101
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Sun T, Chen L, Zhang W. Quantitative Proteomics Reveals Potential Crosstalk between a Small RNA CoaR and a Two-Component Regulator Slr1037 in Synechocystis sp. PCC6803. J Proteome Res 2017; 16:2954-2963. [PMID: 28677390 DOI: 10.1021/acs.jproteome.7b00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of attention these years. Although most studies focused on studying the roles of sRNAs or TCS regulators in stress response in photosynthetic cyanobacteria, limited work has elucidated their potential crosstalk. Our previous work has identified a negative sRNA regulator CoaR and a positive response regulator Slr1037 both related to 1-butanol stress regulation in Synechocystis sp. PCC6803. In this work, the potential crosstalk between CoaR and Slr1307 (i.e., the coregulated genes mediated by CoaR and Slr1037) was identified and validated through quantitative proteomics and quantitative real-time PCR (qRT-PCR), respectively. The results showed that the sensitive phenotype to 1-butanol of Δslr1037 could be rescued by suppressing coaR in Δslr1037, probably due to the fact that some target genes of Slr1037 could be reactivated by repression of CoaR. Twenty-eight coregulated proteins mediated by CoaR and Slr1037 were found through quantitative proteomics, and 10 of the annotated proteins were validated via qRT-PCR. This study proved the existence of crosstalk between sRNAs and response regulators and provided new insights into the coregulation of biofuel resistance in cyanobacteria.
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Affiliation(s)
- Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China.,Center for Biosafety Research and Strategy, Tianjin University , Tianjin 300072, P. R. China
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102
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Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
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103
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Ryan D, Mukherjee M, Suar M. The expanding targetome of small RNAs in Salmonella Typhimurium. Biochimie 2017; 137:69-77. [DOI: 10.1016/j.biochi.2017.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
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104
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Novel DNA Binding and Regulatory Activities for σ 54 (RpoN) in Salmonella enterica Serovar Typhimurium 14028s. J Bacteriol 2017; 199:JB.00816-16. [PMID: 28373272 DOI: 10.1128/jb.00816-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. Salmonella enterica serovar Typhimurium utilizes the housekeeping σ70 and five alternative sigma factors, including σ54 The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. In S. Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54 regulon of S. Typhimurium. The position and context of many of the identified σ54 RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54 regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCE The alternative sigma factor σ54 (RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54 regulon of the versatile pathogen S. Typhimurium has expanded our understanding of the scope of the σ54 regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
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105
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Dersch P, Khan MA, Mühlen S, Görke B. Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets. Front Microbiol 2017; 8:803. [PMID: 28529506 PMCID: PMC5418344 DOI: 10.3389/fmicb.2017.00803] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/23/2023] Open
Abstract
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins. Bacteria respond with extensive changes of their sRNA repertoire to antibiotics. Each antibiotic generates a unique sRNA profile possibly causing downstream effects that may help to overcome the antibiotic challenge. In consequence, regulatory RNAs including sRNAs and their protein interaction partners such as Hfq may prove useful as targets for antimicrobial chemotherapy. Indeed, several compounds have been developed that kill bacteria by mimicking ligands for riboswitches controlling essential genes, demonstrating that regulatory RNA elements are druggable targets. Drugs acting on sRNAs are considered for combined therapies to treat infections. In this review, we address how regulatory RNAs respond to and establish resistance to antibiotics in bacteria. Approaches to target RNAs involved in intrinsic antibiotic resistance or virulence for chemotherapy will be discussed.
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Affiliation(s)
- Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection ResearchBraunschweig, Germany
| | - Muna A Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Sabrina Mühlen
- Department of Molecular Infection Biology, Helmholtz Centre for Infection ResearchBraunschweig, Germany
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
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106
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Smirnov A, Wang C, Drewry LL, Vogel J. Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA. EMBO J 2017; 36:1029-1045. [PMID: 28336682 PMCID: PMC5391140 DOI: 10.15252/embj.201696127] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/05/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022] Open
Abstract
Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown. Here, we report in Salmonella Typhimurium the mode-of-action of RaiZ, a ProQ-dependent sRNA that is made from the 3' end of the mRNA encoding ribosome-inactivating protein RaiA. We show that RaiZ is a base-pairing sRNA that represses in trans the mRNA of histone-like protein HU-α. RaiZ forms an RNA duplex with the ribosome-binding site of hupA mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU-α. Similarities and differences between ProQ- and Hfq-mediated regulation will be discussed.
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Affiliation(s)
- Alexandre Smirnov
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Chuan Wang
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lisa L Drewry
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany .,Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
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107
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Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida. Appl Environ Microbiol 2017; 83:AEM.03236-16. [PMID: 28130298 DOI: 10.1128/aem.03236-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.IMPORTANCE This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least one condition, suggesting their involvement in adaptation to stress conditions and identifying interesting candidates for further functional characterization.
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108
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Maes A, Gracia C, Innocenti N, Zhang K, Aurell E, Hajnsdorf E. Landscape of RNA polyadenylation in E. coli. Nucleic Acids Res 2017; 45:2746-2756. [PMID: 28426097 PMCID: PMC5389530 DOI: 10.1093/nar/gkw894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 11/26/2022] Open
Abstract
Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5΄-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A)polymerase deleted mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A)polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3΄-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.
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Affiliation(s)
- Alexandre Maes
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France
| | - Céline Gracia
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France
| | - Nicolas Innocenti
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 17, SE-10691 Stockholm, Sweden
- Combient AB, Nettovägen 6, SE-175 41 Järfälla, Sweden
| | - Kaiyang Zhang
- Systems Biology Laboratory, Research Programs Unit,Genome-Scale Biology, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finlandepts of Computer Science and Applied Physics, Aalto University, Konemiehentie 2, FI-02150 Espoo, Finland
| | - Erik Aurell
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 17, SE-10691 Stockholm, Sweden
- Departments of Computer Science and Applied Physics, AaltoUniversity, Konemiehentie 2, FI-02150 Espoo, Finlandombient AB, Nettovägen 6, SE-175 41 Järfälla, Sweden
| | - Eliane Hajnsdorf
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France
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109
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Abstract
The major transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) is an increasingly cost-effective technology for the analysis of transcriptomes with several advantages over gene expression microarrays, such as its higher sensitivity and accuracy, broader dynamic range, and the ability to detect novel transcripts, including noncoding RNA molecules, at nucleotide-level resolution. Although these advantages, many microbiology laboratories have not yet applied RNA-seq analyses to their investigations. The high cost of the equipment for next-generation sequencing is no longer an issue, since this intermediate part of the analysis can be provided by commercial or central services. Here, we detail a protocol for the first part of the analysis, the RNA extraction, and an introductory protocol to the bioinformatics analysis of the sequencing data that generates the differential expression results.
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110
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Migault M, Donnou-Fournet E, Galibert MD, Gilot D. Definition and identification of small RNA sponges: Focus on miRNA sequestration. Methods 2016; 117:35-47. [PMID: 27876678 DOI: 10.1016/j.ymeth.2016.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/18/2016] [Indexed: 02/09/2023] Open
Abstract
Targeting RNAs appears as an important opportunity to modulate biological processes. Here, we overviewed critical parameters implied in RNAs competition to bind small RNAs. These competitions influence small RNA availability and thereby gene expression and cell fate. We focused on the ability of RNAs to sequester small RNA, mainly the microRNAs (miRNAs) and proposed experimental workflows to demonstrate the existence and activity of RNA-sponge. From this basic science, we detailed tailored oligonucleotides, developed to challenge the binding of small RNA. In vitro and in vivo, these tailored oligonucleotides efficiently restore small RNA activity by preventing their sequestration on RNA-sponges.
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Affiliation(s)
- Mélodie Migault
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Emmanuelle Donnou-Fournet
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Marie-Dominique Galibert
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France; Department of Medical Genomic, Rennes University Hospital, Rennes, France.
| | - David Gilot
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France.
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111
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Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ. Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E. EMBO J 2016; 36:374-387. [PMID: 27836995 PMCID: PMC5286369 DOI: 10.15252/embj.201694639] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 02/04/2023] Open
Abstract
RNA sequencing studies have identified hundreds of non‐coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV‐crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base‐paired sRNA–mRNA duplexes in association with RNase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA–mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA–mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNAs. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli. Numerous sRNA interactions were also identified with non‐coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.
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Affiliation(s)
- Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sean P McAteer
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Grzegorz Kudla
- MRC Human Genetic Unit, University of Edinburgh, Edinburgh, UK
| | - Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Nandan P Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kai Wen Leong
- Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia
| | - Richard Strugnell
- Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David L Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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112
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Weber L, Thoelken C, Volk M, Remes B, Lechner M, Klug G. The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PLoS One 2016; 11:e0165694. [PMID: 27802301 PMCID: PMC5089854 DOI: 10.1371/journal.pone.0165694] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/17/2016] [Indexed: 11/18/2022] Open
Abstract
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division andcellwall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae.
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Affiliation(s)
- Lennart Weber
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Clemens Thoelken
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcel Volk
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Marcus Lechner
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
- * E-mail:
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113
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Bossi L, Figueroa-Bossi N. Competing endogenous RNAs: a target-centric view of small RNA regulation in bacteria. Nat Rev Microbiol 2016; 14:775-784. [PMID: 27640758 DOI: 10.1038/nrmicro.2016.129] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many bacterial regulatory small RNAs (sRNAs) have several mRNA targets, which places them at the centre of regulatory networks that help bacteria to adapt to environmental changes. However, different mRNA targets of any given sRNA compete with each other for binding to the sRNA; thus, depending on relative abundances and sRNA affinity, competition for regulatory sRNAs can mediate cross-regulation between bacterial mRNAs. This 'target-centric' perspective of sRNA regulation is reminiscent of the competing endogenous RNA (ceRNA) hypothesis, which posits that competition for a limited pool of microRNAs (miRNAs) in higher eukaryotes mediates cross-regulation of mRNAs. In this Opinion article, we discuss evidence that a similar network of RNA crosstalk operates in bacteria, and that this network also includes crosstalk between sRNAs and competition for RNA-binding proteins.
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Affiliation(s)
- Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), The French Alternative Energies and Atomic Energy Commission (CEA), University Paris-Saclay, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), The French Alternative Energies and Atomic Energy Commission (CEA), University Paris-Saclay, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
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114
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Acuña LG, Barros MJ, Peñaloza D, Rodas PI, Paredes-Sabja D, Fuentes JA, Gil F, Calderón IL. A feed-forward loop between SroC and MgrR small RNAs modulates the expression of eptB and the susceptibility to polymyxin B in Salmonella Typhimurium. MICROBIOLOGY-SGM 2016; 162:1996-2004. [PMID: 27571709 DOI: 10.1099/mic.0.000365] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Base-pairing small RNAs (sRNAs) regulate gene expression commonly by direct interaction with cognate mRNAs. Nevertheless, recent studies have expanded this knowledge with the discovery of the RNA 'sponges' which are able to interact and repress the functions of classical base-pairing sRNAs. In this work, we present evidence indicating that the sponge RNA SroC from Salmonella enterica serovar Typhimurium base pairs with the MgrR sRNA, thereby antagonizing its regulatory effects on both gene expression and resistance to the antimicrobial peptide polymyxin B (PMB). By a predictive algorithm, we determined putative SroC-MgrR base-pairing regions flanking the interaction area between MgrR and its target mRNA, eptB, encoding a LPS-modifying enzyme. With a two-plasmid system and compensatory mutations, we confirmed that SroC directly interacts and down-regulates the levels of MgrR, thus relieving the MgrR-mediated repression of eptB mRNA. Since it was previously shown that an Escherichia coli strain carrying an mgrR deletion is more resistant to PMB, we assessed the significance of SroC in the susceptibility of S. Typhimurium to PMB. Whereas the sroC deletion increased the sensitivity to PMB, as compared to the wild-type, the resistance phenotypes between the ΔmgrR and ΔsroCΔmgrR strains were comparable, evidencing that mgrR mutation is epistatic to the sroC mutation. Together, these results indicate that both SroC and MgrR sRNAs compose a coherent feed-forward loop controlling the eptB expression and hence the LPS modification in S. Typhimurium.
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Affiliation(s)
- Lillian G Acuña
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia para la Vida, Santiago, Chile
| | - M José Barros
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Diego Peñaloza
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Paula I Rodas
- Center for Integrative Medicine and Innovative Sciences, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Daniel Paredes-Sabja
- Departamento de Ciencias Biológicas, Microbiota-Host Interaction and Clostridia Research Group, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Fernando Gil
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Iván L Calderón
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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115
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Fröhlich KS, Haneke K, Papenfort K, Vogel J. The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res 2016; 44:10406-10422. [PMID: 27407104 PMCID: PMC5137417 DOI: 10.1093/nar/gkw632] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 12/28/2022] Open
Abstract
Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these ‘core sRNAs’ of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σS and accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.
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Affiliation(s)
- Kathrin S Fröhlich
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Katharina Haneke
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Kai Papenfort
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
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116
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Fröhlich KS, Papenfort K. Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. Mol Microbiol 2016; 101:701-13. [DOI: 10.1111/mmi.13428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Kathrin S. Fröhlich
- Department of Biology I, Microbiology; Ludwig-Maximilians-University Munich; 82152 Martinsried Germany
| | - Kai Papenfort
- Department of Biology I, Microbiology; Ludwig-Maximilians-University Munich; 82152 Martinsried Germany
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117
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The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni. Nat Commun 2016; 7:11667. [PMID: 27229370 PMCID: PMC4894983 DOI: 10.1038/ncomms11667] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/18/2016] [Indexed: 12/12/2022] Open
Abstract
The widespread CsrA/RsmA protein regulators repress translation by binding GGA motifs in bacterial mRNAs. CsrA activity is primarily controlled through sequestration by multiple small regulatory RNAs. Here we investigate CsrA activity control in the absence of antagonizing small RNAs by examining the CsrA regulon in the human pathogen Campylobacter jejuni. We use genome-wide co-immunoprecipitation combined with RNA sequencing to show that CsrA primarily binds flagellar mRNAs and identify the major flagellin mRNA (flaA) as the main CsrA target. The flaA mRNA is translationally repressed by CsrA, but it can also titrate CsrA activity. Together with the main C. jejuni CsrA antagonist, the FliW protein, flaA mRNA controls CsrA-mediated post-transcriptional regulation of other flagellar genes. RNA-FISH reveals that flaA mRNA is expressed and localized at the poles of elongating cells. Polar flaA mRNA localization is translation dependent and is post-transcriptionally regulated by the CsrA-FliW network. Overall, our results suggest a role for CsrA-FliW in spatiotemporal control of flagella assembly and localization of a dual-function mRNA.
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118
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Lee HJ, Gottesman S. sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs. Nucleic Acids Res 2016; 44:6907-23. [PMID: 27137887 PMCID: PMC5001588 DOI: 10.1093/nar/gkw358] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional regulation of transcription factors contributes to regulatory circuits. We created translational reporter fusions for multiple central regulators in Escherichia coli and examined the effect of Hfq-dependent non-coding RNAs on these fusions. This approach yields an 'RNA landscape,' identifying Hfq-dependent sRNAs that regulate a given fusion. No significant sRNA regulation of crp or fnr was detected. hns was regulated only by DsrA, as previously reported. Lrp and SoxS were both found to be regulated post-transcriptionally. Lrp, ' L: eucine-responsive R: egulatory P: rotein,' regulates genes involved in amino acid biosynthesis and catabolism and other cellular functions. sRNAs DsrA, MicF and GcvB each independently downregulate the lrp translational fusion, confirming previous reports for MicF and GcvB. MicF and DsrA interact with an overlapping site early in the lrp ORF, while GcvB acts upstream at two independent sites in the long lrp leader. Surprisingly, GcvB was found to be responsible for significant downregulation of lrp after oxidative stress; MicF also contributed. SoxS, an activator of genes used to combat oxidative stress, is negatively regulated by sRNA MgrR. This study demonstrates that while not all global regulators are subject to sRNA regulation, post-transcriptional control by sRNAs allows multiple environmental signals to affect synthesis of the transcriptional regulator.
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Affiliation(s)
- Hyun-Jung Lee
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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119
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Strobel EJ, Watters KE, Loughrey D, Lucks JB. RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs. Curr Opin Biotechnol 2016; 39:182-191. [PMID: 27132125 DOI: 10.1016/j.copbio.2016.03.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022]
Abstract
RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA 'structomic' methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases.
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Affiliation(s)
- Eric J Strobel
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Kyle E Watters
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - David Loughrey
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Julius B Lucks
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.
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120
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Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J. Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. EMBO J 2016; 35:991-1011. [PMID: 27044921 PMCID: PMC5207318 DOI: 10.15252/embj.201593360] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/26/2016] [Indexed: 12/22/2022] Open
Abstract
The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
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Affiliation(s)
- Erik Holmqvist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany
| | - Lei Li
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert Ludwig University Freiburg, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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121
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Bouloc P, Repoila F. Fresh layers of RNA-mediated regulation in Gram-positive bacteria. Curr Opin Microbiol 2016; 30:30-35. [DOI: 10.1016/j.mib.2015.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023]
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122
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Göpel Y, Khan MA, Görke B. Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage. Nucleic Acids Res 2016; 44:824-37. [PMID: 26531825 PMCID: PMC4737144 DOI: 10.1093/nar/gkv1161] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/07/2015] [Accepted: 10/20/2015] [Indexed: 12/21/2022] Open
Abstract
In E. coli, small RNA GlmZ activates the glmS mRNA by base-pairing in an Hfq dependent manner. When not required, GlmZ is bound by adaptor protein RapZ and recruited to RNase E, which cleaves GlmZ in its base-pairing sequence. Small RNA GlmY counteracts cleavage of GlmZ by sequestration of RapZ. Although both sRNAs are highly homologous, only GlmZ specifically binds Hfq and undergoes cleavage by RNase E. We used domain swapping to identify the responsible modules. Two elements, the 3' terminal oligo(U) stretch and the base-pairing region enable GlmZ to interact with Hfq. Accordingly, Hfq inhibits cleavage of GlmZ, directing it to base-pairing. Intriguingly, the central stem loop of GlmZ is decisive for cleavage, whereas the sequence comprising the actual cleavage site is dispensable. Assisted by RapZ, RNase E cleaves any RNA fused to the 3' end of this module. These results suggest a novel mode for RNase E recognition, in which one of the required handholds in the substrate is replaced by an RNA binding protein. This device can generate RNAs of interest in their 5' monophosphorylated form on demand. As these species are rapidly degraded, this tool allows to regulate gene expression post-transcriptionally by modulation of RapZ levels.
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Affiliation(s)
- Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Muna Ayesha Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr Bohr-Gasse 9, 1030 Vienna, Austria
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123
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Chao Y, Vogel J. A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response. Mol Cell 2016; 61:352-363. [PMID: 26805574 DOI: 10.1016/j.molcel.2015.12.023] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/19/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022]
Abstract
Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an alternative biogenesis pathway releasing the conserved mRNA 3' UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3' UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol.
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Affiliation(s)
- Yanjie Chao
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
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124
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The unmasking of 'junk' RNA reveals novel sRNAs: from processed RNA fragments to marooned riboswitches. Curr Opin Microbiol 2016; 30:16-21. [PMID: 26771674 DOI: 10.1016/j.mib.2015.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/17/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022]
Abstract
While the notion that RNAs can function as regulators dates back to early molecular studies of gene regulation of the lac operon, it is only over the last decade that the ubiquity and diversity of regulatory RNAs are being realized. Advancements in high throughput sequencing and the adoption of these approaches to rapidly sequence genomes and transcriptomes and to examine gene expression and RNA binding protein specificity have revealed an ever-expanding RNA world. In this review, we focus on recent studies revealing that RNA fragments cleaved from larger coding or noncoding RNAs can have regulatory functions. Additionally, we discuss examples of riboswitches that function in trans as mRNA or protein-binding sRNAs, upending the traditional thinking that these are exclusively cis-acting elements.
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125
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Rau MH, Bojanovič K, Nielsen AT, Long KS. Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli. BMC Genomics 2015; 16:1051. [PMID: 26653712 PMCID: PMC4676190 DOI: 10.1186/s12864-015-2231-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 11/18/2015] [Indexed: 01/03/2023] Open
Abstract
Background Bacterial small RNAs (sRNAs) are recognized as posttranscriptional regulators involved in the control of bacterial lifestyle and adaptation to stressful conditions. Although chemical stress due to the toxicity of precursor and product compounds is frequently encountered in microbial bioprocessing applications, the involvement of sRNAs in this process is not well understood. We have used RNA sequencing to map sRNA expression in E. coli under chemical stress and high cell density fermentation conditions with the aim of identifying sRNAs involved in the transcriptional response and those with potential roles in stress tolerance. Results RNA sequencing libraries were prepared from RNA isolated from E. coli K-12 MG1655 cells grown under high cell density fermentation conditions or subjected to chemical stress with twelve compounds including four organic solvent-like compounds, four organic acids, two amino acids, geraniol and decanoic acid. We have discovered 253 novel intergenic transcripts with this approach, adding to the roughly 200 intergenic sRNAs previously reported in E. coli. There are eighty-four differentially expressed sRNAs during fermentation, of which the majority are novel, supporting possible regulatory roles for these transcripts in adaptation during different fermentation stages. There are a total of 139 differentially expressed sRNAs under chemical stress conditions, where twenty-nine exhibit significant expression changes in multiple tested conditions, suggesting that they may be involved in a more general chemical stress response. Among those with known functions are sRNAs involved in regulation of outer membrane proteins, iron availability, maintaining envelope homeostasis, as well as sRNAs incorporated into complex networks controlling motility and biofilm formation. Conclusions This study has used deep sequencing to reveal a wealth of hitherto undescribed sRNAs in E. coli and provides an atlas of sRNA expression during seventeen different growth and stress conditions. Although the number of novel sRNAs with regulatory functions is unknown, several exhibit specific expression patterns during high cell density fermentation and are differentially expressed in the presence of multiple chemicals, suggesting they may play regulatory roles during these stress conditions. These novel sRNAs, together with specific known sRNAs, are candidates for improving stress tolerance and our understanding of the E. coli regulatory network during fed-batch fermentation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2231-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Holm Rau
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
| | - Klara Bojanovič
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
| | - Alex Toftgaard Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
| | - Katherine S Long
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
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126
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs. BIOMED RESEARCH INTERNATIONAL 2015; 2015:153561. [PMID: 26618164 PMCID: PMC4651636 DOI: 10.1155/2015/153561] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE sigma factor and stress responsive two-component systems as well as dedicated small RNAs. LPS composition is highly heterogeneous and dynamically altered upon stress and other challenges in the environment because of the transcriptional activation of RpoE regulon members and posttranslational control by RpoE-regulated Hfq-dependent RybB and MicA sRNAs. The PhoP/Q two-component system further regulates Kdo2-lipid A modification via MgrR sRNA. Some of these structural alterations are critical for antibiotic resistance, OM integrity, virulence, survival in host, and adaptation to specific environmental niches. The heterogeneity arises following the incorporation of nonstoichiometric modifications in the lipid A part and alterations in the composition of inner and outer core of LPS. The biosynthesis of LPS and phospholipids is tightly coupled. This requires the availability of metabolic precursors, whose accumulation is controlled by sRNAs like SlrA, GlmZ, and GlmY.
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127
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Wang J, Liu T, Zhao B, Lu Q, Wang Z, Cao Y, Li W. sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria. Nucleic Acids Res 2015; 44:D248-53. [PMID: 26503244 PMCID: PMC4702819 DOI: 10.1093/nar/gkv1127] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Bacterial sRNAs are a class of small regulatory RNAs of about 40–500 nt in length; they play multiple biological roles through binding to their target mRNAs or proteins. Therefore, elucidating sRNA targets is very important. However, only targets of a few sRNAs have been described. To facilitate sRNA functional studies such as developing sRNA target prediction models, we updated the sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA–mRNA and sRNA–protein interactions, respectively, while 279 had no reported interactions. We also presented detailed information for 316 binding regions of sRNA-target mRNA interactions and related mutation experiments, as well as new features, including NCBI sequence viewer, sRNA regulatory network, target prediction-based GO and pathway annotations, and error report system. The new version provides a comprehensive annotation of validated sRNA-target interactions, and will be a useful resource for bacterial sRNA studies.
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Affiliation(s)
- Jiang Wang
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Tao Liu
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Bo Zhao
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Qixuan Lu
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Zheng Wang
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
| | - Yuan Cao
- Department of Laboratory Medicine, Jinan Military General Hospital, Jinan, Shandong 250031, China
| | - Wuju Li
- Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Haidian district, Beijing 100850, China
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128
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Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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129
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Bruchmann S, Muthukumarasamy U, Pohl S, Preusse M, Bielecka A, Nicolai T, Hamann I, Hillert R, Kola A, Gastmeier P, Eckweiler D, Häussler S. Deep transcriptome profiling of clinicalKlebsiella pneumoniaeisolates reveals strain and sequence type-specific adaptation. Environ Microbiol 2015; 17:4690-710. [DOI: 10.1111/1462-2920.13016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Bruchmann
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
| | - Uthayakumar Muthukumarasamy
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
| | - Sarah Pohl
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Agata Bielecka
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Isabell Hamann
- Medizinisches Labor Ostsachsen; Mikrobiologie; Görlitz Germany
| | - Roger Hillert
- Medizinisches Labor Ostsachsen; Mikrobiologie; Görlitz Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine; Charité University Medicine Berlin; Berlin Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine; Charité University Medicine Berlin; Berlin Germany
| | - Denitsa Eckweiler
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology; Helmholtz Centre for Infection Research; Braunschweig Germany
- Institute for Molecular Bacteriology; Twincore; Centre for Clinical and Experimental Infection Research; A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School; Hannover Germany
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130
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Fuentes DN, Calderón PF, Acuña LG, Rodas PI, Paredes-Sabja D, Fuentes JA, Gil F, Calderón IL. Motility modulation by the small non-coding RNA SroC inSalmonellaTyphimurium. FEMS Microbiol Lett 2015; 362:fnv135. [DOI: 10.1093/femsle/fnv135] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 12/14/2022] Open
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Lalaouna D, Carrier MC, Massé E. The shock absorber: preventing sRNA transcriptional noise. Cell Cycle 2015; 14:2539-40. [PMID: 26066059 DOI: 10.1080/15384101.2015.1060771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- David Lalaouna
- a Department of Biochemistry ; RNA Group; Université de Sherbrooke ; Sherbrooke , QC Canada
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132
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Papenfort K, Vanderpool CK. Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 2015; 39:362-78. [PMID: 25934124 DOI: 10.1093/femsre/fuv016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA Department of Biology I, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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133
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Updegrove TB, Shabalina SA, Storz G. How do base-pairing small RNAs evolve? FEMS Microbiol Rev 2015; 39:379-91. [PMID: 25934120 DOI: 10.1093/femsre/fuv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 01/12/2023] Open
Abstract
The increasing numbers of characterized base-pairing small RNAs (sRNAs) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of sRNA evolution. In this review, we describe some examples of trans-encoded base-pairing sRNAs that are species-specific and others that are more broadly distributed. We also describe examples of sRNA orthologs where different features are conserved. These examples provide the background for a discussion of mechanisms of sRNA evolution and selective pressures on the sRNAs and their mRNA target(s).
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Affiliation(s)
- Taylor B Updegrove
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institutes of Health, Bethesda, MD 20892, USA
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134
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Azam MS, Vanderpool CK. Talk among yourselves: RNA sponges mediate cross talk between functionally related messenger RNAs. EMBO J 2015; 34:1436-8. [PMID: 25916829 DOI: 10.15252/embj.201591492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Muhammad S Azam
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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135
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Regulatory small RNAs from the 3' regions of bacterial mRNAs. Curr Opin Microbiol 2015; 24:132-9. [PMID: 25677420 DOI: 10.1016/j.mib.2015.01.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 12/29/2022]
Abstract
Most studies of small regulatory RNAs in bacteria have focussed on conserved transcripts in intergenic regions. However, several recent developments including single-nucleotide resolution transcriptome profiling by RNA-seq and increased knowledge of the cellular targets of the RNA chaperone Hfq suggest that the bacterial world of functional small RNAs is more diverse. One emerging class are small RNAs that are identical to the 3' regions of known mRNAs, but are produced either by transcription from internal promoters or by mRNA processing. Using several recently discovered examples of such sRNAs, we discuss their biogenesis and modes of action, and illustrate how they can facilitate mRNA crosstalk in various physiological processes.
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