101
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Liu N, Chaudhry MT, Xie Z, Kreth J, Merritt J. Identification of New Degrons in Streptococcus mutans Reveals a Novel Strategy for Engineering Targeted, Controllable Proteolysis. Front Microbiol 2017; 8:2572. [PMID: 29312250 PMCID: PMC5742171 DOI: 10.3389/fmicb.2017.02572] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
Abstract
Recently, controllable, targeted proteolysis has emerged as one of the most promising new strategies to study essential genes and otherwise toxic mutations. One of the principal limitations preventing the wider adoption of this approach is due to the lack of easily identifiable species-specific degrons that can be used to trigger the degradation of target proteins. Here, we report new advancements in the targeted proteolysis concept by creating the first prokaryotic N-terminal targeted proteolysis system. We demonstrate how proteins from the LexA-like protein superfamily can be exploited as species-specific reservoirs of N- and/or C-degrons, which are easily identifiable due to their proximity to strictly conserved residues found among LexA-like proteins. Using the LexA-like regulator HdiR of Streptococcus mutans, we identified two separate N-degrons derived from HdiR that confer highly efficient constitutive proteolysis upon target proteins when added as N-terminal peptide tags. Both degrons mediate degradation via AAA+ family housekeeping proteases with one degron primarily targeting FtsH and the other targeting the ClpP-dependent proteases. To modulate degron activity, our approach incorporates a hybrid N-terminal protein tag consisting of the ubiquitin-like protein NEDD8 fused to an HdiR degron. The NEDD8 fusion inhibits degron function until the NEDD8-specific endopeptidase NEDP1 is heterologously expressed to expose the N-degron. By fusing the NEDD8-degron tag onto GFP, luciferase, and the pleiotropic regulator RNase J2, we demonstrate that the N-terminal proteolysis approach exhibits far superior performance compared to the classic transcriptional depletion approach and is similarly applicable for the study of highly toxic mutations.
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Affiliation(s)
- Nan Liu
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
| | | | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, United States
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
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102
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Zhang YF, Han K, Chandler CE, Tjaden B, Ernst RK, Lory S. Probing the sRNA regulatory landscape of P. aeruginosa: post-transcriptional control of determinants of pathogenicity and antibiotic susceptibility. Mol Microbiol 2017; 106:919-937. [PMID: 28976035 PMCID: PMC5738928 DOI: 10.1111/mmi.13857] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2017] [Indexed: 01/01/2023]
Abstract
During environmental adaptation bacteria use small regulatory RNAs (sRNAs) to repress or activate expression of a large fraction of their proteome. We extended the use of the in vivo RNA proximity ligation method toward probing global sRNA interactions with their targets in Pseudomonas aeruginosa and verified the method with a known regulon controlled by the PrrF1 sRNA. We also identified two sRNAs (Sr0161 and ErsA) that interact with the mRNA encoding the major porin OprD responsible for the uptake of carbapenem antibiotics. These two sRNAs base pair with the 5' UTR of oprD leading to increase in resistance of the bacteria to meropenem. Additional proximity ligation experiments and enrichment for Sr0161 targets identified the mRNA for the regulator of type III secretion system. Interaction between the exsA mRNA and Sr0161 leads to a block in the synthesis of a component of the T3SS apparatus and an effector. Another sRNA, Sr006, positively regulates, without Hfq, the expression of PagL, an enzyme responsible for deacylation of lipid A, reducing its pro-inflammatory property and resulting in polymyxin resistance. Therefore, an analysis of global sRNA-mRNA interactions can lead to discoveries of novel pathways controlling gene expression that are likely integrated into larger regulatory networks.
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Affiliation(s)
- Yi-Fan Zhang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Kook Han
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Courtney E. Chandler
- Department of Microbial Pathogenesis, University of Maryland – Baltimore, School of Dentistry, Baltimore, Maryland, USA
| | - Brian Tjaden
- Computer Science Department, Wellesley College, Wellesley, Massachusetts, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland – Baltimore, School of Dentistry, Baltimore, Maryland, USA
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
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103
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Barvík I, Rejman D, Panova N, Šanderová H, Krásný L. Non-canonical transcription initiation: the expanding universe of transcription initiating substrates. FEMS Microbiol Rev 2017; 41:131-138. [PMID: 27799279 DOI: 10.1093/femsre/fuw041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.
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Affiliation(s)
- Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v. v. i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Natalya Panova
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Šanderová
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences v. v. i., Vídenská 1083, 142 20 Prague 4, Czech Republic
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104
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Kavita K, de Mets F, Gottesman S. New aspects of RNA-based regulation by Hfq and its partner sRNAs. Curr Opin Microbiol 2017; 42:53-61. [PMID: 29125938 PMCID: PMC10367044 DOI: 10.1016/j.mib.2017.10.014] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/15/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Hfq, an RNA chaperone, promotes the pairing of small RNAs (sRNAs) to target mRNAs, mediating post-transcriptional regulation of mRNA stability and translation. This regulation contributes to bacterial adaptation during stress and pathogenesis. Recent advances in sequencing techniques demonstrate the presence of sRNAs encoded not only in intergenic regions but also from the 3' and 5' UTRs of mRNAs, expanding sRNA regulatory networks. Additional layers of regulation by Hfq and its associated RNAs continue to be found. Newly identified RNA sponges modulate the activity of some sRNAs. A subset of sRNAs are proving to be bifunctional, able to pair with targets and also encoding small ORFs or binding other RNA binding proteins, such as CsrA. In addition, there are accumulating examples of Hfq inhibiting mRNA translation in the absence of sRNAs.
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Affiliation(s)
- Kumari Kavita
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Francois de Mets
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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105
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Impact of bacterial sRNAs in stress responses. Biochem Soc Trans 2017; 45:1203-1212. [PMID: 29101308 PMCID: PMC5730939 DOI: 10.1042/bst20160363] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Bacterial life is harsh and involves numerous environmental and internal challenges that are perceived as stresses. Consequently, adequate responses to survive, cope with, and counteract stress conditions have evolved. In the last few decades, a class of small, non-coding RNAs (sRNAs) has been shown to be involved as key players in stress responses. This review will discuss — primarily from an enterobacterial perspective — selected stress response pathways that involve antisense-type sRNAs. These include themes of how bacteria deal with severe envelope stress, threats of DNA damage, problems with poisoning due to toxic sugar intermediates, issues of iron homeostasis, and nutrient limitation/starvation. The examples discussed highlight how stress relief can be achieved, and how sRNAs act mechanistically in regulatory circuits. For some cases, we will propose scenarios that may suggest why contributions from post-transcriptional control by sRNAs, rather than transcriptional control alone, appear to be a beneficial and universally selected feature.
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106
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Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J. In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Mol Cell 2017; 65:39-51. [PMID: 28061332 PMCID: PMC5222698 DOI: 10.1016/j.molcel.2016.11.002] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 01/21/2023]
Abstract
Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3' fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators.
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Affiliation(s)
- Yanjie Chao
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Lei Li
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Dylan Girodat
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Konrad U Förstner
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Nelly Said
- Laboratory of Structural Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Colin Corcoran
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Michał Śmiga
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Kai Papenfort
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Department of Biology I, Microbiology, Ludwig-Maximilians-Universität Munich, 82152 Martinsried, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany.
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107
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van der Meulen SB, de Jong A, Kok J. Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs. Front Microbiol 2017; 8:1704. [PMID: 28959239 PMCID: PMC5603721 DOI: 10.3389/fmicb.2017.01704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/23/2017] [Indexed: 01/02/2023] Open
Abstract
Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in Lactococcus lactis that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in L. lactis, while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in L. lactis, and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of L. lactis NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.
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Affiliation(s)
- Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
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108
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Jiménez-Zurdo JI, Robledo M. RNA silencing in plant symbiotic bacteria: Insights from a protein-centric view. RNA Biol 2017; 14:1672-1677. [PMID: 28805544 DOI: 10.1080/15476286.2017.1356565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions. Here, we discuss current knowledge about RNA silencing in S. meliloti from the perspective of the activity of Hfq and a recently discovered endoribonuclease (YbeY) exhibiting unprecedented catalytic versatility for the cleavage of single- and double-stranded RNA molecules.
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Affiliation(s)
- José I Jiménez-Zurdo
- a Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín , Consejo Superior de Investigaciones Científicas (CSIC) , Granada , Spain
| | - Marta Robledo
- a Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín , Consejo Superior de Investigaciones Científicas (CSIC) , Granada , Spain
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109
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Ivain L, Bordeau V, Eyraud A, Hallier M, Dreano S, Tattevin P, Felden B, Chabelskaya S. An in vivo reporter assay for sRNA-directed gene control in Gram-positive bacteria: identifying a novel sRNA target in Staphylococcus aureus. Nucleic Acids Res 2017; 45:4994-5007. [PMID: 28369640 PMCID: PMC5416835 DOI: 10.1093/nar/gkx190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/11/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, for the most part, are unknown. This is mainly due to difficulties in identifying their targets. To aid in the identification of sRNA targets in Gram-positive bacteria, we set up an in vivo method for fast analysis of sRNA-mediated post-transcriptional control at the 5΄ regions of target mRNAs. The technology is based on the co-expression of an sRNA and a 5΄ sequence of an mRNA target fused to a green fluorescent protein (GFP) reporter. The system was challenged on Staphylococcus aureus, an opportunistic Gram-positive pathogen. We analyzed several established sRNA–mRNA interactions, and in addition, we identified the ecb mRNA as a novel target for SprX2 sRNA. Using our in vivo system in combination with in vitro experiments, we demonstrated that SprX2 uses an antisense mechanism to prevent ecb mRNA translation initiation. Furthermore, we used our reporter assay to validate sRNA regulations in other Gram-positive organisms, Bacillus subtilis and Listeria monocytogenes. Overall, our method is broadly applicable to challenge the predicted sRNA–mRNA interactions in Gram-positive bacteria.
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Affiliation(s)
- Lorraine Ivain
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Valérie Bordeau
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Alex Eyraud
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Marc Hallier
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Stéphane Dreano
- Université de Rennes 1, CNRS UMR 6290 IGDR, BIOSIT, Molecular Bases of Tumorigenesis: VHL Disease Team, 35043 Rennes, France
| | - Pierre Tattevin
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Brice Felden
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
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110
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Xia H, Yang X, Tang Q, Ye J, Wu H, Zhang H. EsrE-A yigP Locus-Encoded Transcript-Is a 3' UTR sRNA Involved in the Respiratory Chain of E. coli. Front Microbiol 2017; 8:1658. [PMID: 28900423 PMCID: PMC5581919 DOI: 10.3389/fmicb.2017.01658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/15/2017] [Indexed: 01/20/2023] Open
Abstract
The yigP locus is widely conserved among γ-proteobacteria. Mutation of the yigP locus impacts aerobic growth of Gram-negative bacteria. However, the underlying mechanism of how the yigP locus influences aerobic growth remains largely unknown. Here, we demonstrated that the yigP locus in Escherichia coli encodes two transcripts; the mRNA of ubiquinone biosynthesis protein, UbiJ, and the 3′ untranslated region small regulatory RNA (sRNA), EsrE. EsrE is an independent transcript that is transcribed using an internal promoter of the yigP locus. Surprisingly, we found that both the EsrE sRNA and UbiJ protein were required for Q8 biosynthesis, and were sufficient to rescue the growth defect ascribed to deletion of the yigP locus. Moreover, our data showed that EsrE targeted multiple mRNAs involved in several cellular processes including murein biosynthesis and the tricarboxylic acid cycle. Among these targets, sdhD mRNA that encodes one subunit of succinate dehydrogenase (SDH), was significantly activated. Our findings provided an insight into the important function of EsrE in bacterial adaptation to various environments, as well as coordinating different aspects of bacterial physiology.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Xichen Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Qiongwei Tang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China.,Department of Applied Biology, East China University of Science and TechnologyShanghai, China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China.,Department of Applied Biology, East China University of Science and TechnologyShanghai, China
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111
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Abstract
Small RNAs (sRNAs) are central regulators of gene expression in bacteria, controlling target genes posttranscriptionally by base pairing with their mRNAs. sRNAs are involved in many cellular processes and have unique regulatory characteristics. In this review, we discuss the properties of regulation by sRNAs and how it differs from and combines with transcriptional regulation. We describe the global characteristics of the sRNA-target networks in bacteria using graph-theoretic approaches and review the local integration of sRNAs in mixed regulatory circuits, including feed-forward loops and their combinations, feedback loops, and circuits made of an sRNA and another regulator, both derived from the same transcript. Finally, we discuss the competition effects in posttranscriptional regulatory networks that may arise over shared targets, shared regulators, and shared resources and how they may lead to signal propagation across the network.
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Affiliation(s)
- Mor Nitzan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; .,Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Rotem Rehani
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel;
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel;
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112
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Tanwer P, Bauer S, Heinrichs E, Panda G, Saluja D, Rudel T, Beier D. Post-transcriptional regulation of target genes by the sRNA FnrS in Neisseria gonorrhoeae. MICROBIOLOGY-SGM 2017; 163:1081-1092. [PMID: 28691898 DOI: 10.1099/mic.0.000484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Small non-coding RNAs (sRNAs) are well-established post-transcriptional regulators of gene expression in bacteria that respond to a variety of environmental stimuli. They usually act by base-pairing with their target mRNAs, which is commonly facilitated by the RNA chaperone Hfq. In this study we initiated the analysis of the sRNA FnrS of Neisseria gonorrhoeae, which is induced under anaerobic conditions. We identified four putative FnrS target genes using bioinformatics approaches and validated these target genes using translational reporter gene fusions in both Escherichia coli and N. gonorrhoeae, thereby demonstrating their downregulation by direct base-pairing between the respective mRNA and FnrS. We demonstrate deregulation of target mRNAs upon deletion of fnrS and provide evidence that the isc gene cluster required for iron-sulfur cluster biosynthesis, which harbours iscS, which is a direct target of FnrS, is coordinately downregulated by the sRNA. By mutational analysis we show that, surprisingly, three distinct regions of FnrS are employed for interaction with different target genes.
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Affiliation(s)
- Pooja Tanwer
- Chair of Microbiology, University of Würzburg, Biocenter, Germany.,Dr B R Ambedkar Center for Biomedical Research, University of Delhi, India
| | - Susanne Bauer
- Chair of Microbiology, University of Würzburg, Biocenter, Germany
| | | | - Gurudutta Panda
- Institute of Network Biology (INET), Helmholtz Zentrum München, Germany
| | - Daman Saluja
- Dr B R Ambedkar Center for Biomedical Research, University of Delhi, India
| | - Thomas Rudel
- Chair of Microbiology, University of Würzburg, Biocenter, Germany
| | - Dagmar Beier
- Chair of Microbiology, University of Würzburg, Biocenter, Germany
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113
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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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114
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Choi HI, Kim M, Jeon J, Han JK, Kim KS. Overexpression of MicA induces production of OmpC-enriched outer membrane vesicles that protect against Salmonella challenge. Biochem Biophys Res Commun 2017; 490:991-996. [PMID: 28666873 DOI: 10.1016/j.bbrc.2017.06.152] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
Abstract
Outer membrane vesicles (OMVs) derived from bacteria are promising candidates for subunit vaccines. Stresses that modulate the composition of outer membrane proteins (OMPs) are important for OMV synthesis. Small RNAs (sRNAs) expressed in response to stress regulate OMPs, although the mechanism underlying sRNA-mediated OMV biogenesis and its utility for developing vaccine platforms remains to be elucidated. Here, we characterized the role of a sRNA, MicA, which regulates OmpA, a major OMP involved in both production of OMVs and reactive immunity against Salmonella challenge. A Salmonella strain overexpressing MicA generated more OMVs than a control strain. In addition, OmpC was the major component of MicA-derived OMV proteins. MicA-derived OMVs induced Th1- and Th17-type immune responses in vitro and reduced Salmonella-mediated lethality in a mouse model. Thus, OmpA-regulatory sRNA-derived OMVs may facilitate production of Salmonella-protective vaccines.
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Affiliation(s)
- Hyun-Il Choi
- Department of Life Science, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongsangbuk-do 37673, South Korea
| | - Moonjeong Kim
- Department of Chemistry, Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Jinseong Jeon
- Department of Life Science, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongsangbuk-do 37673, South Korea
| | - Jin Kwan Han
- Department of Life Science, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongsangbuk-do 37673, South Korea
| | - Kwang-Sun Kim
- Department of Chemistry, Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, South Korea.
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115
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Tronnet S, Garcie C, Brachmann AO, Piel J, Oswald E, Martin P. High iron supply inhibits the synthesis of the genotoxin colibactin by pathogenic Escherichia coli through a non-canonical Fur/RyhB-mediated pathway. Pathog Dis 2017. [DOI: 10.1093/femspd/ftx066] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Sophie Tronnet
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
| | - Christophe Garcie
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
| | - Alexander O. Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), 8093 Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH), 8093 Zurich, Switzerland
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
| | - Patricia Martin
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
- Université Toulouse III Paul Sabatier, 31000 Toulouse, France
- CHU Toulouse, Service de Bactériologie-Hygiène, 31000 Toulouse, France
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116
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Villa JK, Amador P, Janovsky J, Bhuyan A, Saldanha R, Lamkin TJ, Contreras LM. A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response. Appl Environ Microbiol 2017; 83:e00039-17. [PMID: 28411225 PMCID: PMC5452802 DOI: 10.1128/aem.00039-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022] Open
Abstract
Tight regulation of gene expression is important for the survival of Deinococcus radiodurans, a model bacterium of extreme stress resistance. Few studies have examined the use of regulatory RNAs as a possible contributing mechanism to ionizing radiation (IR) resistance, despite their proffered efficient and dynamic gene expression regulation under IR stress. This work presents a transcriptome-based approach for the identification of stress-responsive regulatory 5' untranslated region (5'-UTR) elements in D. radiodurans R1 that can be broadly applied to other bacteria. Using this platform and an in vivo fluorescence screen, we uncovered the presence of a radiation-responsive regulatory motif in the 5' UTR of the DNA gyrase subunit A gene. Additional screens under H2O2-induced oxidative stress revealed the specificity of the response of this element to IR stress. Further examination of the sequence revealed a regulatory motif of the radiation and desiccation response (RDR) in the 5' UTR that is necessary for the recovery of D. radiodurans from high doses of IR. Furthermore, we suggest that it is the preservation of predicted RNA structure, in addition to DNA sequence consensus of the motif, that permits this important regulatory ability.IMPORTANCEDeinococcus radiodurans is an extremely stress-resistant bacterium capable of tolerating up to 3,000 times more ionizing radiation than human cells. As an integral part of the stress response mechanism of this organism, we suspect that it maintains stringent control of gene expression. However, understanding of its regulatory pathways remains incomplete to date. Untranslated RNA elements have been demonstrated to play crucial roles in gene regulation throughout bacteria. In this work, we focus on searching for and characterizing responsive RNA elements under radiation stress and propose that multiple levels of gene regulation work simultaneously to enable this organism to efficiently recover from exposure to ionizing radiation. The model we propose serves as a generic template to investigate similar mechanisms of gene regulation under stress that have likely evolved in other bacterial species.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Paul Amador
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Justin Janovsky
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Arijit Bhuyan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
| | | | - Thomas J Lamkin
- Air Force Research Laboratory/XPRA Wright-Patterson AFB, Ohio, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas,USA
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117
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Huis In 't Veld RAG, Kramer G, van der Ende A, Speijer D, Pannekoek Y. The Hfq regulon of Neisseria meningitidis. FEBS Open Bio 2017; 7:777-788. [PMID: 28593133 PMCID: PMC5458458 DOI: 10.1002/2211-5463.12218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/07/2017] [Accepted: 03/09/2017] [Indexed: 01/09/2023] Open
Abstract
The conserved RNA‐binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed‐phase liquid chromatography combined with data‐independent alternate scanning mass spectrometry (LC‐MSE) was utilized for rapid high‐resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant. Whole‐cell lysates of N. meningitidis serogroup B H44/76 wild‐type (wt) and H44/76Δhfq (Δhfq) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by liquid chromatography (LC) prior to analysis by mass spectrometry (MSE). Differential expression was analyzed by Student's t‐test with control for false discovery rate (FDR). Reliable quantitation of relative expression comparing wt and Δhfq was achieved with 506 proteins (20%). Upon FDR control at q ≤ 0.05, 48 up‐ and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq‐regulated candidates, while 15 proteins were previously found by SDS/PAGE/MS and 24 with microarray analyses. Thus, using LC‐MSE we have expanded the repertoire of Hfq‐regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq‐regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other gram‐negative model systems, suggest still unidentified sRNA analogs in N. meningitidis.
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Affiliation(s)
- Robert A G Huis In 't Veld
- Department of Medical Microbiology Center of Infection and Immunity Amsterdam (CINIMA) Academic Medical Center Amsterdam The Netherlands
| | - Gertjan Kramer
- Clinical Proteomics Facility Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands.,Present address: Genome Biology Unit EMBL Heidelberg Heidelberg Germany
| | - Arie van der Ende
- Department of Medical Microbiology Center of Infection and Immunity Amsterdam (CINIMA) Academic Medical Center Amsterdam The Netherlands.,Reference Laboratory for Bacterial Meningitis Department of Medical Microbiology Academic Medical Center Amsterdam The Netherlands
| | - Dave Speijer
- Clinical Proteomics Facility Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology Center of Infection and Immunity Amsterdam (CINIMA) Academic Medical Center Amsterdam The Netherlands
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118
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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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119
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Prasse D, Förstner KU, Jäger D, Backofen R, Schmitz RA. sRNA 154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. RNA Biol 2017; 14:1544-1558. [PMID: 28296572 DOI: 10.1080/15476286.2017.1306170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The sRNA154 deletion strain showed a significant decrease in growth under N-limitation, pointing toward a regulatory role of sRNA154 in N-metabolism. Aiming to elucidate its regulatory function we characterized sRNA154 by means of biochemical and genetic approaches. 24 homologs of sRNA154 were identified in recently reported draft genomes of Methanosarcina strains, demonstrating high conservation in sequence and predicted secondary structure with two highly conserved single stranded loops. Transcriptome studies of sRNA154 deletion mutants by an RNA-seq approach uncovered nifH- and nrpA-mRNA, encoding the α-subunit of nitrogenase and the transcriptional activator of the nitrogen fixation (nif)-operon, as potential targets besides other components of the N-metabolism. Furthermore, results obtained from stability, complementation and western blot analysis, as well as in silico target predictions combined with electrophoretic mobility shift-assays, argue for a stabilizing effect of sRNA154 on the polycistronic nif-mRNA and nrpA-mRNA by binding with both loops. Further identified N-related targets were studied, which demonstrates that translation initiation of glnA2-mRNA, encoding glutamine synthetase2, appears to be affected by sRNA154 masking the ribosome binding site, whereas glnA1-mRNA appears to be stabilized by sRNA154. Overall, we propose that sRNA154 has a crucial regulatory role in N-metabolism in M. mazei by stabilizing the polycistronic mRNA encoding nitrogenase and glnA1-mRNA, as well as allowing a feed forward regulation of nif-gene expression by stabilizing nrpA-mRNA. Consequently, sRNA154 represents the first archaeal sRNA, for which a positive posttranscriptional regulation is demonstrated as well as inhibition of translation initiation.
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Affiliation(s)
- Daniela Prasse
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Konrad U Förstner
- b Zentrum für Infektionsforschung , Universität Würzburg , Josef Schneider-Str. 2/ Bau D15, Würzburg
| | - Dominik Jäger
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Rolf Backofen
- c Institut für Informatik, Albert-Ludwigs-Universität zu Freiburg , Georges-Koehler-Allee, Freiburg , Germany
| | - Ruth A Schmitz
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
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120
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Giangrossi M, Giuliodori AM, Tran CN, Amici A, Marchini C, Falconi M. VirF Relieves the Transcriptional Attenuation of the Virulence Gene icsA of Shigella flexneri Affecting the icsA mRNA-RnaG Complex Formation. Front Microbiol 2017; 8:650. [PMID: 28458662 PMCID: PMC5394118 DOI: 10.3389/fmicb.2017.00650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
VirF is the master activator of virulence genes of Shigella and its expression is required for the invasion of the human intestinal mucosa by pathogenic bacteria. VirF was shown to directly activate the transcription of virB and icsA, which encode two essential proteins involved in the pathogenicity process, by binding their promoter regions. In this study, we demonstrate by band shift, enzymatic probing and cross-linking experiments that VirF, in addition to DNA, can also bind the icsA transcript and RnaG, an antisense non-coding small RNA that promotes the premature termination of icsA mRNA through a transcriptional attenuation mechanism. Furthermore, we show that VirF binds in vitro also other species of RNAs, although with lower specificity. The existence of VirF–RnaG and VirF-icsA mRNA complexes is confirmed in a pulldown assay carried out under experimental conditions that very close reproduce the in vivo conditions and that allows immobilized VirF to “fish” out RnaG and icsA mRNA from a total RNA extract. The VirF binding sites identified on both icsA mRNA and RnaG contain a 13 nucleotides stretch (5′-UUUUaGYcUuUau-3′) that is the RNA-converted consensus sequence previously proposed for the VirF–DNA interaction. Band-shift assays with a synthetic RNA molecule whose sequence perfectly matches the consensus indicate that this signature plays a key role also in the VirF–RNA interaction, in particular when exposed in a stem–loop structure. To further explore the icsA-RnaG-VirF regulatory system, we developed an in vitro test (RNA–RNA Pairing Assay) in which pairing between icsA mRNA and synthetic RNAs that reproduce the individual stem–loop motifs of RnaG, was analyzed in the presence of VirF. This assay shows that this protein can prevent the formation of the kissing complex, defined as the initial nucleation points for RNA heteroduplex formation, between RnaG and icsA mRNA. Consistently, VirF alleviates the RnaG-mediated repression of icsA transcription in vitro. Therefore VirF, by hindering the icsA transcript-RnaG interaction, exhibits an activity opposed to that usually displayed by proteins, which generally assist the RNA–RNA interaction; this quite uncommon and new function and the regulatory implications of VirF as a potential RNA-binding protein are discussed.
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Affiliation(s)
- Mara Giangrossi
- School of Bioscience and Veterinary Medicine, University of CamerinoCamerino, Italy
| | - Anna M Giuliodori
- School of Bioscience and Veterinary Medicine, University of CamerinoCamerino, Italy
| | - Chi N Tran
- Food Science Department, Can Tho Technical - Economic CollegeCan Tho, Vietnam
| | - Augusto Amici
- School of Bioscience and Veterinary Medicine, University of CamerinoCamerino, Italy
| | - Cristina Marchini
- School of Bioscience and Veterinary Medicine, University of CamerinoCamerino, Italy
| | - Maurizio Falconi
- School of Bioscience and Veterinary Medicine, University of CamerinoCamerino, Italy
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121
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Sun Y, Zhang J, Qin L, Yan C, Zhang X, Liu D. Identification and validation of sRNAs in Edwardsiella tarda S08. PLoS One 2017; 12:e0172783. [PMID: 28267754 PMCID: PMC5340389 DOI: 10.1371/journal.pone.0172783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 02/09/2017] [Indexed: 11/29/2022] Open
Abstract
Bacterial small non-coding RNAs (sRNAs) are known as novel regulators involved in virulence, stress responsibility, and so on. Recently, a lot of new researches have highlighted the critical roles of sRNAs in fine-tune gene regulation in both prokaryotes and eukaryotes. Edwardsiella tarda (E. tarda) is a gram-negative, intracellular pathogen that causes edwardsiellosis in fish. Thus far, no sRNA has been reported in E. tarda. The present study represents the first attempt to identify sRNAs in E. tarda S08. Ten sRNAs were validated by RNA sequencing and quantitative PCR (qPCR). ET_sRNA_1 and ET_sRNA_2 were homolous to tmRNA and GcvB, respectively. However, the other candidate sRNAs have not been reported till now. The cellular abundance of 10 validated sRNA was detected by qPCR at different growth phases to monitor their biosynthesis. Nine candidate sRNAs were expressed in the late-stage of exponential growth and stationary stages of growth (36~60 h). And the expression of the nine sRNAs was growth phase-dependent. But ET_sRNA_10 was almost expressed all the time and reached the highest peak at 48 h. Their targets were predicted by TargetRNA2 and each sRNA target contains some genes that directly or indirectly relate to virulence. These results preliminary showed that sRNAs probably play a regulatory role of virulence in E. tarda.
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Affiliation(s)
- Yuying Sun
- College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, China
| | - Jiquan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
| | - Lei Qin
- College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, China
| | - Cui Yan
- College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, China
| | - Xiaojun Zhang
- College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, China
| | - Dandan Liu
- College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, China
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122
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Abstract
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.
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123
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Pérez-Reytor D, Plaza N, Espejo RT, Navarrete P, Bastías R, Garcia K. Role of Non-coding Regulatory RNA in the Virulence of Human Pathogenic Vibrios. Front Microbiol 2017; 7:2160. [PMID: 28123382 PMCID: PMC5225090 DOI: 10.3389/fmicb.2016.02160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
In recent decades, the identification of small non-coding RNAs in bacteria has revealed an important regulatory mechanism of gene expression involved in the response to environmental signals and to the control of virulence. In the family Vibrionaceae, which includes several human and animal pathogens, small non-coding RNAs (sRNAs) are closely related to important processes including metabolism, quorum sensing, virulence, and fitness. Studies conducted in silico and experiments using microarrays and high-throughput RNA sequencing have led to the discovery of an unexpected number of sRNAs in Vibrios. The present review discusses the most relevant reports regarding the mechanisms of action of sRNAs and their implications in the virulence of the main human pathogens in the family Vibrionaceae: Vibrio parahaemolyticus, V. vulnificus and V. cholerae.
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Affiliation(s)
- Diliana Pérez-Reytor
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile San Miguel, Chile
| | - Nicolás Plaza
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de ChileSan Miguel, Chile; Institute of Nutrition and Food Technology, University of ChileSantiago, Chile
| | - Romilio T Espejo
- Institute of Nutrition and Food Technology, University of Chile Santiago, Chile
| | - Paola Navarrete
- Institute of Nutrition and Food Technology, University of Chile Santiago, Chile
| | - Roberto Bastías
- Laboratory of Microbiology, Institute of Biology, Pontificia Universidad Católica de Valparaíso Valparaíso, Chile
| | - Katherine Garcia
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile San Miguel, Chile
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124
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Kröger C, Kary SC, Schauer K, Cameron ADS. Genetic Regulation of Virulence and Antibiotic Resistance in Acinetobacter baumannii. Genes (Basel) 2016; 8:genes8010012. [PMID: 28036056 PMCID: PMC5295007 DOI: 10.3390/genes8010012] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/18/2016] [Accepted: 12/20/2016] [Indexed: 01/14/2023] Open
Abstract
Multidrug resistant microorganisms are forecast to become the single biggest challenge to medical care in the 21st century. Over the last decades, members of the genus Acinetobacter have emerged as bacterial opportunistic pathogens, in particular as challenging nosocomial pathogens because of the rapid evolution of antimicrobial resistances. Although we lack fundamental biological insight into virulence mechanisms, an increasing number of researchers are working to identify virulence factors and to study antibiotic resistance. Here, we review current knowledge regarding the regulation of virulence genes and antibiotic resistance in Acinetobacter baumannii. A survey of the two-component systems AdeRS, BaeSR, GacSA and PmrAB explains how each contributes to antibiotic resistance and virulence gene expression, while BfmRS regulates cell envelope structures important for pathogen persistence. A. baumannii uses the transcription factors Fur and Zur to sense iron or zinc depletion and upregulate genes for metal scavenging as a critical survival tool in an animal host. Quorum sensing, nucleoid-associated proteins, and non-classical transcription factors such as AtfA and small regulatory RNAs are discussed in the context of virulence and antibiotic resistance.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Stefani C Kary
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Kristina Schauer
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim 85764, Germany.
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK S4S 042, Canada.
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125
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Colameco S, Elliot MA. Non-coding RNAs as antibiotic targets. Biochem Pharmacol 2016; 133:29-42. [PMID: 28012959 DOI: 10.1016/j.bcp.2016.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Antibiotics inhibit a wide range of essential processes in the bacterial cell, including replication, transcription, translation and cell wall synthesis. In many instances, these antibiotics exert their effects through association with non-coding RNAs. This review highlights many classical antibiotic targets (e.g. rRNAs and the ribosome), explores a number of emerging targets (e.g. tRNAs, RNase P, riboswitches and small RNAs), and discusses the future directions and challenges associated with non-coding RNAs as antibiotic targets.
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Affiliation(s)
- Savannah Colameco
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Marie A Elliot
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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126
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GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation. Nat Microbiol 2016; 2:16239. [PMID: 28005055 DOI: 10.1038/nmicrobiol.2016.239] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 10/25/2016] [Indexed: 12/22/2022]
Abstract
The first step in the post-transcriptional regulatory function of most bacterial small non-coding RNAs (sRNAs) is base pairing with partially complementary sequences of targeted transcripts. We present a simple method for identifying sRNA targets in vivo and defining processing sites of the regulated transcripts. The technique, referred to as global small non-coding RNA target identification by ligation and sequencing (GRIL-seq), is based on preferential ligation of sRNAs to the ends of base-paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chimaeras. In addition to the RNA chaperone Hfq, the GRIL-seq method depends on the activity of the pyrophosphorylase RppH. Using PrrF1, an iron-regulated sRNA in Pseudomonas aeruginosa, we demonstrated that direct regulatory targets of this sRNA can readily be identified. Therefore, GRIL-seq represents a powerful tool not only for identifying direct targets of sRNAs in a variety of environments, but also for uncovering novel roles for sRNAs and their targets in complex regulatory networks.
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127
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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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128
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Iron Homeostasis Regulates the Genotoxicity of Escherichia coli That Produces Colibactin. Infect Immun 2016; 84:3358-3368. [PMID: 27620723 DOI: 10.1128/iai.00659-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/03/2016] [Indexed: 01/19/2023] Open
Abstract
The genotoxin colibactin is a secondary metabolite produced by a variety of pathogenic enterobacteria. Its biosynthesis requires the enzymatic activity of the phosphopantetheinyl transferase (PPTase) ClbA. We previously showed that ClbA can also contribute to the production of siderophores. Because the biosynthesis of siderophores is regulated by iron availability, we hypothesized that iron could also modulate the production of colibactin through the transcriptional regulation of clbA This study revealed an increased transcription of clbA under iron-limiting conditions and a decrease of clbA expression in iron-rich media. We demonstrate that clbA transcription is regulated by both the ferric uptake regulator (Fur) and the small regulatory noncoding RNA RyhB. We evidenced that the regulation of the transcription of clbA by Fur and RyhB leads to the regulation of colibactin production. This work highlights the complex mechanism of regulation of an important virulence factor by the two major regulators of bacterial iron homeostasis, making iron a key environmental factor contributing to bacterial virulence and carcinogenesis.
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129
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Tanabe T. Regulation of the Expression of Iron-acquisition System Genes in Pathogenic Vibrio Species. YAKUGAKU ZASSHI 2016; 136:1525-1532. [PMID: 27803484 DOI: 10.1248/yakushi.16-00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Vibrio includes >70 species, of which roughly a dozen cause vibriosis such as gastroenteritis, wound infections, and septicemia. Most bacteria, including Vibrio species, require iron for survival and growth. However, the bioavailability of iron is extremely low because it is usually present as an insoluble ferric complex in an aerobic environment or is bound to iron-binding proteins in mammalian hosts. Therefore many bacteria have developed iron acquisition systems, including biosynthesis and secretion of low-molecular-mass iron-chelating compounds called siderophores, and uptake of iron-bound siderophores into bacterial cells through specific active transport systems. Vibrio parahaemolyticus, a major pathogenic Vibrio species, contains multiple iron-acquisition systems mediated by its own siderophore vibrioferrin and several xenosiderophores produced by other microorganisms. In this review, I have focused on the transcriptional and posttranscriptional regulation of genes encoding iron acquisition systems in V. parahaemolyticus. All genes involved in its iron acquisition systems are repressed by Fur, which acts as a ferrous-dependent transcriptional repressor. Furthermore, the stability of polycistronic mRNA involved in vibrioferrin biosynthesis is positively regulated by a small RNA, RyhB, which is repressed by Fur. Expression of PeuA receptor required for utilization of a xenosiderophore, enterobactin, occurs under iron-limiting conditions at alkaline pH. PeuA expression is induced by a two-component regulatory system, PeuRS, which enhances expression of an alternative peuA transcript without an intrinsic translation-inhibitory structure in response to changes in alkaline pH.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University
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130
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Siqueira FM, de Morais GL, Higashi S, Beier LS, Breyer GM, de Sá Godinho CP, Sagot MF, Schrank IS, Zaha A, de Vasconcelos ATR. Mycoplasma non-coding RNA: identification of small RNAs and targets. BMC Genomics 2016; 17:743. [PMID: 27801290 PMCID: PMC5088518 DOI: 10.1186/s12864-016-3061-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system. Results A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity. Conclusion This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3061-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franciele Maboni Siqueira
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme Loss de Morais
- Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil
| | - Susan Higashi
- Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.,Université Lyon 1, Villeurbanne, France.,CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France
| | - Laura Scherer Beier
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriela Merker Breyer
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Caio Padoan de Sá Godinho
- Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil
| | - Marie-France Sagot
- Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.,Université Lyon 1, Villeurbanne, France.,CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France
| | - Irene Silveira Schrank
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Arnaldo Zaha
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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131
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Arnold WK, Savage CR, Brissette CA, Seshu J, Livny J, Stevenson B. RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs. PLoS One 2016; 11:e0164165. [PMID: 27706236 PMCID: PMC5051733 DOI: 10.1371/journal.pone.0164165] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis.
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Affiliation(s)
- William K Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Christina R Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
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132
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Bhatt S, Egan M, Jenkins V, Muche S, El-Fenej J. The Tip of the Iceberg: On the Roles of Regulatory Small RNAs in the Virulence of Enterohemorrhagic and Enteropathogenic Escherichia coli. Front Cell Infect Microbiol 2016; 6:105. [PMID: 27709103 PMCID: PMC5030294 DOI: 10.3389/fcimb.2016.00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/02/2016] [Indexed: 01/01/2023] Open
Abstract
Enterohemorrhagic and enteropathogenic Escherichia coli are gastrointestinal pathogens that disrupt the intestinal microvilli to form attaching and effacing (A/E) lesions on infected cells and cause diarrhea. This pathomorphological trait is encoded within the pathogenicity island locus of enterocyte effacement (LEE). The LEE houses a type 3 secretion system (T3SS), which upon assembly bridges the bacterial cytosol to that of the host and enables the bacterium to traffic dozens of effectors into the host where they hijack regulatory and signal transduction pathways and contribute to bacterial colonization and disease. Owing to the importance of the LEE to EHEC and EPEC pathogenesis, much of the research on these pathogens has centered on its regulation. To date, over 40 proteinaceous factors have been identified that control the LEE at various hierarchical levels of gene expression. In contrast, RNA-based regulatory mechanisms that converge on the LEE have only just begun to be unraveled. In this minireview, we highlight major breakthroughs in small RNAs (sRNAs)-dependent regulation of the LEE, with an emphasis on their mechanisms of action and/or LEE-encoded targets.
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Affiliation(s)
- Shantanu Bhatt
- Department of Biology, Saint Joseph's University Philadelphia, PA, USA
| | - Marisa Egan
- Department of Biology, Saint Joseph's University Philadelphia, PA, USA
| | - Valerie Jenkins
- Department of Biology, Saint Joseph's University Philadelphia, PA, USA
| | - Sarah Muche
- Department of Biology, Saint Joseph's University Philadelphia, PA, USA
| | - Jihad El-Fenej
- Department of Biology, Saint Joseph's University Philadelphia, PA, USA
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133
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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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134
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Horbal L, Luzhetskyy A. Dual control system - A novel scaffolding architecture of an inducible regulatory device for the precise regulation of gene expression. Metab Eng 2016; 37:11-23. [PMID: 27040671 PMCID: PMC4915818 DOI: 10.1016/j.ymben.2016.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/17/2022]
Abstract
Here, we present a novel scaffolding architecture of an inducible regulatory device. This dual control system is completely silent in the off stage and is coupled to the regulation of gene expression at both the transcriptional and translational levels. This system also functions as an AND gate. We demonstrated the effectiveness of the cumate-riboswitch dual control system for the control of pamamycin production in Streptomyces albus. Placing the cre recombinase gene under the control of this system permitted the construction of synthetic devices with non-volatile memory that sense the signal and respond by altering DNA at the chromosomal level, thereby producing changes that are heritable. In addition, we present a library of synthetic inducible promoters based on the previously described cumate switch. With only one inducer and different promoters, we demonstrate that simultaneous modulation of the expression of several genes to different levels in various operons is possible. Because all modules of the AND gates are functional in bacteria other than Streptomyces, we anticipate that these regulatory devices can be used to control gene expression in other Actinobacteria. The features described in this study make these systems promising tools for metabolic engineering and biotechnology in Actinobacteria.
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Affiliation(s)
- L Horbal
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany
| | - A Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, 66123 Saarbrücken, Germany; University of Saarland, Pharmaceutical Biotechnology, 66123 Saarbrucken, Germany.
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135
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Rossi CC, Bossé JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DMS. A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. RNA (NEW YORK, N.Y.) 2016; 22:1373-85. [PMID: 27402897 PMCID: PMC4986893 DOI: 10.1261/rna.055129.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/24/2016] [Indexed: 05/26/2023]
Abstract
Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.
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Affiliation(s)
- Ciro C Rossi
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Yanwen Li
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Kate A Gould
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Denise M S Bazzolli
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
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136
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Liu Z, Gao X, Wang H, Fang H, Yan Y, Liu L, Chen R, Zhou D, Yang R, Han Y. Plasmid pPCP1-derived sRNA HmsA promotes biofilm formation of Yersinia pestis. BMC Microbiol 2016; 16:176. [PMID: 27492011 PMCID: PMC4973556 DOI: 10.1186/s12866-016-0793-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 11/24/2022] Open
Abstract
Background The ability of Yersinia pestis to form a biofilm is an important characteristic in flea transmission of this pathogen. Y. pestis laterally acquired two plasmids (pPCP1and pMT1) and the ability to form biofilms when it evolved from Yersinia pseudotuberculosis. Small regulatory RNAs (sRNAs) are thought to play a crucial role in the processes of biofilm formation and pathogenesis. Results A pPCP1-derived sRNA HmsA (also known as sR084) was found to contribute to the enhanced biofilm formation phenotype of Y. pestis. The concentration of c-di-GMP was significantly reduced upon deletion of the hmsA gene in Y. pestis. The abundance of mRNA transcripts determining exopolysaccharide production, crucial for biofilm formation, was measured by primer extension, RT-PCR and lacZ transcriptional fusion assays in the wild-type and hmsA mutant strains. HmsA positively regulated biofilm synthesis-associated genes (hmsHFRS, hmsT and hmsCDE), but had no regulatory effect on the biofilm degradation-associated gene hmsP. Interestingly, the recently identified biofilm activator sRNA, HmsB, was rapidly degraded in the hmsA deletion mutant. Two genes (rovM and rovA) functioning as biofilm regulators were also found to be regulated by HmsA, whose regulatory effects were consistent with the HmsA-mediated biofilm phenotype. Conclusion HmsA potentially functions as an activator of biofilm formation in Y. pestis, implying that sRNAs encoded on the laterally acquired plasmids might be involved in the chromosome-based regulatory networks implicated in Y. pestis-specific physiological processes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0793-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zizhong Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,State Key Lab of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Xiaofang Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hongduo Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,College of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Haihong Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Lei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Rong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,The General Hospital of PLA, Beijing, 100853, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
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137
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Broach WH, Weiss A, Shaw LN. Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis. Microb Genom 2016; 2:e000065. [PMID: 28348860 PMCID: PMC5343137 DOI: 10.1099/mgen.0.000065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022] Open
Abstract
Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus with other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, Staphylococcus epidermidis and Staphylococcus carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA contents of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set of between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidishas the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behaviour of these diverse staphylococcal strains.
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Affiliation(s)
- William H Broach
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Andy Weiss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
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138
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Abstract
Enteric pathogens of the family Enterobacteriaceae colonize various niches within animals and humans in which they compete with intestinal commensals and are attacked by the host immune system. To survive these hostile environments they possess complex, multilayer regulatory networks that coordinate the control of virulence factors, host-adapted metabolic functions and stress resistance. An important part of these intricate control networks are RNA-based control systems that enable the pathogen to fine-tune its responses. Recent next-generation sequencing approaches revealed a large repertoire of conserved and species-specific riboregulators, including numerous cis- and trans-acting non-coding RNAs, sensory RNA elements (RNA thermometers, riboswitches), regulatory RNA-binding proteins and RNA degrading enzymes which regulate colonization factors, toxins, host defense processes and virulence-relevant physiological and metabolic processes. All of which are important cues for pathogens to sense and respond to fluctuating conditions during the infection. This review covers infection-relevant riboregulators of E. coli, Salmonella, Shigella and Yersinia, highlights their versatile regulatory mechanisms, complex target regulons and functions, and discusses emerging topics and future challenges to fully understand and exploit RNA-based control to combat bacterial infections.
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Affiliation(s)
- Ann Kathrin Heroven
- a Department of Molecular Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Aaron M Nuss
- a Department of Molecular Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Petra Dersch
- a Department of Molecular Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
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139
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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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140
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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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141
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Wang M, Fleming J, Li Z, Li C, Zhang H, Xue Y, Chen M, Zhang Z, Zhang XE, Bi L. An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:544-53. [PMID: 27174874 DOI: 10.1093/abbs/gmw037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/31/2016] [Indexed: 11/14/2022] Open
Abstract
Deep-sequencing of bacterial transcriptomes using RNA-Seq technology has made it possible to identify small non-coding RNAs, RNA molecules which regulate gene expression in response to changing environments, on a genome-wide scale in an ever-increasing range of prokaryotes. However, a simple and reliable automated method for identifying sRNA candidates in these large datasets is lacking. Here, after generating a transcriptome from an exponential phase culture of Mycobacterium tuberculosis H37Rv, we developed and validated an automated method for the genome-wide identification of sRNA candidate-containing regions within RNA-Seq datasets based on the analysis of the characteristics of reads coverage maps. We identified 192 novel candidate sRNA-encoding regions in intergenic regions and 664 RNA transcripts transcribed from regions antisense (as) to open reading frames (ORF), which bear the characteristics of asRNAs, and validated 28 of these novel sRNA-encoding regions by northern blotting. Our work has not only provided a simple automated method for genome-wide identification of candidate sRNA-encoding regions in RNA-Seq data, but has also uncovered many novel candidate sRNA-encoding regions in M. tuberculosis, reinforcing the view that the control of gene expression in bacteria is more complex than previously anticipated.
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Affiliation(s)
- Ming Wang
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Joy Fleming
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Hongtai Zhang
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunxin Xue
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Zongde Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xian-En Zhang
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijun Bi
- Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan 528000, China
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142
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Vakulskas CA, Leng Y, Abe H, Amaki T, Okayama A, Babitzke P, Suzuki K, Romeo T. Antagonistic control of the turnover pathway for the global regulatory sRNA CsrB by the CsrA and CsrD proteins. Nucleic Acids Res 2016; 44:7896-910. [PMID: 27235416 PMCID: PMC5027483 DOI: 10.1093/nar/gkw484] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 12/20/2022] Open
Abstract
The widely conserved protein CsrA (carbon storage regulator A) globally regulates bacterial gene expression at the post-transcriptional level. In many species, CsrA activity is governed by untranslated sRNAs, CsrB and CsrC in Escherichia coli, which bind to multiple CsrA dimers, sequestering them from lower affinity mRNA targets. Both the synthesis and turnover of CsrB/C are regulated. Their turnover requires the housekeeping endonuclease RNase E and is activated by the presence of a preferred carbon source via the binding of EIIAGlc of the glucose transport system to the GGDEF-EAL domain protein CsrD. We demonstrate that the CsrB 3′ segment contains the features necessary for CsrD-mediated decay. RNase E cleavage in an unstructured segment located immediately upstream from the intrinsic terminator is necessary for subsequent degradation to occur. CsrA stabilizes CsrB against RNase E cleavage by binding to two canonical sites adjacent to the necessary cleavage site, while CsrD acts by overcoming CsrA-mediated protection. Our genetic, biochemical and structural studies establish a molecular framework for sRNA turnover by the CsrD-RNase E pathway. We propose that CsrD evolution was driven by the selective advantage of decoupling Csr sRNA decay from CsrA binding, connecting it instead to the availability of a preferred carbon source.
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Affiliation(s)
- Christopher A Vakulskas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA
| | - Yuanyuan Leng
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA
| | - Hazuki Abe
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Takumi Amaki
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Akihiro Okayama
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Paul Babitzke
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Kazushi Suzuki
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA
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143
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Abstract
In the last few decades, small regulatory RNA (sRNA) molecules emerged as key regulators in every kingdom of life. Resolving the full targetome of sRNAs has however remained a challenge. To address this, we used an in vivo tagging MS2-affinity purification protocol coupled with RNA sequencing technology, namely MAPS, to assemble full bacterial small RNAs targetomes. The impressive potential of MAPS has been supported by a number of reports. Here, we concisely overview RNA-tagging history that preceded the development of the MAPS assay and expose the range of possible uses of this technology.
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Affiliation(s)
- Marie-Claude Carrier
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - David Lalaouna
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - Eric Massé
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
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144
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Huerta JM, Aguilar I, López-Pliego L, Fuentes-Ramírez LE, Castañeda M. The Role of the ncRNA RgsA in the Oxidative Stress Response and Biofilm Formation in Azotobacter vinelandii. Curr Microbiol 2016; 72:671-9. [PMID: 26858204 DOI: 10.1007/s00284-016-1003-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/27/2015] [Indexed: 12/23/2022]
Abstract
Azotobacter vinelandii is a soil bacterium that forms desiccation-resistant cysts, and the exopolysaccharide alginate is essential for this process. A. vinelandii also produces alginate under vegetative growth conditions, and this production has biotechnological significance. Poly-β-hydroxybutyrate (PHB) is another polymer synthetized by A. vinelandii that is of biotechnological interest. The GacS/A two-component signal transduction system plays an important role in regulating alginate production, PHB synthesis, and encystment. GacS/A in turn controls other important regulators such as RpoS and the ncRNAs that belong to the Rsm family. In A. vinelandii, RpoS is necessary for resisting oxidative stress as a result of its control over the expression of the catalase Kat1. In this work, we characterized a new ncRNA in A. vinelandii that is homologous to the P16/RsgA reported in Pseudomonas. We found that the expression of rgsA is regulated by GacA and RpoS and that it was essential for oxidative stress resistance. However, the activity of the catalase Kat1 is unaffected in rgsA mutants. Unlike those reported in Pseudomonas, RgsA in A. vinelandii regulates biofilm formation but not polymer synthesis or the encystment process.
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Affiliation(s)
- Jesús Manuel Huerta
- CICM-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Israel Aguilar
- CICM-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Liliana López-Pliego
- CICM-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | | | - Miguel Castañeda
- CICM-Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
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Balbontín R, Villagra N, Pardos de la Gándara M, Mora G, Figueroa-Bossi N, Bossi L. Expression of IroN, the salmochelin siderophore receptor, requires mRNA activation by RyhB small RNA homologues. Mol Microbiol 2016; 100:139-55. [PMID: 26710935 DOI: 10.1111/mmi.13307] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2015] [Indexed: 12/21/2022]
Abstract
The iroN gene of Salmonella enterica and uropathogenic Escherichia coli encodes the outer membrane receptor of Fe(3+) -bound salmochelin, a siderophore tailored to evade capture by the host's immune system. The iroN gene is under negative control of the Fur repressor and transcribed under iron limiting conditions. We show here that transcriptional de-repression is not sufficient to allow iroN expression, as this also requires activation by either of two partially homologous small RNAs (sRNAs), RyhB1 and RyhB2. The two sRNAs target the same sequence segment approximately in the middle of the 94-nucleotide 5' untranslated region (UTR) of iroN mRNA. Several lines of evidence suggest that base pair interaction stimulates iroN mRNA translation. Activation does not result from the disruption of a secondary structure masking the ribosome binding site; rather it involves sequences at the 5' end of iroN 5' UTR. In vitro 'toeprint' assays revealed that this upstream site binds the 30S ribosomal subunit provided that RyhB1 is paired with the mRNA. Altogether, our data suggest that RyhB1, and to lesser extent RyhB2, activate iroN mRNA translation by promoting entry of the ribosome at an upstream 'standby' site. These findings add yet an additional nuance to the polychromatic landscape of sRNA-mediated regulation.
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Affiliation(s)
- Roberto Balbontín
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Nicolás Villagra
- Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Maria Pardos de la Gándara
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Guido Mora
- Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
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146
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Abstract
Y. pestis exhibits dramatically different traits of pathogenicity and transmission, albeit their close genetic relationship with its ancestor-Y. pseudotuberculosis, a self-limiting gastroenteric pathogen. Y. pestis is evolved into a deadly pathogen and transmitted to mammals and/or human beings by infected flea biting or directly contacting with the infected animals. Various kinds of environmental changes are implicated into its complex life cycle and pathogenesis. Dynamic regulation of gene expression is critical for environmental adaptation or survival, primarily reflected by genetic regulation mediated by transcriptional factors and small regulatory RNAs at the transcriptional and posttranscriptional level, respectively. The effects of genetic regulation have been shown to profoundly influence Y. pestis physiology and pathogenesis such as stress resistance, biofilm formation, intracellular survival, and replication. In this chapter, we mainly summarize the progresses on popular methods of genetic regulation and on regulatory patterns and consequences of many key transcriptional and posttranscriptional regulators, with a particular emphasis on how genetic regulation influences the biofilm and virulence of Y. pestis.
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147
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Schroeder CLC, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK. Bacterial small RNAs in the Genus Rickettsia. BMC Genomics 2015; 16:1075. [PMID: 26679185 PMCID: PMC4683814 DOI: 10.1186/s12864-015-2293-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/14/2015] [Indexed: 01/02/2023] Open
Abstract
Background Rickettsia species are obligate intracellular Gram-negative pathogenic bacteria and the etiologic agents of diseases such as Rocky Mountain spotted fever (RMSF), Mediterranean spotted fever, epidemic typhus, and murine typhus. Genome sequencing revealed that R. prowazekii has ~25 % non-coding DNA, the majority of which is thought to be either “junk DNA” or pseudogenes resulting from genomic reduction. These characteristics also define other Rickettsia genomes. Bacterial small RNAs, whose biogenesis is predominantly attributed to either the intergenic regions (trans-acting) or to the antisense strand of an open reading frame (cis-acting), are now appreciated to be among the most important post-transcriptional regulators of bacterial virulence and growth. We hypothesize that intergenic regions in rickettsial species encode for small, non-coding RNAs (sRNAs) involved in the regulation of its transcriptome, leading to altered virulence and adaptation depending on the host niche. Results We employed a combination of bioinformatics and in vitro approaches to explore the presence of sRNAs in a number of species within Genus Rickettsia. Using the sRNA Identification Protocol using High-throughput Technology (SIPHT) web interface, we predicted over 1,700 small RNAs present in the intergenic regions of 16 different strains representing 13 rickettsial species. We further characterized novel sRNAs from typhus (R. prowazekii and R. typhi) and spotted fever (R. rickettsii and R. conorii) groups for their promoters and Rho-independent terminators using Bacterial Promoter Prediction Program (BPROM) and TransTermHP prediction algorithms, respectively. Strong σ70 promoters were predicted upstream of all novel small RNAs, indicating the potential for transcriptional activity. Next, we infected human microvascular endothelial cells (HMECs) with R. prowazekii for 3 h and 24 h and performed Next Generation Sequencing to experimentally validate the expression of 26 sRNA candidates predicted in R. prowazekii. Reverse transcriptase PCR was also used to further verify the expression of six putative novel sRNA candidates in R. prowazekii. Conclusions Our results yield clear evidence for the expression of novel R. prowazekii sRNA candidates during infection of HMECs. This is the first description of novel small RNAs for a highly pathogenic species of Rickettsia, which should lead to new insights into rickettsial virulence and adaptation mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2293-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Casey L C Schroeder
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Hema P Narra
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Mark Rojas
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Jignesh Patel
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Kamil Khanipov
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Yuriy Fofanov
- Department of Pharmacology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
| | - Sanjeev K Sahni
- Department of Pathology, the University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
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148
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Meißner C, Jahn N, Brantl S. In Vitro Characterization of the Type I Toxin-Antitoxin System bsrE/SR5 from Bacillus subtilis. J Biol Chem 2015; 291:560-71. [PMID: 26565032 DOI: 10.1074/jbc.m115.697524] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Indexed: 11/06/2022] Open
Abstract
BsrE/SR5 is a new type I toxin/antitoxin system located on the prophage-like region P6 of the Bacillus subtilis chromosome. The bsrE gene encoding a 30-amino acid hydrophobic toxin and the antitoxin gene sr5 overlap at their 3' ends by 112 bp. Overexpression of bsrE causes cell lysis on agar plates. Here, we present a detailed in vitro analysis of bsrE/SR5. The secondary structures of SR5, bsrE mRNA, and the SR5/bsrE RNA complex were determined. Apparent binding rate constants (kapp) of wild-type and mutated SR5 species with wild-type bsrE mRNA were calculated, and SR5 regions required for efficient inhibition of bsrE mRNA narrowed down. In vivo studies confirmed the in vitro data but indicated that a so far unknown RNA binding protein might exist in B. subtilis that can promote antitoxin/toxin RNA interaction. Using time course experiments, the binding pathway of SR5 and bsrE RNA was elucidated. A comparison with the previously well characterized type I TA system from the B. subtilis chromosome, bsrG/SR4, reveals similarities but also significant differences.
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Affiliation(s)
- Christin Meißner
- From the AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
| | - Natalie Jahn
- From the AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
| | - Sabine Brantl
- From the AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
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149
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Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing. J Bacteriol 2015; 198:427-35. [PMID: 26553849 DOI: 10.1128/jb.00711-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR. IMPORTANCE Brucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
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