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Deogharia M, Gurha P. The "guiding" principles of noncoding RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1704. [PMID: 34856642 DOI: 10.1002/wrna.1704] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/09/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022]
Abstract
The human genome is pervasively transcribed and yet only a small fraction of these RNAs (less than 2%) are known to code for proteins. The vast majority of the RNAs are classified as noncoding RNAs (ncRNAs) and are further subgrouped as small (shorter than 200 bases) and long noncoding RNAs. The ncRNAs have been identified in all three domains of life and regulate diverse cellular processes through transcriptional and posttranscriptional gene regulation. Most of these RNAs work in conjunction with proteins forming a wide array of base pairing interactions. The determinants of these base pairing interactions are now becoming more evident and show striking similarities among the diverse group of ncRNAs. Here we present a mechanistic overview of pairing between RNA-RNA or RNA-DNA that dictates the function of ncRNAs; we provide examples to illustrate that ncRNAs work through shared evolutionary mechanisms that encompasses a guide-target interaction, involving not only classical Watson-Crick but also noncanonical Wobble and Hoogsteen base pairing. We also highlight the similarities in target selection, proofreading, and the ruler mechanism of ncRNA-protein complexes that confers target specificity and target site selection. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA-Based Catalysis > RNA-Mediated Cleavage RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
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2
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Höfler S, Lukat P, Blankenfeldt W, Carlomagno T. High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain. RNA (NEW YORK, N.Y.) 2021; 27:496-512. [PMID: 33483369 PMCID: PMC7962484 DOI: 10.1261/rna.077396.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Ribosomal RNA (rRNA) carries extensive 2'-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2'-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein-protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Crystallography, X-Ray
- Gene Expression
- Methylation
- Models, Molecular
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Alignment
- Structural Homology, Protein
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Simone Höfler
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
| | - Peer Lukat
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research, Group of NMR-based Structural Chemistry, D-38124 Braunschweig, Germany
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3
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Graziadei A, Gabel F, Kirkpatrick J, Carlomagno T. The guide sRNA sequence determines the activity level of box C/D RNPs. eLife 2020; 9:e50027. [PMID: 32202498 PMCID: PMC7089733 DOI: 10.7554/elife.50027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/08/2020] [Indexed: 12/14/2022] Open
Abstract
2'-O-rRNA methylation, which is essential in eukaryotes and archaea, is catalysed by the Box C/D RNP complex in an RNA-guided manner. Despite the conservation of the methylation sites, the abundance of site-specific modifications shows variability across species and tissues, suggesting that rRNA methylation may provide a means of controlling gene expression. As all Box C/D RNPs are thought to adopt a similar structure, it remains unclear how the methylation efficiency is regulated. Here, we provide the first structural evidence that, in the context of the Box C/D RNP, the affinity of the catalytic module fibrillarin for the substrate-guide helix is dependent on the RNA sequence outside the methylation site, thus providing a mechanism by which both the substrate and guide RNA sequences determine the degree of methylation. To reach this result, we develop an iterative structure-calculation protocol that exploits the power of integrative structural biology to characterize conformational ensembles.
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Affiliation(s)
- Andrea Graziadei
- European Molecular Biology Laboratory, Structural and Computational BiologyHeidelbergGermany
- Leibniz University Hannover, Centre for Biomolecular Drug ResearchHannoverGermany
| | - Frank Gabel
- University Grenoble Alpes, CEA, CNRS IBSGrenobleFrance
- Institut Laue-LangevinGrenobleFrance
| | - John Kirkpatrick
- Leibniz University Hannover, Centre for Biomolecular Drug ResearchHannoverGermany
- Helmholtz Centre for Infection Research, Group of Structural ChemistryBraunschweigGermany
| | - Teresa Carlomagno
- Leibniz University Hannover, Centre for Biomolecular Drug ResearchHannoverGermany
- Helmholtz Centre for Infection Research, Group of Structural ChemistryBraunschweigGermany
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4
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Lui LM, Uzilov AV, Bernick DL, Corredor A, Lowe TM, Dennis PP. Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. Nucleic Acids Res 2019; 46:5678-5691. [PMID: 29771354 PMCID: PMC6009581 DOI: 10.1093/nar/gky284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.
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Affiliation(s)
- Lauren M Lui
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew V Uzilov
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David L Bernick
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Corredor
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick P Dennis
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
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5
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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 (NEW YORK, N.Y.) 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] [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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6
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Abstract
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.
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Affiliation(s)
- Zuxiao Yang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinzhong Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Graziadei A, Masiewicz P, Lapinaite A, Carlomagno T. Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency. RNA (NEW YORK, N.Y.) 2016; 22:764-772. [PMID: 26925607 PMCID: PMC4836650 DOI: 10.1261/rna.054320.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/21/2016] [Indexed: 06/01/2023]
Abstract
RNA modifications confer complexity to the 4-nucleotide polymer; nevertheless, their exact function is mostly unknown. rRNA 2'-O-ribose methylation concentrates to ribosome functional sites and is important for ribosome biogenesis. The methyl group is transferred to rRNA by the box C/D RNPs: The rRNA sequence to be methylated is recognized by a complementary sequence on the guide RNA, which is part of the enzyme. In contrast to their eukaryotic homologs, archaeal box C/D enzymes can be assembled in vitro and are used to study the mechanism of 2'-O-ribose methylation. In Archaea, each guide RNA directs methylation to two distinct rRNA sequences, posing the question whether this dual architecture of the enzyme has a regulatory role. Here we use methylation assays and low-resolution structural analysis with small-angle X-ray scattering to study the methylation reaction guided by the sR26 guide RNA fromPyrococcus furiosus We find that the methylation efficacy at sites D and D' differ substantially, with substrate D' turning over more efficiently than substrate D. This observation correlates well with structural data: The scattering profile of the box C/D RNP half-loaded with substrate D' is similar to that of the holo complex, which has the highest activity. Unexpectedly, the guide RNA secondary structure is not responsible for the functional difference at the D and D' sites. Instead, this difference is recapitulated by the nature of the first base pair of the guide-substrate duplex. We suggest that substrate turnover may occur through a zip mechanism that initiates at the 5'-end of the product.
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Affiliation(s)
- Andrea Graziadei
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Pawel Masiewicz
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Audrone Lapinaite
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany
| | - Teresa Carlomagno
- European Molecular Biology Laboratory, SCB Unit, D-69117 Heidelberg, Germany Leibniz University Hannover, Centre for Biomolecular Drug Research, D-30167 Hannover, Germany Helmholtz Centre for Infection Research, Group of Structural Chemistry, D-38124 Braunschweig, Germany
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8
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Dennis PP, Tripp V, Lui L, Lowe T, Randau L. C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules. BMC Genomics 2015; 16:632. [PMID: 26296872 PMCID: PMC4644070 DOI: 10.1186/s12864-015-1839-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/13/2015] [Indexed: 11/26/2022] Open
Abstract
Background In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2'-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures. Results We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2'-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences. Conclusions This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2'-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1839-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick P Dennis
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. .,Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA.
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
| | - Lauren Lui
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Todd Lowe
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
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9
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Ribonucleoproteins in archaeal pre-rRNA processing and modification. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:614735. [PMID: 23554567 PMCID: PMC3608112 DOI: 10.1155/2013/614735] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/09/2013] [Accepted: 01/15/2013] [Indexed: 12/27/2022]
Abstract
Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.
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10
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Tomkuviene M, Clouet-d'Orval B, Cerniauskas I, Weinhold E, Klimasauskas S. Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases. Nucleic Acids Res 2012; 40:6765-73. [PMID: 22564896 PMCID: PMC3413156 DOI: 10.1093/nar/gks381] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biophysical and mechanistic investigation of RNA function requires site-specific incorporation of spectroscopic and chemical probes, which is difficult to achieve using current technologies. We have in vitro reconstituted a functional box C/D small ribonucleoprotein RNA 2′-O-methyltransferase (C/D RNP) from the thermophilic archaeon Pyrococcus abyssi and demonstrated its ability to transfer a prop-2-ynyl group from a synthetic cofactor analog to a series of preselected target sites in model tRNA and pre-mRNA molecules. Target selection of the RNP was programmed by changing a dodecanucleotide guide sequence in a 64-nt C/D guide RNA leading to efficient derivatization of three out of four new targets in each RNA substrate. We also show that the transferred terminal alkyne can be further appended with a fluorophore using a bioorthogonal azide-alkyne 1,3-cycloaddition (click) reaction. The described approach for the first time permits synthetically tunable sequence-specific labeling of RNA with single-nucleotide precision.
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Affiliation(s)
- Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
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11
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Gagnon KT, Biswas S, Zhang X, Brown BA, Wollenzien P, Mattos C, Maxwell ES. Structurally conserved Nop56/58 N-terminal domain facilitates archaeal box C/D ribonucleoprotein-guided methyltransferase activity. J Biol Chem 2012; 287:19418-28. [PMID: 22496443 DOI: 10.1074/jbc.m111.323253] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Box C/D RNA-protein complexes (RNPs) guide the 2'-O-methylation of nucleotides in both archaeal and eukaryotic ribosomal RNAs. The archaeal box C/D and C'/D' RNP subcomplexes are each assembled with three sRNP core proteins. The archaeal Nop56/58 core protein mediates crucial protein-protein interactions required for both sRNP assembly and the methyltransferase reaction by bridging the L7Ae and fibrillarin core proteins. The interaction of Methanocaldococcus jannaschii (Mj) Nop56/58 with the methyltransferase fibrillarin has been investigated using site-directed mutagenesis of specific amino acids in the N-terminal domain of Nop56/58 that interacts with fibrillarin. Extensive mutagenesis revealed an unusually strong Nop56/58-fibrillarin interaction. Only deletion of the NTD itself prevented dimerization with fibrillarin. The extreme stability of the Nop56/58-fibrillarin heterodimer was confirmed in both chemical and thermal denaturation analyses. However, mutations that did not affect Nop56/58 binding to fibrillarin or sRNP assembly nevertheless disrupted sRNP-guided nucleotide modification, revealing a role for Nop56/58 in methyltransferase activity. This conclusion was supported with the cross-linking of Nop56/58 to the target RNA substrate. The Mj Nop56/58 NTD was further characterized by solving its three-dimensional crystal structure to a resolution of 1.7 Å. Despite low primary sequence conservation among the archaeal Nop56/58 homologs, the overall structure of the archaeal NTD domain is very well conserved. In conclusion, the archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.
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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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12
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Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K. Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature 2011; 469:559-63. [PMID: 21270896 DOI: 10.1038/nature09688] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/19/2010] [Indexed: 11/09/2022]
Abstract
Box C/D RNA protein complexes (RNPs) direct site-specific 2'-O-methylation of RNA and ribosome assembly. The guide RNA in C/D RNP forms base pairs with complementary substrates and selects the modification site using a molecular ruler. Despite many studies of C/D RNP structure, the fundamental questions of how C/D RNAs assemble into RNPs and how they guide modification remain unresolved. Here we report the crystal structure of an entire catalytically active archaeal C/D RNP consisting of a bipartite C/D RNA associated with two substrates and two copies each of Nop5, L7Ae and fibrillarin at 3.15-Å resolution. The substrate pairs with the second through the eleventh nucleotide of the 12-nucleotide guide, and the resultant duplex is bracketed in a channel with flexible ends. The methyltransferase fibrillarin binds to an undistorted A-form structure of the guide-substrate duplex and specifically loads the target ribose into the active site. Because interaction with the RNA duplex alone does not determine the site specificity, fibrillarin is further positioned by non-specific and specific protein interactions. Compared with the structure of the inactive C/D RNP, extensive domain movements are induced by substrate loading. Our results reveal the organization of a monomeric C/D RNP and the mechanism underlying its site-specific methylation activity.
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Affiliation(s)
- Jinzhong Lin
- National Institute of Biological Sciences, Beijing 102206, China
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Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol Cell 2010; 39:939-49. [PMID: 20864039 PMCID: PMC3572848 DOI: 10.1016/j.molcel.2010.08.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 04/20/2010] [Accepted: 07/16/2010] [Indexed: 01/07/2023]
Abstract
Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.
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Affiliation(s)
- Song Xue
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Ruiying Wang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Fangping Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Rebecca M. Terns
- Departments of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Michael P. Terns
- Departments of Biochemistry and Molecular Biology, and Genetics, University of Georgia, Athens, GA 30602, USA
| | - Xinxin Zhang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - E. Stuart Maxwell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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Shin C, Nam JW, Farh KKH, Chiang HR, Shkumatava A, Bartel DP. Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 2010; 38:789-802. [PMID: 20620952 DOI: 10.1016/j.molcel.2010.06.005] [Citation(s) in RCA: 450] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 04/27/2010] [Accepted: 06/03/2010] [Indexed: 12/30/2022]
Abstract
Most metazoan microRNA (miRNA) target sites have perfect pairing to the seed region, located near the miRNA 5' end. Although pairing to the 3' region sometimes supplements seed matches or compensates for mismatches, pairing to the central region has been known to function only at rare sites that impart Argonaute-catalyzed mRNA cleavage. Here, we present "centered sites," a class of miRNA target sites that lack both perfect seed pairing and 3'-compensatory pairing and instead have 11-12 contiguous Watson-Crick pairs to the center of the miRNA. Although centered sites can impart mRNA cleavage in vitro (in elevated Mg(2+)), in cells they repress protein output without consequential Argonaute-catalyzed cleavage. Our study also identified extensively paired sites that are cleavage substrates in cultured cells and human brain. This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many miRNAs are evolutionarily conserved.
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Affiliation(s)
- Chanseok Shin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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Bleichert F, Baserga SJ. Dissecting the role of conserved box C/D sRNA sequences in di-sRNP assembly and function. Nucleic Acids Res 2010; 38:8295-305. [PMID: 20693534 PMCID: PMC3001065 DOI: 10.1093/nar/gkq690] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In all three kingdoms of life, nucleotides in ribosomal RNA (rRNA) are post-transcriptionally modified. One type of chemical modification is 2'-O-ribose methylation, which is, in eukaryotes and archaea, performed by box C/D small ribonucleoproteins (box C/D sRNPs in archaea) and box C/D small nucleolar ribonucleoproteins (box C/D snoRNPs in eukaryotes), respectively. Recently, the first structure of any catalytically active box C/D s(no)RNP determined by electron microscopy and single particle analysis surprisingly demonstrated that they are dimeric RNPs. Mutational analyses of the Nop5 protein interface suggested that di-sRNP formation is also required for the in vitro catalytic activity. We have now analyzed the functional relevance of the second interface, the sRNA interface, within the box C/D di-sRNP. Mutations in conserved sequence elements of the sRNA, which allow sRNP assembly but which severely interfere with the catalytic activity of box C/D sRNPs, prevent formation of the di-sRNP. In addition, we can observe the dimeric box C/D sRNP architecture with a different box C/D sRNP, suggesting that this architecture is conserved. Together, these results provide further support for the functional relevance of the di-sRNP architecture and also provide a structural explanation for the observed defects in catalysis of 2'-O-ribose methylation.
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16
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Faustino I, Aviño A, Marchán I, Luque FJ, Eritja R, Orozco M. Unique Tautomeric and Recognition Properties of Thioketothymines? J Am Chem Soc 2009; 131:12845-53. [DOI: 10.1021/ja904880y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ignacio Faustino
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
| | - Anna Aviño
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
| | - Ivan Marchán
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
| | - F. Javier Luque
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
| | - Ramon Eritja
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
| | - Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1−5, Barcelona 08028, Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain, Institute of Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, Barcelona 08028, Spain, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de
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Structural organization of box C/D RNA-guided RNA methyltransferase. Proc Natl Acad Sci U S A 2009; 106:13808-13. [PMID: 19666563 DOI: 10.1073/pnas.0905128106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.
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18
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Singh SK, Gurha P, Gupta R. Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP. RNA (NEW YORK, N.Y.) 2008; 14:1411-23. [PMID: 18515549 PMCID: PMC2441990 DOI: 10.1261/rna.1003308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 04/16/2008] [Indexed: 05/05/2023]
Abstract
Assembly and guide-target interaction of an archaeal box C/D-guide sRNP was investigated under various conditions by analyzing the lead (II)-induced cleavage of the guide RNA. Guide and target RNAs derived from Haloferax volcanii pre-tRNA(Trp) were used with recombinant Methanocaldococcus jannaschii core proteins in the reactions. Core protein L7Ae binds differentially to C/D and C'/D' motifs of the guide RNA, and interchanging the two motifs relative to the termini of the guide RNA did not affect L7Ae binding or sRNA function. L7Ae binding to the guide RNA exposes its D'-guide sequence first followed by the D guide. These exposures are reduced when aNop5p and aFib proteins are added. The exposed guide sequences did not pair with the target sequences in the presence of L7Ae alone. The D-guide sequence could pair with the target in the presence of L7Ae and aNop5p, suggesting a role of aNop5p in target recruitment and rearrangement of sRNA structure. aFib binding further stabilizes this pairing. After box C/D-guided modification, target-guide pairing at the D-guide sequence is disrupted, suggesting that each round of methylation may require some conformational change or reassembly of the RNP. Asymmetric RNPs containing only one L7Ae at either of the two box motifs can be assembled, but a functional RNP requires L7Ae at the box C/D motif. This arrangement resembles the asymmetric eukaryal snoRNP. Observations of initial D-guide-target pairing and the functional requirement for L7Ae at the box C/D motif are consistent with our previous report of the sequential 2'-O-methylations of the target RNA.
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Affiliation(s)
- Sanjay K Singh
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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19
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Gagnon K, Zhang X, Maxwell ES. In vitro reconstitution and affinity purification of catalytically active archaeal box C/D sRNP complexes. Methods Enzymol 2007; 425:263-82. [PMID: 17673088 DOI: 10.1016/s0076-6879(07)25012-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Archaeal box C/D RNAs guide the site-specific 2'-O-methylation of target nucleotides in ribosomal RNAs and tRNAs. In vitro reconstitution of catalytically active box C/D RNPs by use of in vitro transcribed box C/D RNAs and recombinant core proteins provides model complexes for the study of box C/D RNP assembly, structure, and function. Described here are protocols for assembly of the archaeal box C/D RNP and assessment of its nucleotide modification activity. Also presented is a novel affinity purification scheme that uses differentially tagged core proteins and a sequential three-step affinity selection protocol that yields fully assembled and catalytically active box C/D RNPs. This affinity selection protocol can provide highly purified complex in sufficient quantities not only for biochemical analyses but also for biophysical approaches such as cryoelectron microscopy and X-ray crystallography.
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Affiliation(s)
- Keith Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
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