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Petushkov I, Elkina D, Burenina O, Kubareva E, Kulbachinskiy A. Key interactions of RNA polymerase with 6S RNA and secondary channel factors during pRNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195032. [PMID: 38692564 DOI: 10.1016/j.bbagrm.2024.195032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
Small non-coding 6S RNA mimics DNA promoters and binds to the σ70 holoenzyme of bacterial RNA polymerase (RNAP) to suppress transcription of various genes mainly during the stationary phase of cell growth or starvation. This inhibition can be relieved upon synthesis of short product RNA (pRNA) performed by RNAP from the 6S RNA template. Here, we have shown that pRNA synthesis depends on specific contacts of 6S RNA with RNAP and interactions of the σ finger with the RNA template in the active site of RNAP, and is also modulated by the secondary channel factors. We have adapted a molecular beacon assay with fluorescently labeled σ70 to analyze 6S RNA release during pRNA synthesis. We found the kinetics of 6S RNA release to be oppositely affected by mutations in the σ finger and in the CRE pocket of core RNAP, similarly to the reported role of these regions in promoter-dependent transcription. Secondary channel factors, DksA and GreB, inhibit pRNA synthesis and 6S RNA release from RNAP, suggesting that they may contribute to the 6S RNA-mediated switch in transcription during stringent response. Our results demonstrate that pRNA synthesis depends on a similar set of contacts between RNAP and 6S RNA as in the case of promoter-dependent transcription initiation and reveal that both processes can be regulated by universal transcription factors acting on RNAP.
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Affiliation(s)
- Ivan Petushkov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria Elkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Olga Burenina
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey Kulbachinskiy
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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2
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Vaňková Hausnerová V, Shoman M, Kumar D, Schwarz M, Modrák M, Jirát Matějčková J, Mikesková E, Neva S, Herrmannová A, Šiková M, Halada P, Novotná I, Pajer P, Valášek LS, Převorovský M, Krásný L, Hnilicová J. RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria. Nucleic Acids Res 2024; 52:4604-4626. [PMID: 38348908 PMCID: PMC11077062 DOI: 10.1093/nar/gkae081] [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: 07/21/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/09/2024] Open
Abstract
Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.
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Affiliation(s)
- Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Mahmoud Shoman
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Dilip Kumar
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Marek Schwarz
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Martin Modrák
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Department of Bioinformatics, Second Faculty of Medicine, Charles University, Prague150 06, Czech Republic
| | - Jitka Jirát Matějčková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Eliška Mikesková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Silvia Neva
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Petr Halada
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Vestec252 50, Czech Republic
| | - Iva Novotná
- Military Health Institute, Military Medical Agency, Prague169 02, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague169 02, Czech Republic
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague128 00, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague142 20, Czech Republic
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague128 44, Czech Republic
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3
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Zhu Y, Ponath F, Cosi V, Vogel J. A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum. Nucleic Acids Res 2024; 52:3950-3970. [PMID: 38281181 DOI: 10.1093/nar/gkae010] [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: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
The common oral microbe Fusobacterium nucleatum has recently drawn attention after it was found to colonize tumors throughout the human body. Fusobacteria are also interesting study systems for bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. To search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that co-purified with 19 different sRNAs. This approach revealed strong enrichment of the KH domain proteins KhpA and KhpB with nearly all tested sRNAs, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the stability of several of their target transcripts. Transcriptome studies combined with biochemical and genetic analyses suggest that KhpA/B have several physiological functions, including being required for ethanolamine utilization. Our RBP search and the discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.
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Affiliation(s)
- Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Valentina Cosi
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg D-97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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Wiegard JC, Damm K, Lechner M, Thölken C, Ngo S, Putzer H, Hartmann RK. Processing and decay of 6S-1 and 6S-2 RNAs in Bacillus subtilis. RNA (NEW YORK, N.Y.) 2023; 29:1481-1499. [PMID: 37369528 PMCID: PMC10578484 DOI: 10.1261/rna.079666.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
Noncoding 6S RNAs regulate transcription by binding to the active site of bacterial RNA polymerase holoenzymes. Processing and decay of 6S-1 and 6S-2 RNA were investigated in Bacillus subtilis by northern blot and RNA-seq analyses using different RNase knockout strains, as well as by in vitro processing assays. For both 6S RNA paralogs, we identified a key-but mechanistically different-role of RNase J1. RNase J1 catalyzes 5'-end maturation of 6S-1 RNA, yet relatively inefficient and possibly via the enzyme's "sliding endonuclease" activity. 5'-end maturation has no detectable effect on 6S-1 RNA function, but rather regulates its decay: The generated 5'-monophosphate on matured 6S-1 RNA propels endonucleolytic cleavage in its apical loop region. The major 6S-2 RNA degradation pathway is initiated by endonucleolytic cleavage in the 5'-central bubble to trigger 5'-to-3'-exoribonucleolytic degradation of the downstream fragment by RNase J1. The four 3'-exonucleases of B. subtilis-RNase R, PNPase, YhaM, and particularly RNase PH-are involved in 3'-end trimming of both 6S RNAs, degradation of 6S-1 RNA fragments, and decay of abortive transcripts (so-called product RNAs, ∼14 nt in length) synthesized on 6S-1 RNA during outgrowth from stationary phase. In the case of the growth-retarded RNase Y deletion strain, we were unable to infer a specific role of RNase Y in 6S RNA decay. Yet, a participation of RNase Y in 6S RNA decay still remains possible, as evidence for such a function may have been obscured by overlapping substrate specificities of RNase Y, RNase J1, and RNase J2.
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Affiliation(s)
- Jana Christin Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Katrin Damm
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Marcus Lechner
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Clemens Thölken
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Harald Putzer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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Li Y, Gao J, Wang Y, Cai J, Wu D, Wang L, Pu W, Yu F, Zhu S. The functions of a 5' tRNA-Ala-derived fragment in gene expression. PLANT PHYSIOLOGY 2023; 193:1126-1141. [PMID: 37350495 DOI: 10.1093/plphys/kiad361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/04/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5' tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
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Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Junping Gao
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Dousheng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, China
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7
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Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou VE. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Front Mol Biosci 2023; 10:1219668. [PMID: 37555016 PMCID: PMC10406553 DOI: 10.3389/fmolb.2023.1219668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs). 6S and its complex with a pRNA were structurally characterized using Small Angle X-ray Scattering. The 3D models of 6S and 6S:pRNA complex presented here, demonstrate that the fairly linear and extended structure of 6S undergoes a major conformational change upon binding to pRNA. In particular, 6S:pRNA complex formation is associated with a compaction of the overall 6S size and an expansion of its central domain. Our structural models are consistent with the hypothesis that the resultant particle has a shape and size incompatible with binding to RNA polymerase-σ70. Overall, by use of an optimized in vivo methodological approach, especially useful for structural studies, our study considerably improves our understanding of the structural basis of 6S regulation by offering a mechanistic glimpse of the 6S transcriptional control.
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Affiliation(s)
- Eleni Makraki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Sophia Miliara
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Michalis Pagkalos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
| | - Vasiliki E. Fadouloglou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Komotini, Greece
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8
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Bonar CD, Han J, Wang R, Panchapakesan SSS, Unrau PJ. E. coli 6S RNA complexed to RNA polymerase maintains product RNA synthesis at low cellular ATP levels by initiation with noncanonical initiator nucleotides. RNA (NEW YORK, N.Y.) 2022; 28:1643-1658. [PMID: 36198425 PMCID: PMC9670815 DOI: 10.1261/rna.079356.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The E. coli 6S RNA is an RNA polymerase (RNAP) inhibitor that competes with σ70-dependent DNA promoters for binding to RNAP holoenzyme (RNAP:σ70). The 6S RNA when bound is then used as a template to synthesize a short product RNA (pRNA; usually 13-nt-long). This pRNA changes the 6S RNA structure, triggering the 6S RNA:pRNA complex to release and allowing DNA-dependent housekeeping gene expression to resume. In high nutrient conditions, 6S RNA turnover is extremely rapid but becomes very slow in low nutrient environments. This leads to a large accumulation of inhibited RNAP:σ70 in stationary phase. As pRNA initiates synthesis with ATP, we and others have proposed that the 6S RNA release rate strongly depends on ATP levels as a proxy for sensing the cellular metabolic state. By purifying endogenous 6S RNA:pRNA complexes using RNA Mango and using reverse transcriptase to generate pRNA-cDNA chimeras, we demonstrate that 6S RNA:pRNA formation can be simultaneous with 6S RNA 5' maturation. More importantly, we find a dramatic accumulation of capped pRNAs during stationary phase. This indicates that ATP levels in stationary phase are low enough for noncanonical initiator nucleotides (NCINs) such as NAD+ and NADH to initiate pRNA synthesis. In vitro, mutation of the conserved 6S RNA template sequence immediately upstream of the pRNA transcriptional start site can increase or decrease the pRNA capping efficiency, suggesting that evolution has tuned the biological 6S RNA sequence for an optimal capping rate. NCIN-initiated pRNA synthesis may therefore be essential for cell viability in low nutrient conditions.
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Affiliation(s)
- Christopher D Bonar
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jonathan Han
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, B.C. V6T 1Z3, Canada
| | - Robert Wang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
- Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shanker Shyam Sundhar Panchapakesan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
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Dissanayaka Mudiyanselage SD, Ma J, Pechan T, Pechanova O, Liu B, Wang Y. A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription. PLoS Pathog 2022; 18:e1010850. [PMID: 36121876 PMCID: PMC9521916 DOI: 10.1371/journal.ppat.1010850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.
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Affiliation(s)
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Olga Pechanova
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
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10
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Mahendran G, Jayasinghe OT, Thavakumaran D, Arachchilage GM, Silva GN. Key players in regulatory RNA realm of bacteria. Biochem Biophys Rep 2022; 30:101276. [PMID: 35592614 PMCID: PMC9111926 DOI: 10.1016/j.bbrep.2022.101276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation. sRNAs emerging as major players in global gene regulatory networks. Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding. RNA thermo sensors for temperature-dependent gene expression. Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.
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Affiliation(s)
- Gowthami Mahendran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Oshadhi T. Jayasinghe
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dhanushika Thavakumaran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA
- PTC Therapeutics Inc, South Plainfield, NJ, 07080, USA
| | - Gayathri N. Silva
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Corresponding author.
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11
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Vaňková Hausnerová V, Marvalová O, Šiková M, Shoman M, Havelková J, Kambová M, Janoušková M, Kumar D, Halada P, Schwarz M, Krásný L, Hnilicová J, Pánek J. Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search. Front Microbiol 2022; 13:848536. [PMID: 35633709 PMCID: PMC9130861 DOI: 10.3389/fmicb.2022.848536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/22/2022] [Indexed: 11/15/2022] Open
Abstract
Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes.
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Affiliation(s)
- Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Olga Marvalová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Mahmoud Shoman
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jarmila Havelková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Milada Kambová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Martina Janoušková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Dilip Kumar
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Halada
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czechia
| | - Marek Schwarz
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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12
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Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase. Noncoding RNA 2022; 8:ncrna8010020. [PMID: 35202093 PMCID: PMC8876501 DOI: 10.3390/ncrna8010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022] Open
Abstract
Here we investigated the refolding of Bacillus subtilis 6S-1 RNA and its release from σA-RNA polymerase (σA-RNAP) in vitro using truncated and mutated 6S-1 RNA variants. Truncated 6S-1 RNAs, only consisting of the central bubble (CB) flanked by two short helical arms, can still traverse the mechanistic 6S RNA cycle in vitro despite ~10-fold reduced σA-RNAP affinity. This indicates that the RNA’s extended helical arms including the ‘−35′-like region are not required for basic 6S-1 RNA functionality. The role of the ‘central bubble collapse helix’ (CBCH) in pRNA-induced refolding and release of 6S-1 RNA from σA-RNAP was studied by stabilizing mutations. This also revealed base identities in the 5’-part of the CB (5’-CB), upstream of the pRNA transcription start site (nt 40), that impact ground state binding of 6S-1 RNA to σA-RNAP. Stabilization of the CBCH by the C44/45 double mutation shifted the pRNA length pattern to shorter pRNAs and, combined with a weakened P2 helix, resulted in more effective release from RNAP. We conclude that formation of the CBCH supports pRNA-induced 6S-1 RNA refolding and release. Our mutational analysis also unveiled that formation of a second short hairpin in the 3′-CB is detrimental to 6S-1 RNA release. Furthermore, an LNA mimic of a pRNA as short as 6 nt, when annealed to 6S-1 RNA, retarded the RNA’s gel mobility and interfered with σA-RNAP binding. This effect incrementally increased with pLNA 7- and 8-mers, suggesting that restricted conformational flexibility introduced into the 5’-CB by base pairing with pRNAs prevents 6S-1 RNA from adopting an elongated shape. Accordingly, atomic force microscopy of free 6S-1 RNA versus 6S-1:pLNA 8- and 14-mer complexes revealed that 6S-1:pRNA hybrid structures, on average, adopt a more compact structure than 6S-1 RNA alone. Overall, our findings also illustrate that the wild-type 6S-1 RNA sequence and structure ensures an optimal balance of the different functional aspects involved in the mechanistic cycle of 6S-1 RNA.
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13
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6S-Like scr3559 RNA Affects Development and Antibiotic Production in Streptomyces coelicolor. Microorganisms 2021; 9:microorganisms9102004. [PMID: 34683325 PMCID: PMC8539372 DOI: 10.3390/microorganisms9102004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Regulatory RNAs control a number of physiological processes in bacterial cells. Here we report on a 6S-like RNA transcript (scr3559) that affects both development and antibiotic production in Streptomyces coelicolor. Its expression is enhanced during the transition to stationary phase. Strains that over-expressed the scr3559 gene region exhibited a shortened exponential growth phase in comparison with a control strain; accelerated aerial mycelium formation and spore maturation; alongside an elevated production of actinorhodin and undecylprodigiosin. These observations were supported by LC-MS analyses of other produced metabolites, including: germicidins, desferrioxamines, and coelimycin. A subsequent microarray differential analysis revealed increased expression of genes associated with the described morphological and physiological changes. Structural and functional similarities between the scr3559 transcript and 6S RNA, and its possible employment in regulating secondary metabolite production are discussed.
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14
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Prezza G, Ryan D, Mädler G, Reichardt S, Barquist L, Westermann AJ. Comparative genomics provides structural and functional insights into Bacteroides RNA biology. Mol Microbiol 2021; 117:67-85. [PMID: 34379855 DOI: 10.1111/mmi.14793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of the RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homologue to have an RNA-related function. We apply an in-silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions, and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic co-conservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.
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Affiliation(s)
- Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Gohar Mädler
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Sarah Reichardt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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15
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Abstract
Viroids are small, single-stranded, circular RNAs infecting plants. Composed of only a few hundred nucleotides and being unable to code for proteins, viroids represent the lowest level of complexity for an infectious agent, even below that of the smallest known viruses. Despite the relatively small size, viroids contain RNA structural elements embracing all the information needed to interact with host factors involved in their infectious cycle, thus providing models for studying structure-function relationships of RNA. Viroids are specifically targeted to nuclei (family Pospiviroidae) or chloroplasts (family Avsunviroidae), where replication based on rolling-circle mechanisms takes place. They move locally and systemically through plasmodesmata and phloem, respectively, and may elicit symptoms in the infected host, with pathogenic pathways linked to RNA silencing and other plant defense responses. In this review, recent advances in the dissection of the complex interplay between viroids and plants are presented, highlighting knowledge gaps and perspectives for future research. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
| | - Ricardo Flores
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Polytechnic University of Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
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16
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Burenina OY, Oretskaya TS, Kubareva EA. Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Gerovac M, Vogel J, Smirnov A. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Front Mol Biosci 2021; 8:661448. [PMID: 33898526 PMCID: PMC8058203 DOI: 10.3389/fmolb.2021.661448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.
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Affiliation(s)
- Milan Gerovac
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Alexandre Smirnov
- UMR 7156—Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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18
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A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. mBio 2021; 12:mBio.03454-20. [PMID: 33563827 PMCID: PMC8545117 DOI: 10.1128/mbio.03454-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.
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19
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Wang Y. Current view and perspectives in viroid replication. Curr Opin Virol 2021; 47:32-37. [PMID: 33460914 DOI: 10.1016/j.coviro.2020.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. The noncoding nature indicates that viroids must harness their RNA genomes to redirect host machinery for infection. Therefore, the viroid model provides invaluable opportunities for delineating fundamental principles of RNA structure-function relationships and for dissecting the composition and mechanism of RNA-related cellular machinery. There are two viroid families, Pospiviroidae and Avsunviroidae. Members of both families replicate via the RNA-based rolling-circle mechanism with some variations. Viroid replication is generally divided into three steps: transcription, cleavage, and ligation. Decades of studies have uncovered numerous viroid RNA structures with a regulatory role in replication and multiple enzymes critical for the three replication steps. This review discusses these findings and highlights the latest discoveries. Future studies will continue to elucidate regulatory factors and mechanism of host machinery exploited by viroids and provide new insights into host-viroid interactions in the context of pathogenesis.
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Affiliation(s)
- Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA.
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20
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Pei HH, Hilal T, Chen ZA, Huang YH, Gao Y, Said N, Loll B, Rappsilber J, Belogurov GA, Artsimovitch I, Wahl MC. The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Nat Commun 2020; 11:6418. [PMID: 33339827 PMCID: PMC7749165 DOI: 10.1038/s41467-020-20159-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA polymerases (RNAPs) can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. In Bacillus subtilis, the RNAP δ subunit and NTPase HelD have been implicated in RNAP recycling. We structurally analyzed Bacillus subtilis RNAP-δ-HelD complexes. HelD has two long arms: a Gre cleavage factor-like coiled-coil inserts deep into the RNAP secondary channel, dismantling the active site and displacing RNA, while a unique helical protrusion inserts into the main channel, prying the β and β' subunits apart and, aided by δ, dislodging DNA. RNAP is recycled when, after releasing trapped nucleic acids, HelD dissociates from the enzyme in an ATP-dependent manner. HelD abundance during slow growth and a dimeric (RNAP-δ-HelD)2 structure that resembles hibernating eukaryotic RNAP I suggest that HelD might also modulate active enzyme pools in response to cellular cues.
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Affiliation(s)
- Hao-Hong Pei
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany
| | - Tarek Hilal
- Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy and Core Facility BioSupraMol, Freie Universität Berlin, Fabeckstr. 36a, 14195, Berlin, Germany
| | - Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Yong-Heng Huang
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany
| | - Yuan Gao
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany
| | - Nelly Said
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany
| | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
- University of Edinburgh, Wellcome Centre for Cell Biology, Edinburgh, EH9 3BF, UK
| | | | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraβe 6, 14195, Berlin, Germany.
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489, Berlin, Germany.
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21
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Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti. J Microbiol 2020; 58:945-956. [PMID: 33125669 DOI: 10.1007/s12275-020-0283-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ∼13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ∼75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.
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22
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Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol 2020; 19:95-109. [PMID: 33122819 DOI: 10.1038/s41579-020-00450-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. Diverse mechanisms are used among and within the different branches to regulate transcription initiation. Mechanistic studies of transcription initiation in bacteria are especially amenable because the promoter recognition and melting steps are much less complicated than in eukaryotes or archaea. Also, bacteria have critical roles in human health as pathogens and commensals, and the bacterial RNA polymerase is a proven target for antibiotics. Recent biophysical studies of RNA polymerases and their inhibition, as well as transcription initiation and transcription factors, have detailed the mechanisms of transcription initiation in phylogenetically diverse bacteria, inspiring this Review to examine unifying and diverse themes in this process.
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23
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Ryan D, Prezza G, Westermann AJ. An RNA-centric view on gut Bacteroidetes. Biol Chem 2020; 402:55-72. [PMID: 33544493 DOI: 10.1515/hsz-2020-0230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/21/2020] [Indexed: 01/26/2023]
Abstract
Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany.,Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
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24
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Thüring M, Ganapathy S, Schlüter MAC, Lechner M, Hartmann RK. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol 2020; 18:79-92. [PMID: 32862759 DOI: 10.1080/15476286.2020.1795408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Bacterial 6S RNA regulates transcription via binding to the active site of RNA polymerase holoenzymes. 6S RNA has been identified in the majority of bacteria, in most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two 6S RNA paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that the regulatory role of 6S RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed 6S RNA deletion mutants of the undomesticated B. subtilis wild-type strain NCIB 3610. We observed a strong phenotype for the ∆6S-2 RNA strain that showed increased biofilm formation on solid media and the ability to form surface-attached biofilms in liquid culture. This phenotype remained undetected in derived laboratory strains (168, PY79) that are defective in biofilm formation. Quantitative RT-PCR data revealed transcriptional upregulation of biofilm marker genes such as tasA, epsA and bslA in the ∆6S-2 RNA strain, particularly during transition from exponential to stationary growth phase. Salt stress, which blocks sporulation at a very early stage, was found to override the derepressed biofilm phenotype of the ∆6S-2 RNA strain. Furthermore, the ∆6S-2 RNA strain showed retarded swarming activity and earlier spore formation. Finally, the ∆6S-1&2 RNA double deletion strain showed a prolonged lag phase of growth under oxidative, high salt and alkaline stress conditions, suggesting that the interplay of both 6S RNAs in B. subtilis optimizes and fine-tunes transcriptomic adaptations, thereby contributing to the fitness of B. subtilis under the unsteady and temporarily harsh conditions encountered in natural habitats.
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Affiliation(s)
- Marietta Thüring
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Sweetha Ganapathy
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - M Amri C Schlüter
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Bioinformatics Core Facility , Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
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25
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Jain N, Blauch LR, Szymanski MR, Das R, Tang SKY, Yin YW, Fire AZ. Transcription polymerase-catalyzed emergence of novel RNA replicons. Science 2020; 368:eaay0688. [PMID: 32217750 PMCID: PMC7445081 DOI: 10.1126/science.aay0688] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Transcription polymerases can exhibit an unusual mode of regenerating certain RNA templates from RNA, yielding systems that can replicate and evolve with RNA as the information carrier. Two classes of pathogenic RNAs (hepatitis delta virus in animals and viroids in plants) are copied by host transcription polymerases. Using in vitro RNA replication by the transcription polymerase of T7 bacteriophage as an experimental model, we identify hundreds of new replicating RNAs, define three mechanistic hallmarks of replication (subterminal de novo initiation, RNA shape-shifting, and interrupted rolling-circle synthesis), and describe emergence from DNA seeds as a mechanism for the origin of novel RNA replicons. These results inform models for the origins and replication of naturally occurring RNA genetic elements and suggest a means by which diverse RNA populations could be propagated as hereditary material in cellular contexts.
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Affiliation(s)
- Nimit Jain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lucas R Blauch
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Michal R Szymanski
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Y Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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26
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Evidence Supporting That RNA Polymerase II Catalyzes De Novo Transcription Using Potato Spindle Tuber Viroid Circular RNA Templates. Viruses 2020; 12:v12040371. [PMID: 32230827 PMCID: PMC7232335 DOI: 10.3390/v12040371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Transcription is a fundamental process that mediates the interplay between genetic information and phenotype. Emerging evidence indicates that RNA polymerase II (Pol II) can catalyze transcription using both DNA and RNA templates. It is well established that Pol II initiates de novo transcription on DNA templates. However, it is unclear whether Pol II performs de novo transcription or relies on primers for initiation (primed transcription) on RNA templates. Using potato spindle tuber viroid (PSTVd) as a model, we presented evidence showing that circular PSTVd templates are critical for the synthesis of longer-than-unit-length (-)-strand products, which supports the de novo transcription based on the asymmetric rolling circle model of PSTVd replication. We further showed that the crucial factor for primed transcription, transcription factor IIS (TFIIS), is dispensable for PSTVd replication in cells. Together, our data support the de novo transcription on PSTVd RNA templates catalyzed by Pol II. This result has significant implications in understanding the mechanism and machinery underlying Pol II-catalyzed transcription using other RNA templates.
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27
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Fang X, Liu Y, Zhao Y, Chen Y, Liu R, Qin QL, Li G, Zhang YZ, Chan W, Hess WR, Zeng Q. Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products. Environ Microbiol 2019; 21:2015-2028. [PMID: 30585375 DOI: 10.1111/1462-2920.14513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Viral infection of marine phytoplankton releases a variety of dissolved organic matter (DOM). The impact of viral DOM (vDOM) on the uninfected co-occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of vDOM on the cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. Using Prochlorococcus MIT9313, we showed that its growth was not affected by vDOM, but many tRNAs increased in abundance. We tested tRNA-gly and found that its abundance increased upon addition of glycine. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds in vDOM. Addition of vDOM to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO2 fixation while increasing its respiration rate, consistent with differentially abundant transcripts related to photosynthesis and respiration. One of the highest positive fold-changes was observed for the 6S RNA, a noncoding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds.
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Affiliation(s)
- Xiaoting Fang
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yaxin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yao Zhao
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yue Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Riyue Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qi-Long Qin
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology (CAS), Guangzhou, China
| | - Yu-Zhong Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Germany
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,HKUST Shenzhen Research Institute, Shenzhen, China
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28
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Esyunina D, Pupov D, Kulbachinskiy A. Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase. FEBS Lett 2018; 593:361-368. [PMID: 30536890 DOI: 10.1002/1873-3468.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Bacterial RNA polymerase (RNAP) serves as a primase during replication of single-stranded plasmids and filamentous phages. Primer RNA (prRNA) synthesis from the origin regions of these replicons depends on the σ factor that normally participates in promoter recognition. However, it was proposed that σ may not be required for origin recognition but is rather involved in RNA extension by RNAP. Here, by analyzing the natural replication origin of bacteriophage M13 and synthetic ssDNA templates, we show that interactions of σ with promoter-like motifs stabilize priming complexes and can control prRNA synthesis by trapping RNAP on the template. Thus, the σ factor is involved in both DNA recognition and RNA priming, unifying its functions in transcription initiation from double- and single-stranded templates.
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Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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29
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Šiková M, Janoušková M, Ramaniuk O, Páleníková P, Pospíšil J, Bartl P, Suder A, Pajer P, Kubičková P, Pavliš O, Hradilová M, Vítovská D, Šanderová H, Převorovský M, Hnilicová J, Krásný L. Ms1 RNA increases the amount of RNA polymerase in Mycobacterium smegmatis. Mol Microbiol 2018; 111:354-372. [PMID: 30427073 DOI: 10.1111/mmi.14159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2018] [Indexed: 01/13/2023]
Abstract
Ms1 is a sRNA recently found in mycobacteria and several other actinobacterial species. Ms1 interacts with the RNA polymerase (RNAP) core devoid of sigma factors, which differs from 6S RNA that binds to RNAP holoenzymes containing the primary sigma factor. Here we show that Ms1 is the most abundant non-rRNA transcript in stationary phase in Mycobacterium smegmatis. The accumulation of Ms1 stems from its high-level synthesis combined with decreased degradation. We identify the Ms1 promoter, PMs1 , and cis-acting elements important for its activity. Furthermore, we demonstrate that PNPase (an RNase) contributes to the differential accumulation of Ms1 during growth. Then, by comparing the transcriptomes of wt and ΔMs1 strains from stationary phase, we reveal that Ms1 affects the intracellular level of RNAP. The absence of Ms1 results in decreased levels of the mRNAs encoding β and β' subunits of RNAP, which is also reflected at the protein level. Thus, the ΔMs1 strain has a smaller pool of RNAPs available when the transcriptional demand increases. This contributes to the inability of the ΔMs1 strain to rapidly react to environmental changes during outgrowth from stationary phase.
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Affiliation(s)
- Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Janoušková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague, Czech Republic
| | - Olga Ramaniuk
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Páleníková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Pospíšil
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Bartl
- Faculty of Nuclear Science and Physical Engineering, Department of Nuclear Chemistry, Czech Technical University in Prague, Prague, Czech Republic
| | - Agnieszka Suder
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Pavla Kubičková
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Ota Pavliš
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Miluše Hradilová
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Dragana Vítovská
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Převorovský
- Faculty of Science, Department of Cell Biology, Charles University, Prague, Czech Republic
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
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30
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Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA. G3-GENES GENOMES GENETICS 2018; 8:2079-2089. [PMID: 29686109 PMCID: PMC5982834 DOI: 10.1534/g3.118.200265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In Escherichia coli, the sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, while σ38 directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ70, and the non-coding 6S RNA which binds to the RNA polymerase-σ70 holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show that Rsd and 6S RNA facilitate σ38 activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.
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31
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Wassarman KM. 6S RNA, a Global Regulator of Transcription. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0019-2018. [PMID: 29916345 PMCID: PMC6013841 DOI: 10.1128/microbiolspec.rwr-0019-2018] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 01/06/2023] Open
Abstract
6S RNA is a small RNA regulator of RNA polymerase (RNAP) that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNAP resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity, including (i) addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; (ii) the nature of the 6S RNA-RNAP interaction through examination of variant proteins and mutant RNAs, cross-linking approaches, and ultimately a cryo-electron microscopic structure; (iii) the physiological consequences of 6S RNA function through identification of the 6S RNA regulon and promoter features that determine 6S RNA sensitivity; and (iv) the mechanism and cellular impact of 6S RNA-directed synthesis of product RNAs (i.e., pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action, and how it is regulated; yet much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53562
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32
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Greenlee EB, Stav S, Atilho RM, Brewer KI, Harris KA, Malkowski SN, Mirihana Arachchilage G, Perkins KR, Sherlock ME, Breaker RR. Challenges of ligand identification for the second wave of orphan riboswitch candidates. RNA Biol 2018; 15:377-390. [PMID: 29135333 PMCID: PMC5927730 DOI: 10.1080/15476286.2017.1403002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022] Open
Abstract
Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn2+, and the metabolites guanidine and PRPP. Such studies also yield useful linkages between the ligands sensed by the riboswitches and numerous biochemical pathways. In the current report, we describe the known characteristics of 30 distinct classes of orphan riboswitch candidates - some of which have remained unsolved for over a decade. We also discuss the prospects for uncovering novel biological insights via focused studies on these RNAs. Lastly, we make recommendations for experimental objectives along the path to finding ligands for these mysterious RNAs.
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Affiliation(s)
- Etienne B. Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ruben M. Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kenneth I. Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kimberly A. Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | | | - Kevin R. Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Madeline E. Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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33
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6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiol 2017; 17:229. [PMID: 29216826 PMCID: PMC5721685 DOI: 10.1186/s12866-017-1137-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria. Electronic supplementary material The online version of this article (10.1186/s12866-017-1137-9) contains supplementary material, which is available to authorized users.
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34
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Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 2017; 68:388-397.e6. [PMID: 28988932 DOI: 10.1016/j.molcel.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023]
Abstract
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ70-holoenzyme (Eσ70) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ70 determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
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Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shili Feng
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Leon
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zongli Li
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
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35
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Panchapakesan SSS, Ferguson ML, Hayden EJ, Chen X, Hoskins AA, Unrau PJ. Ribonucleoprotein purification and characterization using RNA Mango. RNA (NEW YORK, N.Y.) 2017; 23:1592-1599. [PMID: 28747322 PMCID: PMC5602116 DOI: 10.1261/rna.062166.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/12/2017] [Indexed: 05/04/2023]
Abstract
The characterization of RNA-protein complexes (RNPs) is a difficult but increasingly important problem in modern biology. By combining the compact RNA Mango aptamer with a fluorogenic thiazole orange desthiobiotin (TO1-Dtb or TO3-Dtb) ligand, we have created an RNA tagging system that simplifies the purification and subsequent characterization of endogenous RNPs. Mango-tagged RNP complexes can be immobilized on a streptavidin solid support and recovered in their native state by the addition of free biotin. Furthermore, Mango-based RNP purification can be adapted to different scales of RNP isolation ranging from pull-down assays to the isolation of large amounts of biochemically defined cellular RNPs. We have incorporated the Mango aptamer into the S. cerevisiae U1 small nuclear RNA (snRNA), shown that the Mango-snRNA is functional in cells, and used the aptamer to pull down a U1 snRNA-associated protein. To demonstrate large-scale isolation of RNPs, we purified and characterized bacterial RNA polymerase holoenzyme (HE) in complex with a Mango-containing 6S RNA. We were able to use the combination of a red-shifted TO3-Dtb ligand and eGFP-tagged HE to follow the binding and release of the 6S RNA by two-color native gel analysis as well as by single-molecule fluorescence cross-correlation spectroscopy. Together these experiments demonstrate how the Mango aptamer in conjunction with simple derivatives of its flurophore ligands enables the purification and characterization of endogenous cellular RNPs in vitro.
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Affiliation(s)
- Shanker Shyam S Panchapakesan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew L Ferguson
- Department of Physics, Boise State University, Boise, Idaho 83725, USA
- Department of Biological Science and Biomolecular Sciences Graduate Program, Boise State University, Boise, Idaho 83725, USA
| | - Eric J Hayden
- Department of Biological Science and Biomolecular Sciences Graduate Program, Boise State University, Boise, Idaho 83725, USA
| | - Xin Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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36
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Elkina D, Weber L, Lechner M, Burenina O, Weisert A, Kubareva E, Hartmann RK, Klug G. 6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. RNA Biol 2017; 14:1627-1637. [PMID: 28692405 DOI: 10.1080/15476286.2017.1342933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ΔssrS strain when grown in the presence of 250 mM NaCl.
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Affiliation(s)
- Daria Elkina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Lennart Weber
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Marcus Lechner
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Olga Burenina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Andrea Weisert
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Elena Kubareva
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Roland K Hartmann
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Gabriele Klug
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
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37
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Choi YS, Edwards LO, DiBello A, Jose AM. Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs. Nucleic Acids Res 2017; 45:e87. [PMID: 28180294 PMCID: PMC5449620 DOI: 10.1093/nar/gkx091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/02/2017] [Indexed: 12/21/2022] Open
Abstract
Changes in small non-coding RNAs such as micro RNAs (miRNAs) can serve as indicators of disease and can be measured using next-generation sequencing of RNA (RNA-seq). Here, we highlight the need for approaches that complement RNA-seq, discover that northern blotting of small RNAs is biased against short sequences and develop a protocol that removes this bias. We found that multiple small RNA-seq datasets from the worm Caenorhabditis elegans had shorter forms of miRNAs that appear to be degradation products that arose during the preparatory steps required for RNA-seq. When using northern blotting during these studies, we discovered that miRNA-length probes can have ∼1000-fold bias against detecting even synthetic sequences that are 8 nt shorter. By using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable nearly equivalent detection of 24 to 14 nt RNAs. Our protocol can discriminate RNAs that differ by a single nucleotide and can detect specific miRNAs present in total RNA from C. elegans and pRNAs in total RNA from bacteria. This improved northern blotting is particularly useful to analyze products of RNA processing or turnover, and functional RNAs that are shorter than typical miRNAs.
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Affiliation(s)
- Yun S Choi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Lanelle O Edwards
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Aubrey DiBello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College, Park, MD 20742, USA
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. RNA Biol 2016; 13:177-95. [PMID: 26580233 PMCID: PMC4829319 DOI: 10.1080/15476286.2015.1110674] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
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Affiliation(s)
- Anaïs Le Rhun
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Yan Yan Beer
- b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Johan Reimegård
- c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden
| | - Krzysztof Chylinski
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria
| | - Emmanuelle Charpentier
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.,e Hannover Medical School (MHH), D-30625 , Hannover , Germany.,f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany
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40
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Chen H, Dutta T, Deutscher MP. Growth Phase-dependent Variation of RNase BN/Z Affects Small RNAs: REGULATION OF 6S RNA. J Biol Chem 2016; 291:26435-26442. [PMID: 27875308 DOI: 10.1074/jbc.m116.757450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/07/2016] [Indexed: 01/01/2023] Open
Abstract
RNase BN, the RNase Z family member in E. coli, can participate in the processing of tRNA precursors. However, this function only becomes apparent when other processing enzymes are absent, raising the question of its primary physiological role. Here, we show that RNase BN itself is subject to growth phase-dependent regulation, because both rbn mRNA and RNase BN protein are at their highest levels in early exponential phase, but then decrease dramatically and are essentially absent in stationary phase. As a consequence of this variation, certain small RNAs, such as 6S RNA, remain low in exponential phase cells, and increase greatly in stationary phase. RNase BN affects 6S RNA abundance by decreasing its stability in exponential phase. RNase BN levels increase rapidly as cells exit stationary phase and are primarily responsible for the decrease in 6S RNA that accompanies this process. Purified RNase BN directly cleaves 6S RNA as shown by in vitro assays, and the 6S RNA:pRNA duplex is an even more favorable substrate of RNase BN. The exoribonuclease activity of RNase BN is unnecessary because all its action on 6S RNA is due to endonucleolytic cleavages. These data indicate that RNase BN plays an important role in determining levels of the global transcription regulator, 6S RNA, throughout the growth cycle.
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Affiliation(s)
- Hua Chen
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Tanmay Dutta
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Murray P Deutscher
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
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41
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Bergkessel M, Basta DW, Newman DK. The physiology of growth arrest: uniting molecular and environmental microbiology. Nat Rev Microbiol 2016; 14:549-62. [PMID: 27510862 PMCID: PMC10069271 DOI: 10.1038/nrmicro.2016.107] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Most bacteria spend the majority of their time in prolonged states of very low metabolic activity and little or no growth, in which electron donors, electron acceptors and/or nutrients are limited, but cells are poised to undergo rapid division cycles when resources become available. These non-growing states are far less studied than other growth states, which leaves many questions regarding basic bacterial physiology unanswered. In this Review, we discuss findings from a small but diverse set of systems that have been used to investigate how growth-arrested bacteria adjust metabolism, regulate transcription and translation, and maintain their chromosomes. We highlight major questions that remain to be addressed, and suggest that progress in answering them will be aided by recent methodological advances and by dialectic between environmental and molecular microbiology perspectives.
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42
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Wang Y, Qu J, Ji S, Wallace AJ, Wu J, Li Y, Gopalan V, Ding B. A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II. THE PLANT CELL 2016; 28:1094-107. [PMID: 27113774 PMCID: PMC4904678 DOI: 10.1105/tpc.16.00100] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/11/2016] [Accepted: 04/22/2016] [Indexed: 05/05/2023]
Abstract
Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP PSTVd replication in the nucleoplasm generates (-)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (-)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes.
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Affiliation(s)
- Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210
| | - Jie Qu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210
| | - Shaoyi Ji
- College of Life Sciences, Peking University, Beijing, China
| | - Andrew J Wallace
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210
| | - Jian Wu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Yi Li
- College of Life Sciences, Peking University, Beijing, China
| | - Venkat Gopalan
- The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Biao Ding
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210 Center for Applied Plant Sciences, Ohio State University, Columbus, Ohio 43210 Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
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43
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Hoch PG, Schlereth J, Lechner M, Hartmann RK. Bacillus subtilis 6S-2 RNA serves as a template for short transcripts in vivo. RNA (NEW YORK, N.Y.) 2016; 22:614-622. [PMID: 26873600 PMCID: PMC4793215 DOI: 10.1261/rna.055616.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The global transcriptional regulator 6S RNA is abundant in a broad range of bacteria. The RNA competes with DNA promoters for binding to the housekeeping RNA polymerase (RNAP) holoenzyme. When bound to RNAP, 6S RNA serves as a transcription template for RNAP in an RNA-dependent RNA polymerization reaction. The resulting short RNA transcripts (so-called product RNAs = pRNAs) can induce a stable structural rearrangement of 6S RNA when reaching a certain length. This rearrangement leads to the release of RNAP and thus the recovery of transcription at DNA promoters. While most bacteria express a single 6S RNA, some harbor a second 6S RNA homolog (termed 6S-2 RNA in Bacillus subtilis). Bacillus subtilis 6S-2 RNA was recently shown to exhibit essentially all hallmark features of a bona fide 6S RNA in vitro, but evidence for the synthesis of 6S-2 RNA-derived pRNAs in vivo has been lacking so far. This raised the question of whether the block of RNAP by 6S-2 RNA might be lifted by a mechanism other than pRNA synthesis. However, here we demonstrate that 6S-2 RNA is able to serve as a template for pRNA synthesis in vivo. We verify this finding by using three independent approaches including a novel primer extension assay. Thus, we demonstrate the first example of an organism that expresses two distinct 6S RNAs that both exhibit all mechanistic features defined for this type of regulatory RNA.
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Affiliation(s)
- Philipp G Hoch
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Julia Schlereth
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
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44
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Fadouloglou VE, Lin HTV, Tria G, Hernández H, Robinson CV, Svergun DI, Luisi BF. Maturation of 6S regulatory RNA to a highly elongated structure. FEBS J 2015; 282:4548-64. [PMID: 26367381 PMCID: PMC7610929 DOI: 10.1111/febs.13516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 09/04/2015] [Accepted: 09/10/2015] [Indexed: 12/11/2022]
Abstract
As bacterial populations leave the exponential growth phase and enter the stationary phase, their patterns of gene expression undergo marked changes. A key effector of this change is 6S RNA, which is a highly conserved regulatory RNA that impedes the transcription of genes associated with exponential growth by forming an inactivating ternary complex with RNA polymerase and sigma factor σ(70) (σ(70)-RNAP). In Escherichia coli, the endoribonuclease RNase E generates 6S RNA by specific cleavage of a precursor that is nearly twice the size of the 58 kDa mature form. We have explored recognition of the precursor by RNase E, and observed that processing is inhibited under conditions of excess substrate. This finding supports a largely distributive mechanism, meaning that each round of catalysis results in enzyme dissociation and re-binding to the substrate. We show that the precursor molecule and the mature 6S share a structural core dominated by an A-type helix, indicating that processing is not accompanied by extensive refolding. Both precursor and mature forms of 6S have a highly stable secondary structure, adopt an elongated shape, and show the potential to form dimers under specific conditions; nonetheless, 6S has a high structural plasticity that probably enables it to be structurally adapted upon binding to its cognate protein partners. Analysis of the 6S-σ(70)-RNAP complex by native mass spectrometry reveals a stable association with a stoichiometry of 1:1:1. A theoretical 3D model of mature 6S is presented, which is consistent with the experimental data and supports a previously proposed structure with a small stem-loop inside the central bubble.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Biochemistry, University of Cambridge, UK
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Outstation, European Molecular Biology Laboratory/Deutsches Elektronen Synchrotron, Hamburg, Germany
| | | | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, European Molecular Biology Laboratory/Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, UK
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45
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van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate. Nucleic Acids Res 2015; 44:2577-92. [PMID: 26609136 PMCID: PMC4824073 DOI: 10.1093/nar/gkv1302] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/08/2015] [Indexed: 11/23/2022] Open
Abstract
Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAP in vivo and in vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins.
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Affiliation(s)
- Rob W van Nues
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
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46
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Burenina OY, Elkina DA, Hartmann RK, Oretskaya TS, Kubareva EA. Small noncoding 6S RNAs of bacteria. BIOCHEMISTRY (MOSCOW) 2015; 80:1429-46. [DOI: 10.1134/s0006297915110048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Mondragón E, Maher LJ. Anti-Transcription Factor RNA Aptamers as Potential Therapeutics. Nucleic Acid Ther 2015; 26:29-43. [PMID: 26509637 PMCID: PMC4753637 DOI: 10.1089/nat.2015.0566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.
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Affiliation(s)
- Estefanía Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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48
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Abstract
6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.
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Affiliation(s)
- Stefanie Wehner
- a Department for Bioinformatics; Faculty of Mathematics and Computer Science ; Friedrich-Schiller-University of Jena , Jena , Germany
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49
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Oliva G, Sahr T, Buchrieser C. Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev 2015; 39:331-349. [DOI: 10.1093/femsre/fuv022] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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50
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Köhler K, Duchardt-Ferner E, Lechner M, Damm K, Hoch PG, Salas M, Hartmann RK. Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus. Biochimie 2015; 117:72-86. [PMID: 25771336 DOI: 10.1016/j.biochi.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/03/2015] [Indexed: 01/26/2023]
Abstract
Bacterial 6S RNAs competitively inhibit binding of RNA polymerase (RNAP) holoenzymes to DNA promoters, thereby globally regulating transcription. RNAP uses 6S RNA itself as a template to synthesize short transcripts, termed pRNAs (product RNAs). Longer pRNAs (approx. ≥ 10 nt) rearrange the 6S RNA structure and thereby disrupt the 6S RNA:RNAP complex, which enables the enzyme to resume transcription at DNA promoters. We studied 6S RNA of the hyperthermophilic bacterium Aquifex aeolicus, representing the thermodynamically most stable 6S RNA known so far. Applying structure probing and NMR, we show that the RNA adopts the canonical rod-shaped 6S RNA architecture with little structure formation in the central bulge (CB) even at moderate temperatures (≤37 °C). 6S RNA:pRNA complex formation triggers an internal structure rearrangement of 6S RNA, i.e. formation of a so-called central bulge collapse (CBC) helix. The persistence of several characteristic NMR imino proton resonances upon pRNA annealing demonstrates that defined helical segments on both sides of the CB are retained in the pRNA-bound state, thus representing a basic framework of the RNA's architecture. RNA-seq analyses revealed pRNA synthesis from 6S RNA in A. aeolicus, identifying 9 to ∼17-mers as the major length species. A. aeolicus 6S RNA can also serve as a template for in vitro pRNA synthesis by RNAP from the mesophile Bacillus subtilis. Binding of a synthetic pRNA to A. aeolicus 6S RNA blocks formation of 6S RNA:RNAP complexes. Our findings indicate that A. aeolicus 6S RNA function in its hyperthermophilic host is mechanistically identical to that of other bacterial 6S RNAs. The use of artificial pRNA variants, designed to disrupt helix P2 from the 3'-CB instead of the 5'-CB but preventing formation of the CBC helix, indicated that the mechanism of pRNA-induced RNAP release has been evolutionarily optimized for transcriptional pRNA initiation in the 5'-CB.
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MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Base Sequence
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Bacterial
- Hot Temperature
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- RNA Stability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sequence Analysis, RNA
- Substrate Specificity
- Transcription, Genetic
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Affiliation(s)
- Karen Köhler
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Elke Duchardt-Ferner
- Goethe-Universität Frankfurt am Main, Institut für Molekulare Biowissenschaften, Max-von-Laue-Straße 9, D-60438 Frankfurt am Main, Germany; Zentrum für biomagnetische Resonanzspektroskopie (BMRZ), Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.
| | - Marcus Lechner
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Katrin Damm
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Philipp G Hoch
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Margarita Salas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| | - Roland K Hartmann
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
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