1
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FinO/ProQ-family proteins: an evolutionary perspective. Biosci Rep 2023; 43:232566. [PMID: 36787218 PMCID: PMC9977716 DOI: 10.1042/bsr20220313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/15/2023] Open
Abstract
RNA-binding proteins are key actors of post-transcriptional networks. Almost exclusively studied in the light of their interactions with RNA ligands and the associated functional events, they are still poorly understood as evolutionary units. In this review, we discuss the FinO/ProQ family of bacterial RNA chaperones, how they evolve and spread across bacterial populations and what properties and opportunities they provide to their host cells. We reflect on major conserved and divergent themes within the family, trying to understand how the same ancestral RNA-binding fold, augmented with additional structural elements, could yield either highly specialised proteins or, on the contrary, globally acting regulatory hubs with a pervasive impact on gene expression. We also consider dominant convergent evolutionary trends that shaped their RNA chaperone activity and recurrently implicated the FinO/ProQ-like proteins in bacterial DNA metabolism, translation and virulence. Finally, we offer a new perspective in which FinO/ProQ-family regulators emerge as active evolutionary players with both negative and positive roles, significantly impacting the evolutionary modes and trajectories of their bacterial hosts.
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2
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Guimarães VA, Le Scornet A, Khemici V, Hausmann S, Armitano J, Prados J, Jousselin A, Manzano C, Linder P, Redder P. RNase J1 and J2 Are Host-Encoded Factors for Plasmid Replication. Front Microbiol 2021; 12:586886. [PMID: 34017314 PMCID: PMC8129170 DOI: 10.3389/fmicb.2021.586886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids need to ensure their transmission to both daughter-cells when their host divides, but should at the same time avoid overtaxing their hosts by directing excessive host-resources toward production of plasmid factors. Naturally occurring plasmids have therefore evolved regulatory mechanisms to restrict their copy-number in response to the volume of the cytoplasm. In many plasmid families, copy-number control is mediated by a small plasmid-specified RNA, which is continuously produced and rapidly degraded, to ensure that its concentration is proportional to the current plasmid copy-number. We show here that pSA564 from the RepA_N-family is regulated by a small antisense RNA (RNA1), which, when over-expressed in trans, blocks plasmid replication and cures the bacterial host. The 5' untranslated region (5'UTR) of the plasmid replication initiation gene (repA) potentially forms two mutually exclusive secondary structures, ON and OFF, where the latter both sequesters the repA ribosome binding site and acts as a rho-independent transcriptional terminator. Duplex formation between RNA1 and the 5'UTR shifts the equilibrium to favor the putative OFF-structure, enabling a single small RNA to down-regulate repA expression at both transcriptional and translational levels. We further examine which sequence elements on the antisense RNA and on its 5'UTR target are needed for this regulation. Finally, we identify the host-encoded exoribonucleases RNase J1 and J2 as the enzymes responsible for rapidly degrading the replication-inhibiting section of RNA1. This region accumulates and blocks RepA expression in the absence of either RNase J1 or J2, which are therefore essential host factors for pSA564 replication in Staphylococcus aureus.
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Affiliation(s)
- Vanessa Andrade Guimarães
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Alexandre Le Scornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Paul Sabatier University, Toulouse, France
| | - Vanessa Khemici
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Hausmann
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joshua Armitano
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ambre Jousselin
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Paul Sabatier University, Toulouse, France
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Redder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Paul Sabatier University, Toulouse, France
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3
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Germain-Amiot N, Augagneur Y, Camberlein E, Nicolas I, Lecureur V, Rouillon A, Felden B. A novel Staphylococcus aureus cis-trans type I toxin-antitoxin module with dual effects on bacteria and host cells. Nucleic Acids Res 2019; 47:1759-1773. [PMID: 30544243 PMCID: PMC6393315 DOI: 10.1093/nar/gky1257] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/29/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Bacterial type I toxin–antitoxin (TA) systems are widespread, and consist of a stable toxic peptide whose expression is monitored by a labile RNA antitoxin. We characterized Staphylococcus aureus SprA2/SprA2AS module, which shares nucleotide similarities with the SprA1/SprA1AS TA system. We demonstrated that SprA2/SprA2AS encodes a functional type I TA system, with the cis-encoded SprA2AS antitoxin acting in trans to prevent ribosomal loading onto SprA2 RNA. We proved that both TA systems are distinct, with no cross-regulation between the antitoxins in vitro or in vivo. SprA2 expresses PepA2, a toxic peptide which internally triggers bacterial death. Conversely, although PepA2 does not affect bacteria when it is present in the extracellular medium, it is highly toxic to other host cells such as polymorphonuclear neutrophils and erythrocytes. Finally, we showed that SprA2AS expression is lowered during osmotic shock and stringent response, which indicates that the system responds to specific triggers. Therefore, the SprA2/SprA2AS module is not redundant with SprA1/SprA1AS, and its PepA2 peptide exhibits an original dual mode of action against bacteria and host cells. This suggests an altruistic behavior for S. aureus in which clones producing PepA2 in vivo shall die as they induce cytotoxicity, thereby promoting the success of the community.
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Affiliation(s)
- Noëlla Germain-Amiot
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Yoann Augagneur
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Emilie Camberlein
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Irène Nicolas
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Valérie Lecureur
- Université de Rennes 1, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) UMR_S 1085, 35000 Rennes, France
| | - Astrid Rouillon
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Brice Felden
- Université de Rennes 1, Inserm, BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
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4
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Pluta R, Espinosa M. Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1500. [PMID: 30074293 DOI: 10.1002/wrna.1500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/27/2018] [Accepted: 07/01/2018] [Indexed: 12/27/2022]
Abstract
Bacterial plasmids constitute a wealth of shared DNA amounting to about 20% of the total prokaryotic pangenome. Plasmids replicate autonomously and control their replication by maintaining a fairly constant number of copies within a given host. Plasmids should acquire a good fitness to their hosts so that they do not constitute a genetic load. Here we review some basic concepts in plasmid biology, pertaining to the control of replication and distribution of plasmid copies among daughter cells. A particular class of plasmids is constituted by those that replicate by the rolling circle mode (rolling circle-replicating [RCR]-plasmids). They are small double-stranded DNA molecules, with a rather high number of copies in the original host. RCR-plasmids control their replication by means of a small short-lived antisense RNA, alone or in combination with a plasmid-encoded transcriptional repressor protein. Two plasmid prototypes have been studied in depth, namely the staphylococcal plasmid pT181 and the streptococcal plasmid pMV158, each corresponding to the two types of replication control circuits, respectively. We further discuss possible applications of the plasmid-encoded antisense RNAs and address some future directions that, in our opinion, should be pursued in the study of these small molecules. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Radoslaw Pluta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
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5
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Kong HK, Liu X, Lo WU, Pan Q, Law COK, Chan TF, Ho PL, Lau TCK. Identification of Plasmid-Encoded sRNAs in a blaNDM-1-Harboring Multidrug-Resistance Plasmid pNDM-HK in Enterobacteriaceae. Front Microbiol 2018; 9:532. [PMID: 29636732 PMCID: PMC5880898 DOI: 10.3389/fmicb.2018.00532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/08/2018] [Indexed: 01/15/2023] Open
Abstract
Small RNAs (sRNAs) play significant roles in regulating gene expression post-transcriptionally in response to environmental changes in bacteria. In this work, we identified and characterized six novel sRNAs from an emerging multidrug-resistance (MDR) plasmid pNDM-HK, a New Delhi metallo-β-lactamase 1 gene (blaNDM−1)-carrying IncL/M plasmid that has caused worldwide threat in recent years. These sRNAs are located at different regions of pNDM-HK, such as replication, stability, and variable regions. Moreover, one of the plasmid-encoded sRNAs (NDM-sR3) functions in an Hfq-dependent manner and possibly plays roles in the fitness of pNDM-HK carrying bacteria. In addition, we attempted to construct the phylogenetic tree based on these novel sRNAs and surprisingly, the sRNA-phylogenetic tree provided significant information about the evolutionary pathway of pNDM-HK, including possible gene acquisition and insertion from relevant plasmids. Moreover, the sRNA-phylogenetic tree can specifically cluster the IncM2 type and distinguish it from other IncL/M subtypes. In summary, this is the first study to systematically identify and characterize sRNAs from clinically-isolated MDR plasmids. We believe that these newly found sRNAs could lead to further understanding and new directions to study the evolution and dissemination of the clinically MDR bacterial plasmids.
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Affiliation(s)
- Hoi-Kuan Kong
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xuan Liu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Wai U Lo
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Qing Pan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Carmen O K Law
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ting F Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Pak L Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Terrence C K Lau
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
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6
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Gerdes K. Hypothesis: type I toxin-antitoxin genes enter the persistence field-a feedback mechanism explaining membrane homoeostasis. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0189. [PMID: 27672159 DOI: 10.1098/rstb.2016.0189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Bacteria form persisters, cells that are tolerant to multiple antibiotics and other types of environmental stress. Persister formation can be induced either stochastically in single cells of a growing bacterial ensemble, or by environmental stresses, such as nutrient starvation, in a subpopulation of cells. In many cases, the molecular mechanisms underlying persistence are still unknown. However, there is growing evidence that, in enterobacteria, both stochastically and environmentally induced persistence are controlled by the second messenger (p)ppGpp. For example, the 'alarmone' (p)ppGpp activates Lon, which, in turn, activates type II toxin-antitoxin (TA) modules to thereby induce persistence. Recently, it has been shown that a type I TA module, hokB/sokB, also can induce persistence. In this case, the underlying mechanism depends on the universally conserved GTPase Obg and, surprisingly, also (p)ppGpp. In the presence of (p)ppGpp, Obg stimulates hokB transcription and induces persistence. HokB toxin expression is under both negative and positive control: SokB antisense RNA inhibits hokB mRNA translation, while (p)ppGpp and Obg together stimulate hokB transcription. HokB is a small toxic membrane protein that, when produced in modest amounts, leads to membrane depolarization, cell stasis and persistence. By contrast, overexpression of HokB disrupts the membrane potential and kills the cell. These observations raise the question of how expression of HokB is regulated. Here, I propose a homoeostatic control mechanism that couples HokB expression to the membrane-bound RNase E that degrades and inactivates SokB antisense RNA.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Kenn Gerdes
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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7
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Piatek MJ, Henderson V, Zynad HS, Werner A. Natural antisense transcription from a comparative perspective. Genomics 2016; 108:56-63. [PMID: 27241791 PMCID: PMC4996343 DOI: 10.1016/j.ygeno.2016.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/08/2016] [Accepted: 05/25/2016] [Indexed: 12/28/2022]
Abstract
Natural antisense transcripts (NATs) can interfere with the expression of complementary sense transcripts with exquisite specificity. We have previously cloned NATs of Slc34a loci (encoding Na-phosphate transporters) from fish and mouse. Here we report the cloning of a human SLC34A1-related NAT that represents an alternatively spliced PFN3 transcript (Profilin3). The transcript is predominantly expressed in testis. Phylogenetic comparison suggests two distinct mechanisms producing Slc34a-related NATs: Alternative splicing of a transcript from a protein coding downstream gene (Pfn3, human/mouse) and transcription from the bi-directional promoter (Rbpja, zebrafish). Expression analysis suggested independent regulation of the complementary Slc34a mRNAs. Analysis of randomly selected bi-directionally transcribed human/mouse loci revealed limited phylogenetic conservation and independent regulation of NATs. They were reduced on X chromosomes and clustered in regions that escape inactivation. Locus structure and expression pattern suggest a NATs-associated regulatory mechanisms in testis unrelated to the physiological role of the sense transcript encoded protein.
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Affiliation(s)
- Monica J Piatek
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Victoria Henderson
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Hany S Zynad
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Andreas Werner
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom.
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8
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Abstract
Plasmids are selfish genetic elements that normally constitute a burden for the bacterial host cell. This burden is expected to favor plasmid loss. Therefore, plasmids have evolved mechanisms to control their replication and ensure their stable maintenance. Replication control can be either mediated by iterons or by antisense RNAs. Antisense RNAs work through a negative control circuit. They are constitutively synthesized and metabolically unstable. They act both as a measuring device and a regulator, and regulation occurs by inhibition. Increased plasmid copy numbers lead to increasing antisense-RNA concentrations, which, in turn, result in the inhibition of a function essential for replication. On the other hand, decreased plasmid copy numbers entail decreasing concentrations of the inhibiting antisense RNA, thereby increasing the replication frequency. Inhibition is achieved by a variety of mechanisms, which are discussed in detail. The most trivial case is the inhibition of translation of an essential replication initiator protein (Rep) by blockage of the rep-ribosome binding site. Alternatively, ribosome binding to a leader peptide mRNA whose translation is required for efficient Rep translation can be prevented by antisense-RNA binding. In 2004, translational attenuation was discovered. Antisense-RNA-mediated transcriptional attenuation is another mechanism that has, so far, only been detected in plasmids of Gram-positive bacteria. ColE1, a plasmid that does not need a plasmid-encoded replication initiator protein, uses the inhibition of primer formation. In other cases, antisense RNAs inhibit the formation of an activator pseudoknot that is required for efficient Rep translation.
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9
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López-Aguilar C, Romero-López C, Espinosa M, Berzal-Herranz A, Del Solar G. The 5'-tail of antisense RNAII of pMV158 plays a critical role in binding to the target mRNA and in translation inhibition of repB. Front Genet 2015; 6:225. [PMID: 26175752 PMCID: PMC4485353 DOI: 10.3389/fgene.2015.00225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/12/2015] [Indexed: 02/05/2023] Open
Abstract
Rolling-circle replication of streptococcal plasmid pMV158 is controlled by the concerted action of two trans-acting elements, namely transcriptional repressor CopG and antisense RNAII, which inhibit expression of the repB gene encoding the replication initiator protein. The pMV158-encoded antisense RNAII exerts its activity of replication control by inhibiting translation of the essential repB gene. RNAII is the smallest and simplest among the characterized antisense RNAs involved in control of plasmid replication. Structure analysis of RNAII revealed that it folds into an 8-bp-long stem containing a 1-nt bulge and closed by a 6-nt apical loop. This hairpin is flanked by a 17-nt-long single-stranded 5′-tail and an 8-nt-long 3′-terminal U-rich stretch. Here, the 3′ and 5′ regions of the 5′-tail of RNAII are shown to play a critical role in the binding to the target mRNA and in the inhibition of repB translation, respectively. In contrast, the apical loop of the single hairpin of RNAII plays a rather secondary role and the upper stem region hardly contributes to the binding or inhibition processes. The entire 5′-tail is required for efficient inhibition of repB translation, though only the 8-nt-long region adjacent to the hairpin seems to be essential for rapid binding to the mRNA. These results show that a “kissing” interaction involving base-pairing between complementary hairpin loops in RNAII and mRNA is not critical for efficient RNA/RNA binding or repB translation inhibition. A singular binding mechanism is envisaged whereby initial pairing between complementary single-stranded regions in the antisense and sense RNAs progresses upwards into the corresponding hairpin stems to form the intermolecular duplex.
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Affiliation(s)
- Celeste López-Aguilar
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
| | - Cristina Romero-López
- Molecular Biology Department, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC) Granada, Spain
| | - Manuel Espinosa
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
| | - Alfredo Berzal-Herranz
- Molecular Biology Department, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC) Granada, Spain
| | - Gloria Del Solar
- Molecular Microbiology and Infection Biology Department, Centro de Investigaciones Biológicas (CIB-CSIC) Madrid, Spain
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10
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Brantl S, Jahn N. sRNAs in bacterial type I and type III toxin-antitoxin systems. FEMS Microbiol Rev 2015; 39:413-27. [PMID: 25808661 DOI: 10.1093/femsre/fuv003] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 01/17/2023] Open
Abstract
Toxin-antitoxin (TA) loci consist of two genes: a stable toxin whose overexpression kills the cell or causes growth stasis and an unstable antitoxin that neutralizes the toxin action. Currently, five TA systems are known. Here, we review type I and type III systems in which the antitoxins are regulatory RNAs. Type I antitoxins act by a base-pairing mechanism on toxin mRNAs. By contrast, type III antitoxins are RNA pseudoknots that bind their cognate toxins directly in an RNA-protein interaction. Whereas for a number of plasmid-encoded systems detailed information on structural requirements, kinetics of interaction with their targets and regulatory mechanisms employed by the antitoxin RNAs is available, the investigation of chromosomal systems is still in its infancy. Here, we summarize our current knowledge on that topic. Furthermore, we compare factors and conditions that induce antitoxins or toxins and different mechanisms of toxin action. Finally, we discuss biological roles for chromosome-encoded TA systems.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
| | - Natalie Jahn
- AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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12
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Holmstrom ED, Polaski JT, Batey RT, Nesbitt DJ. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch. J Am Chem Soc 2014; 136:16832-43. [PMID: 25325398 PMCID: PMC4277777 DOI: 10.1021/ja5076184] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Riboswitches
represent a family of highly structured regulatory
elements found primarily in the leader sequences of bacterial mRNAs.
They function as molecular switches capable of altering gene expression;
commonly, this occurs via a conformational change in a regulatory
element of a riboswitch that results from ligand binding in the aptamer
domain. Numerous studies have investigated the ligand binding process,
but little is known about the structural changes in the regulatory
element. A mechanistic description of both processes is essential
for deeply understanding how riboswitches modulate gene expression.
This task is greatly facilitated by studying all aspects of riboswitch
structure/dynamics/function in the same model system. To this end,
single-molecule fluorescence resonance energy transfer (smFRET) techniques
have been used to directly observe the conformational dynamics of
a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work
is unique in that it contains all of the structural elements both
necessary and sufficient for regulation of gene expression in a biological
context. The results of this investigation reveal that the undocking
rate constant associated with the disruption of a long-range kissing-loop
(KL) interaction is substantially decreased when the ligand is bound
to the RNA, resulting in a preferential stabilization of the docked
conformation. Notably, the formation of this tertiary KL interaction
directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome
binding site) via base-pairing, thus preventing translation initiation.
These results reveal that the conformational dynamics of this regulatory
switch are quantitatively described by a four-state kinetic model,
whereby ligand binding promotes formation of the KL interaction. The
results of complementary cell-based gene expression experiments conducted
in Escherichia coli are highly correlated
with the smFRET results, suggesting that KL formation is directly
responsible for regulating gene expression.
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Affiliation(s)
- Erik D Holmstrom
- JILA, University of Colorado and National Institute of Standards and Technology, and ‡Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0440, United States
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Brantl S. Antisense-RNA mediated control of plasmid replication - pIP501 revisited. Plasmid 2014; 78:4-16. [PMID: 25108234 DOI: 10.1016/j.plasmid.2014.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/24/2014] [Accepted: 07/26/2014] [Indexed: 02/02/2023]
Abstract
Over the past decade, a wealth of small noncoding RNAs (sRNAs) have been discovered in the genomes of almost all bacterial species, where they constitute the most abundant class of posttranscriptional regulators. These sRNAs are key-players in prokaryotic metabolism, stress response and virulence. However, the first bona-fide antisense RNAs had been found already in 1981 in plasmids, where they regulate replication or maintenance. Antisense RNAs involved in plasmid replication control - meanwhile investigated in depth for almost 35 years - employ a variety of mechanisms of action: They regulate primer maturation, inhibit translation of essential replication initiator proteins (Rep proteins) as well as leader peptides or the formation of activator pseudoknots required for efficient rep translation. Alternatively they attenuate transcription or translation of rep mRNAs. Some antisense RNAs collaborate with transcriptional repressors to ensure proper copy-number control. Here, I summarize our knowledge on replication control of the broad-host range plasmid pIP501 that was originally isolated from Streptococcus agalactiae. Plasmid pIP501 uses two copy number-control elements, RNAIII, a cis-encoded antisense RNA, and transcriptional repressor CopR. RNA III mediates transcription attenuation, a rather widespread concept that found its culmination in the recent discovery of riboswitches. A peculiarity of pIP501 is the unusual stability of RNA III, which requires a second function of CopR: CopR does not only repress transcription from the essential repR promoter, but also prevents convergent transcription between rep mRNA and RNAIII, thereby indirectly increasing the amount of RNAIII. The concerted action of these two control elements is necessary to prevent plasmid loss at dangerously low copy numbers.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
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14
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Abstract
Type I toxin–antitoxin systems encoded on bacterial chromosomes became the focus of research during the past years. However, little is known in terms of structural requirements, kinetics of interaction with their targets and regulatory mechanisms of the antitoxin RNAs. Here, we present a combined in vitro and in vivo analysis of the bsrG/SR4 type I toxin–antitoxin system from Bacillus subtilis. The secondary structures of SR4 and bsrG mRNA and of the SR4/bsrG RNA complex were determined, apparent binding rate constants calculated and functional segments required for complex formation narrowed down. The initial contact between SR4 and its target was shown to involve the SR4 terminator loop and loop 3 of bsrG mRNA. Additionally, a contribution of the stem of SR4 stem-loop 3 to target binding was found. On SR4/bsrG complex formation, a 4 bp double-stranded region sequestering the bsrG Shine Dalgarno (SD) sequence was extended to 8 bp. Experimental evidence was obtained that this extended region caused translation inhibition of bsrG mRNA. Therefore, we conclude that SR4 does not only promote degradation of the toxin mRNA but also additionally inhibit its translation. This is the first case of a dual-acting antitoxin RNA.
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Affiliation(s)
| | - Sabine Brantl
- *To whom correspondence should be addressed. Tel: +49 3641 949570; Fax: +49 3641 949302;
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15
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Brantl S. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiol 2012; 7:853-71. [DOI: 10.2217/fmb.12.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
sRNAs that act by base pairing were first discovered in plasmids, phages and transposons, where they control replication, maintenance and transposition. Since 2001, however, computational searches were applied that led to the discovery of a plethora of sRNAs in bacterial chromosomes. Whereas the majority of these chromsome-encoded sRNAs have been investigated in Escherichia coli, Salmonella and other Gram-negative bacteria, only a few well-studied examples are known from Gram-positive bacteria. Here, the author summarizes our current knowledge on plasmid- and chromosome-encoded sRNAs from Gram-positive species, thereby focusing on regulatory mechanisms used by these RNAs and their biological role in complex networks. Furthermore, regulatory factors that control the expression of these RNAs will be discussed and differences between sRNAs from Gram-positive and Gram-negative bacteria highlighted. The main emphasis of this review is on sRNAs that act by base pairing (i.e., by an antisense mechanism). Thereby, both plasmid-encoded and chromosome-encoded sRNAs will be considered.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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16
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Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophys J 2012; 102:1097-107. [PMID: 22404932 DOI: 10.1016/j.bpj.2011.12.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 12/22/2011] [Accepted: 12/30/2011] [Indexed: 11/22/2022] Open
Abstract
Kissing hairpin interactions form when the loop residues of two hairpins have Watson-Crick complementarity. In a unimolecular context, kissing interactions are important for tertiary folding and pseudoknot formation, whereas in a bimolecular context, they provide a basis for molecular recognition. In some cases, kissing complexes can be a prelude to strand displacement reactions where the two hairpins resolve to form a stable extended intermolecular duplex. The kinetics and thermodynamics of kissing-complex formation and their subsequent strand-displacement reactions are poorly understood. Here, biophysical techniques including isothermal titration calorimetry, surface plasmon resonance, and single-molecule fluorescence have been employed to probe the factors that govern the stability of kissing complexes and their subsequent structural rearrangements. We show that the general understanding of RNA duplex formation can be extended to kissing complexes but that kissing complexes display an unusual level of stability relative to simple duplexes of the same sequence. These interactions form and break many times at room temperature before becoming committed to a slow, irreversible forward transition to the strand-displaced form. Furthermore, using smFRET we show that the primary difference between stable and labile kissing complexes is based almost completely on their off rates. Both stable and labile complexes form at the same rate within error, but less stable species dissociate rapidly, allowing us to understand how these complexes can help generate specificity along a folding pathway or during a gene regulation event.
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17
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Le Roux F, Davis BM, Waldor MK. Conserved small RNAs govern replication and incompatibility of a diverse new plasmid family from marine bacteria. Nucleic Acids Res 2010; 39:1004-13. [PMID: 20923782 PMCID: PMC3035462 DOI: 10.1093/nar/gkq852] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Plasmids are autonomously replicating extrachromosomal DNA molecules that often impart key phenotypes to their bacterial hosts. Plasmids are abundant in marine bacteria, but there is scant knowledge of the mechanisms that control their replication in these hosts. Here, we identified and characterized the factors governing replication of a new family of plasmids from marine bacteria, typified by the virulence-linked plasmid pB1067 of Vibrio nigripulchritudo. Members of this family are prevalent among, yet restricted to, the Vibrionaceae. Unlike almost all plasmid families characterized to date, the ori regions of these plasmids do not encode a Rep protein to initiate DNA replication; instead, the ori regions encode two partially complementary RNAs. The smaller, termed RNA I, is ∼68-nt long and functions as a negative regulator and the key determinant of plasmid incompatibility. This Marine RNA-based (MRB) plasmid family is the first characterized family of replicons derived from marine bacteria. Only one other plasmid family (the ColE1 family) has previously been reported to rely on RNA-mediated replication initiation. However, since the sequences and structures of MRB RNA I transcripts are not related to those of ColE1 replicons, these two families of RNA-dependent replicons likely arose by convergent evolution.
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Affiliation(s)
- Frédérique Le Roux
- IFREMER, Laboratoire de Génétique et Pathologie, Ifremer, 17390 La Tremblade, France.
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18
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Giangrossi M, Prosseda G, Tran CN, Brandi A, Colonna B, Falconi M. A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri. Nucleic Acids Res 2010; 38:3362-75. [PMID: 20129941 PMCID: PMC2879508 DOI: 10.1093/nar/gkq025] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 12/30/2009] [Accepted: 01/11/2010] [Indexed: 12/26/2022] Open
Abstract
The virulence gene icsA of Shigella flexneri encodes an invasion protein crucial for host colonization by pathogenic bacteria. Within the intergenic region virA-icsA, we have discovered a new gene that encodes a non-translated antisense RNA (named RnaG), transcribed in cis on the complementary strand of icsA. In vitro transcription assays show that RnaG promotes premature termination of transcription of icsA mRNA. Transcriptional inhibition is also observed in vivo by monitoring the expression profile in Shigella by real-time polymerase chain reaction and when RnaG is provided in trans. Chemical and enzymatic probing of the leader region of icsA mRNA either free or bound to RnaG indicate that upon hetero-duplex formation an intrinsic terminator, leading to transcription block, is generated on the nascent icsA mRNA. Mutations in the hairpin structure of the proposed terminator impair the RnaG mediated-regulation of icsA transcription. This study represents the first evidence of transcriptional attenuation mechanism caused by a small RNA in Gram-negative bacteria. We also present data on the secondary structure of the antisense region of RnaG. In addition, alternatively silencing icsA and RnaG promoters, we find that transcription from the strong RnaG promoter reduces the activity of the weak convergent icsA promoter through the transcriptional interference regulation.
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Affiliation(s)
- Mara Giangrossi
- Laboratory of Molecular Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino, MC, Italy
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19
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Han K, Kim KS, Bak G, Park H, Lee Y. Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family. Nucleic Acids Res 2010; 38:5851-66. [PMID: 20453032 PMCID: PMC2943612 DOI: 10.1093/nar/gkq292] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Five Sib antitoxin RNAs, members of a family of cis-encoded small regulatory RNAs (sRNAs) in Escherichia coli, repress their target mRNAs, which encode Ibs toxins. This target repression occurs only between cognate sRNA–mRNA pairs with an exception of ibsA. We performed co-transformation assays to assess the ability of SibC derivatives to repress ibsC expression, thereby revealing the regions of SibC that are essential for ibsC mRNA recognition. SibC has two target recognition domains, TRD1 and TRD2, which function independently. The target site for TRD1 is located within the ORF of ibsC, whereas the target site for TRD2 is located in the translational initiation region. The TRD1 sequence is sufficient to repress ibsC expression. In contrast, TRD2 requires a specific structure in addition to the recognition sequence. An in vitro structural probing analysis showed that the initial interactions at these two recognition sites allowed base-pairing to progress into the flanking sequences. Displacement of the TRD1 and TRD2 domains of SibC by the corresponding domains of SibD changed the target specificity of SibC from ibsC to ibsD, suggesting that these two elements modulate the cognate target recognition of each Sib RNA by discriminating among non-cognate ibs mRNAs.
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Affiliation(s)
- Kook Han
- Department of Chemistry, KAIST, Daejeon 305-701 and Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea
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20
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Silveira ACG, Robertson KL, Lin B, Wang Z, Vora GJ, Vasconcelos ATR, Thompson FL. Identification of non-coding RNAs in environmental vibrios. MICROBIOLOGY-SGM 2010; 156:2452-2458. [PMID: 20447992 DOI: 10.1099/mic.0.039149-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The discovery of non-coding RNA (ncRNA) has been mainly limited to laboratory model systems and human pathogenic bacteria. In this study, we begin to explore the ncRNA diversity in four recently sequenced environmental Vibrio species (Vibrio alginolyticus 40B, Vibrio communis 1DA3, Vibrio mimicus VM573 and Vibrio campbellii BAA-1116) by performing in silico searches using Infernal and Rfam for the identification of putative ncRNA-encoding genes. This search method resulted in the identification of 31-38 putative ncRNA genes per species and the total ncRNA catalogue spanned an assortment of regulatory mechanisms (riboswitches, cis-encoded ncRNAs, trans-encoded ncRNAs, modulators of protein activity, ribonucleoproteins, transcription termination ncRNAs and unknown). We chose to experimentally validate the identifications for V. campbellii BAA-1116 using a microarray-based expression profiling strategy. Transcript hybridization to tiled probes targeting annotated V. campbellii BAA-1116 intergenic regions revealed that 21 of the 38 predicted ncRNA genes were expressed in mid-exponential-phase cultures grown in nutrient-rich medium. The microarray findings were confirmed by testing a subset of three highly expressed (6S, tmRNA and TPP-2) and three moderately expressed (CsrB, GcvB and purine) ncRNAs via reverse transcription PCR. Our findings provide new information on the diversity of ncRNA in environmental vibrios while simultaneously promoting a more accurate annotation of genomic intergenic regions.
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Affiliation(s)
- Ana Cristina G Silveira
- National Laboratory for Scientific Computing (LNCC), Petrópolis, RJ, Brazil.,Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Kelly L Robertson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | - Zheng Wang
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | - Gary J Vora
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
| | | | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, CEP 21941-590, Brazil
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21
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Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d. J Bacteriol 2010; 192:3268-78. [PMID: 20435728 DOI: 10.1128/jb.00118-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Replication and segregation of the Rhizobium etli symbiotic plasmid (pRetCFN42d) depend on the presence of a repABC operon, which carries all the plasmid-encoded elements required for these functions. All repABC operons share three protein-encoding genes (repA, repB, and repC), an antisense RNA (ctRNA) coding gene, and at least one centromere-like region (parS). The products of repA and repB, in conjunction with the parS region, make up the segregation system, and they negatively regulate operon transcription. The last gene of the operon, repC, encodes the initiator protein. The ctRNA is a negative posttranscriptional regulator of repC. In this work, we analyzed the secondary structures of the ctRNA and its target and mapped the motifs involved in the complex formed between them. Essential residues for the effective interaction localize at the unpaired 5' end of the antisense molecule and the loop of the target mRNA. In light of our results, we propose a model explaining the mechanism of action of this ctRNA in the regulation of plasmid replication in R. etli.
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22
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Shokeen S, Johnson CM, Greenfield TJ, Manias DA, Dunny GM, Weaver KE. Structural analysis of the Anti-Q-Qs interaction: RNA-mediated regulation of E. faecalis plasmid pCF10 conjugation. Plasmid 2010; 64:26-35. [PMID: 20332003 DOI: 10.1016/j.plasmid.2010.03.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/08/2010] [Accepted: 03/17/2010] [Indexed: 11/18/2022]
Abstract
Conjugation of the E. faecalis plasmid pCF10 is triggered in response to peptide sex pheromone cCF10 produced by potential recipients. Regulation of this response is complex and multi-layered and includes a small regulatory RNA, Anti-Q that participates in a termination/antitermination decision controlling transcription of the conjugation structural genes. In this study, the secondary structure of the Anti-Q transcript and its sites of interaction with its target, Qs, were determined. The primary site of interaction occurred at a centrally-located loop whose sequence showed high variability in analogous molecules on other pheromone-responsive plasmids. This loop, designated the specificity loop, was demonstrated to be important but not sufficient for distinguishing between Qs molecules from pCF10 and another pheromone-responsive plasmid pAD1. A loop 5' from the specificity loop which carries a U-turn motif played no demonstrable role in Anti-Q-Qs interaction or regulation of the termination/antitermination decision. These results provide direct evidence for a critical role of Anti-Q-Qs interactions in posttranscriptional regulation of pCF10 transfer functions.
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Affiliation(s)
- Sonia Shokeen
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E Clark St. Vermillion, SD 57069, USA
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23
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Abstract
Bioinformatic approaches are described for the discovery of small regulatory RNAs (srRNAs) in the biomining microorganism Acidithiobacillus ferrooxidans. Intergenic regions of the annotated genome were extracted and computationally searched for srRNAs. Candidate srRNAs that were associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for further study. Experimental validation is presented for 6S srRNA and frr. srRNAs are known to control gene expression in a wide variety of microorganisms, usually at the post-transcriptional level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with regulatory proteins. srRNAs are involved in the regulation of a large variety of processes. Frr is an RNA antisense to fur; the latter encodes a global regulator involved the control of a large number of genes involved in iron uptake and homeostasis. Because of the widespread occurrence and extensive repertoire of regulatory functions afforded by srRNAs, it is expected that their discovery functional analysis in biomining microorganisms will contribute to improving our understanding of the microbiology of bioleaching processes.
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24
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Abstract
Small RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life. Until 1999, only about 10 abundant sRNAs had been identified in Escherichia coli, but the function of most of them remained elusive for a long time. However, since 2001, a series of systematic computational approaches have revealed that bacteria encode a tremendous number of sRNAs. In E. coli more than 100 sRNAs are now known. However, approximately only 20 of them have been assigned a biological function, indicating that this is still a challenging issue. Systematic searches have been performed for a few Gram-positive bacterial species, too. sRNAs can be divided into two major groups: the first group comprises so-called bona fide antisense RNAs, which regulate gene expression by a base-pairing mechanism with mRNA. The second group of sRNAs encompasses RNAs that act by binding to small proteins.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.
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25
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Williams JA, Carnes AE, Hodgson CP. Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production. Biotechnol Adv 2009; 27:353-70. [PMID: 19233255 DOI: 10.1016/j.biotechadv.2009.02.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/02/2009] [Accepted: 02/07/2009] [Indexed: 10/21/2022]
Abstract
Critical molecular and cellular biological factors impacting design of licensable DNA vaccine vectors that combine high yield and integrity during bacterial production with increased expression in mammalian cells are reviewed. Food and Drug Administration (FDA), World Health Organization (WHO) and European Medical Agencies (EMEA) regulatory guidance's are discussed, as they relate to vector design and plasmid fermentation. While all new vectors will require extensive preclinical testing to validate safety and performance prior to clinical use, regulatory testing burden for follow-on products can be reduced by combining carefully designed synthetic genes with existing validated vector backbones. A flowchart for creation of new synthetic genes, combining rationale design with bioinformatics, is presented. The biology of plasmid replication is reviewed, and process engineering strategies that reduce metabolic burden discussed. Utilizing recently developed low metabolic burden seed stock and fermentation strategies, optimized vectors can now be manufactured in high yields exceeding 2 g/L, with specific plasmid yields of 5% total dry cell weight.
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26
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Stenvang J, Kauppinen S. MicroRNAs as targets for antisense-based therapeutics. Expert Opin Biol Ther 2008; 8:59-81. [PMID: 18081537 DOI: 10.1517/14712598.8.1.59] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are a novel class of endogenous non-coding single-stranded RNAs, which regulate gene expression post-transcriptionally by base pairing with their target mRNAs. So far > 5000 miRNA entries have been registered and miRNAs have been implicated in most, if not all, central cellular processes and several diseases. As the mechanism of action for miRNA regulation of target mRNAs is mediated by Watson-Crick base pairing, antisense oligonucleotides targeting the miRNAs appear as an obvious choice to specifically inhibit miRNA function. Indeed, miRNAs can be antagonized in vivo by oligonucleotides composed of high-affinity nucleotide mimics. Lessons learned from traditional antisense strategies and small-interfering RNA approaches, that is from potent nucleotide mimics, design rules, pharmacokinetics, administration and safety issues, are likely to pave the way for future clinical trials of miRNA-antagonizing oligonucleotides.
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Affiliation(s)
- Jan Stenvang
- University of Copenhagen, Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
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27
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Discovery of Small Regulatory RNAs Extends Our Understanding of Gene Regulation in the Acidithiobacillus Genus. ACTA ACUST UNITED AC 2007. [DOI: 10.4028/www.scientific.net/amr.20-21.535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small regulatory RNAs (srRNAs) control gene expression in Bacteria, usually at the posttranscriptional
level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with
regulatory proteins. srRNAs are involved in the regulation of a large variety of processes such as
plasmid replication, transposition and global genetic circuits that respond to environmental changes.
Since their discovery a few years ago, it has become apparent that they are prolific and widespread. In
this study, we describe bioinformatic approaches to srRNA discovery in the biomining microorganisms
Acidithiobacillus ferrooxidans, A. caldus and A. thiooxidans. Intergenic regions of the annotated
genomes were extracted and computationally searched for srRNAs. Candidate srRNAs that were
associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for
further study. The resulting potential srRNAs include known examples from other microorganisms and
some novel candidates and reveal interesting underlying biology of the Acidithiobacillus genus.
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28
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Abstract
In Vibrio cholerae, bioinformatic approaches have been used to predict the locations of numerous small RNA (sRNA)-encoding genes, but biological roles have been determined for very few. Here, we describe the expression, processing and biological role of an sRNA (previously known as A10) that was identified through such analyses. We have renamed this sRNA MicX as, like the Escherichia coli sRNAs MicA, MicC and MicF, it regulates expression of an outer membrane protein (OMP). MicX appears to be a direct negative regulator of vc0972, which encodes an uncharacterized OMP, and vc0620, which encodes the periplasmic component of a peptide ABC transporter. Hfq is apparently not required for MicX's interactions with and regulation of these targets. The sequence encoding MicX overlaps with vca0943; however, primary transcripts of MicX are processed in an RNase E- and Hfq-dependent fashion to a shorter, still active and much more stable form consisting largely of the vca0943 3′ untranslated region. Our data suggest that processing of MicX enhances its effectiveness, and that sRNA cleavage is not simply a means to sRNA inactivation and clearance.
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Affiliation(s)
- Brigid M Davis
- Channing Laboratory, Brigham and Women's Hospital, and Howard Hughes Medical Institute, Boston, MA 02111, USA.
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29
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Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 2007; 10:102-9. [PMID: 17387036 DOI: 10.1016/j.mib.2007.03.012] [Citation(s) in RCA: 224] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 03/14/2007] [Indexed: 12/13/2022]
Abstract
Bacterial small regulatory RNAs that act by base-pairing can be divided into two classes: cis-encoded and trans-encoded antisense RNAs. The former--mainly discovered in plasmids, phages and transposons--are encoded in the same DNA locus and are therefore completely complementary to their targets over a long sequence stretch. Regulatory mechanisms employed by these RNAs encompass inhibition of primer maturation or RNA pseudoknot formation, transcriptional attenuation, inhibition of translation or promotion of RNA degradation or cleavage. Although the final product of antisense RNA/target RNA binding is a full duplex that is degraded by RNase III, inhibition does not require complete duplex formation. By contrast, in many cases, partially paired binding intermediates have been shown to be sufficient for the biological function.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.
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30
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Heidrich N, Brantl S. Antisense RNA-mediated transcriptional attenuation in plasmid pIP501: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA. Microbiology (Reading) 2007; 153:420-427. [PMID: 17259613 DOI: 10.1099/mic.0.2006/002329-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcal plasmid pIP501 uses antisense RNA-mediated transcriptional attenuation to regulate its replication. Previous in vitro assays suggested that binding intermediates between RNAII (sense RNA) and RNAIII (antisense RNA) are sufficient for inhibition, and a U-turn structure on RNAII loop L1 was found to be crucial for the interaction with RNAIII. Here, sequence and structural requirements for an efficient RNAII-RNAIII interaction were investigated. A detailed probing of RNA secondary structure combined with in vitro single-round transcription assays indicated that complex formation between the two molecules progresses into the lower stems of both loop pairs of the sense and antisense RNAs, but that the complex between RNAII and RNAIII is not a full duplex. Stem-loops L3 and L4 were required to be linked to one other for efficient contact with the complementary loops L2 and L1 of the sense RNA, indicating a simultaneous interaction between these two loop pairs. Thereby, the sequence and length of the spacer connecting L3 and L4 were shown not to be important for inhibition.
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Affiliation(s)
- Nadja Heidrich
- Friedrich-Schiller-Universität Jena, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany
| | - Sabine Brantl
- Friedrich-Schiller-Universität Jena, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany
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31
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Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res 2006; 16:922-33. [PMID: 16769979 PMCID: PMC1484459 DOI: 10.1101/gr.5210006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Given that humans have about the same number of genes as mice and not so many more than worm, what makes us more complex? Antisense transcripts are implicated in many aspects of gene regulation. Is there a functional connection between antisense transcription and organismic complexity, that is, is antisense regulation especially prevalent in humans? We used the same robust protocol to identify antisense transcripts in humans and five other metazoan genomes (mouse, rat, chicken, fruit fly, and nematode), and found that the estimated proportions of genes involved in antisense transcription are highly sensitive to the number of transcripts included in the analysis. By controlling for transcript abundance, we find that the probability that any given transcript is putatively involved in sense-antisense regulation is no higher in humans than in other vertebrates but appears unusually high in flies and especially low in nematodes. Similarly, there is no evidence that the proportion of sense-antisense transcripts is especially higher in humans than other vertebrates in a given subset of transcript sequences such as mRNAs, coding sequences, conserved, or nonconserved transcripts. Although antisense transcription might be enriched in mammalian brains compared with nonbrain tissues, it is no more enriched in human brain than in mouse brain. Overall, therefore, while we see striking variation between multicellular animals in the abundance of antisense transcripts, there is no evidence for a link between antisense transcription and organismic complexity. More particularly, we see no evidence that humans are in any way unusual among the vertebrates in this regard. Instead, our results suggest that antisense transcription might be prevalent in almost all metazoan genomes, nematodes being an unexplained exception.
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Affiliation(s)
- Miao Sun
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Laurence D. Hurst
- Department of Biology and Biochemistry, University of Bath, Somerset, BA2 7AY, United Kingdom
- Corresponding authors.E-mail ; fax (773) 702-3002.E-mail ; fax 44 (0)1225-386779
| | - Gordon G. Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06030-3301, USA
| | - Jianjun Chen
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Corresponding authors.E-mail ; fax (773) 702-3002.E-mail ; fax 44 (0)1225-386779
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32
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Abstract
Small regulatory RNAs can modify the activity of proteins and the stability and translation of mRNAs. They have now been found in a wide range of organisms, and can play previously unsuspected critical regulatory roles. The bacterial small RNAs include two major classes. The largest family(with at least 20 members in Escherichia coli K12) acts by base pairing with target mRNAs to modify mRNA translation or stability; this class of RNAs also uses an RNA chaperone protein, Hfq. DsrA is the best-studied example of this family of RNAs. It has been shown to positively regulate translation of the transcription factor RpoS by opening an inhibitory hairpin in the mRNA, and to negatively regulate translation of hns by pairing just beyond the translation initiation codon. The class of RNAs that modify activity of proteins is exemplified by CsrB and CsrC of E. coli, two RNAs that bind to and inhibit CsrA, a protein translational regulator. Homologs of CsrA and related regulatory RNAs have been implicated in the regulation of gluconeogenesis, biofilm formation,and virulence factor expression in plant and human pathogens.
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Affiliation(s)
- Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
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33
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Bois JS, Venkataraman S, Choi HMT, Spakowitz AJ, Wang ZG, Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res 2005; 33:4090-5. [PMID: 16043632 PMCID: PMC1180668 DOI: 10.1093/nar/gki721] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.
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Affiliation(s)
| | - Suvir Venkataraman
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
| | - Harry M. T. Choi
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
| | | | | | - Niles A. Pierce
- Department of Bioengineering, California Institute of TechnologyPasadena, CA 91125, USA
- Department of Applied and Computational Mathematics, California Institute of TechnologyPasadena, CA 91125, USA
- To whom correspondence should be addressed at Caltech, Mail Code 114-96, Pasadena, CA 91125, USA. Tel: +1 626 395 8086; Fax: +1 626 395 8845;
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34
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Munroe SH. Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns. J Cell Biochem 2005; 93:664-71. [PMID: 15389973 DOI: 10.1002/jcb.20252] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High-throughput analysis of RNA molecules in multicellular eukaryotes has revealed an abundance of complementary antisense RNAs that are transcribed from separate or overlapping genes. In mammals these include many novel non-coding RNAs of unknown function. This unexpected complexity of the mammalian transcriptome suggests that expression of many genes is regulated post-transcriptionally by mechanisms mediated by RNA-RNA base pairing. The recent discovery of the widespread expression of microRNAs in animals and plants provides a prototypic example of such regulation in eukaryotes. However, there are likely to be numerous other types of antisense regulation in eukaryotes, many as yet uncharacterized.
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Affiliation(s)
- Stephen H Munroe
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA.
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35
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Gottesman S. Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 2005; 21:399-404. [PMID: 15913835 DOI: 10.1016/j.tig.2005.05.008] [Citation(s) in RCA: 388] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/17/2005] [Accepted: 05/09/2005] [Indexed: 11/25/2022]
Abstract
Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent studies have led to the identification of numerous small regulatory RNAs in Escherichia coli and in other bacteria. As in eukaryotic cells, a major class of these small RNAs acts by base-pairing with target mRNAs, resulting in changes in the translation and stability of the mRNA. Roles for these non-coding pairing RNAs in bacteria have been demonstrated in several cases. Because these non-coding RNAs act post-transcriptionally, they impose a regulatory step that is independent of and epistatic to any transcriptional signals for their target mRNAs.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA.
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36
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Denap JCB, Thomas JR, Musk DJ, Hergenrother PJ. Combating drug-resistant bacteria: small molecule mimics of plasmid incompatibility as antiplasmid compounds. J Am Chem Soc 2005; 126:15402-4. [PMID: 15563166 DOI: 10.1021/ja044207u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major mechanism for bacterial resistance to antibiotics is through the acquisition of a plasmid coding for resistance-mediating proteins. Described herein is a strategy to eliminate these plasmids from bacteria, thus resensitizing the bacteria to antibiotics. This approach involves mimicking a natural mechanism for plasmid elimination, known as plasmid incompatibility. The compound apramycin was identified as a tight binder to SLI RNA (Kd = 93 nM), the in vivo target of the plasmid incompatibility determinate RNA I, and footprinting/mutagenesis studies indicate apramycin binds SLI in the important regulatory region that dictates plasmid replication control and incompatibility. In vivo studies demonstrate that this compound causes significant plasmid loss and resensitizes bacteria to conventional antibiotics. The demonstration that a small molecule can mimic incompatibility, cause plasmid elimination, and resensitize bacteria to antibiotics opens up new targets for antibacterial research.
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Affiliation(s)
- Johna C B Denap
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL 61801, USA
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37
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Abstract
Small noncoding RNAs have been found in all organisms, primarily as regulators of translation and message stability. The most exhaustive searches have taken place in E. coli, resulting in identification of more than 50 small RNAs, or 1%-2% of the number of protein-coding genes. One large class of these small RNAs uses the RNA chaperone Hfq; members of this class act by pairing to target messenger RNAs. Among the members of this class are DsrA and RprA, which positively regulate rpoS translation, OxyS, which negatively regulates rpoS translation and fhlA translation, RyhB, which reapportions iron use in the cell by downregulating translation of many genes that encode Fe-containing proteins, and Spot 42, which changes the polarity of translation in the gal operon. The promoters of these small RNAs are tightly regulated, frequently as part of well-understood regulons. Lessons learned from the study of small RNAs in E. coli can be applied to finding these important regulators in other organisms.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA.
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38
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Muñoz-Gómez AJ, Santos-Sierra S, Berzal-Herranz A, Lemonnier M, Díaz-Orejas R. Insights into the specificity of RNA cleavage by the Escherichia coli MazF toxin. FEBS Lett 2004; 567:316-20. [PMID: 15178344 DOI: 10.1016/j.febslet.2004.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 04/29/2004] [Accepted: 05/03/2004] [Indexed: 02/08/2023]
Abstract
The mazEF (chpA) toxin-antitoxin system of Escherichia coli is involved in the cell response to nutritional and antibiotic stresses as well as in bacterial-programmed cell death. Valuable information on the MazF toxin was derived from the determination of the crystal structure of the MazE/MazF complex and from in vivo data, suggesting that MazF promoted ribosome-dependent cleavage of messenger RNA. However, it was concluded from recent in vitro analyses using a MazF-(His6) fusion protein that MazF was an endoribonuclease that cleaved messenger RNA specifically at 5'-ACA-3' sites situated in single-stranded regions. In contrast, our work reported here shows that native MazF protein cleaves RNA at the 5' side of residue A in 5'-NAC-3' sequences (where N is preferentially U or A). MazF-dependent cleavage occurred at target sequences situated either in single- or double-stranded RNA regions. These activities were neutralized by a His6-MazE antitoxin. Although essentially consistent with previous in vivo reports on the substrate specificity of MazF, our results strongly suggest that the endoribonuclease activity of MazF may be modulated by additional factors to cleave messenger and other cellular RNAs.
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Affiliation(s)
- Ana J Muñoz-Gómez
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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39
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Kwong SM, Skurray RA, Firth N. Staphylococcus aureus multiresistance plasmid pSK41: analysis of the replication region, initiator protein binding and antisense RNA regulation. Mol Microbiol 2004; 51:497-509. [PMID: 14756789 DOI: 10.1046/j.1365-2958.2003.03843.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The vast majority of large staphylococcal plasmids characterized to date appear to possess an evolutionarily common replication system, which has clearly had a major impact on the evolution of antimicrobial resistant staphylococci worldwide. Related systems have also been found in plasmids from other Gram-positive genera, including enterococci, streptococci and bacilli. The 46.4 kb plasmid pSK41 is the prototype of a family of conjugative staphylococcal multiresistance plasmids. The replication region of pSK41 encodes a protein product, Rep, which was shown to be essential for replication; mutations that truncated Rep could be complemented in trans. Rep was found to bind in vitro to four tandem repeat sequences located centrally within the rep coding region. An A + T-rich inverted repeat sequence upstream of rep was required for efficient replication, whereas no sequences downstream of rep were necessary. An antisense countertranscript, RNAI, encoded upstream of rep was identified and transcriptional start points for both RNAI and the rep-mRNA were defined.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Chloramphenicol O-Acetyltransferase/chemistry
- Chloramphenicol O-Acetyltransferase/genetics
- DNA Primers
- DNA Replication/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA-Binding Proteins/metabolism
- Drug Resistance, Multiple/genetics
- Escherichia coli/genetics
- Evolution, Molecular
- Gene Expression Regulation, Bacterial/genetics
- Genetic Vectors
- Molecular Sequence Data
- Plasmids/genetics
- Polymerase Chain Reaction
- RNA, Antisense/genetics
- RNA, Bacterial/genetics
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Replication Origin/genetics
- Staphylococcus aureus/genetics
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Affiliation(s)
- Stephen M Kwong
- School of Biological Sciences, University of Sydney, New South Wales 2006, Australia
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40
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Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EGH. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 2004; 31:6435-43. [PMID: 14602901 PMCID: PMC275561 DOI: 10.1093/nar/gkg867] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (<2 to >32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
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Affiliation(s)
- Jörg Vogel
- Institute of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden.
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41
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Slagter-Jäger JG, Wagner EGH. Loop swapping in an antisense RNA/target RNA pair changes directionality of helix progression. J Biol Chem 2003; 278:35558-63. [PMID: 12819201 DOI: 10.1074/jbc.m304867200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The binding pathway of the natural antisense RNA CopA to its target CopT proceeds through a hierarchical order of steps. It initiates by reversible loop-loop contacts followed by unidirectional helix progression into the upper stems. This involves extensive breakage of intramolecular base pairs and the subsequent formation of two intermolecular helices, B and B'. Based on the known tRNA anticodon loop structure and on results from the Sok/Hok antisense/target RNA system, it had been suggested that a U-turn (or pi-turn) in the loop of CopT might determine the directionality of helix progression. Data presented here show that the putative U-turn is one of the structural elements of antisense/target RNA pairs required to achieve fast binding kinetics. Swapping of the hypothetical U-turn structure from the target RNA to the antisense RNA retained regulatory performance in vivo and binding rates in vitro but altered the binding pathway by changing the direction in which the initiating helix was extended. In addition, our data indicate that a helical stem immediately adjacent to the target loop sequence is required to provide a scaffold for the U-turn.
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Affiliation(s)
- Jacoba G Slagter-Jäger
- Institute of Cell and Molecular Biology, Department of Microbiology, Biomedical Center, Uppsala University, Box 596, Husargatan 3, S-75124 Uppsala, Sweden
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42
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Gubbins MJ, Arthur DC, Ghetu AF, Glover JNM, Frost LS. Characterizing the structural features of RNA/RNA interactions of the F-plasmid FinOP fertility inhibition system. J Biol Chem 2003; 278:27663-71. [PMID: 12748195 DOI: 10.1074/jbc.m303186200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
F-like plasmid transfer is mediated by the FinOP fertility inhibition system. Expression of the F positive regulatory protein, TraJ, is controlled by the action of the antisense RNA, FinP, and the RNA-binding protein FinO. FinO binds to and protects FinP from degradation and promotes duplex formation between FinP and traJ mRNA, leading to repression of both traJ expression and conjugative F transfer. FinP antisense RNA secondary structure is composed of two stem-loops separated by a 4-base single-stranded spacer and flanked on each side by single-stranded tails. Here we show that disruption of the expected Watson-Crick base pairing between the loops of FinP stem-loop I and its cognate RNA binding partner, traJ mRNA stem-loop Ic, led to a moderate reduction in the rate of duplex formation in vitro. In vivo, alterations of the anti-ribosome binding site region in the loop of FinP stem-loop I reduced the ability of the mutant FinP to mediate fertility inhibition and to inhibit TraJ expression when expressed in trans at an elevated copy number. Alterations of intermolecular complementarity between the stems of these RNAs reduced the rate of duplex formation. Our results suggest that successful interaction between stem-loop I of FinP and stem-loop Ic of traJ mRNA requires that base pairing must proceed from an initial loop-loop interaction through the top portion of the stems for stable duplex formation to occur.
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Affiliation(s)
- Michael J Gubbins
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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43
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Thompson JK, Collins MA. Completed sequence of plasmid pIP501 and origin of spontaneous deletion derivatives. Plasmid 2003; 50:28-35. [PMID: 12826055 DOI: 10.1016/s0147-619x(03)00042-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The sequence of plasmid pIP501 (30,603 bp) was completed using previously published and newly acquired data. The sites at which two spontaneous deletions had occurred were identified. One was between tracts of repeated heptamers and the other between regions of secondary structure associated with plasmid replication. A high level of identity ( >95%) between plasmid pIP501 and part of plasmid pRE25, which had been isolated from Enterococcus faecalis associated with a food source, was confirmed.
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Affiliation(s)
- J K Thompson
- Department of Food Science (Food Microbiology), Department of Agriculture and Rural Development for Northern Ireland, Newforge Lane, Belfast BT9 5PX, Northern Ireland, UK.
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44
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA.
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45
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Abstract
The search for small RNAs which might act as riboregulators became successful over the past two years both in prokaryotes and in eukaryotes. Moreover, artificially designed antisense RNAs have become powerful tools to downregulate the expression of targeted genes. It seems that antisense RNAs as regulatory molecules are most likely to be found everywhere. However, the first naturally occuring antisense RNAs were identified in plasmids and other prokaryotic accessory DNA elements. The thorough and detailed analyses of these systems have provided deep insights into structure and function of prokaryotic antisense RNAs and the kinetics of antisense/sense RNA interaction. Here, I focus on the role of antisense RNAs in plasmid replication and maintenance.
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Affiliation(s)
- Sabine Brantl
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 10, Jena D-07745, Germany.
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46
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Abstract
In this review, we describe a variety of mechanisms that bacteria use to regulate transcription elongation in order to control gene expression in response to changes in their environment. Together, these mechanisms are known as attenuation and antitermination, and both involve controlling the formation of a transcription terminator structure in the RNA transcript prior to a structural gene or operon. We examine attenuation and antitermination from the point of view of the different biomolecules that are used to influence the RNA structure. Attenuation of many amino acid biosynthetic operons, particularly in enteric bacteria, is controlled by ribosomes translating leader peptides. RNA-binding proteins regulate attenuation, particularly in gram-positive bacteria such as Bacillus subtilis. Transfer RNA is also used to bind to leader RNAs and influence transcription antitermination in a large number of amino acyl tRNA synthetase genes and several biosynthetic genes in gram-positive bacteria. Finally, antisense RNA is involved in mediating transcription attenuation to control copy number of several plasmids.
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Affiliation(s)
- Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA.
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47
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Abstract
RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.
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Affiliation(s)
- Christine Brunel
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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48
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Møller T, Franch T, Udesen C, Gerdes K, Valentin-Hansen P. Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 2002; 16:1696-706. [PMID: 12101127 PMCID: PMC186370 DOI: 10.1101/gad.231702] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The physiological role of Escherichia coli Spot 42 RNA has remained obscure, even though the 109-nucleotide RNA was discovered almost three decades ago. Structural features of Spot 42 RNA and previous work suggested to us that the RNA might be a regulator of discoordinate gene expression of the galactose operon, a control that is only understood at the phenomenological level. The effects of controlled expression of Spot 42 RNA or deleting the gene (spf) encoding the RNA supported this hypothesis. Down-regulation of galK expression, the third gene in the gal operon, was only observed in the presence of Spot 42 RNA and required growth conditions that caused derepression of the spf gene. Subsequent biochemical studies showed that Spot 42 RNA specifically bound at the galK Shine-Dalgarno region of the galETKM mRNA, thereby blocking ribosome binding. We conclude that Spot 42 RNA is an antisense RNA that acts to differentially regulate genes that are expressed from the same transcription unit. Our results reveal an interesting mechanism by which the expression of a promoter distal gene in an operon can be modulated and underline the importance of antisense control in bacterial gene regulation.
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Affiliation(s)
- Thorleif Møller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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49
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Abstract
For a long time, RNA has been merely regarded as a molecule that can either function as a messenger (mRNA) or as part of the translational machinery (tRNA, rRNA). Meanwhile, it became clear that RNAs are versatile molecules that do not only play key roles in many important biological processes like splicing, editing, protein export and others, but can also--like enzymes--act catalytically. Two important aspects of RNA function--antisense-RNA control and RNA interference (RNAi)--are emphasized in this review. Antisense-RNA control functions in all three kingdoms of life--although the majority of examples are known from bacteria. In contrast, RNAi, gene silencing triggered by double-stranded RNA, the oldest and most ubiquitous antiviral system, is exclusively found in eukaryotes. Our current knowledge about occurrence, biological roles and mechanisms of action of antisense RNAs as well as the recent findings about involved genes/enzymes and the putative mechanism of RNAi are summarized. An interesting intersection between both regulatory mechanisms is briefly discussed.
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Affiliation(s)
- Sabine Brantl
- Institut für Molekularbiologie, Friedrich Schiller Univ. Jena, Winzerlaer Str. 10, D-07745 Jena, Germany.
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50
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Brantl S, Wagner EGH. An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli. J Bacteriol 2002; 184:2740-7. [PMID: 11976303 PMCID: PMC135013 DOI: 10.1128/jb.184.10.2740-2747.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antisense RNA-mediated transcriptional attenuation is a regulatory mechanism operating in the replication control of two groups of plasmids in gram-positive bacteria, the pT181 group and the inc18 family, represented by pIP501. In contrast, this control mechanism has so far not been identified in gram-negative bacteria or their plasmids. In this work we asked whether such a mechanism can be supported by Escherichia coli. The core replication control regions of plasmids pT181 and pIP501 were transferred into this heterologous host. In vivo lacZ reporter gene assays showed that the antisense RNAs of these plasmids can inhibit lacZ expression and that most of this effect can be accounted for by reduced mRNA readthrough. Northern analyses confirmed that the ratio of attenuated to readthrough target RNA was increased in the presence of the cognate antisense RNA, as expected for this mechanism. Similarly, both antisense RNAs induced premature termination of their cognate target RNAs in an E. coli in vitro transcription system, whereas the noncognate antisense RNAs had no effect. Thus, this report shows that antisense RNA-mediated transcriptional attenuation is supported by at least one gram-negative host, although the data indicate that inhibitory efficiencies are lower than those for, e.g., Bacillus subtilis. Possible explanations for the apparent absence of this control mode in plasmids of gram-negative bacteria are discussed.
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Affiliation(s)
- Sabine Brantl
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Strasse 10, Jena D-07745, Germany.
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