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Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008; 29:499-509. [PMID: 18313387 DOI: 10.1016/j.molcel.2007.12.013] [Citation(s) in RCA: 354] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/24/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
Noncoding RNAs (ncRNAs) have recently been discovered to regulate mRNA transcription in trans, a role traditionally reserved for proteins. The breadth of ncRNAs as transacting transcriptional regulators and the diversity of signals to which they respond are only now becoming recognized. Here we show that human Alu RNA, transcribed from short interspersed elements (SINEs), is a transacting transcriptional repressor during the cellular heat shock response. Alu RNA blocks transcription by binding RNA polymerase II (Pol II) and entering complexes at promoters in vitro and in human cells. Transcriptional repression by Alu RNA involves two loosely structured domains that are modular, a property reminiscent of classical protein transcriptional regulators. Two other SINE RNAs, human scAlu RNA and mouse B1 RNA, also bind Pol II but do not repress transcription in vitro. These studies provide an explanation for why mouse cells harbor two major classes of SINEs, whereas human cells contain only one.
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Affiliation(s)
- Peter D Mariner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, CO 80309-0215, USA
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102
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Neußer T, Gildehaus N, Wurm R, Wagner R. Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation. Biol Chem 2008; 389:285-97. [DOI: 10.1515/bc.2008.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe small bacterial 6S RNA has been recognized as a transcriptional regulator, facilitating the transition from exponential to stationary growth phase by preferentially inhibiting Eσ70RNA polymerase holoenzyme transcription. Consistent with this function, the cellular concentration of 6S RNA increases with stationary phase. We have studied the underlying mechanisms responsible for the growth phase-dependent differences in 6S RNA concentration. To this aim, we have analyzed the effects of the typical bacterial growth phase and stress regulators FIS, H-NS, LRP and StpA on 6S RNA expression. Measurements of 6S RNA accumulation in strains deficient in each one of these proteins support their contribution as potential regulators. Specific binding of the four proteins to DNA fragments containing 6S RNA promoters was demonstrated by gel retardation and DNase I footprinting. Moreover,in vitrotranscription analysis with both RNA polymerase holoenzymes, Eσ70and Eσ38, demonstrated a direct inhibition of 6S RNA transcription by H-NS, StpA and LRP, while FIS seems to act as a dual regulator.In vitrotranscription in the presence of ppGpp indicates that 6S RNA promoters are not stringently regulated. Our results underline that regulation of 6S RNA transcription depends on a complex network, involving a set of bacterial regulators with general importance in the adaptation to changing growth conditions.
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103
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Abstract
During the past decade, numerous ncRNAs (non-coding RNAs) have been identified as regulators of transcription. This review focuses on a few examples of ncRNAs that directly interact with and regulate components of the transcription machinery. Artificial RNA aptamers have been selected against components of the transcriptional machinery. The bacterial 6S RNA and the eukaryotic B2 RNA directly target RNA polymerases. The 7SK RNA, U1 snRNA (small nuclear RNA) and SRA (steroid receptor RNA activator) RNA bind to and regulate the activity of transcription factors. Xist (X-inactive-specific transcript) and roX (RNA on the X) RNAs are involved in epigenetic regulation of transcription through the recruitment of histone-modifying enzymes.
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104
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Cavanagh AT, Klocko AD, Liu X, Wassarman KM. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol Microbiol 2008; 67:1242-56. [PMID: 18208528 DOI: 10.1111/j.1365-2958.2008.06117.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6S RNA binds sigma70-RNA polymerase and downregulates transcription at many sigma70-dependent promoters, but others escape regulation even during stationary phase when the majority of the transcription machinery is bound by the RNA. We report that core promoter elements determine this promoter specificity; a weak -35 element allows a promoter to be 6S RNA sensitive, and an extended -10 element similarly determines 6S RNA inhibition except when a consensus -35 element is present. These two features together predicted that hundreds of mapped Escherichia coli promoters might be subject to 6S RNA dampening in stationary phase. Microarray analysis confirmed 6S RNA-dependent downregulation of expression from 68% of the predicted genes, which corresponds to 49% of the expressed genes containing mapped E. coli promoters and establishes 6S RNA as a global regulator in stationary phase. We also demonstrate a critical role for region 4.2 of sigma70 in RNA polymerase interactions with 6S RNA. Region 4.2 binds the -35 element during transcription initiation; therefore we propose one mechanism for 6S RNA regulation of transcription is through competition for binding region 4.2 of sigma70.
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Affiliation(s)
- Amy T Cavanagh
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
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105
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Ulvé VM, Sevin EW, Chéron A, Barloy-Hubler F. Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics 2007; 8:467. [PMID: 18093320 PMCID: PMC2245857 DOI: 10.1186/1471-2164-8-467] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 12/19/2007] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years. RESULTS We used a combination of in silico comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between Sinorhizobium meliloti and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization. CONCLUSION Small non coding RNA (sra) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium.
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Affiliation(s)
- Vincent M Ulvé
- CNRS UMR6061 Génétique et Développement, Groupe Modèles Génétiques, Université de Rennes 1, IFR140 GFAS, Faculté de médecine, 2 avenue du Professeur Léon Bernard, CS 34317, 35043 Rennes Cedex, France.
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106
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Abstract
The past decade has seen an explosion in discovery of small, non-coding RNAs in all organisms. As functions for many of the small RNAs have been identified, it has become increasingly clear that they are important components in regulating gene expression. A multitude of RNAs target mRNAs for regulation at the level of translation or stability, including the microRNAs in higher eukaryotes and the Hfq binding RNAs in bacteria. Other RNAs regulate transcription, such as murine B2 RNA, mammalian 7SK RNA and the bacterial 6S RNA, which will be the focus of this review. Details of 6S RNA interactions with RNA polymerase, how 6S RNA regulates transcription, and how 6S RNA function contributes to cellular survival are discussed.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, USA.
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107
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Discovery of Small Regulatory RNAs Extends Our Understanding of Gene Regulation in the Acidithiobacillus Genus. ACTA ACUST UNITED AC 2007. [DOI: 10.4028/www.scientific.net/amr.20-21.535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small regulatory RNAs (srRNAs) control gene expression in Bacteria, usually at the posttranscriptional
level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with
regulatory proteins. srRNAs are involved in the regulation of a large variety of processes such as
plasmid replication, transposition and global genetic circuits that respond to environmental changes.
Since their discovery a few years ago, it has become apparent that they are prolific and widespread. In
this study, we describe bioinformatic approaches to srRNA discovery in the biomining microorganisms
Acidithiobacillus ferrooxidans, A. caldus and A. thiooxidans. Intergenic regions of the annotated
genomes were extracted and computationally searched for srRNAs. Candidate srRNAs that were
associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for
further study. The resulting potential srRNAs include known examples from other microorganisms and
some novel candidates and reveal interesting underlying biology of the Acidithiobacillus genus.
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108
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Axmann IM, Holtzendorff J, Voss B, Kensche P, Hess WR. Two distinct types of 6S RNA in Prochlorococcus. Gene 2007; 406:69-78. [PMID: 17640832 DOI: 10.1016/j.gene.2007.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 02/12/2007] [Accepted: 06/04/2007] [Indexed: 11/21/2022]
Abstract
Different forms of the 6S non-coding RNA (ncRNA) exist in enterobacteria and in B. subtilis but there is only limited information about this RNA from other groups of bacteria. Prochlorococcus is an oceanic, ecologically important, cyanobacterium. It possesses the most streamlined genome within the cyanobacterial phylum, lacking many regulatory proteins and mechanisms well-known from other bacteria. Here we show the accumulation of two distinct types of 6S RNA in Prochlorococcus MED4. One of these RNAs is transcribed from a specific promoter located 23 nucleotides downstream the terminal codon of the purK gene, whereas the longer transcript is produced by processing from a purK-6S RNA precursor. The expression of both 6S transcripts is under diel control, reaching maxima during the day and minima coinciding with the S- and G2-like phases which are typical for synchronized cultures of this prokaryote. Based on data from four closely related Prochlorococcus strains and 11 environmental sequences from the Sargasso Sea, a previously unknown structural element is predicted within the 6S RNA 5' domain by comparative computational analysis. The divergent expression in synchronized cultures and unusual structural domains that were detected based on metagenomic data sets indicate that 6S RNA is an extremely important global regulator in these marine cyanobacteria.
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Affiliation(s)
- Ilka M Axmann
- Humboldt University Berlin, Institute for Theoretical Biology, Invalidenstrasse 43, D-10115 Berlin, Germany
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109
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Gottesman S, McCullen C, Guillier M, Vanderpool C, Majdalani N, Benhammou J, Thompson K, FitzGerald P, Sowa N, FitzGerald D. Small RNA regulators and the bacterial response to stress. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:1-11. [PMID: 17381274 PMCID: PMC3592358 DOI: 10.1101/sqb.2006.71.016] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent studies have uncovered dozens of regulatory small RNAs in bacteria. A large number of these small RNAs act by pairing to their target mRNAs. The outcome of pairing can be either stimulation or inhibition of translation. Pairing in vivo frequently depends on the RNA-binding protein Hfq. Synthesis of these small RNAs is tightly regulated at the level of transcription; many of the well-studied stress response regulons have now been found to include a regulatory RNA. Expression of the small RNA can help the cell cope with environmental stress by redirecting cellular metabolism, exemplified by RyhB, a small RNA expressed upon iron starvation. Although small RNAs found in Escherichia coli can usually be identified by sequence comparison to closely related enterobacteria, other approaches are necessary to find the equivalent RNAs in other bacterial species. Nonetheless, it is becoming increasingly clear that many if not all bacteria encode significant numbers of these important regulators. Tracing their evolution through bacterial genomes remains a challenge.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
- Corresponding author: Bldg. 37, Rm. 5132, National Cancer Institute, Bethesda, MD. 20892; phone: 301-496-3524; fax: 301-496-3875;
| | - Colleen McCullen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Maude Guillier
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Carin Vanderpool
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Jihane Benhammou
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Karl Thompson
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Peter FitzGerald
- Genome Analysis Unit, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - Nathaniel Sowa
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
| | - David FitzGerald
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD. 20892
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110
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Storz G, Opdyke JA, Wassarman KM. Regulating bacterial transcription with small RNAs. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:269-73. [PMID: 17381306 DOI: 10.1101/sqb.2006.71.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, the combinations of computational and molecular approaches have led to the identification of an increasing number of small, noncoding RNAs encoded by bacteria and their plasmids and phages. Most of the characterized small RNAs have been shown to operate at a posttranscriptional level, modulating mRNA stability or translation by base-pairing with the 5' regions of the target mRNAs. However, a subset of small RNAs has been found to regulate transcription. One example is the abundant 6S RNA that has been proposed to compete for DNA binding of RNA polymerase by mimicking the open conformation of promoter DNA. Other small RNAs affect transcription termination via base-pairing interactions with sequences in the mRNA. Here, we discuss current understanding and questions regarding the roles of small RNAs in regulating transcription.
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Affiliation(s)
- G Storz
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Bethesda, Maryland 20892-5430, USA
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111
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Heidrich N, Moll I, Brantl S. In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucleic Acids Res 2007; 35:4331-46. [PMID: 17576690 PMCID: PMC1935000 DOI: 10.1093/nar/gkm439] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. However, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense RNAs. Here, we present a detailed in vitro analysis of SR1, a sRNA of Bacillus subtilis that is involved in regulation of arginine catabolism by basepairing with its target, ahrC mRNA. The secondary structures of SR1 species of different lengths and of the SR1/ahrC RNA complex were determined and functional segments required for complex formation narrowed down. The initial contact between SR1 and its target was shown to involve the 5′ part of the SR1 terminator stem and a region 100 bp downstream from the ahrC transcriptional start site. Toeprinting studies and secondary structure probing of the ahrC/SR1 complex indicated that SR1 inhibits translation initiation by inducing structural changes downstream from the ahrC RBS. Furthermore, it was demonstrated that Hfq, which binds both SR1 and ahrC RNA was not required to promote ahrC/SR1 complex formation but to enable the translation of ahrC mRNA. The intracellular concentrations of SR1 were calculated under different growth conditions.
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Affiliation(s)
- Nadja Heidrich
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany and Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
| | - Isabella Moll
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany and Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
| | - Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany and Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
- *To whom correspondence should be addressed. +49 3641 949570/571
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112
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Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K. Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol 2007; 5:25. [PMID: 17577407 PMCID: PMC1914338 DOI: 10.1186/1741-7007-5-25] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 06/18/2007] [Indexed: 01/06/2023] Open
Abstract
Background Non-coding RNAs (ncRNAs) are an emerging focus for both computational analysis and experimental research, resulting in a growing number of novel, non-protein coding transcripts with often unknown functions. Whole genome screens in higher eukaryotes, for example, provided evidence for a surprisingly large number of ncRNAs. To supplement these searches, we performed a computational analysis of seven yeast species and searched for new ncRNAs and RNA motifs. Results A comparative analysis of the genomes of seven yeast species yielded roughly 2800 genomic loci that showed the hallmarks of evolutionary conserved RNA secondary structures. A total of 74% of these regions overlapped with annotated non-coding or coding genes in yeast. Coding sequences that carry predicted structured RNA elements belong to a limited number of groups with common functions, suggesting that these RNA elements are involved in post-transcriptional regulation and/or cellular localization. About 700 conserved RNA structures were found outside annotated coding sequences and known ncRNA genes. Many of these predicted elements overlapped with UTR regions of particular classes of protein coding genes. In addition, a number of RNA elements overlapped with previously characterized antisense transcripts. Transcription of about 120 predicted elements located in promoter regions and other, previously un-annotated, intergenic regions was supported by tiling array experiments, ESTs, or SAGE data. Conclusion Our computational predictions strongly suggest that yeasts harbor a substantial pool of several hundred novel ncRNAs. In addition, we describe a large number of RNA structures in coding sequences and also within antisense transcripts that were previously characterized using tiling arrays.
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Affiliation(s)
- Stephan Steigele
- Wilhelm-Schickard-Institut für Informatik, ZBIT-Center for Bioinformatics Tübingen, University of Tübingen, Sand-14, D-72076 Tübingen, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Wolfgang Huber
- EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claudia Stocsits
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
- Department of Theoretical Chemistry University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Kay Nieselt
- Wilhelm-Schickard-Institut für Informatik, ZBIT-Center for Bioinformatics Tübingen, University of Tübingen, Sand-14, D-72076 Tübingen, Germany
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113
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Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA (NEW YORK, N.Y.) 2007; 13:583-96. [PMID: 17307818 PMCID: PMC1831867 DOI: 10.1261/rna.310307] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We previously found that the SINE-encoded mouse B2 RNA binds RNA polymerase II and represses mRNA transcription during the cellular heat-shock response. In vitro B2 RNA assembles into preinitiation complexes on promoter DNA via its interaction with the polymerase, thus rendering the complexes inactive. With the goal of understanding which regions of B2 RNA are important for high-affinity binding to RNA polymerase II and repression of transcription, we performed a structural and deletion analysis of a 178 nucleotide (nt) B2 RNA. We describe an experimentally derived secondary structure model for B2 RNA, and show that RNA polymerase II protects a specific region from RNase digestion. Deletion studies revealed that a 51-nt region of B2 RNA is sufficient for high-affinity binding to RNA polymerase II, association with preinitiation complexes, and repression of transcription in vitro, the latter of which involves a large predominately single-stranded region within the RNA. In addition, this piece of B2 RNA blocked the polymerase from properly associating with template DNA during the assembly of elongation complexes. Further deletion revealed that a 33-nt piece of B2 RNA binds RNA polymerase II, associates with preinitiation complexes, but cannot repress transcription. These results support a model in which RNA polymerase II contains a high-affinity ncRNA docking site to which a distinct region of B2 RNA binds, thereby allowing another region of the RNA to repress transcription. Moreover, the mechanism of transcriptional repression by B2 RNA likely involves disrupting critical contacts between RNA polymerase II and the promoter DNA.
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Affiliation(s)
- Celso A Espinoza
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA
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114
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Wassarman KM. 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 2007; 10:164-8. [PMID: 17383220 DOI: 10.1016/j.mib.2007.03.008] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2006] [Accepted: 03/12/2007] [Indexed: 11/16/2022]
Abstract
Appreciation for the prevalence and diversity of noncoding, small RNAs (sRNAs) has grown enormously in the past decade. A major role for sRNAs in all organisms is to regulate gene expression, often at the level of mRNA translation or stability. However, a few sRNAs have been shown to function by regulating transcription. The bacterial 6S RNA was the first sRNA shown to inhibit transcription by binding directly to the housekeeping holoenzyme form of RNA polymerase (i.e. sigma70-RNA polymerase in E. coli). It resides within the active site of RNA polymerase, blocks access to promoter DNA and, surprisingly, is used as a template for RNA synthesis. 6S RNA regulation of transcription leads to altered cell survival, perhaps by redirecting resource utilization under nutrient-limiting conditions.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA.
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115
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Typas A, Barembruch C, Possling A, Hengge R. Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels. EMBO J 2007; 26:1569-78. [PMID: 17332743 PMCID: PMC1829388 DOI: 10.1038/sj.emboj.7601629] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 02/06/2007] [Indexed: 11/08/2022] Open
Abstract
Upon environmental changes, bacteria reschedule gene expression by directing alternative sigma factors to core RNA polymerase (RNAP). This sigma factor switch is achieved by regulating relative amounts of alternative sigmas and by decreasing the competitiveness of the dominant housekeeping sigma(70). Here we report that during stationary phase, the unorthodox Crl regulator supports a specific sigma factor, sigma(S) (RpoS), in its competition with sigma(70) for core RNAP by increasing the formation of sigma(S)-containing RNAP holoenzyme, Esigma(S). Consistently, Crl has a global regulatory effect in stationary phase gene expression exclusively through sigma(S), that is, on sigma(S)-dependent genes only. Not a specific promoter motif, but sigma(S) availability determines the ability of Crl to exert its function, rendering it of major importance at low sigma(S) levels. By promoting the formation of Esigma(S), Crl also affects partitioning of sigma(S) between RNAP core and the proteolytic sigma(S)-targeting factor RssB, thereby playing a dual role in fine-tuning sigma(S) proteolysis. In conclusion, Crl has a key role in reorganising the Escherichia coli transcriptional machinery and global gene expression during entry into stationary phase.
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Affiliation(s)
- Athanasios Typas
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Berlin, Germany
| | - Claudia Barembruch
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Berlin, Germany
| | - Alexandra Possling
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Berlin, Germany
| | - Regine Hengge
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Berlin, Germany
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany. Tel.: +49 30 838 53119; Fax: +49 30 838 53118; E-mail:
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116
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Typas A, Becker G, Hengge R. The molecular basis of selective promoter activation by the ?Ssubunit of RNA polymerase. Mol Microbiol 2007; 63:1296-306. [PMID: 17302812 DOI: 10.1111/j.1365-2958.2007.05601.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Different environmental stimuli cause bacteria to exchange the sigma subunit in the RNA polymerase (RNAP) and, thereby, tune their gene expression according to the newly emerging needs. Sigma factors are usually thought to recognize clearly distinguishable promoter DNA determinants, and thereby activate distinct gene sets, known as their regulons. In this review, we illustrate how the principle sigma factor in stationary phase and in stressful conditions in Escherichia coli, sigmaS (RpoS), can specifically target its large regulon in vivo, although it is known to recognize the same core promoter elements in vitro as the housekeeping sigma factor, sigma70 (RpoD). Variable combinations of cis-acting promoter features and trans-acting protein factors determine whether a promoter is recognized by RNAP containing sigmaS or sigma70, or by both holoenzymes. How these promoter features impose sigmaS selectivity is further discussed. Moreover, additional pathways allow sigmaS to compete more efficiently than sigma70 for limiting amounts of core RNAP (E) and thereby enhance EsigmaS formation and effectiveness. Finally, these topics are discussed in the context of sigma factor evolution and the benefits a cell gains from retaining competing and closely related sigma factors with overlapping sets of target genes.
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Affiliation(s)
- Athanasios Typas
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany
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117
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Gildehaus N, Neußer T, Wurm R, Wagner R. Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res 2007; 35:1885-96. [PMID: 17332013 PMCID: PMC1874619 DOI: 10.1093/nar/gkm085] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/30/2007] [Accepted: 01/30/2007] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the conserved secondary structure and previous functional studies, had been suggested to interfere with transcription. Selective inhibition of sigma-70 holoenzymes, preferentially at extended -10 promoters, but not stationary-phase-specific transcription was described, suggesting a direct role of 6S RNA in the transition from exponential to stationary phase. To elucidate the underlying mechanism, we have analysed 6S RNA interactions with different forms of RNA polymerase by gel retardation and crosslinking. Preferred binding of 6S RNA to Esigma(70) was confirmed, however weaker binding to Esigma(38) was also observed. The crosslinking analysis revealed direct contact between a central 6S RNA sequence element and the beta/beta' and sigma subunits. Promoter complex formation and in vitro transcription analysis with exponential- and stationary-phase-specific promoters and the corresponding holoenzymes demonstrated that 6S RNA interferes with transcription initiation but does not generally distinguish between exponential- and stationary-phase-specific promoters. Moreover, we show for the first time that 6S RNA acts as a template for the transcription of defined RNA molecules in the absence of DNA. In conclusion, this study reveals new aspects of 6S RNA function.
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MESH Headings
- Binding Sites
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial
- Promoter Regions, Genetic
- RNA/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/physiology
- RNA, Untranslated/chemistry
- RNA, Untranslated/metabolism
- RNA, Untranslated/physiology
- Sigma Factor/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
| | | | | | - Rolf Wagner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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118
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Abstract
Here, I review three new structural studies from our laboratory. First, the crystal structure of RNA polymerase (Pol) II in complex with an RNA inhibitor revealed that this RNA blocks transcription initiation by preventing DNA loading into the active-centre cleft. Secondly, the structure of the SRI (Set2 Rpb1-interacting) domain of the histone methyltransferase Set2 revealed a novel fold for specific interaction with the doubly phosphorylated CTD (C-terminal repeat domain) of Pol II. Finally, we obtained the first structural information on Pol III, in the form of an 11-subunit model obtained by combining a homology model of the nine-subunit core enzyme with a new X-ray structure of the subcomplex C17/25.
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Affiliation(s)
- P Cramer
- Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
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119
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120
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Heidrich N, Chinali A, Gerth U, Brantl S. The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol Microbiol 2007; 62:520-36. [PMID: 17020585 DOI: 10.1111/j.1365-2958.2006.05384.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whereas about 70 small non-coding RNAs have been found in the Escherichia coli genome, relatively little is known about regulatory RNAs from Gram-positive bacteria. Here, we demonstrate that the recently identified small untranslated RNA SR1 from the Bacillus subtilis genome is a regulatory RNA involved in fine-tuning of arginine catabolism. 2D protein gel electrophoresis indicated three possible SR1 targets that are regulated by the transcriptional activator AhrC, which was shown to be the primary target of SR1. In vitro pairing studies and an in vivo reporter gene test demonstrated a specific interaction between SR1 and ahrC mRNA. This interaction did not lead to degradation of ahrC mRNA, but inhibited translation at a post-initiation stage. Our data show that the Hfq chaperone was not required for the stabilization of SR1 in vivo. The amount of SR1 was increased upon addition of l-arginine and l-ornithine, but not l-citrulline or l-proline.
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Affiliation(s)
- Nadja Heidrich
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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121
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Abstract
Noncoding small RNAs regulate gene expression in all organisms, in some cases through direct association with RNA polymerase (RNAP). Here we report that the mechanism of 6S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding. In fact, the DNA-dependent RNAP uses bound 6S RNA as a template for RNA synthesis, producing 14-to 20-nucleotide RNA products (pRNA). These results demonstrate that 6S RNA is functionally engaged in the active site of RNAP. Synthesis of pRNA destabilizes 6S RNA-RNAP complexes leading to release of the pRNA-6S RNA hybrid. In vivo, 6S RNA-directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/antagonists & inhibitors
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- RNA Stability
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sigma Factor/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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122
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Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR. Identification of a large noncoding RNA in extremophilic eubacteria. Proc Natl Acad Sci U S A 2006; 103:19490-5. [PMID: 17164334 PMCID: PMC1748253 DOI: 10.1073/pnas.0607493103] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Indexed: 12/14/2022] Open
Abstract
We have discovered a large and highly conserved RNA motif that typically resides in a noncoding section of a multigene messenger RNA in extremophilic Gram-positive eubacteria. RNAs of this class adopt an ornate secondary structure, are large compared with most other noncoding RNAs, and have been identified only in certain extremophilic bacteria. These ornate, large, extremophilic (OLE) RNAs have a length of approximately 610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. Structural probing of the OLE RNA from Bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. The patterns of structural conservation, and its unique phylogenetic distribution, suggest that OLE RNA carries out a complex and critical function only in certain extremophilic bacteria.
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Affiliation(s)
| | - Jeffrey E. Barrick
- Molecular Biophysics and Biochemistry, and
- Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103
| | - Ronald R. Breaker
- Departments of *Molecular, Cellular, and Developmental Biology and
- Molecular Biophysics and Biochemistry, and
- Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103
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123
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Abstract
Large noncoding RNAs (lncRNAs) have emerged as key players in regulating various fundamental cellular processes. Recent reports identify a functional lncRNA, Evf-2, that operates during development to control the expression of specific homeodomain proteins, and they provide important insights into the mechanism of cooperation between a newly discovered nuclear receptor co-repressor protein (SLIRP) and steroid receptor activator RNA. Evf-2 is the first example of lncRNA directly involved in organogenesis in vertebrates.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/physiology
- Alternative Splicing
- Amino Acid Motifs
- Animals
- Cell Line, Tumor
- Enhancer Elements, Genetic
- Gene Expression Regulation/genetics
- Gene Expression Regulation/physiology
- Genes, Reporter
- Histone Acetyltransferases/genetics
- Histone Acetyltransferases/physiology
- Homeodomain Proteins/genetics
- Homeodomain Proteins/physiology
- Humans
- Mice
- Nuclear Receptor Coactivator 1
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- RNA/genetics
- RNA/physiology
- RNA, Small Interfering/pharmacology
- RNA-Binding Proteins/physiology
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transcription, Genetic/physiology
- Transfection
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Affiliation(s)
- Ilya Shamovsky
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
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124
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Trotochaud AE, Wassarman KM. 6S RNA regulation of pspF transcription leads to altered cell survival at high pH. J Bacteriol 2006; 188:3936-43. [PMID: 16707685 PMCID: PMC1482906 DOI: 10.1128/jb.00079-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6S RNA is a highly abundant small RNA that regulates transcription through direct interaction with RNA polymerase. Here we show that 6S RNA directly inhibits transcription of pspF, which subsequently leads to inhibition of pspABCDE and pspG expression. Cells without 6S RNA are able to survive at elevated pH better than wild-type cells due to loss of 6S RNA-regulation of pspF. This 6S RNA-dependent phenotype is eliminated in pspF-null cells, indicating that 6S RNA effects are conferred through PspF. Similar growth phenotypes are seen when PspF levels are increased in a 6S RNA-independent manner, signifying that changes to pspF expression are sufficient. Changes in survival at elevated pH most likely result from altered expression of pspABCDE and/or pspG, both of which require PspF for transcription and are indirectly regulated by 6S RNA. 6S RNA provides another layer of regulation in response to high pH during stationary phase. We propose that the normal role of 6S RNA at elevated pH is to limit the extent of the psp response under conditions of nutrient deprivation, perhaps facilitating appropriate allocation of diminishing resources.
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Affiliation(s)
- Amy E Trotochaud
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA
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125
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Willkomm DK, Hartmann RK. 6S RNA - an ancient regulator of bacterial RNA polymerase rediscovered. Biol Chem 2006; 386:1273-7. [PMID: 16336121 DOI: 10.1515/bc.2005.144] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The bacterial riboregulator 6S RNA was one of the first non-coding RNAs to be discovered in the late 1960s, but its cellular role remained enigmatic until the year 2000. 6S RNA, only recognized to be ubiquitous among bacteria in 2005, binds to RNA polymerase in a sigma factor-dependent manner to repress transcription from a subgroup of promoters. The common feature of a double-stranded rod with a central bulge has led to the proposal that 6S RNA may mimic an open promoter complex.
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Affiliation(s)
- Dagmar K Willkomm
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany.
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126
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Silvaggi JM, Perkins JB, Losick R. Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol 2006; 188:532-41. [PMID: 16385044 PMCID: PMC1347314 DOI: 10.1128/jb.188.2.532-541.2006] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The process of sporulation in the bacterium Bacillus subtilis is known to involve the programmed activation of several hundred protein-coding genes. Here we report the discovery of previously unrecognized genes under sporulation control that specify small, non-protein-coding RNAs (sRNAs). Genes for sRNAs were identified by transcriptional profiling with a microarray bearing probes for intergenic regions in the genome and by use of a comparative genomics algorithm that predicts regions of conserved RNA secondary structure. The gene for one such sRNA, SurA, which is located in the region between yndK and yndL, was induced at the start of development under the indirect control of the master regulator for entry into sporulation, Spo0A. The gene for a second sRNA, SurC, located in the region between dnaJ and dnaK, was switched on at a late stage of sporulation by the RNA polymerase sigma factor sigmaK, which directs gene transcription in the mother cell compartment of the developing sporangium. Finally, a third intergenic region, that between polC and ylxS, which specified several sRNAs, including two transcripts produced under the control of the forespore-specific sigma factor sigmaG and a third transcript generated by sigmaK, was identified. Our results indicate that the full repertoire of sporulation-specific gene expression involves the activation of multiple genes for small, noncoding RNAs.
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Affiliation(s)
- Jessica M Silvaggi
- Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave., Harvard University, Cambridge, MA 02138, USA
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127
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Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006; 34:635-46. [PMID: 16436800 PMCID: PMC1351373 DOI: 10.1093/nar/gkj469] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 12/12/2022] Open
Abstract
Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.
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Affiliation(s)
- Alexander Hüttenhofer
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria.
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128
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Kettenberger H, Eisenführ A, Brueckner F, Theis M, Famulok M, Cramer P. Structure of an RNA polymerase II–RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat Struct Mol Biol 2005; 13:44-8. [PMID: 16341226 DOI: 10.1038/nsmb1032] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Accepted: 11/03/2005] [Indexed: 11/08/2022]
Abstract
The noncoding RNA B2 and the RNA aptamer FC bind RNA polymerase (Pol) II and inhibit messenger RNA transcription initiation, but not elongation. We report the crystal structure of FC(*), the central part of FC RNA, bound to Pol II. FC(*) RNA forms a double stem-loop structure in the Pol II active center cleft. B2 RNA may bind similarly, as it competes with FC(*) RNA for Pol II interaction. Both RNA inhibitors apparently prevent the downstream DNA duplex and the template single strand from entering the cleft after DNA melting and thus interfere with open-complex formation. Elongation is not inhibited, as nucleic acids prebound in the cleft would exclude the RNA inhibitors. The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.
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Affiliation(s)
- Hubert Kettenberger
- Gene Center, University of Munich, Department of Chemistry and Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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129
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Abstract
AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.
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MESH Headings
- Cloning, Molecular
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Eukaryotic Cells/metabolism
- Gene Expression Regulation, Bacterial
- Genome, Bacterial
- Host Factor 1 Protein/chemistry
- Host Factor 1 Protein/genetics
- Host Factor 1 Protein/metabolism
- Oligonucleotide Array Sequence Analysis
- RNA Processing, Post-Transcriptional
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
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Affiliation(s)
- Jörg Vogel
- Max Planck Institute for Infection Biology, RNA Biology, Schumannstr. 21/22, D-10117 Berlin, Germany.
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130
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Winkler WC. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol 2005; 9:594-602. [PMID: 16226486 DOI: 10.1016/j.cbpa.2005.09.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 09/27/2005] [Indexed: 12/22/2022]
Abstract
Microorganisms use a plethora of genetic strategies to regulate expression of their genes. In recent years there has been an increase in the discovery and characterization of riboswitches, cis-acting regulatory RNAs that function as direct receptors for intracellular metabolites. Nine classes have been uncovered that together regulate many essential biochemical pathways. Two classes, responding to either glucosamine-6-phosphate (GlcN6P) or glycine, have been found to employ novel mechanisms of genetic control. Additionally, progress has been achieved in elucidating molecular details for regulation by the other riboswitches, via X-ray crystallography and biochemical analyses of riboswitch-metabolite interactions. The complete repertoire of metabolite-sensing RNAs and extent of their usage in modern organisms remains to be determined; however, these current data assist in establishing a foundation from which to build future expectations.
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Affiliation(s)
- Wade C Winkler
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA.
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131
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Pichon C, Felden B. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci U S A 2005; 102:14249-54. [PMID: 16183745 PMCID: PMC1242290 DOI: 10.1073/pnas.0503838102] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small RNA (sRNA) genes are expressed in all organisms, primarily as regulators of translation and message stability. We have developed comparative genomic approaches to identify sRNAs that are expressed by Staphylococcus aureus, the most common cause of hospital-acquired infections. This study represents an in-depth analysis of the RNome of a Gram-positive bacterium. A set of sRNAs candidates were identified in silico within intergenic regions, and their expression levels were monitored by using microarrays and confirmed by Northern blot hybridizations. Two sRNAs were also detected directly from purification and RNA sequence determination. In total, at least 12 sRNAs are expressed from the S. aureus genome, five from the core genome and seven from pathogenicity islands that confer virulence and antibiotic resistance. Three sRNAs are present in multiple (two to five) copies. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods. In vitro binding assays indicate that one sRNA encoded within a pathogenicity island is a trans-encoded antisense RNA regulating the expression of target genes at the posttranscriptional level. Some of these RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence.
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Affiliation(s)
- Christophe Pichon
- Biochimie Pharmaceutique, Université de Rennes I, Unité Propre de Recherche de l'Enseignement Supérieur JE 2311, Inserm ESPRI, 2 Avenue du Professeur Léon Bernard, 35043 Rennes, France
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132
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