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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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2
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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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3
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Ruszkowska A, Zheng YY, Mao S, Ruszkowski M, Sheng J. Structural Insights Into the 5′UG/3′GU Wobble Tandem in Complex With Ba2+ Cation. Front Mol Biosci 2022; 8:762786. [PMID: 35096964 PMCID: PMC8793689 DOI: 10.3389/fmolb.2021.762786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA]2, providing detailed structural insights into the tandem motif I (5′UG/3′GU) complexed with Ba2+ cation. We compare the electrostatic potential of the presented motif I major groove with previously published structures of tandem motifs I, II (5′GU/3′UG), and III (5′GG/3′UU). A local patch of a strongly negative electrostatic potential in the major groove of the presented structure forms the metal binding site with the contributions of three oxygen atoms from the tandem. These results give us a better understanding of the G•U tandem motif I as a divalent metal binder, a feature essential for RNA functions.
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Affiliation(s)
| | - Ya Ying Zheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Song Mao
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
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4
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Aseev LV, Koledinskaya LS, Bychenko OS, Boni IV. Regulation of Ribosomal Protein Synthesis in Mycobacteria: The Autogenous Control of rpsO. Int J Mol Sci 2021; 22:9679. [PMID: 34575857 PMCID: PMC8470358 DOI: 10.3390/ijms22189679] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/23/2023] Open
Abstract
The autogenous regulation of ribosomal protein (r-protein) synthesis plays a key role in maintaining the stoichiometry of ribosomal components in bacteria. In this work, taking the rpsO gene as a classic example, we addressed for the first time the in vivo regulation of r-protein synthesis in the mycobacteria M. smegmatis (Msm) and M. tuberculosis (Mtb). We used a strategy based on chromosomally integrated reporters under the control of the rpsO regulatory regions and the ectopic expression of Msm S15 to measure its impact on the reporter expression. Because the use of E. coli as a host appeared inefficient, a fluorescent reporter system was developed by inserting Msm or Mtb rpsO-egfp fusions into the Msm chromosome and expressing Msm S15 or E. coli S15 in trans from a novel replicative shuttle vector, pAMYC. The results of the eGFP expression measurements in Msm cells provided evidence that the rpsO gene in Msm and Mtb was feedback-regulated at the translation level. The mutagenic analysis showed that the folding of Msm rpsO 5'UTR in a pseudoknot appeared crucial for repression by both Msm S15 and E. coli S15, thus indicating a striking resemblance of the rpsO feedback control in mycobacteria and in E. coli.
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Affiliation(s)
| | | | | | - Irina V. Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.V.A.); (L.S.K.); (O.S.B.)
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5
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Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fåhraeus R. The p53 mRNA: an integral part of the cellular stress response. Nucleic Acids Res 2019; 47:3257-3271. [PMID: 30828720 PMCID: PMC6468297 DOI: 10.1093/nar/gkz124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulated via a hierarchical order of post-translational modifications and regulated protein-protein interactions. The mechanisms governing these processes provide a model for how cells optimize the genetic information for maximal diversity. The p53 mRNA also plays a role in this process and this review aims to illustrate how protein and RNA interactions throughout the p53 mRNA in response to different signalling pathways control RNA stability, translation efficiency or alternative initiation of translation. We also describe how a p53 mRNA platform shows riboswitch-like features and controls the rate of p53 synthesis, protein stability and modifications of the nascent p53 protein. A single cancer-derived synonymous mutation disrupts the folding of this platform and prevents p53 activation following DNA damage. The role of the p53 mRNA as a target for signalling pathways illustrates how mRNA sequences have co-evolved with the function of the encoded protein and sheds new light on the information hidden within mRNAs.
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Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y cáncer. Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona universitaria, 78290 SLP, México
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | - Robin Fåhraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden.,Inserm U1162, 27 rue Juliette Dodu, 75010 Paris, France.,ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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6
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Pei S, Slinger BL, Meyer MM. Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15. BMC Bioinformatics 2017; 18:298. [PMID: 28587636 PMCID: PMC5461778 DOI: 10.1186/s12859-017-1704-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 05/22/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Proteins recognize many different aspects of RNA ranging from single stranded regions to discrete secondary or tertiary structures. High-throughput sequencing (HTS) of in vitro selected populations offers a large scale method to study RNA-proteins interactions. However, most existing analysis methods require that the binding motifs are enriched in the population relative to earlier rounds, and that motifs are found in a loop or single stranded region of the potential RNA secondary structure. Such methods do not generalize to all RNA-protein interaction as some RNA binding proteins specifically recognize more complex structures such as double stranded RNA. RESULTS In this study, we use HT-SELEX derived populations to study the landscape of RNAs that interact with Geobacillus kaustophilus ribosomal protein S15. Our data show high sequence and structure diversity and proved intractable to existing methods. Conventional programs identified some sequence motifs, but these are found in less than 5-10% of the total sequence pool. Therefore, we developed a novel framework to analyze HT-SELEX data. Our process accounts for both sequence and structure components by abstracting the overall secondary structure into smaller substructures composed of a single base-pair stack, which allows us to leverage existing approaches already used in k-mer analysis to identify enriched motifs. By focusing on secondary structure motifs composed of specific two base-pair stacks, we identified significantly enriched or depleted structure motifs relative to earlier rounds. CONCLUSIONS Discrete substructures are likely to be important to RNA-protein interactions, but they are difficult to elucidate. Substructures can help make highly diverse sequence data more tractable. The structure motifs provide limited accuracy in predicting enrichment suggesting that G. kaustophilus S15 can either recognize many different secondary structure motifs or some aspects of the interaction are not captured by the analysis. This highlights the importance of considering secondary and tertiary structure elements and their role in RNA-protein interactions.
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Affiliation(s)
- Shermin Pei
- Boston College, 140 Commonwealth Ave., 02467, Chestnut Hill, USA
| | - Betty L Slinger
- Boston College, 140 Commonwealth Ave., 02467, Chestnut Hill, USA
| | - Michelle M Meyer
- Boston College, 140 Commonwealth Ave., 02467, Chestnut Hill, USA.
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7
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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8
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Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res 2013; 41:9033-48. [PMID: 23901011 PMCID: PMC3799429 DOI: 10.1093/nar/gkt654] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data.
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Affiliation(s)
- Michael C Chao
- Division of Infectious Disease, Brigham & Women's Hospital, Boston, MA 02115, USA, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA, Howard Hughes Medical Institute, Boston, MA 02115, USA, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA and Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
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9
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Ligand-inducible formation of RNA pseudoknot. Bioorg Med Chem Lett 2013; 23:3539-41. [DOI: 10.1016/j.bmcl.2013.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/23/2022]
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10
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Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM. Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria. Nucleic Acids Res 2013; 41:3491-503. [PMID: 23396277 PMCID: PMC3616713 DOI: 10.1093/nar/gkt055] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/02/2013] [Accepted: 01/10/2013] [Indexed: 01/30/2023] Open
Abstract
In Escherichia coli, 12 distinct RNA structures within the transcripts encoding ribosomal proteins interact with specific ribosomal proteins to allow autogenous regulation of expression from large multi-gene operons, thus coordinating ribosomal protein biosynthesis across multiple operons. However, these RNA structures are typically not represented in the RNA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution is largely unknown. To investigate the extent to which these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger RNA (mRNA) structures in E. coli. We find that while three RNA structures are widely distributed across many phyla of bacteria, seven of the RNAs are narrowly distributed to a few orders of Gammaproteobacteria. To experimentally validate our computational predictions, we biochemically confirmed dual L1-binding sites identified in many Firmicute species. This work reveals that RNA-based regulation of ribosomal protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that regulate ribosomal protein biosynthesis in E. coli are narrowly distributed. These results highlight the limits of our knowledge regarding ribosomal protein biosynthesis regulation outside of E. coli, and the potential for alternative RNA structures responsible for regulating ribosomal proteins in other eubacteria.
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Affiliation(s)
| | | | | | - Michelle M. Meyer
- Department of Biology, Boston College, 140 Commonwealth Ave. Chestnut Hill, MA 02467, USA
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11
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Huang Q, Purzycka KJ, Lusvarghi S, Li D, LeGrice SF, Boeke JD. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. RNA (NEW YORK, N.Y.) 2013; 19:320-32. [PMID: 23329695 PMCID: PMC3677243 DOI: 10.1261/rna.035535.112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/26/2012] [Indexed: 05/04/2023]
Abstract
Ty1 retrotransposon RNA has the potential to fold into a variety of distinct structures, mutation of which affects retrotransposition frequencies. We show here that one potential functional structure is located at the 5' end of the genome and can assume a pseudoknot conformation. Chemoenzymatic probing of wild-type and mutant mini-Ty1 RNAs supports the existence of such a structure, while molecular genetic analyses show that mutations disrupting pseudoknot formation interfere with retrotransposition, indicating that it provides a critical biological function. These defects are enhanced at higher temperatures. When these mutants are combined with compensatory changes, retrotransposition is restored, consistent with pseudoknot architecture. Analyses of mutants suggest a defect in Ty1 reverse transcription. Collectively, our data allow modeling of a three-dimensional structure for this novel critical cis-acting signal of the Ty1 genome.
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Affiliation(s)
- Qing Huang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Katarzyna J. Purzycka
- National Cancer Institute, Frederick, Maryland 21702, USA
- Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | | | - Donghui Li
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Jef D. Boeke
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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12
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Abstract
Despite the fact that ribosomal proteins are the constituents of an organelle that is present in every cell, they show a surprising level of regulation, and several of them have also been shown to have other extra-ribosomal functions, such in replication, transcription, splicing or even ageing. This review provides a comprehensive summary of these important aspects.
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Affiliation(s)
- Rital B Bhavsar
- Department of Biology, University of Dayton, OH 45469-2320, USA
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13
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Abstract
Sgm methyltransferase from Micromonospora zionensis and KgmB methyltransferase from Streptoalloteichus tenebrarius are resistant to aminoglycoside antibiotics as a result of their ability to specifically methylate G1405 within the bacterial 16S rRNA A-site. The (C)CGCCC motif, assumed to be a regulatory sequence responsible for the autoregulation of the sgm gene, could most likely also be responsible for the autoregulation of the kgmB gene. This sequence, found within the 5' untranslated region of both sgm and kgmB mRNAs, as indicated by in silico prediction, may be involved in the formation of a specific stem-loop structure. Sgm and KgmB are mutually down-regulated and it is likely that they share the same cis-acting elements. Structure probing experiments confirmed the existence of a stable secondary structure within the 5' UTR of the sgm mRNA, while the analysis of kgmB mRNA failed to confirm the predicted structure. .
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14
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Xu D, Landon T, Greenbaum NL, Fenley MO. The electrostatic characteristics of G.U wobble base pairs. Nucleic Acids Res 2007; 35:3836-47. [PMID: 17526525 PMCID: PMC1920249 DOI: 10.1093/nar/gkm274] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
G.U wobble base pairs are the most common and highly conserved non-Watson-Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G.U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson-Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G.U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G.U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G.U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G.U sites in RNA are most likely to bind cationic ligands.
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Affiliation(s)
- Darui Xu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
| | - Theresa Landon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
| | - Nancy L. Greenbaum
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
- *To whom correspondence should be addressed. Marcia O. Fenley. +1-850-644-7961+1-850-644-7244 Correspondence may also be addressed to Nancy L. Greenbaum. +1-850-644-2005 +1-850-644-8281
| | - Marcia O. Fenley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
- *To whom correspondence should be addressed. Marcia O. Fenley. +1-850-644-7961+1-850-644-7244 Correspondence may also be addressed to Nancy L. Greenbaum. +1-850-644-2005 +1-850-644-8281
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15
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Scott LG, Williamson JR. The binding interface between Bacillus stearothermophilus ribosomal protein S15 and its 5'-translational operator mRNA. J Mol Biol 2005; 351:280-90. [PMID: 16005889 DOI: 10.1016/j.jmb.2005.06.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 06/07/2005] [Accepted: 06/10/2005] [Indexed: 11/26/2022]
Abstract
The Bacillus stearothermophilus ribosomal protein S15 (BS15) binds a purine-rich three-helix junction motif in the central domain of 16S ribosomal RNA (rRNA) as well as a translational operator located in the 5'-untranslated region (5'-UTR) of its cognate messenger RNA (mRNA). An in-frame fusion between the 5'-UTR of the BS15 gene and beta-galactosidase (lacZ) was prepared, and tested for BS15-dependent translational repression of lacZ activity in Escherichia coli. The presence of BS15 in trans represses lacZ activity 24-fold. A series of detailed point mutations in BS15 were tested for their effects upon translational repression of lacZ activity. These point mutations demonstrated that the 5'-UTR-BS15 binding interface utilizes many of the same conserved amino acid residues implicated in the binding of BS15 to 16S rRNA. The data demonstrate that the S15 protein can bind to an RNA target motif based primarily upon appropriate minor groove and sugar-phosphate backbone contacts, irrespective of the specific RNA sequence.
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Affiliation(s)
- Lincoln G Scott
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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16
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Vajic S, Anastasov N, Vasiljevic B. The kgmB gene, encoding ribosomal RNA methylase from Streptomyces tenebrarius, is autogenously regulated. Arch Microbiol 2004; 182:475-81. [PMID: 15578257 DOI: 10.1007/s00203-004-0731-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Revised: 08/02/2004] [Accepted: 08/31/2004] [Indexed: 11/28/2022]
Abstract
The KgmB methylase (the kanamycin-gentamicin resistance methylase from Streptomyces tenebrarius) acts at G-1405 of 16S rRNA within the sequence CGUCA that is also found 6 bp in front of ribosomal binding site of the kgmB gene. The kgmBColon, two colonslacZ gene and operon fusions were used in order to test for translational autoregulation of kgmB gene. Overexpression of kgmB either in cis or in trans drastically decreased the level of expression of the fusion protein. However, mutagenesis eliminated any role for the CGUCA sequence in translational autoregulation. Hence, the role of second putative regulatory sequence (CGCCC) that was shown to be involved in regulation of another methylase, Sgm (sisomicin-gentamicin methylase gene from Micromonospora zionensis) was examined. It was shown that the Sgm methylase can also decrease the level of expression of the kgmBColon, two colonslacZ fusion protein.
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Affiliation(s)
- Sandra Vajic
- Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444a, P.O. Box 446, 11001 Belgrade, Serbia and Montenegro
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17
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Mathy N, Pellegrini O, Serganov A, Patel DJ, Ehresmann C, Portier C. Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation. Mol Microbiol 2004; 52:661-75. [PMID: 15101974 PMCID: PMC4693643 DOI: 10.1111/j.1365-2958.2004.04005.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ribosomal protein S15 binds to 16S rRNA, during ribosome assembly, and to its own mRNA (rpsO mRNA), affecting autocontrol of its expression. In both cases, the RNA binding site is bipartite with a common subsite consisting of a G*U/G-C motif. The second subsite is located in a three-way junction in 16S rRNA and in the distal part of a stem forming a pseudoknot in Escherichia coli rpsO mRNA. To determine the extent of mimicry between these two RNA targets, we determined which amino acids interact with rpsO mRNA. A plasmid carrying rpsO (the S15 gene) was mutagenized and introduced into a strain lacking S15 and harbouring an rpsO-lacZ translational fusion. Analysis of deregulated mutants shows that each subsite of rpsO mRNA is recognized by a set of amino acids known to interact with 16S rRNA. In addition to the G*U/G-C motif, which is recognized by the same amino acids in both targets, the other subsite interacts with amino acids also involved in contacts with helix H22 of 16S rRNA, in the region adjacent to the three-way junction. However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Mimicry
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Protein Structure, Secondary
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Recombinant Fusion Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Sequence Alignment
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Affiliation(s)
- Nathalie Mathy
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Pellegrini
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Alexander Serganov
- Laboratory of Nucleic Acid and Protein Structures, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Dinshaw J. Patel
- Laboratory of Nucleic Acid and Protein Structures, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Chantal Ehresmann
- UPR9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France
| | - Claude Portier
- UPR9073 du CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- For correspondence. ; Tel. (+33) 1 58 41 51 27; Fax (+33) 1 58 41 50 20
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18
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Springer M, Portier C. More than one way to skin a cat: translational autoregulation by ribosomal protein S15. Nat Struct Mol Biol 2003; 10:420-2. [PMID: 12768202 DOI: 10.1038/nsb0603-420] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Serganov A, Polonskaia A, Ehresmann B, Ehresmann C, Patel DJ. Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J 2003; 22:1898-908. [PMID: 12682022 PMCID: PMC154462 DOI: 10.1093/emboj/cdg170] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 16S rRNA-binding ribosomal protein S15 is a key component in the assembly of the small ribosomal subunit in bacteria. We have shown that S15 from the extreme thermophile Thermus thermophilus represses the translation of its own mRNA in vitro, by interacting with the leader segment of its mRNA. The S15 mRNA-binding site was characterized by footprinting experiments, deletion analysis and site-directed mutagenesis. S15 binding triggers a conformational rearrangement of its mRNA into a fold that mimics the conserved three-way junction of the S15 rRNA-binding site. This conformational change masks the ribosome entry site, as demonstrated by direct competition between the ribosomal subunit and S15 for mRNA binding. A comparison of the T.thermophilus and Escherichia coli regulation systems reveals that the two regulatory mRNA targets do not share any similarity and that the mechanisms of translational inhibition are different. Our results highlight an astonishing plasticity of mRNA in its ability to adapt to evolutionary constraints, that contrasts with the extreme conservation of the rRNA-binding site.
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Affiliation(s)
- Alexander Serganov
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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20
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Serganov A, Ennifar E, Portier C, Ehresmann B, Ehresmann C. Do mRNA and rRNA binding sites of E.coli ribosomal protein S15 share common structural determinants? J Mol Biol 2002; 320:963-78. [PMID: 12126618 DOI: 10.1016/s0022-2836(02)00553-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Escherichia coli ribosomal protein S15 recognizes two RNA targets: a three-way junction in 16S rRNA and a pseudoknot structure on its own mRNA. Binding to mRNA occurs when S15 is expressed in excess over its rRNA target, resulting in an inhibition of translation start. The sole apparent similarity between the rRNA and mRNA targets is the presence of a G-U/G-C motif that contributes only modestly to rRNA binding but is essential for mRNA. To get more information on the structural determinants used by S15 to bind its mRNA target as compared to its rRNA site, we used site-directed mutagenesis, substitution by nucleotide analogs, footprinting experiments on both RNA and protein, and graphic modeling. The size of the mRNA-binding site could be reduced to 45 nucleotides, without loss of affinity. This short RNA preferentially folds into a pseudoknot, the formation of which depends on magnesium concentration and temperature. The size of the loop L2 that bridges the two stems of the pseudoknot through the minor groove could not be reduced below nine nucleotides. Then we showed that the pseudoknot recognizes the same side of S15 as 16S rRNA, although shielding a smaller surface area. It turned out that the G-U/G-C motif is recognized from the minor groove in both cases, and that the G-C pair is recognized in a very similar manner. However, the wobble G-U pair of the mRNA is not directly contacted by S15, as in rRNA, but is most likely involved in building a precise conformation of the RNA, essential for binding. Otherwise, unique specific features are utilized, such as the three-way junction in the case of 16S rRNA and the looped out A(-46) for the mRNA pseudoknot.
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Affiliation(s)
- Alexander Serganov
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 cedex, Strasbourg, France
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21
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Scott LG, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5'-translational operator mRNA. J Mol Biol 2001; 314:413-22. [PMID: 11846555 DOI: 10.1006/jmbi.2001.5165] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Bacillus stearothermophilus ribosomal protein S15 (BS15) binds both a three-helix junction in the central domain of 16 S ribosomal RNA and its cognate mRNA. Native gel mobility-shift assays show that BS15 interacts specifically and with high affinity to the 5'-untranslated region (5'-UTR) of this cognate mRNA with an apparent dissociation constant of 3(+/-0.3) nM. In order to localize the structural elements that are essential for BS15 recognition, a series of deletion mutants of the full cognate mRNA were prepared and tested in the same gel-shift assay. The minimal binding site for BS15 is a 50 nucleotide RNA showing a close secondary structure resemblance to the BS15 binding region from 16 S rRNA. There are two major structural motifs that must be maintained for high-affinity binding. The first being a purine-rich three-helix junction, and the second being an internal loop. The sequence identity of the internal loops differs greatly between the BS15 mRNA and rRNA sites, and this difference is correlated to discrimination between wild-type BS15 and a BS15(H45R) mutant. The association and dissociation kinetics measured for the 5'-UTR-BS15 interaction are quite slow, but are typical for a ribosomal protein-RNA interaction. The BS15 mRNA and 16 S rRNA binding sites share a common secondary structure yet have little sequence identity. The mRNA and rRNA may in fact present similar if not identical structural elements that confer BS15 recognition.
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MESH Headings
- 5' Untranslated Regions/chemistry
- 5' Untranslated Regions/genetics
- 5' Untranslated Regions/metabolism
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- Electrophoretic Mobility Shift Assay
- Geobacillus stearothermophilus/genetics
- Geobacillus stearothermophilus/metabolism
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Mutation/genetics
- Nucleic Acid Conformation
- Operator Regions, Genetic/genetics
- Protein Biosynthesis/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/metabolism
- Substrate Specificity
- Titrimetry
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Affiliation(s)
- L G Scott
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, MB33, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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22
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Robert F, Brakier-Gingras L. Ribosomal protein S7 from Escherichia coli uses the same determinants to bind 16S ribosomal RNA and its messenger RNA. Nucleic Acids Res 2001; 29:677-82. [PMID: 11160889 PMCID: PMC30405 DOI: 10.1093/nar/29.3.677] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ribosomal protein S7 from Escherichia coli binds to the lower half of the 3' major domain of 16S rRNA and initiates its folding. It also binds to its own mRNA, the str mRNA, and represses its translation. Using filter binding assays, we show in this study that the same mutations that interfere with S7 binding to 16S rRNA also weaken its affinity for its mRNA. This suggests that the same protein regions are responsible for mRNA and rRNA binding affinities, and that S7 recognizes identical sequence elements within the two RNA targets, although they have dissimilar secondary structures. Overexpression of S7 is known to inhibit bacterial growth. This phenotypic growth defect was relieved in cells overexpressing S7 mutants that bind poorly the str mRNA, confirming that growth impairment is controlled by the binding of S7 to its mRNA. Interestingly, a mutant with a short deletion at the C-terminus of S7 was more detrimental to cell growth than wild-type S7. This suggests that the C-terminal portion of S7 plays an important role in ribosome function, which is perturbed by the deletion.
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MESH Headings
- Base Sequence
- Binding Sites
- Binding, Competitive
- Cell Division/genetics
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genotype
- Molecular Sequence Data
- Molecular Structure
- Mutation
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
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Affiliation(s)
- F Robert
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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23
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Serganov A, Bénard L, Portier C, Ennifar E, Garber M, Ehresmann B, Ehresmann C. Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15. J Mol Biol 2001; 305:785-803. [PMID: 11162092 DOI: 10.1006/jmbi.2000.4354] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosomal protein S15 recognizes a highly conserved target on 16 S rRNA, which consists of two distinct binding regions. Here, we used extensive site-directed mutagenesis on a Escherichia coli 16 S rRNA fragment containing the S15 binding site, to investigate the role of conserved nucleotides in protein recognition and to evaluate the relative contribution of the two sites. The effect of mutations on S15 recognition was studied by measuring the relative binding affinity, RNA probing and footprinting. The crystallographic structure of the Thermus thermophilus complex allowed molecular modelling of the E. coli complex and facilitated interpretation of biochemical data. Binding is essentially driven by site 1, which includes a three-way junction constrained by a conserved base triple and cross-strand stacking. Recognition is based mainly on shape complementarity, and the role of conserved nucleotides is to maintain a unique backbone geometry. The wild-type base triple is absolutely required for protein interaction, while changes in the conserved surrounding nucleotides are partially tolerated. Site 2, which provides functional groups in a conserved G-U/G-C motif, contributes only modestly to the stability of the interaction. Binding to this motif is dependent on binding at site 1 and is allowed only if the two sites are in the correct relative orientation. Non-conserved bulged nucleotides as well as a conserved purine interior loop, although not directly involved in recognition, are used to provide an appropriate flexibility between the two sites. In addition, correct binding at the two sites triggers conformational adjustments in the purine interior loop and in a distal region, which are known to be involved for subsequent binding of proteins S6 and S18. Thus, the role of site 1 is to anchor S15 to the rRNA, while binding at site 2 is aimed to induce a cascade of events required for subunit assembly.
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Affiliation(s)
- A Serganov
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France
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24
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Varani G, McClain WH. The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep 2000; 1:18-23. [PMID: 11256617 PMCID: PMC1083677 DOI: 10.1093/embo-reports/kvd001] [Citation(s) in RCA: 323] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The G x U wobble base pair is a fundamental unit of RNA secondary structure that is present in nearly every class of RNA from organisms of all three phylogenetic domains. It has comparable thermodynamic stability to Watson-Crick base pairs and is nearly isomorphic to them. Therefore, it often substitutes for G x C or A x U base pairs. The G x U wobble base pair also has unique chemical, structural, dynamic and ligand-binding properties, which can only be partially mimicked by Watson-Crick base pairs or other mispairs. These features mark sites containing G x U pairs for recognition by proteins and other RNAs and allow the wobble pair to play essential functional roles in a remarkably wide range of biological processes.
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Affiliation(s)
- G Varani
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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25
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Abstract
The wobble GoU pairs have been implicated in several biological processes where RNA molecules play a key role. We review the geometrical and conformational properties of wobble GoU pairs on the basis of available crystal structures of RNAs at high resolution. The similarities with the wobble A+oC pairs and UoU pairs are illustrated, while the differences with the recently discovered bifurcated G x U pairs are contrasted.
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Affiliation(s)
- B Masquida
- Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR9002, Strasbourg, France
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26
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Strazewski P, Biala E, Gabriel K, McClain WH. The relationship of thermodynamic stability at a G x U recognition site to tRNA aminoacylation specificity. RNA (NEW YORK, N.Y.) 1999; 5:1490-4. [PMID: 10580477 PMCID: PMC1369870 DOI: 10.1017/s1355838299991586] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The G x U pair at the third position in the acceptor helix of Escherichia coli tRNA(Ala) is critical for aminoacylation. The features that allow G x U recognition are likely to include direct interaction of alanyl-tRNA synthetase with distinctive atomic groups and indirect recognition of the structural and stability information encoded in the sequence of G x U and its immediate context. The present work investigates the thermodynamic stability and acceptor activity for a comprehensive set of variant RNAs with substitutions of the G x U pair of E. coli tRNA(Ala). The four RNAs with Watson-Crick substitutions had a lower acceptor activity and a higher stability relative to the G x U RNA. On the other hand, the RNAs with mispair substitutions had a lower stability, but either a higher or a lower acceptor activity. Thus, the entire set of variant RNAs does not exhibit a correlation between thermodynamic stability of the free, unbound tRNA and its acceptor activity. The substantial acceptor activity of tRNAs with particular mispair substitutions may be explained by their ability to assume the conformational preferences of alanyl-tRNA synthetase. Moreover, the G x U pair may provide a point of deformability for the substrate tRNA to adapt to the enzyme's active site.
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Affiliation(s)
- P Strazewski
- Institute of Organic Chemistry, University of Basel, Switzerland.
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27
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Abstract
Equilibrium unfolding (folding) studies reveal that the autoregulatory RNA pseudoknots derived from the bacteriophage T2 and T4 gene 32 mRNAs exhibit significant stabilization by increasing concentrations of divalent metal ions in solution. In this report, the apparent affinities of exchange inert trivalent Co(NH(3))(3+)(6) have been determined, relative to divalent Mg(2+), for the folded, partially folded (K(f)), and fully unfolded (K(u)) conformations of these molecules. A general nonspecific, delocalized ion binding model was developed and applied to the analysis of the metal ion concentration dependence of individual two-state unfolding transitions. Trivalent Co(NH(3))(3+)(6) was found to associate with the fully folded and partially unfolded pseudoknotted forms of these RNAs with a K(f) of 5-8 x 10(4) M(-1) in a background of 0.10 M K(+), or 3- to 5-fold larger than the K(f) obtained for two model RNA hairpins and hairpin unfolding intermediates, and approximately 40-50-fold larger than K(f) for Mg(2+). The magnitude of K(f) was found to be strongly dependent on the monovalent salt concentration in a manner qualitatively consistent with polyelectrolyte theory, with K(f) reaching 1.2 x 10(5) M(-1) in 50 mM K(+). Two RNA hairpins were found to have affinities for Co(NH(3))(3+)(6) and Ru(NH(3))(3+)(6) of 1-2 x10(4) M(-1), or approximately 15-fold larger than the K(f) of approximately 1000 M(-1) observed for Mg(2+). Additionally, the K(u) of 4,800 M(-1) for the trivalent ligands is approximately 8-fold larger than the K(u) of 600 M(-1) observed for Mg(2+). These findings suggest that the T2 and T4 gene 32 mRNA pseudoknots possess a site(s) for Mg(2+) and Co(NH(3))(3+)(6) binding of significantly higher affinity than a "duplexlike" delocalized ion binding site that is strongly linked to the thermodynamic stability of these molecules. Imino proton perturbation nmr spectroscopy suggests that this site(s) lies near the base of the pseudoknot stem S2, near a patch of high negative electrostatic potential associated with the region where the single loop L1 adenosine crosses the major groove of stem S2.
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Affiliation(s)
- P L Nixon
- Department of Biochemistry and Biophysics, Center for Macromolecular Design, Texas A&M University, College Station, TX 77843-2128, USA
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28
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McClain WH, Jou YY, Bhattacharya S, Gabriel K, Schneider J. The reliability of in vivo structure-function analysis of tRNA aminoacylation. J Mol Biol 1999; 290:391-409. [PMID: 10390340 DOI: 10.1006/jmbi.1999.2884] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The G.U wobble base-pair in the acceptor helix of Escherichia coli tRNAAlais critical for aminoacylation by the alanine synthetase. Previous work by several groups probed the mechanism of enzyme recognition of G.U by a structure-function analysis of mutant tRNAs using either a cell assay (amber suppressor tRNA) or a test tube assay (phage T7 tRNA substrate and purified enzyme). However, the aminoacylation capacity of particular mutant tRNAs was about 10(4)-fold higher in the cell assay. This led us to scrutinize the cell assay to determine if any parameter exaggerates the extent of aminoacylation in mutants forming substantial amounts of alanyl-tRNAAla. In doing so, we have refined and developed experimental designs to analyze tRNA function. We examined the level of aminoacylation of amber suppressor tRNAAlawith respect to the method of isolating aminoacyl-tRNA, the rate of cell growth, the cellular levels of alanine synthetase and elongation factor TU (EF-Tu), the amount of tRNA and the characteristics of EF-Tu binding. Within the precision of our measurements, none of these parameters varied in a way that could significantly amplify cellular alanyl-tRNAAla. A key observation is that the extent of aminoacylation of tRNAAlawas independent of tRNAAlaconcentration over a 75-fold range. Therefore, the cellular assay of tRNAAlareflects the substrate quality of the molecule for formation of alanyl-tRNAAla. These experiments support the authenticity of the cellular assay and imply that a condition or factor present in the cell assay may be absent in the test tube assay.
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MESH Headings
- Acylation
- Alanine-tRNA Ligase/metabolism
- Base Sequence
- Blotting, Northern
- Escherichia coli/cytology
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Genes, Suppressor/genetics
- Guanosine Triphosphate/metabolism
- Lysine/analysis
- Mutation
- Peptide Elongation Factor Tu/metabolism
- Protein Binding
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Bacterial/metabolism
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ala/isolation & purification
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/isolation & purification
- RNA, Transfer, Amino Acyl/metabolism
- Reproducibility of Results
- Structure-Activity Relationship
- Suppression, Genetic
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Affiliation(s)
- W H McClain
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706-1567, USA.
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29
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Gilley D, Blackburn EH. The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein. Proc Natl Acad Sci U S A 1999; 96:6621-5. [PMID: 10359761 PMCID: PMC21964 DOI: 10.1073/pnas.96.12.6621] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes telomeric DNA. A pseudoknot structure is phylogenetically conserved within the RNA component of telomerase in all ciliated protozoans examined. Here, we report that disruptions of the pseudoknot base pairing within the telomerase RNA from Tetrahymena thermophila prevent the stable assembly in vivo of an active telomerase. Restoring the base-pairing potential of the pseudoknot by compensatory changes restores telomerase activity to essentially wild-type levels. Therefore, the pseudoknot topology rather than sequence is critical for an active telomerase. Furthermore, we show that disruption of the pseudoknot prevents the association of the RNA with the reverse transcriptase protein subunit of telomerase. Thus, we provide an example of a structural motif within the telomerase RNA that is required for telomerase function and identify the domain that is required for telomerase complex formation. Hence, we identify a biological role for a pseudoknot: promoting the stable assembly of a catalytically active ribonucleoprotein.
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Affiliation(s)
- D Gilley
- Department of Microbiology and Immunology, Box 0414, University of California, San Francisco, CA 94143-0414, USA
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30
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Liphardt J, Napthine S, Kontos H, Brierley I. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting. J Mol Biol 1999; 288:321-35. [PMID: 10329145 PMCID: PMC7141562 DOI: 10.1006/jmbi.1999.2689] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA pseudoknots are structural elements that participate in a variety of biological processes. At -1 ribosomal frameshifting sites, several types of pseudoknot have been identified which differ in their organisation and functionality. The pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived pseudoknot into a highly efficient, kinked frameshifter pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked pseudoknot) was not sufficient to create a functional pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G.C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3'-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those pseudoknots with a short loop 2.
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Affiliation(s)
- Jan Liphardt
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Sawsan Napthine
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Harry Kontos
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ian Brierley
- Division of Virology Department of Pathology University of Cambridge Tennis Court Road, Cambridge CB2 1QP, UK
- Corresponding author
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31
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Mizutani T, Tanabe K, Yamada K. A G.U base pair in the eukaryotic selenocysteine tRNA is important for interaction with SePF, the putative selenocysteine-specific elongation factor. FEBS Lett 1998; 429:189-93. [PMID: 9650587 DOI: 10.1016/s0014-5793(98)00589-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In Escherichia coli, selenocysteine biosynthesis and incorporation into selenoproteins requires the action of four gene products, including the specialized selenocysteine tRNA(Sec) and elongation factor SELB, different from the universal EF-Tu. In this regard, the situation is less clear in eukaryotes, but we previously reported the existence of SePF, a putative SELB homologue. The secondary structure of the tRNA(Sec) differs slightly in eukaryotes, due to a change in the lengths of several stems. Two non-Watson-Crick base pairs, G5a x U67b and U6 x U67, reside in the acceptor stem and are conserved in the course of evolution. Since it has already been reported that changing them to Watson-Crick base pairs did not affect the serylation or selenylation levels of tRNA(Sec), we asked whether these non-Watson-Crick base pairs are required for the interaction with SePF. To this end, tRNA(Sec) variants carrying Watson-Crick changes at these positions were tested for their ability to maintain the interaction with SePF. In these assays, the tRNA(Sec)-SePF interaction was determined by the protective action it confers against hydrolysis of the amino acid ester bond, under basic conditions. All the changes introduced at U6 x U67 did not significantly affect the interaction. Interestingly, however, the G5a x U67b to G5a-C67b substitution was sufficient, by itself, to lead to unprotection of the ester bond. Therefore, our finding strongly suggests that SePF is unable to interact with a tRNA(Sec) mutant version carrying a Watson-Crick G5a-C67b instead of the wild-type G5a x U67b base pair, establishing that G5a x U67b constitutes a structural determinant for SePF interaction.
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Affiliation(s)
- T Mizutani
- Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.
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