:c.400A-->G, p.D86G in the 18S ribosome assembly protein EMG1 as the probable cause of BCS. This mutation segregated with disease, was not found in 414 non-Hutterite alleles, and altered a highly conserved aspartic acid (D) residue. A structural model of human EMG1 suggested that the D86 residue formed a salt bridge with arginine 84 that would be disrupted by the glycine (G) substitution. EMG1 mRNA was detected in all human adult and fetal tissues tested. In BCS patient fibroblasts, EMG1 mRNA levels did not differ from those of normal cells, but EMG1 protein was dramatically reduced in comparison to that of normal controls. In mammalian cells, overexpression of EMG1 harboring the D86G mutation decreased the level of soluble EMG1 protein, and in yeast two-hybrid analysis, the D86G substitution increased interaction between EMG1 subunits. These findings suggested that the D-to-G mutation caused aggregation of EMG1, thereby reducing the level of the protein and causing BCS.
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