1
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Kolberg T, von Löhneysen S, Ozerova I, Wellner K, Hartmann R, Stadler P, Mörl M. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA. Nucleic Acids Res 2023; 51:e63. [PMID: 37114986 PMCID: PMC10287922 DOI: 10.1093/nar/gkad312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals. However, these methods address only one side of the RT stop or misincorporation position. Here, we describe Led-Seq, a new approach based on lead-induced cleavage of unpaired RNA positions, where both resulting cleavage products are investigated. The RNA fragments carrying 2', 3'-cyclic phosphate or 5'-OH ends are selectively ligated to oligonucleotide adapters by specific RNA ligases. In a deep sequencing analysis, the cleavage sites are identified as ligation positions, avoiding possible false positive signals based on premature RT stops. With a benchmark set of transcripts in Escherichia coli, we show that Led-Seq is an improved and reliable approach based on metal ion-induced phosphodiester hydrolysis to investigate RNA structures in vivo.
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Affiliation(s)
- Tim Kolberg
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Sarah von Löhneysen
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Iuliia Ozerova
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Roland K Hartmann
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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2
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Twittenhoff C, Brandenburg VB, Righetti F, Nuss AM, Mosig A, Dersch P, Narberhaus F. Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions. Nucleic Acids Res 2020; 48:e71. [PMID: 32463449 PMCID: PMC7337928 DOI: 10.1093/nar/gkaa404] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/08/2020] [Accepted: 05/06/2020] [Indexed: 12/24/2022] Open
Abstract
The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed 'Lead-seq', provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5'-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.
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Affiliation(s)
| | | | | | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
| | - Axel Mosig
- Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
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3
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Savage JC, Shinde P, Bächinger HP, Davare MA, Shinde U. A ribose modification of Spinach aptamer accelerates lead(ii) cation association in vitro. Chem Commun (Camb) 2019; 55:5882-5885. [PMID: 31037281 DOI: 10.1039/c9cc01697j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Spinach aptamer fluorescence requires formation of a tripartite complex composed of folded RNA, a GFP-like fluorophore, and selective cation coordination. 2'F pyrimidine modified Spinach has retained fluorescence, increased chemical stability, and accelerated cation association via increased G-quadruplex dynamics, thereby reducing readout time and enhancing Spinach utility for aqueous Pb2+ detection.
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Affiliation(s)
- Jonathan C Savage
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
| | - Pushkar Shinde
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA. and MSC181105, Emory University Main Campus, 1762 Clifton Rd, Atlanta, GA 30022, USA
| | - Hans Peter Bächinger
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA. and Research Department, Shriners Hospital, Portland, OR 97239, USA
| | - Monika A Davare
- Papé Pediatric Research Institute, Division of Pediatric Hematology/Oncology, Department of Pediatrics, Oregon Health & Sciences University, Portland, OR, USA
| | - Ujwal Shinde
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
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4
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Lackey L, Coria A, Woods C, McArthur E, Laederach A. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. RNA (NEW YORK, N.Y.) 2018; 24:513-528. [PMID: 29317542 PMCID: PMC5855952 DOI: 10.1261/rna.064469.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 05/22/2023]
Abstract
The impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next-generation sequencing to obtain experimental structure data, such as SHAPE-MaP, can reveal structural effects of mutations, especially when these data are incorporated into structure modeling. Here, we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single-nucleotide mutations. We find that allele-specific sorting greatly improved our detection ability. Thus, we used SHAPE-MaP with a novel combination of clone-free robotic mutagenesis and allele-specific sorting to perform a rapid, comprehensive survey of noncoding somatic and inherited riboSNitches in two cancer-associated mRNAs, TPT1 and LCP1 Using rigorous thermodynamic modeling of the Boltzmann suboptimal ensemble, we identified a subset of mutations that change TPT1 and LCP1 RNA structure, with approximately 14% of all variants identified as riboSNitches. To confirm that these in vitro structures were biologically relevant, we tested how dependent TPT1 and LCP1 mRNA structures were on their environments. We performed SHAPE-MaP on TPT1 and LCP1 mRNAs in the presence or absence of cellular proteins and found that both mRNAs have similar overall folds in all conditions. RiboSNitches identified within these mRNAs in vitro likely exist under biological conditions. Overall, these data reveal a robust mRNA structural landscape where differences in environmental conditions and most sequence variants do not significantly alter RNA structural ensembles. Finally, predicting riboSNitches in mRNAs from sequence alone remains particularly challenging; these data will provide the community with benchmarks for further algorithmic development.
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Affiliation(s)
- Lela Lackey
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Aaztli Coria
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Chanin Woods
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Evonne McArthur
- School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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5
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Ledda M, Aviran S. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biol 2018; 19:28. [PMID: 29495968 PMCID: PMC5833111 DOI: 10.1186/s13059-018-1399-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.
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Affiliation(s)
- Mirko Ledda
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
- Integrative Genetics and Genomics Graduate Group, UC Davis, 1 Shields Ave, Davis, 95616 USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
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6
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Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017; 5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. RESULTS We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. CONCLUSIONS To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.
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Affiliation(s)
| | | | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA 95616, USA
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7
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Wu S, Mao G, Kirsebom LA. Inhibition of Bacterial RNase P RNA by Phenothiazine Derivatives. Biomolecules 2016; 6:biom6030038. [PMID: 27618117 PMCID: PMC5039424 DOI: 10.3390/biom6030038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/19/2022] Open
Abstract
There is a need to identify novel scaffolds and targets to develop new antibiotics. Methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. Here, we show that different phenothiazine derivatives and pyronine G inhibited the activities of three structurally different bacterial RNase P RNAs (RPRs), including that from Mycobacterium tuberculosis, with Ki values in the lower μM range. Interestingly, three antipsychotic phenothiazines (chlorpromazine, thioridazine, and trifluoperazine), which are known to have antibacterial activities, also inhibited the activity of bacterial RPRs, albeit with higher Ki values than methylene blue. Phenothiazines also affected lead(II)-induced cleavage of bacterial RPR and inhibited yeast tRNA(Phe), indicating binding of these drugs to functionally important regions. Collectively, our findings provide the first experimental data showing that long, noncoding RNAs could be targeted by different phenothiazine derivatives.
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Affiliation(s)
- Shiying Wu
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
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8
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Righetti F, Narberhaus F. How to find RNA thermometers. Front Cell Infect Microbiol 2014; 4:132. [PMID: 25279353 PMCID: PMC4166951 DOI: 10.3389/fcimb.2014.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/02/2014] [Indexed: 11/27/2022] Open
Abstract
Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, we describe how such RNA thermometers (RNATs) have been discovered one by one upstream of heat shock and virulence genes in the past, and how next-generation sequencing approaches are able to reveal novel temperature-responsive RNA structures on a global scale.
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9
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Wildauer M, Zemora G, Liebeg A, Heisig V, Waldsich C. Chemical probing of RNA in living cells. Methods Mol Biol 2014; 1086:159-76. [PMID: 24136603 DOI: 10.1007/978-1-62703-667-2_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
RNAs need to adopt a specific architecture to exert their task in cells. While significant progress has been made in describing RNA folding landscapes in vitro, understanding intracellular RNA structure formation is still in its infancy. This is in part due to the complex nature of the cellular environment but also to the limited availability of suitable methodologies. To assess the intracellular structure of large RNAs, we recently applied a chemical probing technique and a metal-induced cleavage assay in vivo. These methods are based on the fact that small molecules, like dimethyl sulfate (DMS), or metal ions, such as Pb(2+), penetrate and spread throughout the cell very fast. Hence, these chemicals are able to modify accessible RNA residues or to induce cleavage of the RNA strand in the vicinity of a metal ion in living cells. Mapping of these incidents allows inferring information on the intracellular conformation, metal ion binding sites or ligand-induced structural changes of the respective RNA molecule. Importantly, in vivo chemical probing can be easily adapted to study RNAs in different cell types.
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Affiliation(s)
- Michael Wildauer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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10
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Koh DC, Edelman GM, Mauro VP. Physical evidence supporting a ribosomal shunting mechanism of translation initiation for BACE1 mRNA. ACTA ACUST UNITED AC 2013; 1:e24400. [PMID: 26824018 PMCID: PMC4718059 DOI: 10.4161/trla.24400] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/06/2013] [Accepted: 03/21/2013] [Indexed: 12/22/2022]
Abstract
In Alzheimer disease, elevated levels of the BACE1 enzyme are correlated with increased production of amyloid peptides and disease pathology. The increase in BACE1 levels is post-transcriptional and may involve altered translation efficiency. Earlier studies have indicated that translation of BACE1 mRNA is cap-dependent. As ribosomal subunits move from the cap-structure to the initiation codon, they fail to recognize several AUG codons in the 5′ leader. In this study, we looked for physical evidence of the mechanism underlying ribosomal scanning or shunting along the BACE1 5′ leader by investigating structural stability in the 5′ leaders of endogenous mRNAs in vivo. To perform this analysis, we probed RNAs using lead(II) acetate, a cell-permeable chemical that induces cleavage of unpaired nucleotides having conformational flexibility. The data revealed that the ≈440-nt 5′ leader was generally resistant to cleavage except for a region upstream of the initiation codon. Cleavage continued into the coding region, consistent with destabilization of secondary structures by translating ribosomes. Evidence that a large segment of the BACE1 5′ leader was not cleaved indicates that this region is structurally stable and suggests that it is not scanned. The data support a mechanism of translation initiation in which ribosomal subunits bypass (shunt) part of the BACE1 5′ leader to reach the initiation codon. We suggest that a nucleotide bias in the 5′ leader may predispose the initiation codon to be more accessible than other AUG codons in the 5′ leader, leading to an increase in its relative utilization.
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Affiliation(s)
- Dora C Koh
- Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA
| | - Gerald M Edelman
- Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA
| | - Vincent P Mauro
- Department of Cell and Molecular Biology; The Scripps Research Institute; La Jolla, CA USA
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11
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Kraut S, Bebenroth D, Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme. Nucleic Acids Res 2011; 40:1318-30. [PMID: 21976731 PMCID: PMC3273808 DOI: 10.1093/nar/gkr812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.
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Affiliation(s)
- Stefanie Kraut
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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12
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Abstract
RNA folding is the most essential process underlying RNA function. While significant progress has been made in understanding the forces driving RNA folding in vitro, exploring the rules governing intracellular RNA structure formation is still in its infancy. The cellular environment hosts a great diversity of factors that potentially influence RNA folding in vivo. For example, the nature of transcription and translation is known to shape the folding landscape of RNA molecules. Trans-acting factors such as proteins, RNAs and metabolites, among others, are also able to modulate the structure and thus the fate of an RNA. Here we summarize the ongoing efforts to uncover how RNA folds in living cells.
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Affiliation(s)
- Georgeta Zemora
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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13
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Abstract
RNA folding is the most fundamental process underlying RNA function. RNA structure and associated folding paradigms have been intensively studied in vitro. However, in vivo RNA structure formation has only been explored to a limited extent. To determine the influence of the cellular environment, which differs significantly from the in vitro refolding conditions, on RNA architecture, we have applied a chemical probing technique to assess the structure of catalytic RNAs in living cells. This method is based on the fact that chemicals like dimethyl sulfate readily penetrate cells and modify specific atoms of RNA bases (N1-A, N3-C), provided that these positions are solvent accessible. By mapping the modified residues, one gains substantial information on the architecture of the target RNA on the secondary and tertiary structure level. This method also allows exploration of interactions of the target RNA with ligands such as proteins, metabolites, or other RNA molecules and associated conformational changes. In brief, in vivo chemical probing is a powerful tool to investigate RNA structure in its natural environment and can be easily adapted to study RNAs in different cell types.
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14
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Brännvall M, Kikovska E, Wu S, Kirsebom LA. Evidence for Induced Fit in Bacterial RNase P RNA-mediated Cleavage. J Mol Biol 2007; 372:1149-64. [PMID: 17719605 DOI: 10.1016/j.jmb.2007.07.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/06/2007] [Accepted: 07/09/2007] [Indexed: 11/26/2022]
Abstract
RNase P with its catalytic RNA subunit is involved in the processing of a number of RNA precursors with different structures. However, precursor tRNAs are the most abundant substrates for RNase P. Available data suggest that a tRNA is folded into its characteristic structure already at the precursor state and that RNase P recognizes this structure. The tRNA D-/T-loop domain (TSL-region) is suggested to interact with the specificity domain of RNase P RNA while residues in the catalytic domain interact with the cleavage site. Here, we have studied the consequences of a productive interaction between the TSL-region and its binding site (TBS) in the specificity domain using tRNA precursors and various hairpin-loop model substrates. The different substrates were analyzed with respect to cleavage site recognition, ground-state binding, cleavage as a function of the concentration of Mg(2+) and the rate of cleavage under conditions where chemistry is suggested to be rate limiting using wild-type Escherichia coli RNase P RNA, M1 RNA, and M1 RNA variants with structural changes in the TBS-region. On the basis of our data, we conclude that a productive TSL/TBS interaction results in a conformational change in the M1 RNA substrate complex that has an effect on catalysis. Moreover, it is likely that this conformational change comprises positioning of chemical groups (and Mg(2+)) at and in the vicinity of the cleavage site. Hence, our findings are consistent with an induced-fit mechanism in RNase P RNA-mediated cleavage.
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Affiliation(s)
- Mathias Brännvall
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden
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15
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Lapouge K, Sineva E, Lindell M, Starke K, Baker CS, Babitzke P, Haas D. Mechanism of
hcnA
mRNA recognition in the Gac/Rsm signal transduction pathway of
Pseudomonas fluorescens. Mol Microbiol 2007; 66:341-56. [PMID: 17850261 DOI: 10.1111/j.1365-2958.2007.05909.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the plant-beneficial bacterium Pseudomonas fluorescens CHA0, the expression of antifungal exoproducts is controlled by the GacS/GacA two-component system. Two RNA binding proteins (RsmA, RsmE) ensure effective translational repression of exoproduct mRNAs. At high cell population densities, GacA induces three small RNAs (RsmX, RsmY, RsmZ) which sequester both RsmA and RsmE, thereby relieving translational repression. Here we systematically analyse the features that allow the RNA binding proteins to interact strongly with the 5' untranslated leader mRNA of the P. fluorescens hcnA gene (encoding hydrogen cyanide synthase subunit A). We obtained evidence for three major RsmA/RsmE recognition elements in the hcnA leader, based on directed mutagenesis, RsmE footprints and toeprints, and in vivo expression data. Two recognition elements were found in two stem-loop structures whose existence in the 5' leader region was confirmed by lead(II) cleavage analysis. The third recognition element, which overlapped the hcnA Shine-Dalgarno sequence, was postulated to adopt either an open conformation, which would favour ribosome binding, or a stem-loop structure, which may form upon interaction with RsmA/RsmE and would inhibit access of ribosomes. Effective control of hcnA expression by the Gac/Rsm system appears to result from the combination of the three appropriately spaced recognition elements.
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Affiliation(s)
- Karine Lapouge
- Département de Microbiologie Fondamentale, Université de Lausanne, Bâtiment Biophore, CH-1015 Lausanne, Switzerland
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16
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Felden B. RNA structure: experimental analysis. Curr Opin Microbiol 2007; 10:286-91. [PMID: 17532253 DOI: 10.1016/j.mib.2007.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 03/09/2007] [Accepted: 05/14/2007] [Indexed: 11/25/2022]
Abstract
Among all of the biological macromolecules, the functional versatility of RNAs is unique including encoding or transferring genetic information and performing catalysis. These biological functions are highly dependent upon RNA folding and structure. Since the discovery of catalytic RNAs in the early 1980s, a recent breakthrough came from the identification of a wealth of micro RNAs, small interfering RNAs and regulatory RNAs, all involved in modulation of gene expression. The structure of these novel RNAs, either free or in complex with specific ligands, can be analyzed using various experimental strategies, including X-ray crystallography, cryo-electron microscopy, nuclear magnetic resonance spectroscopy, structure-specific probes, with some that can be used in living cells, RNA engineering, thermal denaturation and mass spectrometry. Among these, X-ray crystallography has recently enabled determination of the structures of several large and complex RNAs, as well as of ribonucleoprotein complexes. The database of RNA structure has grown tremendously since the recent crystal structure analyses of the prokaryotic ribosome and its subunits. These methods are now widely applied to a variety of biologically relevant RNAs.
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Affiliation(s)
- Brice Felden
- Université de Rennes I, Upres JE2311, Inserm U835 Biochimie Pharmaceutique, 2 Avenue du Prof. Léon Bernard, 35043 Rennes, France.
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17
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Wegscheid B, Hartmann RK. In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3'-CCA. Nucleic Acids Res 2007; 35:2060-73. [PMID: 17355991 PMCID: PMC1874595 DOI: 10.1093/nar/gkm005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For catalysis by bacterial type B RNase P, the importance of a specific interaction with p(recursor)tRNA 3'-CCA termini is yet unclear. We show that mutation of one of the two G residues assumed to interact with 3'-CCA in type B RNase P RNAs inhibits cell growth, but cell viability is at least partially restored at increased RNase P levels due to RNase P protein overexpression. The in vivo defects of the mutant enzymes correlated with an enzyme defect at low Mg(2+) in vitro. For Bacillus subtilis RNase P, an isosteric C259-G(74) bp fully and a C258-G(75) bp slightly rescued catalytic proficiency, demonstrating Watson-Crick base pairing to tRNA 3'-CCA but also emphasizing the importance of the base identity of the 5'-proximal G residue (G258). We infer the defect of the mutant enzymes to primarily lie in the recruitment of catalytically relevant Mg(2+), with a possible contribution from altered RNA folding. Although with reduced efficiency, B. subtilis RNase P is able to cleave CCA-less ptRNAs in vitro and in vivo. We conclude that the observed in vivo defects upon disruption of the CCA interaction are either due to a global deceleration in ptRNA maturation or severe inhibition of 5'-maturation for a ptRNA subset.
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Wegscheid B, Hartmann RK. The precursor tRNA 3'-CCA interaction with Escherichia coli RNase P RNA is essential for catalysis by RNase P in vivo. RNA (NEW YORK, N.Y.) 2006; 12:2135-48. [PMID: 17135488 PMCID: PMC1664727 DOI: 10.1261/rna.188306] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The L15 region of Escherichia coli RNase P RNA forms two Watson-Crick base pairs with precursor tRNA 3'-CCA termini (G292-C75 and G293-C74). Here, we analyzed the phenotypes associated with disruption of the G292-C75 or G293-C74 pair in vivo. Mutant RNase P RNA alleles (rnpBC292 and rnpBC293) caused severe growth defects in the E. coli rnpB mutant strain DW2 and abolished growth in the newly constructed mutant strain BW, in which chromosomal rnpB expression strictly depended on the presence of arabinose. An isosteric C293-G74 base pair, but not a C292-G75 pair, fully restored catalytic performance in vivo, as shown for processing of precursor 4.5S RNA. This demonstrates that the base identity of G292, but not G293, contributes to the catalytic process in vivo. Activity assays with mutant RNase P holoenzymes assembled in vivo or in vitro revealed that the C292/293 mutations cause a severe functional defect at low Mg2+ concentrations (2 mM), which we infer to be on the level of catalytically important Mg2+ recruitment. At 4.5 mM Mg2+, activity of mutant relative to the wild-type holoenzyme, was decreased only about twofold, but 13- to 24-fold at 2 mM Mg2+. Moreover, our findings make it unlikely that the C292/293 phenotypes include significant contributions from defects in protein binding, substrate affinity, or RNA degradation. However, native PAGE experiments revealed nonidentical RNA folding equilibria for the wild-type versus mutant RNase P RNAs, in a buffer- and preincubation-dependent manner. Thus, we cannot exclude that altered folding of the mutant RNAs may have also contributed to their in vivo defect.
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Affiliation(s)
- Barbara Wegscheid
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
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Adilakshmi T, Lease RA, Woodson SA. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res 2006; 34:e64. [PMID: 16682443 PMCID: PMC1458516 DOI: 10.1093/nar/gkl291] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We used a high flux synchrotron X-ray beam to map the structure of 16S rRNA and RNase P in viable bacteria in situ. A 300 ms exposure to the X-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. The in vivo footprints of the 16S rRNA in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the RNA backbone to hydroxyl radical. Protection or enhanced cleavage of certain nucleotides in vivo can be explained by interactions with tRNA and perturbation of the subunit interface. Thus, short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA–protein complexes with nucleotide resolution in living cells.
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Affiliation(s)
| | | | - Sarah A. Woodson
- To whom correspondence should be addressed. Tel: +1 410 516 2015; Fax: +1 410 516 4118;
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