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Bandyra KJ, Fröhlich KS, Vogel J, Rodnina M, Goyal A, Luisi B. Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance. Nucleic Acids Res 2024; 52:9161-9173. [PMID: 38842944 PMCID: PMC11347162 DOI: 10.1093/nar/gkae455] [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: 11/02/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 08/28/2024] Open
Abstract
The ompD transcript, encoding an outer membrane porin in Salmonella, harbors a controlling element in its coding region that base-pairs imperfectly with a 'seed' region of the small regulatory RNA (sRNA) MicC. When tagged with the sRNA, the ompD mRNA is cleaved downstream of the pairing site by the conserved endoribonuclease RNase E, leading to transcript destruction. We observe that the sRNA-induced cleavage site is accessible to RNase E in vitro upon recruitment of ompD into the 30S translation pre-initiation complex (PIC) in the presence of the degradosome components. Evaluation of substrate accessibility suggests that the paused 30S PIC presents the mRNA for targeted recognition and degradation. Ribonuclease activity on PIC-bound ompD is critically dependent on the recruitment of RNase E into the multi-enzyme RNA degradosome, and our data suggest a process of substrate capture and handover to catalytic sites within the degradosome, in which sequential steps of seed matching and duplex remodelling contribute to cleavage efficiency. Our findings support a putative mechanism of surveillance at translation that potentially terminates gene expression efficiently and rapidly in response to signals provided by regulatory RNA.
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Affiliation(s)
- Katarzyna J Bandyra
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kathrin S Fröhlich
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Akanksha Goyal
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ben F Luisi
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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2
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Shenkutie AM, Gebrelibanos D, Yao M, Bedada Hundie G, Chow FWN, Leung PHM. Impairment of novel non-coding small RNA00203 inhibits biofilm formation and reduces biofilm-specific antibiotic resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2023; 62:106889. [PMID: 37315907 DOI: 10.1016/j.ijantimicag.2023.106889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/12/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
Small RNAs (sRNAs) are post-transcriptional regulators of many biological processes in bacteria, including biofilm formation and antibiotic resistance. The mechanisms by which sRNA regulates the biofilm-specific antibiotic resistance in Acinetobacter baumannii have not been reported to date. This study aimed to investigate the influence of sRNA00203 (53 nucleotides) on biofilm formation, antibiotic susceptibility, and expression of genes associated with biofilm formation and antibiotic resistance. The results showed that deletion of the sRNA00203-encoding gene decreased the biomass of biofilm by 85%. Deletion of the sRNA00203-encoding gene also reduced the minimum biofilm inhibitory concentrations for imipenem and ciprofloxacin 1024- and 128-fold, respectively. Knocking out of sRNA00203 significantly downregulated genes involved in biofilm matrix synthesis (pgaB), efflux pump production (novel00738), lipopolysaccharide biosynthesis (novel00626), preprotein translocase subunit (secA) and the CRP transcriptional regulator. Overall, the suppression of sRNA00203 in an A. baumannii ST1894 strain impaired biofilm formation and sensitized the biofilm cells to imipenem and ciprofloxacin. As sRNA00203 was found to be conserved in A. baumannii, a therapeutic strategy targeting sRNA00203 may be a potential solution for the treatment of biofilm-associated infections caused by A. baumannii. To the best of the authors' knowledge, this is the first study to show the impact of sRNA00203 on biofilm formation and biofilm-specific antibiotic resistance in A. baumannii.
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Affiliation(s)
- Abebe Mekuria Shenkutie
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China; Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Daniel Gebrelibanos
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Mianzhi Yao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Gadissa Bedada Hundie
- Department of Microbiology, Immunology and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Franklin W N Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Polly H M Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
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3
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Zheng T, Jing M, Gong T, Yan J, Wang X, Xu M, Zhou X, Zeng J, Li Y. Regulatory mechanisms of exopolysaccharide synthesis and biofilm formation in Streptococcus mutans. J Oral Microbiol 2023; 15:2225257. [PMID: 37346997 PMCID: PMC10281425 DOI: 10.1080/20002297.2023.2225257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
Background Dental caries is a chronic, multifactorial and biofilm-mediated oral bacterial infection affecting almost every age group and every geographical region. Streptococcus mutans is considered an important pathogen responsible for the initiation and development of dental caries. It produces exopolysaccharides in situ to promote the colonization of cariogenic bacteria and coordinate dental biofilm development. Objective The understanding of the regulatory mechanism of S. mutans biofilm formation can provide a theoretical basis for the prevention and treatment of caries. Design At present, an increasing number of studies have identified many regulatory systems in S. mutans that regulate biofilm formation, including second messengers (e.g. c-di-AMP, Ap4A), transcription factors (e.g. EpsR, RcrR, StsR, AhrC, FruR), two-component systems (e.g. CovR, VicR), small RNA (including sRNA0426, srn92532, and srn133489), acetylation modifications (e.g. ActG), CRISPR-associated proteins (e.g. Cas3), PTS systems (e.g. EIIAB), quorum-sensing signaling system (e.g. LuxS), enzymes (including Dex, YidC, CopZ, EzrA, lmrB, SprV, RecA, PdxR, MurI) and small-molecule metabolites. Results This review summarizes the recent progress in the molecular regulatory mechanisms of exopolysaccharides synthesis and biofilm formation in S. mutans.
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Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mai Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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4
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Mohanty BK, Kushner SR. Regulation of mRNA decay in E. coli. Crit Rev Biochem Mol Biol 2022; 57:48-72. [PMID: 34547957 PMCID: PMC9973670 DOI: 10.1080/10409238.2021.1968784] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.
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Affiliation(s)
| | - Sidney R. Kushner
- Department of Genetics, University of Georgia, Athens GA 30602
- Department of Microbiology, University of Georgia, Athens GA 30602
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5
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Dwijayanti A, Storch M, Stan GB, Baldwin GS. A modular RNA interference system for multiplexed gene regulation. Nucleic Acids Res 2022; 50:1783-1793. [PMID: 35061908 PMCID: PMC8860615 DOI: 10.1093/nar/gkab1301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
The rational design and realisation of simple-to-use genetic control elements that are modular, orthogonal and robust is essential to the construction of predictable and reliable biological systems of increasing complexity. To this effect, we introduce modular Artificial RNA interference (mARi), a rational, modular and extensible design framework that enables robust, portable and multiplexed post-transcriptional regulation of gene expression in Escherichia coli. The regulatory function of mARi was characterised in a range of relevant genetic contexts, demonstrating its independence from other genetic control elements and the gene of interest, and providing new insight into the design rules of RNA based regulation in E. coli, while a range of cellular contexts also demonstrated it to be independent of growth-phase and strain type. Importantly, the extensibility and orthogonality of mARi enables the simultaneous post-transcriptional regulation of multi-gene systems as both single-gene cassettes and poly-cistronic operons. To facilitate adoption, mARi was designed to be directly integrated into the modular BASIC DNA assembly framework. We anticipate that mARi-based genetic control within an extensible DNA assembly framework will facilitate metabolic engineering, layered genetic control, and advanced genetic circuit applications.
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Affiliation(s)
| | - Marko Storch
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Bessemer Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Geoff S Baldwin
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Life Sciences, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
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Svensson SL, Sharma CM. RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist. eLife 2021; 10:69064. [PMID: 34843430 PMCID: PMC8687705 DOI: 10.7554/elife.69064] [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: 04/02/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the food-borne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome-binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that can antagonize bacterial sRNAs.
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Affiliation(s)
- Sarah Lauren Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia Mira Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Oogai Y, Nakata M. Small regulatory RNAs of oral streptococci and periodontal bacteria. JAPANESE DENTAL SCIENCE REVIEW 2021; 57:209-216. [PMID: 34745393 PMCID: PMC8551640 DOI: 10.1016/j.jdsr.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/27/2022] Open
Abstract
Small regulatory RNAs (sRNAs) belong to a family of non-coding RNAs, and many of which regulate expression of genes via interaction with mRNA. The recent popularity of high-throughput next generation sequencers have presented abundant sRNA-related data, including sRNAs of several different oral bacterial species. Some sRNA candidates have been validated in terms of their expression and interaction with target mRNAs. Since the oral cavity is an environment constantly exposed to various stimuli, such as fluctuations in temperature and pH, and osmotic pressure, as well as changes in nutrient availability, oral bacteria require rapid control of gene expression for adaptation to such diverse conditions, while regulation via interactions of sRNAs with mRNA provides advantages for rapid adaptation. This review summarizes methods effective for identification and validation of sRNAs, as well as sRNAs identified to be associated with oral bacterial species, including cariogenic and periodontal pathogens, together with their confirmed and putative target genes.
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Affiliation(s)
- Yuichi Oogai
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 890-8544, Japan
| | - Masanobu Nakata
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 890-8544, Japan
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Apura P, Gonçalves LG, Viegas SC, Arraiano CM. The world of ribonucleases from pseudomonads: a short trip through the main features and singularities. Microb Biotechnol 2021; 14:2316-2333. [PMID: 34427985 PMCID: PMC8601179 DOI: 10.1111/1751-7915.13890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/30/2021] [Indexed: 11/27/2022] Open
Abstract
The development of synthetic biology has brought an unprecedented increase in the number molecular tools applicable into a microbial chassis. The exploration of such tools into different bacteria revealed not only the challenges of context dependency of biological functions but also the complexity and diversity of regulatory layers in bacterial cells. Most of the standardized genetic tools and principles/functions have been mostly based on model microorganisms, namely Escherichia coli. In contrast, the non-model pseudomonads lack a deeper understanding of their regulatory layers and have limited molecular tools. They are resistant pathogens and promising alternative bacterial chassis, making them attractive targets for further studies. Ribonucleases (RNases) are key players in the post-transcriptional control of gene expression by degrading or processing the RNA molecules in the cell. These enzymes act according to the cellular requirements and can also be seen as the recyclers of ribonucleotides, allowing a continuous input of these cellular resources. This makes these post-transcriptional regulators perfect candidates to regulate microbial physiology. This review summarizes the current knowledge and unique properties of ribonucleases in the world of pseudomonads, taking into account genomic context analysis, biological function and strategies to use ribonucleases to improve biotechnological processes.
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Affiliation(s)
- Patrícia Apura
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Luis G. Gonçalves
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Sandra C. Viegas
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
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Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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RNase III and RNase E Influence Posttranscriptional Regulatory Networks Involved in Virulence Factor Production, Metabolism, and Regulatory RNA Processing in Bordetella pertussis. mSphere 2021; 6:e0065021. [PMID: 34406853 PMCID: PMC8386462 DOI: 10.1128/msphere.00650-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis has been shown to encode regulatory RNAs, yet the posttranscriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. Transcriptome sequencing (RNA-Seq) analysis showed differential expression of ∼25% of the B. pertussis transcriptome in each mutant, with only 28% overlap between data sets. Both endonucleases exhibited substantial impact on genes involved in amino acid uptake (e.g., ABC transporters) and in virulence (e.g., the type III secretion system and the autotransporters vag8, tcfA, and brkA). Interestingly, mutations in RNase III and RNase E drove the stability of many transcripts, including those involved in virulence, in opposite directions, a result that was validated by qPCR and immunoblotting for tcfA and brkA. Of note, whereas similar mutations to RNase E in Escherichia coli have subtle effects on transcript stability, a striking >20-fold reduction in four gene transcripts, including tcfA and vag8, was observed in B. pertussis. We further compared our data set to the regulon controlled by the RNA chaperone Hfq to identify B. pertussis loci influenced by regulatory RNAs. This analysis identified ∼120 genes and 19 operons potentially regulated at the posttranscriptional level. Thus, our findings revealed how changes in RNase III- and RNase E-mediated RNA turnover influence pathways associated with virulence and cellular homeostasis. Moreover, we highlighted loci potentially influenced by regulatory RNAs, providing insights into the posttranscriptional regulatory networks involved in fine-tuning B. pertussis gene expression. IMPORTANCE Noncoding, regulatory RNAs in bacterial pathogens are critical components required for rapid changes in gene expression profiles. However, little is known about the role of regulatory RNAs in the growth and pathogenesis of Bordetella pertussis. To address this, mutants separately lacking ribonucleases central to regulatory RNA processing, RNase III and RNase E, were analyzed by RNA-Seq. Here, we detail the first transcriptomic analysis of the impact of altered RNA degradation in B. pertussis. Each mutant showed approximately 1,000 differentially expressed genes, with significant changes in the expression of pathways associated with metabolism, bacterial secretion, and virulence factor production. Our analysis suggests an important role for these ribonucleases during host colonization and provides insights into the breadth of posttranscriptional regulation in B. pertussis, further informing our understanding of B. pertussis pathogenesis.
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Lin Y, Chen J, Zhou X, Li Y. Inhibition of Streptococcus mutans biofilm formation by strategies targeting the metabolism of exopolysaccharides. Crit Rev Microbiol 2021; 47:667-677. [PMID: 33938347 DOI: 10.1080/1040841x.2021.1915959] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Dental caries is one of the most prevalent and costly biofilm-associated infectious diseases affecting most of the world's population. In particular, dental caries is driven by dysbiosis of the dental biofilm adherent to the enamel surface. Specific types of acid-producing bacteria, especially Streptococcus mutans, colonize the dental surface and cause damage to the hard tooth structure in the presence of fermentable carbohydrates. Streptococcus mutans has been established as the major cariogenic pathogen responsible for human dental caries, with a high ability to form biofilms. The exopolysaccharide (EPS) matrix, mainly contributed by S. mutans, has been considered as a virulence determinant of cariogenic biofilm. As EPS is an important virulence factor, targeting EPS metabolism could be useful in preventing cariogenic biofilm formation. This review summarizes plausible strategies targeting S. mutans biofilms by degrading EPS structure, inhibiting EPS production, and disturbing the EPS metabolism-related gene expression and regulatory systems.
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Affiliation(s)
- Yongwang Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiamin Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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12
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Lee M, Ryu M, Joo M, Seo YJ, Lee J, Kim HM, Shin E, Yeom JH, Kim YH, Bae J, Lee K. Endoribonuclease-mediated control of hns mRNA stability constitutes a key regulatory pathway for Salmonella Typhimurium pathogenicity island 1 expression. PLoS Pathog 2021; 17:e1009263. [PMID: 33524062 PMCID: PMC7877770 DOI: 10.1371/journal.ppat.1009263] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/11/2021] [Accepted: 01/01/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteria utilize endoribonuclease-mediated RNA processing and decay to rapidly adapt to environmental changes. Here, we report that the modulation of hns mRNA stability by the endoribonuclease RNase G plays a key role in Salmonella Typhimurium pathogenicity. We found that RNase G determines the half-life of hns mRNA by cleaving its 5′ untranslated region and that altering its cleavage sites by genome editing stabilizes hns mRNA, thus decreasing S. Typhimurium virulence in mice. Under anaerobic conditions, the FNR-mediated transcriptional repression of rnc encoding RNase III, which degrades rng mRNA, and simultaneous induction of rng transcription resulted in rapid hns mRNA degradation, leading to the derepression of genes involved in the Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS). Together, our findings show that RNase III and RNase G levels-mediated control of hns mRNA abundance acts as a regulatory pathway upstream of a complex feed-forward loop for SPI-1 expression. Recent studies have shown that pathogenic bacteria with ribonuclease mutations display attenuated virulence, impaired mobility, and reduced proliferation in host cells. However, the molecular mechanisms underlying ribonuclease-associated pathogenesis have not yet been characterised. Here, we provide strong experimental evidence that the coordinated modulation of endoribonuclease activity constitutes an additional regulatory layer upstream of a complex feed-forward loop controlling global regulatory systems in the Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS). In addition, we showed that this regulatory pathway plays a key role in the virulence of S. Typhimurium in the host. Thus, our study improves the understanding of the mechanisms through which bacterial pathogens sense the host environment and respond precisely by expressing gene products required for adaptation to that particular niche.
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Affiliation(s)
- Minho Lee
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Minkyung Ryu
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Minju Joo
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Jaejin Lee
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Hong-Man Kim
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Eunkyoung Shin
- Department of Pharmacy, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
| | - Yong-Hak Kim
- Department of Microbiology, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
- * E-mail: (Y-HK); (JB); (KL)
| | - Jeehyeon Bae
- Department of Pharmacy, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
- * E-mail: (Y-HK); (JB); (KL)
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Dongjak-Gu, Seoul, Republic of Korea
- * E-mail: (Y-HK); (JB); (KL)
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13
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Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments. Microorganisms 2021; 9:microorganisms9020250. [PMID: 33530561 PMCID: PMC7911923 DOI: 10.3390/microorganisms9020250] [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: 01/01/2021] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.
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14
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Reuscher CM, Klug G. Antisense RNA asPcrL regulates expression of photosynthesis genes in Rhodobacter sphaeroides by promoting RNase III-dependent turn-over of puf mRNA. RNA Biol 2021; 18:1445-1457. [PMID: 33258405 DOI: 10.1080/15476286.2020.1857520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anoxygenic photosynthesis is an important pathway for Rhodobacter sphaeroides to produce ATP under oxygen-limiting conditions. The expression of its photosynthesis genes is tightly regulated at transcriptional and post-transcriptional levels in response to light and oxygen signals, to avoid photooxidative stress by the simultaneous presence of pigments, light and oxygen. The puf operon encodes pigment-binding proteins of the light-harvesting complex I (genes pufB and pufA), of the reaction centre (genes pufL and pufM), a scaffold protein (gene pufX) and includes the gene for sRNA PcrX. Segmental differences in the stability of the pufBALMX-pcrX mRNA contribute to the stoichiometry of LHI to RC complexes. With asPcrL we identified the third sRNA and the first antisense RNA that is involved in balancing photosynthesis gene expression in R. sphaeroides. asPcrL influences the stability of the pufBALMX-pcrX mRNA but not of the pufBA mRNA and consequently the stoichiometry of photosynthetic complexes. By base pairing to the pufL region asPcrL promotes RNase III-dependent degradation of the pufBALMX-prcX mRNA. Since asPcrL is activated by the same protein regulators as the puf operon including PcrX it is part of an incoherent feed-forward loop that fine-tunes photosynthesis gene expression.[Figure: see text].
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Affiliation(s)
- Carina M Reuscher
- Institut Für Mikro- Und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Giessen, Germany
| | - Gabriele Klug
- Institut Für Mikro- Und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Giessen, Germany
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15
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Layton E, Fairhurst AM, Griffiths-Jones S, Grencis RK, Roberts IS. Regulatory RNAs: A Universal Language for Inter-Domain Communication. Int J Mol Sci 2020; 21:E8919. [PMID: 33255483 PMCID: PMC7727864 DOI: 10.3390/ijms21238919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.
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Affiliation(s)
- Emma Layton
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Anna-Marie Fairhurst
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore;
| | - Sam Griffiths-Jones
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Richard K. Grencis
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
| | - Ian S. Roberts
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; (E.L.); (S.G.-J.)
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16
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The Endoribonuclease RNase E Coordinates Expression of mRNAs and Small Regulatory RNAs and Is Critical for the Virulence of Brucella abortus. J Bacteriol 2020; 202:JB.00240-20. [PMID: 32747427 DOI: 10.1128/jb.00240-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
RNases are key regulatory components in prokaryotes, responsible for the degradation and maturation of specific RNA molecules at precise times. Specifically, RNases allow cells to cope with changes in their environment through rapid alteration of gene expression. To date, few RNases have been characterized in the mammalian pathogen Brucella abortus In the present work, we sought to investigate several RNases in B. abortus and determine what role, if any, they have in pathogenesis. Of the 4 RNases reported in this study, the highly conserved endoribonuclease, RNase E, was found to play an integral role in the virulence of B. abortus Although rne, which encodes RNase E, is essential in B. abortus, we were able to generate a strain encoding a defective version of RNase E lacking the C-terminal portion of the protein, and this strain (rne-tnc) was attenuated in a mouse model of Brucella infection. RNA-sequencing analysis revealed massive RNA dysregulation in B. abortus rne-tnc, with 122 upregulated and 161 downregulated transcripts compared to the parental strain. Interestingly, several mRNAs related to metal homeostasis were significantly decreased in the rne-tnc strain. We also identified a small regulatory RNA (sRNA), called Bsr4, that exhibited significantly elevated levels in rne-tnc, demonstrating an important role for RNase E in sRNA-mediated regulatory pathways in Brucella Overall, these data highlight the importance of RNase E in B. abortus, including the role of RNase E in properly controlling mRNA levels and contributing to virulence in an animal model of infection.IMPORTANCE Brucellosis is a debilitating disease of humans and animals globally, and there is currently no vaccine to combat human infection by Brucella spp. Moreover, effective antibiotic treatment in humans is extremely difficult and can lead to disease relapse. Therefore, it is imperative that systems and pathways be identified and characterized in the brucellae so new vaccines and therapies can be generated. In this study, we describe the impact of the endoribonuclease RNase E on the control of mRNA and small regulatory RNA (sRNA) levels in B. abortus, as well as the importance of RNase E for the full virulence of B. abortus This work greatly enhances our understanding of ribonucleases in the biology and pathogenesis of Brucella spp.
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Quendera AP, Seixas AF, Dos Santos RF, Santos I, Silva JPN, Arraiano CM, Andrade JM. RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria. Front Mol Biosci 2020; 7:78. [PMID: 32478092 PMCID: PMC7237705 DOI: 10.3389/fmolb.2020.00078] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
Small non-coding RNAs (sRNAs) are critical post-transcriptional regulators of gene expression. Distinct RNA-binding proteins (RBPs) influence the processing, stability and activity of bacterial small RNAs. The vast majority of bacterial sRNAs interact with mRNA targets, affecting mRNA stability and/or its translation rate. The assistance of RNA-binding proteins facilitates and brings accuracy to sRNA-mRNA basepairing and the RNA chaperones Hfq and ProQ are now recognized as the most prominent RNA matchmakers in bacteria. These RBPs exhibit distinct high affinity RNA-binding surfaces, promoting RNA strand interaction between a trans-encoding sRNA and its mRNA target. Nevertheless, some organisms lack ProQ and/or Hfq homologs, suggesting the existence of other RBPs involved in sRNA function. Along this line of thought, the global regulator CsrA was recently shown to facilitate the access of an sRNA to its target mRNA and may represent an additional factor involved in sRNA function. Ribonucleases (RNases) can be considered a class of RNA-binding proteins with nucleolytic activity that are responsible for RNA maturation and/or degradation. Presently RNase E, RNase III, and PNPase appear to be the main players not only in sRNA turnover but also in sRNA processing. Here we review the current knowledge on the most important bacterial RNA-binding proteins affecting sRNA activity and sRNA-mediated networks.
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Affiliation(s)
- Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João P N Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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18
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Apura P, Saramago M, Peregrina A, Viegas SC, Carvalho SM, Saraiva LM, Arraiano CM, Domingues S. Tailor-made sRNAs: a plasmid tool to control the expression of target mRNAs in Pseudomonas putida. Plasmid 2020; 109:102503. [PMID: 32209400 DOI: 10.1016/j.plasmid.2020.102503] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 11/25/2022]
Abstract
Pseudomonas putida is a highly attractive production system for industrial needs. However, for its improvement as a biocatalyst at the industrial level, modulation of its gene expression is urgently needed. We report the construction of a plasmid expressing a small RNA-based system with the potential to be used for different purposes. Due to the small RNAs modular composition, the design facilities and ability to tune gene expression, they constitute a powerful tool in genetic and metabolic engineering. In the tool presented here, customized sRNAs are expressed from a plasmid and specifically directed to any region of a chosen target. Expression of these customized sRNAs is shown to differentially modulate the level of endogenous and heterologous reporter genes. The antisense interaction of the sRNA with the mRNA produces different outcomes. Depending on the particularity of each sRNA-target mRNA pair, we demonstrate the duality of this system, which is able either to decrease or increase the expression of the same given gene. This system combines high specificity with the potential to be widely applied, due to its predicted ability to modulate the expression of virtually any given gene. This plasmid can be used to redesign P. putida metabolism, fulfilling an important industrial gap.
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Affiliation(s)
- Patrícia Apura
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Margarida Saramago
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexandra Peregrina
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sandra C Viegas
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Sandra M Carvalho
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lígia M Saraiva
- Molecular Mechanisms of Pathogen Resistance Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Susana Domingues
- Control of Gene Expression Lab, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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19
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Hör J, Matera G, Vogel J, Gottesman S, Storz G. Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0030-2019. [PMID: 32213244 PMCID: PMC7112153 DOI: 10.1128/ecosalplus.esp-0030-2019] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 12/20/2022]
Abstract
The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Gianluca Matera
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892
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20
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Reprogramming bacteria with RNA regulators. Biochem Soc Trans 2019; 47:1279-1289. [DOI: 10.1042/bst20190173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022]
Abstract
Abstract
The revolution of genomics and growth of systems biology urged the creation of synthetic biology, an engineering discipline aiming at recreating and reprogramming cellular functions for industrial needs. There has been a huge effort in synthetic biology to develop versatile and programmable genetic regulators that would enable the precise control of gene expression. Synthetic RNA components have emerged as a solution, offering a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their compactness, structure and way of action, several types of RNA devices that act on DNA, RNA and protein have been characterized and applied in synthetic biology. RNA-based approaches are more ‘economical' for the cell, since they are generally not translated. These RNA-based strategies act on a much shorter time scale than transcription-based ones and can be more efficient than protein-based mechanisms. In this review, we explore these RNA components as building blocks in the RNA synthetic biology field, first by explaining their natural mode of action and secondly discussing how these RNA components have been exploited to rewire bacterial regulatory circuitry.
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21
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Phillips JO, Butt LE, Henderson CA, Devonshire M, Healy J, Conway SJ, Locker N, Pickford AR, Vincent HA, Callaghan AJ. High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions. Nucleic Acids Res 2019; 46:e86. [PMID: 29846708 PMCID: PMC6101487 DOI: 10.1093/nar/gky410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/02/2018] [Indexed: 12/13/2022] Open
Abstract
We are just beginning to unravel the myriad of interactions in which non-coding RNAs participate. The intricate RNA interactome is the foundation of many biological processes, including bacterial virulence and human disease, and represents unexploited resources for the development of potential therapeutic interventions. However, identifying specific associations of a given RNA from the multitude of possible binding partners within the cell requires robust high-throughput systems for their rapid screening. Here, we present the first demonstration of functional-RNA arrays as a novel platform technology designed for the study of such interactions using immobilized, active RNAs. We have generated high-density RNA arrays by an innovative method involving surface-capture of in vitro transcribed RNAs. This approach has significant advantages over existing technologies, particularly in its versatility in regards to binding partner character. Indeed, proof-of-principle application of RNA arrays to both RNA–small molecule and RNA–RNA pairings is demonstrated, highlighting their potential as a platform technology for mapping RNA-based networks and for pharmaceutical screening. Furthermore, the simplicity of the method supports greater user-accessibility over currently available technologies. We anticipate that functional-RNA arrays will find broad utility in the expanding field of RNA characterization.
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Affiliation(s)
- Jack O Phillips
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Martin Devonshire
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Jess Healy
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7HX, UK
| | - Andrew R Pickford
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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22
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Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res 2019; 46:10380-10394. [PMID: 30113670 PMCID: PMC6212723 DOI: 10.1093/nar/gky684] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/18/2018] [Indexed: 12/02/2022] Open
Abstract
Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3′ overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.
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Affiliation(s)
- Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Niv Reiss
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ehud Karavani
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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23
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Chen ICK, Satinsky BM, Velicer GJ, Yu YTN. sRNA-pathway genes regulating myxobacterial development exhibit clade-specific evolution. Evol Dev 2019; 21:82-95. [PMID: 30762281 DOI: 10.1111/ede.12281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Small non-coding RNAs (sRNAs) control bacterial gene expression involved in a wide range of important cellular processes. In the highly social bacterium Myxococcus xanthus, the sRNA Pxr prevents multicellular fruiting-body development when nutrients are abundant. Pxr was discovered from the evolution of a developmentally defective strain (OC) into a developmentally proficient strain (PX). In OC, Pxr is constitutively expressed and blocks development even during starvation. In PX, one mutation deactivates Pxr allowing development to proceed. We screened for transposon mutants that suppress the OC defect and thus potentially reveal new Pxr-pathway components. Insertions significantly restoring development were found in four genes-rnd, rnhA, stkA and Mxan_5793-not previously associated with an sRNA activity. Phylogenetic analysis suggests that the Pxr pathway was constructed within the Cystobacterineae suborder both by co-option of genes predating the Myxococcales order and incorporation of a novel gene (Mxan_5793). Further, the sequence similarity of rnd, rnhA and stkA homologs relative to M. xanthus alleles was found to decrease greatly among species beyond the Cystobacterineae suborder compared to the housekeeping genes examined. Finally, ecological context differentially affected the developmental phenotypes of distinct mutants, with implications for the evolution of development in variable environments.
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Affiliation(s)
- I-Chen Kimberly Chen
- Department of Biology, Indiana University, Bloomington, Indiana.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | | | - Gregory J Velicer
- Department of Biology, Indiana University, Bloomington, Indiana.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Department of Biology, Indiana University, Bloomington, Indiana.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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24
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SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA. Proc Natl Acad Sci U S A 2019; 116:3042-3051. [PMID: 30718400 DOI: 10.1073/pnas.1811589116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription termination is a critical step in the control of gene expression. One of the major termination mechanisms is mediated by Rho factor that dissociates the complex mRNA-DNA-RNA polymerase upon binding with RNA polymerase. Rho promotes termination at the end of operons, but it can also terminate transcription within leader regions, performing regulatory functions and avoiding pervasive transcription. Transcription of rho is autoregulated through a Rho-dependent attenuation in the leader region of the transcript. In this study, we have included an additional player in this pathway. By performing MS2-affinity purification coupled with RNA sequencing (MAPS), rho transcript was shown to directly interact with the small noncoding RNA SraL. Using bioinformatic in vivo and in vitro experimental analyses, SraL was shown to base pair with the 5'-UTR of rho mRNA upregulating its expression in several growth conditions. This base pairing was shown to prevent the action of Rho over its own message. Moreover, the results obtained indicate that both ProQ and Hfq are associated with this regulation. We propose a model that contemplates the action of Salmonella SraL sRNA in the protection of rho mRNA from premature transcription termination by Rho. Note that since the interaction region between both RNAs corresponds to a very-well-conserved sequence, it is plausible to admit that this regulation also occurs in other enterobacteria.
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Saramago M, Robledo M, Matos RG, Jiménez-Zurdo JI, Arraiano CM. Sinorhizobium meliloti RNase III: Catalytic Features and Impact on Symbiosis. Front Genet 2018; 9:350. [PMID: 30210532 PMCID: PMC6121014 DOI: 10.3389/fgene.2018.00350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the ribonuclease (RNase) III family of enzymes are metal-dependent double-strand specific endoribonucleases. They are ubiquitously found and eukaryotic RNase III-like enzymes include Dicer and Drosha, involved in RNA processing and RNA interference. In this work, we have addressed the primary characterization of RNase III from the symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti. The S. meliloti rnc gene does encode an RNase III-like protein (SmRNase III), with recognizable catalytic and double-stranded RNA (dsRNA)-binding domains that clusters in a branch with its α–proteobacterial counterparts. Purified SmRNase III dimerizes, is active at neutral to alkaline pH and behaves as a strict metal cofactor-dependent double-strand endoribonuclease, with catalytic features distinguishable from those of the prototypical member of the family, the Escherichia coli ortholog (EcRNase III). SmRNase III prefers Mn2+ rather than Mg2+ as metal cofactor, cleaves the generic structured R1.1 substrate at a site atypical for RNase III cleavage, and requires higher cofactor concentrations and longer dsRNA substrates than EcRNase III for optimal activity. Furthermore, the ultraconserved E125 amino acid was shown to play a major role in the metal-dependent catalysis of SmRNase III. SmRNase III degrades endogenous RNA substrates of diverse biogenesis with different efficiency, and is involved in the maturation of the 23S rRNA. SmRNase III loss-of-function neither compromises viability nor alters morphology of S. meliloti cells, but influences growth, nodulation kinetics, the onset of nitrogen fixation and the overall symbiotic efficiency of this bacterium on the roots of its legume host, alfalfa, which ultimately affects plant growth. Our results support an impact of SmRNase III on nodulation and symbiotic nitrogen fixation in plants.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnología Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Rute G Matos
- Instituto de Tecnología Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José I Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Cecília M Arraiano
- Instituto de Tecnología Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Cheah HL, Raabe CA, Lee LP, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang TH. Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 2018; 53:335-355. [PMID: 29793351 DOI: 10.1080/10409238.2018.1473330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, RNA-deep sequencing has uncovered copious non-protein coding RNAs (npcRNAs) in bacteria. Many of them are key players in the regulation of gene expression, taking part in various regulatory circuits, such as metabolic responses to different environmental stresses, virulence, antibiotic resistance, and host-pathogen interactions. This has contributed to the high adaptability of bacteria to changing or even hostile environments. Their mechanisms include the regulation of transcriptional termination, modulation of translation, and alteration of messenger RNA (mRNA) stability, as well as protein sequestration. Here, the mechanisms of gene expression by regulatory bacterial npcRNAs are comprehensively reviewed and supplemented with well-characterized examples. This class of molecules and their mechanisms of action might be useful targets for the development of novel antibiotics.
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Affiliation(s)
- Hong-Leong Cheah
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Carsten A Raabe
- b Institute of Experimental Pathology, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany.,c Brandenburg Medical School (MHB) , Neuruppin , Germany.,d Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation , University of Münster , Münster , Germany
| | - Li-Pin Lee
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Timofey S Rozhdestvensky
- e Medical Faculty, Transgenic Mouse and Genome Engineering Model Core Facility (TRAM) , University of Münster , Münster , Germany
| | - Marimuthu Citartan
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Siti Aminah Ahmed
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
| | - Thean-Hock Tang
- a Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia , Kepala Batas , Malaysia
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27
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Mohanty BK, Kushner SR. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0011-2017. [PMID: 29676246 PMCID: PMC5912700 DOI: 10.1128/microbiolspec.rwr-0011-2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Indexed: 02/08/2023] Open
Abstract
Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, we discuss the various enzymes that control transcription, translation, and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5' and 3' termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript are matured to individual 16S, 23S, and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and nontranslated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions, Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase, as well as proteins that regulate the catalytic activity of particular RNases. Under certain stress conditions, an additional group of specialized endonucleases facilitate the cell's ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I, participate in multiple RNA processing and decay pathways.
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Affiliation(s)
| | - Sidney R Kushner
- Department of Genetics
- Department of Microbiology, University of Georgia, Athens, GA 30602
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28
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Mao MY, Li M, Lei L, Yin JX, Yang YM, Hu T. The Regulator Gene rnc Is Closely Involved in Biofilm Formation in Streptococcus mutans. Caries Res 2018; 52:347-358. [PMID: 29510413 DOI: 10.1159/000486431] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/18/2017] [Indexed: 11/19/2022] Open
Abstract
Streptococcus mutans is an important factor in the etiology and pathogenesis of dental caries, largely owing to its ability to form a stable biofilm. Previous animal studies have indicated that rnc could decrease the amount of sulcal caries, and that the downregulation of cariogenicity might be due to its capacity to disrupt biofilm formation. However, the biofunctions by which rnc is involved in biofilm formation remain to be elucidated. In this study, we further investigate the role of rnc based on the study of mature biofilm. Scanning electron microscopy and the crystal violet assay were used to detect the biofilm forming ability. The production and distribution of exopolysaccharides within biofilm was analyzed by exopolysaccharide staining. Gel permeation chromatography was used to perform molecular weight assessment. Its adhesion force was measured by atomic force microscopy. The expression of biofilm formation-associated genes was analyzed at the mRNA level by qPCR. Here, we found that rnc could occur and function in biofilm formation by assembling well-structured, exopolysaccharide-encased, stable biofilms in S. mutans. The weakened biofilm forming ability of rnc-deficient strains was associated with the reduction of exopolysaccharide production and bacterial adhesion. Over all, these data illustrate an interesting situation in which an unappreciated regulatory gene acquired for virulence, rnc, most likely has been coopted as a potential regulator of biofilm formation in S. mutans. Further characterization of rnc may lead to the identification of a possible pathogenic biofilm-specific treatment for dental caries.
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Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli. Methods Mol Biol 2018; 1737:231-248. [PMID: 29484597 DOI: 10.1007/978-1-4939-7634-8_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Regulation of RNA turnover is of utmost importance for controlling the concentration of transcripts and consequently cellular protein levels. Among the processes controlling RNA decay, small noncoding regulatory RNAs (sRNAs) have recently emerged as major new players. In this chapter, we describe and discuss protocols that can be used to measure sRNA concentration in vivo and to assess sRNA decay rates in Gram-negative bacteria. Precisely, we focus our analyses on the Escherichia coli Gram-negative bacterium as a model. The information described in this chapter provides a guideline to help develop a protocol in order to assess these important parameters and to identify RNA-processing enzymes involved in sRNA degradation processes.
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30
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Rath EC, Pitman S, Cho KH, Bai Y. Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data. BMC Bioinformatics 2017; 18:540. [PMID: 29297355 PMCID: PMC5751559 DOI: 10.1186/s12859-017-1897-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III. The endoribonuclease RNase III cleaves double stranded RNAs, which can be formed during the interaction between an sRNA and target mRNAs. Results For this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type. First, we developed a custom script that can detect intergenic regions of the S. pyogenes genome. A differential expression analysis with Cufflinks and Stringtie was then performed to identify the intergenic regions whose expression was influenced by the RNase III gene deletion. Conclusion This analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs. This study not only expanded our knowledge on novel sRNAs but would also give us new insight into sRNA degradation.
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Affiliation(s)
- Ethan C Rath
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Stephanie Pitman
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA.
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. .,The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN, 47809, USA.
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31
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Saramago M, Peregrina A, Robledo M, Matos RG, Hilker R, Serrania J, Becker A, Arraiano CM, Jiménez-Zurdo JI. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. Nucleic Acids Res 2017; 45:1371-1391. [PMID: 28180335 PMCID: PMC5388416 DOI: 10.1093/nar/gkw1234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 01/23/2023] Open
Abstract
Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
- These authors contributed equally to the work as the first authors
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Rolf Hilker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Cecilia M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - José I. Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- To whom correspondence should be addressed. Tel: +34 958181600; Fax: +34 958181609;
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Chen ICK, Velicer GJ, Yu YTN. Divergence of functional effects among bacterial sRNA paralogs. BMC Evol Biol 2017; 17:199. [PMID: 28830343 PMCID: PMC5568312 DOI: 10.1186/s12862-017-1037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus. Specifically, Pxr prevents the initiation of fruiting body development when nutrients are abundant. Previous work has shown that Pxr appears to have a recent origin within a sub-clade of the myxobacteria, which allowed us to infer the most recent common ancestor of pxr and examine the divergence of Pxr since its origin. RESULTS To test for inter-specific divergence in functional effects, extant pxr homologs from several species and their inferred ancestor were introduced into an M. xanthus deletion mutant lacking pxr. Both the inferred ancestral pxr and all extant alleles from species containing only one copy of pxr were found to control development in M. xanthus in a qualitatively similar manner to the native M. xanthus allele. However, multiple paralogs present in Cystobacter species exhibited divergent effects, with two paralogs controlling M. xanthus development but two others failing to do so. These differences may have occurred through changes in gene expression caused by apparent structural differences in the sRNA variants encoded by these paralogs. CONCLUSIONS Taken together, our results suggest that Pxr plays a common fundamental role in developmental gene regulation across diverse species of myxobacteria but also that the functional effects of some Pxr variants may be evolving in some lineages.
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Affiliation(s)
- I-Chen Kimberly Chen
- Department of Biology, Indiana University, Bloomington, IN47405, USA. .,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland. .,Present address: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332, USA.
| | - Gregory J Velicer
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
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Mao MY, Yang YM, Li KZ, Lei L, Li M, Yang Y, Tao X, Yin JX, Zhang R, Ma XR, Hu T. The rnc Gene Promotes Exopolysaccharide Synthesis and Represses the vicRKX Gene Expressions via MicroRNA-Size Small RNAs in Streptococcus mutans. Front Microbiol 2016; 7:687. [PMID: 27242713 PMCID: PMC4861726 DOI: 10.3389/fmicb.2016.00687] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023] Open
Abstract
Dental caries is a biofilm-dependent disease that largely relies on the ability of Streptococcus mutans to synthesize exopolysaccharides. Although the rnc gene is suggested to be involved in virulence mechanisms in many other bacteria, the information regarding it in S. mutans is very limited. Here, using deletion or overexpression mutant assay, we demonstrated that rnc in S. mutans significantly positively regulated exopolysaccharide synthesis and further altered biofilm formation. Meanwhile, the cariogenecity of S. mutans was decreased by deletion of rnc in a specific pathogen-free (SPF) rat model. Interestingly, analyzing the expression at mRNA level, we found the downstream vic locus was repressed by rnc in S. mutans. Using deep sequencing and bioinformatics analysis, for the first time, three putative microRNA-size small RNAs (msRNAs) targeting vicRKX were predicted in S. mutans. The expression levels of these msRNAs were negatively correlated with vicRKX but positively correlated with rnc, indicating rnc probably repressed vicRKX expression through msRNAs at the post-transcriptional level. In all, the results present that rnc has a potential role in the regulation of exopolysaccharide synthesis and can affect vicRKX expressions via post-transcriptional repression in S. mutans. This study provides an alternative avenue for further research aimed at preventing caries.
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Affiliation(s)
- Meng-Ying Mao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ying-Ming Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ke-Zeng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu, China; Department of Dentistry, Yan'an Hospital Affiliated to Kunming Medical UniversityKunming, China
| | - Lei Lei
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Meng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Yan Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, China
| | - Jia-Xin Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
| | - Ru Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan UniversityChengdu, China; Department of Endodontics and Operative Dentistry School of Stomatology, Capital Medical UniversityBeijing, China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences Chengdu, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, China
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Gone S, Alfonso-Prieto M, Paudyal S, Nicholson AW. Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation. Sci Rep 2016; 6:25448. [PMID: 27150669 PMCID: PMC4858673 DOI: 10.1038/srep25448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/15/2016] [Indexed: 12/15/2022] Open
Abstract
Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.
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Affiliation(s)
- Swapna Gone
- Department of Chemistry, Philadelphia PA, 19122, USA
| | | | - Samridhdi Paudyal
- Department of Biology, Temple University, Philadelphia PA, 19122, USA
| | - Allen W Nicholson
- Department of Chemistry, Philadelphia PA, 19122, USA.,Department of Biology, Temple University, Philadelphia PA, 19122, USA
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35
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Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
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36
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Kim JN. Roles of two RyhB paralogs in the physiology of Salmonella enterica. Microbiol Res 2016; 186-187:146-52. [PMID: 27242152 DOI: 10.1016/j.micres.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 11/18/2022]
Abstract
Salmonella has evolved complicated regulatory systems to regulate the expression of virulence determinants that are acquired by horizontal gene transfer in response to various environmental niches. Among these, small RNA (sRNA)-mediated regulation exhibits unique features, distinct from those of protein factor-mediated regulation, which may provide benefits for a pathogen coping with the complex stress conditions encountered during host infection. Specifically, iron acquisition by this pathogenic bacterium is important for cellular processes such as energy metabolism and DNA replication. Many studies on the role of RyhB sRNA have begun to unveil the essential nature of iron acquisition in allowing the organism to persist and develop pathogenicity. The Salmonella genome encodes two RyhB paralogs, RyhB-1 and RyhB-2, which are known to act singularly or together on target expression. Based on the mechanism of Escherichia coli RyhB function, this review proposes a possible model to show how two Salmonella RyhB paralogs regulate the level of target mRNAs by sensing environmental inputs or conditions. This review also describes the involvement of Salmonella RyhBs in diverse functions including nitrate homeostasis, adaptive system to oxidative stress, and intracellular survival. Thus, the two Salmonella RyhBs play a critical role in the regulation of gene expression that appears to be essential for persistence and pathogenesis of Salmonella spp.
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Affiliation(s)
- Jeong Nam Kim
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610, United States.
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37
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Yang L, Wang YL, Dai JC, Liu M, Li X, Tang H. Biochemical properties of Bacillus Calmette Guerin ribonuclease III. J Basic Microbiol 2015; 56:392-404. [PMID: 26632143 DOI: 10.1002/jobm.201500360] [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: 06/05/2015] [Accepted: 10/18/2015] [Indexed: 11/11/2022]
Abstract
Double-stranded RNA (dsRNA) is discovered to participate in the regulation of gene expression in both bacterial and eukaryotic cells. Members of ribonuclease III (RNase III) family recognize RNA motifs and cleave substrates at specific sites in a divalent-metal-ion-dependent manner. In this study, we find the RNase III from Bacillus Calmette Guerin (BCG-RNase III) cleaves small hairpin RNA based on the conserved stem structure associated with Mycobacterium 16S ribosomal RNA precursor at specific sites which are not determined. To evaluate the influence of remnant endogenous ribonucleases from expression host on RNA cleavage assays for RNase III, we use E44A and D48A mutant of the enzyme to perform RNA cleavage assays and find that remnant ribonucleases have no effect on cleavage assays. The RNA cleavage activity of the enzyme can be supported by Mg(2+), Mn(2+), and Co(2+) and enhanced with the increasing salt concentration. The catalytic activity of the enzyme is exhibited when the temperature of the reaction buffer ranges from 30 to 55 °C and the pH of the buffer from 7.0 to 10.0. Two major cleavage sites in RNA substrate are identified using RNA Ligase Mediated Rapid Amplification of cDNA Ends (RLM-RACE).
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Affiliation(s)
- Lei Yang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China.,Department of Clinical Laboratory, Tianjin First Center Hospital, Tianjin, China
| | - Yan-Li Wang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China.,Department of Clinical Laboratory, Tianjin Hospital of ITCWM Nankai Hospital, Tianjin, China
| | - Jin-Chuan Dai
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Min Liu
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Xin Li
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
| | - Hua Tang
- Tianjin Life Science Research Center and Basic Medical School, Tianjin Medical University, Tianjin, China
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Van Puyvelde S, Vanderleyden J, De Keersmaecker SCJ. Experimental approaches to identify small RNAs and their diverse roles in bacteria--what we have learnt in one decade of MicA research. Microbiologyopen 2015; 4:699-711. [PMID: 25974745 PMCID: PMC4618604 DOI: 10.1002/mbo3.263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 01/12/2023] Open
Abstract
Nowadays the identification of small RNAs (sRNAs) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. Compared to the study of other components of bacterial cells, this is a relatively new but fast-growing research field. Although reports on new sRNAs appear regularly, some sRNAs are already subject of research for a longer time. One of such sRNAs is MicA, a sRNA best described for its role in outer membrane remodeling, but probably having a much broader function than anticipated. An overview of what we have learnt from MicA led to the conclusion that even for this well-described sRNA, we still do not have the overall picture. More general, the story of MicA might become an experimental lead for unraveling the many sRNAs with unknown functions. In this review, three important topics in the sRNA field are covered, exemplified from the perspective of MicA: (i) identification of new sRNAs, (ii) target identification and unraveling the biological function, (iii) structural analysis. The complex mechanisms of action of MicA deliver some original insights in the sRNA field which includes the existence of dimer formation or simultaneous cis and trans regulation, and might further inspire the understanding of the function of other sRNAs.
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Affiliation(s)
- Sandra Van Puyvelde
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Heverlee, Belgium.,Department of Biomedical Sciences, Diagnostic Bacteriology Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, Belgium
| | - Jozef Vanderleyden
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Heverlee, Belgium
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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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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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Möller P, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F. Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PLoS One 2014; 9:e110427. [PMID: 25330313 PMCID: PMC4201532 DOI: 10.1371/journal.pone.0110427] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/14/2014] [Indexed: 01/18/2023] Open
Abstract
As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens.
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Affiliation(s)
- Philip Möller
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | | | - Konrad U. Förstner
- Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany
| | - Tuan-Nan Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Cynthia M. Sharma
- Research Center for Infectious Diseases (ZINF), Julius-Maximilian's University of Würzburg, Würzburg, Germany
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
- * E-mail:
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Development, antibiotic production, and ribosome assembly in Streptomyces venezuelae are impacted by RNase J and RNase III deletion. J Bacteriol 2014; 196:4253-67. [PMID: 25266378 DOI: 10.1128/jb.02205-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA metabolism is a critical but frequently overlooked control element affecting virtually every cellular process in bacteria. RNA processing and degradation is mediated by a suite of ribonucleases having distinct cleavage and substrate specificity. Here, we probe the role of two ribonucleases (RNase III and RNase J) in the emerging model system Streptomyces venezuelae. We show that each enzyme makes a unique contribution to the growth and development of S. venezuelae and further affects the secondary metabolism and antibiotic production of this bacterium. We demonstrate a connection between the action of these ribonucleases and translation, with both enzymes being required for the formation of functional ribosomes. RNase III mutants in particular fail to properly process 23S rRNA, form fewer 70S ribosomes, and show reduced translational processivity. The loss of either RNase III or RNase J additionally led to the appearance of a new ribosomal species (the 100S ribosome dimer) during exponential growth and dramatically sensitized these mutants to a range of antibiotics.
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Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E. Riboregulation in plant-associated α-proteobacteria. RNA Biol 2014; 11:550-62. [PMID: 25003187 DOI: 10.4161/rna.29625] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The symbiotic α-rhizobia Sinorhizobium meliloti, Bradyrhizobium japonicum, Rhizobium etli and the related plant pathogen Agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. These metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. Here we summarize the recent knowledge on their small non-coding RNAs (sRNAs) including conservation, function, and interaction of the sRNAs with the RNA chaperone Hfq. In each of these organisms, an inventory of hundreds of cis- and trans-encoded sRNAs with regulatory potential was uncovered by high-throughput approaches and used for the construction of 39 sRNA family models. Genome-wide analyses of hfq mutants and co-immunoprecipitation with tagged Hfq revealed a major impact of the RNA chaperone on the physiology of plant-associated α-proteobacteria including symbiosis and virulence. Highly conserved members of the SmelC411 family are the AbcR sRNAs, which predominantly regulate ABC transport systems. AbcR1 of A. tumefaciens controls the uptake of the plant-generated signaling molecule GABA and is a central regulator of nutrient uptake systems. It has similar functions in S. meliloti and the human pathogen Brucella abortus. As RNA degradation is an important process in RNA-based gene regulation, a short overview on ribonucleases in plant-associated α-proteobacteria concludes this review.
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Affiliation(s)
- Anke Becker
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | | | - Jan-Philip Schlüter
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Jan Reinkensmeier
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
| | - Marta Robledo
- LOEWE Centre for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; Marburg, Germany
| | - Robert Giegerich
- Center for Biotechnology (CeBiTec); Bielefeld University; Bielefeld, Germany
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Rische-Grahl T, Weber L, Remes B, Förstner KU, Klug G. RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides. RNA Biol 2014; 11:855-64. [PMID: 24922065 PMCID: PMC4179960 DOI: 10.4161/rna.29440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
All bacteria contain multiple exoribonucleases to ensure a fast breakdown of different RNA molecules, either for maturation or for complete degradation to the level of mononucleotides. This efficient RNA degradation plays pivotal roles in the post-transcriptional gene regulation, in RNA processing and maturation as well as in RNA quality control mechanisms and global adaption to stress conditions. Besides different 3'-to-5' exoribonucleases mostly with overlapping functions in vivo many bacteria additionally possess the 5'-to-3' exoribonuclease, RNase J, to date the only known bacterial ribonuclease with this activity. An RNA-seq approach was applied to identify specific targets of RNase J in the α-proteobacterium Rhodobacter sphaeroides. Only few transcripts were strongly affected by the lack of RNase J implying that its function is mostly required for specific processing/degradation steps in this bacterium. The accumulation of diverse RNA fragments in the RNase J deletion mutant points to RNA features that apparently cannot be targeted by the conventional 3'-exoribonucleases in Gram-negative bacteria.
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Affiliation(s)
- Tom Rische-Grahl
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Germany
| | - Lennart Weber
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Germany
| | - Bernhard Remes
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Germany
| | - Konrad U Förstner
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Research Center for Infectious Diseases, University of Würzburg, 97080 Würzburg, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Germany
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Rapid degradation of Hfq-free RyhB in Yersinia pestis by PNPase independent of putative ribonucleolytic complexes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:798918. [PMID: 24818153 PMCID: PMC4003864 DOI: 10.1155/2014/798918] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/10/2014] [Accepted: 03/15/2014] [Indexed: 11/17/2022]
Abstract
The RNA chaperone Hfq in bacteria stabilizes sRNAs by protecting them from the attack of ribonucleases. Upon release from Hfq, sRNAs are preferably degraded by PNPase. PNPase usually forms multienzyme ribonucleolytic complexes with endoribonuclease E and/or RNA helicase RhlB to facilitate the degradation of the structured RNA. However, whether PNPase activity on Hfq-free sRNAs is associated with the assembly of RNase E or RhlB has yet to be determined. Here we examined the roles of the main endoribonucleases, exoribonucleases, and ancillary RNA-modifying enzymes in the degradation of Y. pestis RyhB in the absence of Hfq. Expectedly, the transcript levels of both RyhB1 and RyhB2 increase only after inactivating PNPase, which confirms the importance of PNPase in sRNA degradation. By contrast, the signal of RyhB becomes barely perceptible after inactivating of RNase III, which may be explained by the increase in PNPase levels resulting from the exemption of pnp mRNA from RNase III processing. No significant changes are observed in RyhB stability after deletion of either the PNPase-binding domain of RNase E or rhlB. Therefore, PNPase acts as a major enzyme of RyhB degradation independent of PNPase-containing RNase E and RhlB assembly in the absence of Hfq.
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Saramago M, Bárria C, Dos Santos RF, Silva IJ, Pobre V, Domingues S, Andrade JM, Viegas SC, Arraiano CM. The role of RNases in the regulation of small RNAs. Curr Opin Microbiol 2014; 18:105-15. [PMID: 24704578 DOI: 10.1016/j.mib.2014.02.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 12/20/2022]
Abstract
Ribonucleases (RNases) are key factors in the control of biological processes, since they modulate the processing, degradation and quality control of RNAs. This review gives many illustrative examples of the role of RNases in the regulation of small RNAs (sRNAs). RNase E and PNPase have been shown to degrade the free pool of sRNAs. RNase E can also be recruited to cleave mRNAs when they are interacting with sRNAs. RNase III cleaves double-stranded structures, and can cut both the sRNA and its RNA target when they are hybridized. Overall, ribonucleases act as conductors in the control of sRNAs. Therefore, it is very important to further understand their role in the post-transcriptional control of gene expression.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Cátia Bárria
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Inês J Silva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Susana Domingues
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.
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Göpel Y, Khan MA, Görke B. Ménage à trois: post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic. RNA Biol 2014; 11:433-42. [PMID: 24667238 PMCID: PMC4152352 DOI: 10.4161/rna.28301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In Escherichia coli, small RNAs GlmY and GlmZ feedback control synthesis of glucosamine-6-phosphate (GlcN6P) synthase GlmS, a key enzyme required for synthesis of the cell envelope. Both small RNAs are highly similar, but only GlmZ is able to activate the glmS mRNA by base-pairing. Abundance of GlmZ is controlled at the level of decay by RNase adaptor protein RapZ. RapZ binds and targets GlmZ to degradation by RNase E via protein–protein interaction. GlmY activates glmS indirectly by protecting GlmZ from degradation. Upon GlcN6P depletion, GlmY accumulates and sequesters RapZ in an RNA mimicry mechanism, thus acting as an anti-adaptor. As a result, this regulatory circuit adjusts synthesis of GlmS to the level of its enzymatic product, thereby mediating GlcN6P homeostasis. The interplay of RNase adaptor proteins and anti-adaptors provides an elegant means how globally acting RNases can be re-programmed to cleave a specific transcript in response to a cognate stimulus.
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Affiliation(s)
- Yvonne Göpel
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Muna A Khan
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
| | - Boris Görke
- Max F. Perutz Laboratories; Department of Microbiology; Immunobiology and Genetics; Center of Molecular Biology; University of Vienna; Vienna, Austria
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Abstract
Campylobacter jejuni is a foodborne bacterial pathogen, which is now considered as a leading cause of human bacterial gastroenteritis. The information regarding ribonucleases in C. jejuni is very scarce but there are hints that they can be instrumental in virulence mechanisms. Namely, PNPase (polynucleotide phosphorylase) was shown to allow survival of C. jejuni in refrigerated conditions, to facilitate bacterial swimming, cell adhesion, colonization and invasion. In several microorganisms PNPase synthesis is auto-controlled in an RNase III (ribonuclease III)-dependent mechanism. Thereby, we have cloned, overexpressed, purified and characterized Cj-RNase III (C. jejuni RNase III). We have demonstrated that Cj-RNase III is able to complement an Escherichia coli rnc-deficient strain in 30S rRNA processing and PNPase regulation. Cj-RNase III was shown to be active in an unexpectedly large range of conditions, and Mn2+ seems to be its preferred co-factor, contrarily to what was described for other RNase III orthologues. The results lead us to speculate that Cj-RNase III may have an important role under a Mn2+-rich environment. Mutational analysis strengthened the function of some residues in the catalytic mechanism of action of RNase III, which was shown to be conserved.
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Kim T, Lee J, Kim KS. Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator. BMC Microbiol 2013; 13:266. [PMID: 24267348 PMCID: PMC4222554 DOI: 10.1186/1471-2180-13-266] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 11/21/2013] [Indexed: 12/03/2022] Open
Abstract
Background Ribonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli). YmdB, a member of the macrodomain protein family, is one of known trans-acting regulators of RNase III activity; however, the significance of its regulatory role in specific bacterial cellular processes and related genes has not been determined. YmdB overexpression was used to model YmdB-induced RNase III inhibition in vivo, and microarray analysis identified gene targets and cellular processes related to RNase III inhibition. Results The expression of >2,000 E. coli genes was modulated by YmdB induction; 129 genes were strongly regulated, of which 80 have not been reported as RNase III targets. Of these, ten are involved in biofilm formation. Significantly, YmdB overexpression also inhibited biofilm formation via a process that is not uniquely dependent upon RNase III inhibition. Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB. Conclusions This is the first global profile of target genes modulated by YmdB-induced RNase III inhibition in E. coli, and the data reveal a novel, hitherto unrecognized regulatory role for YmdB in biofilm modulation.
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Affiliation(s)
- Taeyeon Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea.
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