1
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Fuchs M, Lamm-Schmidt V, Lenče T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F. A network of small RNAs regulates sporulation initiation in Clostridioides difficile. EMBO J 2023:e112858. [PMID: 37140366 DOI: 10.15252/embj.2022112858] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic-resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues and molecular mechanisms that regulate sporulation initiation remain ill-defined. Here, by using RIL-seq to globally capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.
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Affiliation(s)
- Manuela Fuchs
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Vanessa Lamm-Schmidt
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Tina Lenče
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Johannes Sulzer
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Arne Bublitz
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Janet Wackenreuter
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Milan Gerovac
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Franziska Faber
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
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2
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A Sporulation-Specific sRNA Bvs196 Contributing to the Developing Spore in Bacillus velezensis. Microorganisms 2022; 10:microorganisms10051015. [PMID: 35630459 PMCID: PMC9147052 DOI: 10.3390/microorganisms10051015] [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: 04/20/2022] [Revised: 05/07/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Many putative sRNAs have been characterized using bioinformatic analysis and high-throughput sequencing in Gram-positive Bacillus strains, but there are only a few functional studies on the sRNAs involved in the spore formation developmental process. In particular, there is no sRNA confirmed experimentally to regulate the late stages of sporulation. Bvs196 is an sRNA with a length of 294 nucleotides that is abundantly expressed in the stationary phase of several media and independently transcribed in Bacillus velezensis strain PEBA20, as validated by RNA-seq and Northern blot,. It is also confirmed, by qRT-PCR, that Bvs196 is transcribed abundantly throughout the intermediate and late stages of sporulation. Using the gfpmut3a gene transcriptional reporter demonstrates that Bvs196 is expressed specifically in the forespore during sporulation and controlled by σF and σG (mainly by σG). This was observed by fluorescence microscopy and multi-function microplate reader. Further evolutionary conservation analysis found that Bvs196 is widely present in Bacillus with a strongly conserved and stable secondary structure. Resistance phenotypic assays of spores formed from the Bvs196 deletion mutant, the overexpressed Bvs196 mutant, and the wild-type strain revealed that the absence of Bvs196 led to reduced heat and UV resistance and enhanced formaldehyde resistance. We determined, by MST analysis, that Bvs196 can directly interact with spo0A and sspN-tlp mRNAs in vitro, and that short incomplete complementary paired bases affect the binding affinity of Bvs196 to target mRNAs. Our results suggest that Bvs196 is a novel sporulation-specific sRNA of B. velezensis, 294 nt in length, independently transcribed under the control of σF and σG in the forespore during sporulation, and that it affects spore resistance, and is able to directly interact with spo0A and sspN-tlp mRNAs. The remarkable conservation and impressive expression level of Bvs196 imply that it acts as an important conservative regulator, presumably by interacting with many other unknown targets in the forespore, and therefore contributing to spore properties. This work provides new clues for further understanding of the spore formation regulatory network.
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3
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The Heterocyst-Specific Small RNA NsiR1 Regulates the Commitment to Differentiation in Nostoc. Microbiol Spectr 2022; 10:e0227421. [PMID: 35230129 PMCID: PMC9045159 DOI: 10.1128/spectrum.02274-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Heterocysts are specialized cells that filamentous cyanobacteria differentiate for the fixation of atmospheric nitrogen when other nitrogen sources are not available. Heterocyst differentiation at semiregular intervals along the filaments requires complex structural and metabolic changes that are under the control of the master transcriptional regulator HetR. NsiR1 (nitrogen stress-induced RNA 1) is a HetR-dependent noncoding RNA that is expressed from multiple chromosomal copies, some identical, some slightly divergent in sequence, specifically in heterocysts from very early stages of differentiation. We have previously shown that NsiR1 inhibits translation of the overlapping hetF mRNA by an antisense mechanism. Here, we identify alr3234, a hetP-like gene involved in the regulation of commitment (point of no return) to heterocyst differentiation, as a target of NsiR1. A strain overexpressing one of the identical copies of NsiR1 commits to heterocyst development earlier than the wild type. The posttranscriptional regulation exerted by NsiR1 on the expression of two genes involved in heterocyst differentiation and commitment, hetF and alr3234, adds a new level of complexity to the network of transcriptional regulation and protein-protein interactions that participate in heterocyst differentiation. IMPORTANCE Heterocysts are nitrogen-fixing specialized cells that appear at semiregular intervals along cyanobacterial filaments upon nitrogen starvation. The differentiation and patterning of heterocysts is a model for the study of cell differentiation in multicellular prokaryotes. The regulation of differentiation, which is only partially understood, includes transcriptional changes, factor diffusion between cells, and protein-protein interactions. This work describes the identification of a novel target for NsiR1, a small RNA (sRNA) encoded in multiple slightly divergent copies, and shows how different copies of “sibling” sRNAs regulate the expression of different targets involved in one of the few examples of a differentiation process in prokaryotes.
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4
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Ul Haq I, Brantl S, Müller P. A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation. Nucleic Acids Res 2021; 49:10589-10603. [PMID: 34478554 PMCID: PMC8501984 DOI: 10.1093/nar/gkab747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/27/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022] Open
Abstract
SR1 is a dual-function sRNA from Bacillus subtilis. It inhibits translation initiation of ahrC mRNA encoding the transcription activator of the arginine catabolic operons. Base-pairing is promoted by the RNA chaperone CsrA, which induces a slight structural change in the ahrC mRNA to facilitate SR1 binding. Additionally, SR1 encodes the small protein SR1P that interacts with glyceraldehyde-3P dehydrogenase A to promote binding to RNase J1 and enhancing J1 activity. Here, we describe a new target of SR1, kinA mRNA encoding the major histidine kinase of the sporulation phosphorelay. SR1 and kinA mRNA share 7 complementary regions. Base-pairing between SR1 and kinA mRNA decreases kinA translation without affecting kinA mRNA stability and represses transcription of the KinA/Spo0A downstream targets spoIIE, spoIIGA and cotA. The initial interaction between SR1 and kinA mRNA occurs 10 nt downstream of the kinA start codon and is decisive for inhibition. The sr1 encoded peptide SR1P is dispensable for kinA regulation. Deletion of sr1 accelerates sporulation resulting in low quality spores with reduced stress resistance and altered coat protein composition which can be compensated by sr1 overexpression. Neither CsrA nor Hfq influence sporulation or spore properties.
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Affiliation(s)
- Inam Ul Haq
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Sabine Brantl
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Peter Müller
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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5
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Durand S, Callan-Sidat A, McKeown J, Li S, Kostova G, Hernandez-Fernaud JR, Alam MT, Millard A, Allouche D, Constantinidou C, Condon C, Denham EL. Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis. Nucleic Acids Res 2021; 49:6399-6419. [PMID: 34096591 PMCID: PMC8216469 DOI: 10.1093/nar/gkab444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 02/05/2023] Open
Abstract
sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA-RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA-sRNA pairings are rare (compared with sRNA-mRNA), we identify a robust example involving the conserved sRNA RoxS and an unstudied sRNA RosA (Regulator of sRNA A). We show RosA to be the first confirmed RNA sponge described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. The RosA/RoxS interaction not only affects the levels of RoxS but also its processing and regulatory activity. We also found that the transcription of RosA is repressed by CcpA, the key regulator of carbon-metabolism in B. subtilis. Since RoxS is already known to be transcriptionally controlled by malate via the transcriptional repressor Rex, its post-transcriptional regulation by CcpA via RosA places RoxS in a key position to control central metabolism in response to varying carbon sources.
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Affiliation(s)
- Sylvain Durand
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Adam Callan-Sidat
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Josie McKeown
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Stephen Li
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Gergana Kostova
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Juan R Hernandez-Fernaud
- School of Life Sciences, Proteomics Research Technology Platform, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Mohammad Tauqeer Alam
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Andrew Millard
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Delphine Allouche
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chrystala Constantinidou
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Ciarán Condon
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Emma L Denham
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, UK
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6
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Boudry P, Piattelli E, Drouineau E, Peltier J, Boutserin A, Lejars M, Hajnsdorf E, Monot M, Dupuy B, Martin-Verstraete I, Gautheret D, Toffano-Nioche C, Soutourina O. Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile. RNA Biol 2021; 18:1931-1952. [PMID: 33629931 PMCID: PMC8583004 DOI: 10.1080/15476286.2021.1882180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogen Clostridioides (Clostridium) difficile. Some of them are trans-encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq in C. difficile with the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting with C. difficile Hfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs in C. difficile. Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition to trans-encoded RNAs, new categories of Hfq ligands were found including cis-antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile. Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.
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Affiliation(s)
- Pierre Boudry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Emma Piattelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Emilie Drouineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Johann Peltier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Anaïs Boutserin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Maxence Lejars
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Biomics Platform, C2RT, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Institut Universitaire de France (IUF), Paris, France
| | - Daniel Gautheret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Institut Universitaire de France (IUF), Paris, France
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7
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Brenes‐Álvarez M, Minguet M, Vioque A, Muro‐Pastor AM. NsiR1, a smallRNAwith multiple copies, modulates heterocyst differentiation in the cyanobacteriumNostocsp.PCC7120. Environ Microbiol 2020; 22:3325-3338. [DOI: 10.1111/1462-2920.15103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Manuel Brenes‐Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla Spain
| | - Marina Minguet
- Instituto de Bioquímica Vegetal y Fotosíntesis Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla Spain
| | - Alicia M. Muro‐Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla Spain
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8
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Abstract
Small regulatory RNAs are now recognized as key regulators of gene expression in bacteria. They accumulate under specific conditions, most often because their synthesis is directly controlled by transcriptional regulators, including but not limited to alternative sigma factors and response regulators of two-component systems. In turn, small RNAs regulate, mostly at the posttranscriptional level, expression of multiple genes, among which are genes encoding transcriptional regulators. Small RNAs are thus embedded in mixed regulatory circuits combining transcriptional and posttranscriptional controls, and whose properties are discussed here.
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9
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Little GT, Willson BJ, Heap JT, Winzer K, Minton NP. The Butanol Producing MicrobeClostridium beijerinckiiNCIMB 14988 Manipulated Using Forward and Reverse Genetic Tools. Biotechnol J 2018; 13:e1700711. [DOI: 10.1002/biot.201700711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/15/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Gareth T. Little
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Benjamin J. Willson
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - John T. Heap
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
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10
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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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11
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Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR. Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol Cell 2016; 65:220-230. [PMID: 27989440 DOI: 10.1016/j.molcel.2016.11.019] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 01/25/2023]
Abstract
The guanidyl moiety is a component of fundamental metabolites, including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse, and no biological receptors that specifically recognize this compound have been previously identified. We report that many members of the ykkC motif RNA, the longest unresolved riboswitch candidate, naturally sense and respond to guanidine. This RNA is found throughout much of the bacterial domain of life, where it commonly controls the expression of proteins annotated as urea carboxylases and multidrug efflux pumps. Our analyses reveal that these proteins likely function as guanidine carboxylases and guanidine transporters, respectively. Furthermore, we demonstrate that bacteria are capable of endogenously producing guanidine. These and related findings demonstrate that free guanidine is a biologically relevant compound, and several gene families that can alleviate guanidine toxicity exist.
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Affiliation(s)
- James W Nelson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Madeline E Sherlock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Randy B Stockbridge
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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12
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Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression. Microbiol Mol Biol Rev 2016; 80:1029-1057. [PMID: 27784798 DOI: 10.1128/mmbr.00026-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis.
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Panda G, Tanwer P, Ansari S, Khare D, Bhatnagar R. Regulation and RNA-binding properties of Hfq-like RNA chaperones in Bacillus anthracis. Biochim Biophys Acta Gen Subj 2015; 1850:1661-8. [DOI: 10.1016/j.bbagen.2015.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/05/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
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Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N, Nicolas P, Romby P, Condon C. A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis. PLoS Genet 2015; 11:e1004957. [PMID: 25643072 PMCID: PMC4409812 DOI: 10.1371/journal.pgen.1004957] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022] Open
Abstract
RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD+/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5′ end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA. Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms. These signals modify the expression of genes, allowing bacteria to adapt to altered redox environments and to maintain homeostasis. Studies in Enterobacteriaceae have shown that sRNAs play central roles in adaptation to oxidative stress. We show here that the conserved sRNA, RoxS is induced by the presence of nitric oxide (NO) in the medium, through the ResDE and SrrAB two-component systems of Bacillus subtilis and Staphylococcus aureus, respectively. B. subtilis RoxS regulates functions related to oxidation-reduction reactions and acts as an antisense RNA to control translation initiation and the degradation of ppnKB mRNA, encoding an NAD+/NADH kinase. Interestingly, RNase Y processes the 5′ end of the RoxS sRNA leading to a truncated sRNA that in turn interacts more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase. Taken together this work shows that RoxS is part of a complex regulatory network that allows the cell to sense and respond to redox perturbations, and revealed a novel process that allows an expansion of the repertoire of sRNA targets.
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Affiliation(s)
- Sylvain Durand
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Frédérique Braun
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Efthimia Lioliou
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Cédric Romilly
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Anne-Catherine Helfer
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Laurianne Kuhn
- Plateforme Protéomique Esplanade, IBMC, Strasbourg, France
| | - Noé Quittot
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pierre Nicolas
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (CC); (PR)
| | - Ciarán Condon
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
- * E-mail: (CC); (PR)
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Abstract
ABSTRACT
Clostridia are Gram-positive, anaerobic, endospore-forming bacteria, incapable of dissimilatory sulfate reduction. Comprising approximately 180 species, the genus
Clostridium
is one of the largest bacterial genera. Physiology is mostly devoted to acid production. Numerous pathways are known, such as the homoacetate fermentation by acetogens, the propionate fermentation by
Clostridium propionicum
, and the butyrate/butanol fermentation by
C. acetobutylicum
, a well-known solvent producer. Clostridia degrade sugars, alcohols, amino acids, purines, pyrimidines, and polymers such as starch and cellulose. Energy conservation can be performed by substrate-level phosphorylation as well as by the generation of ion gradients. Endospore formation resembles the mechanism elucidated in
Bacillus
. Morphology, contents, and properties of spores are very similar to bacilli endospores. Sporulating clostridia usually form swollen mother cells and accumulate the storage substance granulose. However, clostridial sporulation differs by not employing the so-called phosphorelay. Initiation starts by direct phosphorylation of the master regulator Spo0A. The cascade of sporulation-specific sigma factors is again identical to what is known from
Bacillus
. The onset of sporulation is coupled in some species to either solvent (acetone, butanol) or toxin (e.g.,
C. perfringens
enterotoxin) formation. The germination of spores is often induced by various amino acids, often in combination with phosphate and sodium ions. In medical applications,
C. butyricum
spores are used as a
C. difficile
prophylaxis and as treatment against diarrhea. Recombinant spores are currently under investigation and testing as antitumor agents, because they germinate only in hypoxic tissues (i.e., tumor tissue), allowing precise targeting and direct killing of tumor cells.
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Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile. J Bacteriol 2014; 196:3234-48. [PMID: 24982306 DOI: 10.1128/jb.01923-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. In an effort to understand the function of the RNA chaperone protein Hfq, we constructed and characterized an Hfq-depleted strain in C. difficile. Hfq depletion led to a growth defect, morphological changes, an increased sensitivity to stresses, and a better ability to sporulate and to form biofilms. The transcriptome analysis revealed pleiotropic effects of Hfq depletion on gene expression in C. difficile, including genes encoding proteins involved in sporulation, stress response, metabolic pathways, cell wall-associated proteins, transporters, and transcriptional regulators and genes of unknown function. Remarkably, a great number of genes of the regulon dependent on sporulation-specific sigma factor, SigK, were upregulated in the Hfq-depleted strain. The altered accumulation of several sRNAs and interaction of Hfq with selected sRNAs suggest potential involvement of Hfq in these regulatory RNA functions. Altogether, these results suggest the pleiotropic role of Hfq protein in C. difficile physiology, including processes important for the C. difficile infection cycle, and expand our knowledge of Hfq-dependent regulation in Gram-positive bacteria.
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18
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Dong H, Peng X, Wang N, Wu Q. Identification of novel sRNAs inBrucella abortus2308. FEMS Microbiol Lett 2014; 354:119-25. [DOI: 10.1111/1574-6968.12433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Hao Dong
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiaowei Peng
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Ning Wang
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Qingmin Wu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture; College of Veterinary Medicine; China Agricultural University; Beijing China
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Abstract
Small regulatory RNAs (sRNAs) that act by base-pairing were first discovered in so-called accessory DNA elements—plasmids, phages, and transposons—where they control replication, maintenance, and transposition. Since 2001, a huge body of work has been performed to predict and identify sRNAs in a multitude of bacterial genomes. The majority of chromosome-encoded sRNAs have been investigated in E. coli and other Gram-negative bacteria. However, during the past five years an increasing number of sRNAs were found in Gram-positive bacteria. Here, we outline our current knowledge on chromosome-encoded sRNAs from low-GC Gram-positive species that act by base-pairing, i.e., an antisense mechanism. We will focus on sRNAs with known targets and defined regulatory mechanisms with special emphasis on Bacillus subtilis.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena; Biologisch-Pharmazeutische Fakultät; AG Bakteriengenetik; Philosophenweg 12; Jena, Germany
| | - Reinhold Brückner
- Mikrobiologie; TU Kaiserslautern; Paul-Ehrlich-Str. 23; D-67663 Kaiserslautern, Germany
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20
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Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR. Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol 2013; 9:834-9. [PMID: 24141192 PMCID: PMC3830699 DOI: 10.1038/nchembio.1363] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/10/2013] [Indexed: 11/28/2022]
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a recently discovered bacterial second messenger implicated in the control of cell wall metabolism, osmotic stress responses and sporulation. However, the mechanisms by which c-di-AMP triggers these physiological responses have remained largely unknown. Notably, a candidate riboswitch class called ydaO associates with numerous genes involved in these same processes. Although a representative ydaO motif RNA recently was reported to weakly bind ATP, we report that numerous members of this noncoding RNA class selectively respond to c-di-AMP with subnanomolar affinity. Our findings resolve the mystery regarding the primary ligand for this extremely common riboswitch class and expose a major portion of the super-regulon of genes that are controlled by the widespread bacterial second messenger c-di-AMP.
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Affiliation(s)
- James W. Nelson
- Department of Chemistry, Yale University, Box 208107, New Haven, CT 06520, USA
| | - Narasimhan Sudarsan
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Joy X. Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
| | - Ronald R. Breaker
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520, USA
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Wiegand S, Dietrich S, Hertel R, Bongaerts J, Evers S, Volland S, Daniel R, Liesegang H. RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 2013; 14:667. [PMID: 24079885 PMCID: PMC3871023 DOI: 10.1186/1471-2164-14-667] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/25/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis. RESULTS A detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases. CONCLUSION The hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains.
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Affiliation(s)
- Sandra Wiegand
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Norddeutsches Zentrum für Mikrobielle Genomforschung, Georg-August-Universität Göttingen, Grisebachstr, 8, D-37077 Göttingen, Germany.
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Dambach M, Irnov I, Winkler WC. Association of RNAs with Bacillus subtilis Hfq. PLoS One 2013; 8:e55156. [PMID: 23457461 PMCID: PMC3574147 DOI: 10.1371/journal.pone.0055156] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/23/2012] [Indexed: 11/18/2022] Open
Abstract
The prevalence and characteristics of small regulatory RNAs (sRNAs) have not been well characterized for Bacillus subtilis, an important model system for Gram-positive bacteria. However, B. subtilis was recently found to synthesize many candidate sRNAs during stationary phase. In the current study, we performed deep sequencing on Hfq-associated RNAs and found that a small subset of sRNAs associates with Hfq, an enigmatic RNA-binding protein that stabilizes sRNAs in Gram-negatives, but whose role is largely unknown in Gram-positive bacteria. We also found that Hfq associated with antisense RNAs, antitoxin transcripts, and many mRNA leaders. Several new candidate sRNAs and mRNA leader regions were also discovered by this analysis. Additionally, mRNA fragments overlapping with start or stop codons associated with Hfq, while, in contrast, relatively few full-length mRNAs were recovered. Deletion of hfq reduced the intracellular abundance of several representative sRNAs, suggesting that B. subtilis Hfq-sRNA interactions may be functionally significant in vivo. In general, we anticipate this catalog of Hfq-associated RNAs to serve as a resource in the functional characterization of Hfq in B. subtilis.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/metabolism
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Host Factor 1 Protein/analysis
- Host Factor 1 Protein/genetics
- Host Factor 1 Protein/metabolism
- Open Reading Frames
- RNA, Antisense/analysis
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Michael Dambach
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Irnov Irnov
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Wade C. Winkler
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, United States of America
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23
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Brantl S. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiol 2012; 7:853-71. [DOI: 10.2217/fmb.12.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
sRNAs that act by base pairing were first discovered in plasmids, phages and transposons, where they control replication, maintenance and transposition. Since 2001, however, computational searches were applied that led to the discovery of a plethora of sRNAs in bacterial chromosomes. Whereas the majority of these chromsome-encoded sRNAs have been investigated in Escherichia coli, Salmonella and other Gram-negative bacteria, only a few well-studied examples are known from Gram-positive bacteria. Here, the author summarizes our current knowledge on plasmid- and chromosome-encoded sRNAs from Gram-positive species, thereby focusing on regulatory mechanisms used by these RNAs and their biological role in complex networks. Furthermore, regulatory factors that control the expression of these RNAs will be discussed and differences between sRNAs from Gram-positive and Gram-negative bacteria highlighted. The main emphasis of this review is on sRNAs that act by base pairing (i.e., by an antisense mechanism). Thereby, both plasmid-encoded and chromosome-encoded sRNAs will be considered.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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Esre: a novel essential non-coding RNA in Escherichia coli. FEBS Lett 2012; 586:1195-200. [PMID: 22575655 DOI: 10.1016/j.febslet.2012.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/04/2012] [Accepted: 03/05/2012] [Indexed: 11/21/2022]
Abstract
YigP gene (GeneID: 948915) locates between ubiquinone biosynthetic genes ubiE and ubiB in Escherichia coli. GeneBank annotates yigP as a putative protein-coding gene. In this study, we found a new essential sRNA gene, esre, locates within the region of yigP. The E. coli strain with inactive esre must rely on a complementary plasmid to survive. Moreover, RACE experiments showed esre encodes an RNA molecule of 252 nt. Further experiments revealed esre gene is immune to frame shift mutations and the function of esre depends mostly on the RNA secondary structure, which are typical traits of sRNA. Since it is difficult to predict the target of an essential sRNA, more research is needed to reveal the function and mechanism of esre.
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Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. BMC Genomics 2012; 13:69. [PMID: 22333191 PMCID: PMC3814617 DOI: 10.1186/1471-2164-13-69] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 02/14/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. RESULTS Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. CONCLUSION DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world.
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Ott A, Idali A, Marchais A, Gautheret D. NAPP: the Nucleic Acid Phylogenetic Profile Database. Nucleic Acids Res 2011; 40:D205-9. [PMID: 21984475 PMCID: PMC3245103 DOI: 10.1093/nar/gkr807] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.
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Affiliation(s)
- Alban Ott
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, bâtiment 400, 91405 Orsay Cedex, France
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