1
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Svensson SL, Sharma CM. RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist. eLife 2021; 10:69064. [PMID: 34843430 PMCID: PMC8687705 DOI: 10.7554/elife.69064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the food-borne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome-binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that can antagonize bacterial sRNAs.
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Affiliation(s)
- Sarah Lauren Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Cynthia Mira Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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2
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Denham EL. The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194565. [PMID: 32475775 DOI: 10.1016/j.bbagrm.2020.194565] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
In bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Sponge RNAs modulate free sRNA levels in the cell through RNA-RNA interactions that sequester ("soak up") the sRNA and/or promote degradation of the target sRNA or the sponge RNA-sRNA complex. The development of complex RNA sequencing strategies for the detection of RNA-RNA interactions has enabled identification of several sponge RNAs, as well as previously known regulatory RNAs able to act as both regulators and sponges. This review highlights techniques that have enabled the identification of these sponge RNAs, the origins of sponge RNAs and the mechanisms by which they function in the post-transcriptional network.
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Affiliation(s)
- Emma L Denham
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom.
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3
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Bossi L, Figueroa-Bossi N, Bouloc P, Boudvillain M. Regulatory interplay between small RNAs and transcription termination factor Rho. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194546. [PMID: 32217107 DOI: 10.1016/j.bbagrm.2020.194546] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/12/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5' end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to transcriptional steps, most notably transcription termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and termination factor Rho. Two general mechanisms have emerged. One mechanism operates in translated regions subjected to sRNA repression. By inhibiting ribosome binding co-transcriptionally, the sRNA uncouples translation from transcription, allowing Rho to bind the nascent RNA and promote termination. In the second mechanism, which functions in 5' untranslated regions, the sRNA antagonizes termination directly by interfering with Rho binding to the RNA or the subsequent translocation along the RNA. Here, we review the above literature in the context of other mechanisms that underlie the participation of Rho-dependent transcription termination in gene regulation. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France
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4
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Grüll MP, Massé E. Mimicry, deception and competition: The life of competing endogenous RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1525. [PMID: 30761752 DOI: 10.1002/wrna.1525] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets. While some ceRNAs seem to be expressed constitutively, others are intricately regulated according to environmental conditions. The outcome of ceRNA binding to a sRNA reaches beyond simple sequestration. Various effects observed on sRNA functions extend from reducing transcriptional noise to promote RNA turnover. Here, we present a historical perspective of the discovery of ceRNAs in eukaryotic organisms and mainly focus on the synthesis and function of select, well-described, ceRNAs in bacterial cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Marc P Grüll
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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5
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Sinha D, Matz LM, Cameron TA, De Lay NR. Poly(A) polymerase is required for RyhB sRNA stability and function in Escherichia coli. RNA (NEW YORK, N.Y.) 2018; 24:1496-1511. [PMID: 30061117 PMCID: PMC6191717 DOI: 10.1261/rna.067181.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/24/2018] [Indexed: 05/05/2023]
Abstract
Small regulatory RNAs (sRNAs) are an important class of bacterial post-transcriptional regulators that control numerous physiological processes, including stress responses. In Gram-negative bacteria including Escherichia coli, the RNA chaperone Hfq binds many sRNAs and facilitates pairing to target transcripts, resulting in changes in mRNA transcription, translation, or stability. Here, we report that poly(A) polymerase (PAP I), which promotes RNA degradation by exoribonucleases through the addition of poly(A) tails, has a crucial role in the regulation of gene expression by Hfq-dependent sRNAs. Specifically, we show that deletion of pcnB, encoding PAP I, paradoxically resulted in an increased turnover of certain Hfq-dependent sRNAs, including RyhB. RyhB instability in the pcnB deletion strain was suppressed by mutations in hfq or ryhB that disrupt pairing of RyhB with target RNAs, by mutations in the 3' external transcribed spacer of the glyW-cysT-leuZ transcript (3'ETSLeuZ) involved in pairing with RyhB, or an internal deletion in rne, which encodes the endoribonuclease RNase E. Finally, the reduced stability of RyhB in the pcnB deletion strain resulted in impaired regulation of some of its target mRNAs, specifically sodB and sdhCDAB. Altogether our data support a model where PAP I plays a critical role in ensuring the efficient decay of the 3'ETSLeuZ In the absence of PAP I, the 3'ETSLeuZ transcripts accumulate, bind Hfq, and pair with RyhB, resulting in its depletion via RNase E-mediated decay. This ultimately leads to a defect in RyhB function in a PAP I deficient strain.
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Affiliation(s)
- Dhriti Sinha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Lisa M Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas 77030, USA
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6
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Coherent Feedforward Regulation of Gene Expression by Caulobacter σ T and GsrN during Hyperosmotic Stress. J Bacteriol 2018; 200:JB.00349-18. [PMID: 30012732 DOI: 10.1128/jb.00349-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 07/12/2018] [Indexed: 01/05/2023] Open
Abstract
GsrN is a conserved small RNA that is under transcriptional control of the general stress sigma factor, σT, and that functions as a posttranscriptional regulator of Caulobacter crescentus survival under multiple stress conditions. We have defined features of GsrN structure that determine survival under hyperosmotic stress, and we have applied transcriptomic and proteomic methods to identify regulatory targets of GsrN under hyperosmotic conditions. The 5' end of GsrN, which includes a conserved cytosine-rich stem-loop structure, is necessary for cell survival after osmotic upshock. GsrN both activates and represses gene expression in this stress condition. Expression of an uncharacterized open reading frame predicted to encode a glycine zipper protein, osrP, is strongly activated by GsrN. Our data support a model in which GsrN physically interacts with osrP mRNA through its 5' C-rich stem-loop to enhance OsrP protein expression. We conclude that sigT, gsrN, and osrP form a coherent feedforward loop in which σT activates gsrN and osrP transcription during stress and GsrN activates OsrP protein expression at the posttranscriptional level. This study delineates transcriptional and posttranscriptional layers of Caulobacter gene expression control during hyperosmotic stress, uncovers a new regulatory target of GsrN, and defines a coherent feedforward motif in the Caulobacter general stress response (GSR) regulatory network.IMPORTANCE Bacteria inhabit diverse niches and must adapt their physiology to constant environmental fluctuations. A major response to environmental perturbation is to change gene expression. Caulobacter and other alphaproteobacteria initiate a complex gene expression program known as the general stress response (GSR) under conditions including oxidative stress, osmotic stress, and nutrient limitation. The GSR enables cell survival in these environments. Understanding how bacteria survive stress requires that we dissect gene expression responses, such as the GSR, at the molecular level. This study is significant, as it defines transcriptional and posttranscriptional layers of gene expression regulation in response to hyperosmotic stress. We further provide evidence that a coherent feedforward motif influences the system properties of the Caulobacter GSR pathway.
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7
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Abstract
ABSTRACT
Most noncoding small RNAs (sRNAs) that regulate gene expression do so by base-pairing with mRNAs, affecting their translation and/or stability. Regulators as evolutionarily distant as the
trans
-encoded sRNAs of bacteria and the microRNAs (miRNAs) of higher eukaryotes share the property of targeting short sequence segments that occur in multiple copies in bacterial and eukaryotic transcriptomes. This target promiscuity has major implications for sRNA function. On the one hand, it allows the sRNA to coordinately control several different targets and thus be at the center of regulatory networks. On the other hand, it allows the existence of target mimics or decoys that divert the sRNA/miRNA away from bona fide targets and thus serve as mechanisms to regulate the regulator. In addition, by competing for pairing with the same sRNA, bona fide targets establish a cross talk that can impact on each other’s expression levels. Here we review evidence that target mimicry and competition are important components of the regulatory architecture of bacterial sRNA networks.
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8
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Durica-Mitic S, Göpel Y, Görke B. Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs. Microbiol Spectr 2018; 6. [PMID: 29573258 DOI: 10.1128/microbiolspec.rwr-0013-2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Survival of bacteria in ever-changing habitats with fluctuating nutrient supplies requires rapid adaptation of their metabolic capabilities. To this end, carbohydrate metabolism is governed by complex regulatory networks including posttranscriptional mechanisms that involve small regulatory RNAs (sRNAs) and RNA-binding proteins. sRNAs limit the response to substrate availability and set the threshold or time required for induction and repression of carbohydrate utilization systems. Carbon catabolite repression (CCR) also involves sRNAs. In Enterobacteriaceae, sRNA Spot 42 cooperates with the transcriptional regulator cyclic AMP (cAMP)-receptor protein (CRP) to repress secondary carbohydrate utilization genes when a preferred sugar is consumed. In pseudomonads, CCR operates entirely at the posttranscriptional level, involving RNA-binding protein Hfq and decoy sRNA CrcZ. Moreover, sRNAs coordinate fluxes through central carbohydrate metabolic pathways with carbohydrate availability. In Gram-negative bacteria, the interplay between RNA-binding protein CsrA and its cognate sRNAs regulates glycolysis and gluconeogenesis in response to signals derived from metabolism. Spot 42 and cAMP-CRP jointly downregulate tricarboxylic acid cycle activity when glycolytic carbon sources are ample. In addition, bacteria use sRNAs to reprogram carbohydrate metabolism in response to anaerobiosis and iron limitation. Finally, sRNAs also provide homeostasis of essential anabolic pathways, as exemplified by the hexosamine pathway providing cell envelope precursors. In this review, we discuss the manifold roles of bacterial sRNAs in regulation of carbon source uptake and utilization, substrate prioritization, and metabolism.
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Affiliation(s)
- Svetlana Durica-Mitic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
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9
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10
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Soysa HSM, Schulte A, Suginta W. Functional analysis of an unusual porin-like channel that imports chitin for alternative carbon metabolism in Escherichia coli. J Biol Chem 2017; 292:19328-19337. [PMID: 28972167 DOI: 10.1074/jbc.m117.812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/22/2017] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli have the genetic potential to use chitin as a carbon source in the absence of glucose, importing it via the chitin-uptake channel EcChiP for processing by the glucosamine catabolic pathway. The chip gene is usually not expressed when E. coli are grown on glucose-enriched nutrients, providing a general regulatory mechanism for the pathway. EcChiP is unusual in that it is homologous to porins and monomeric instead of trimeric, the typical form of sugar-specific channels, making it unclear how this channel operates. We recently reported that EcChiP could form a stable channel in lipid membranes and that the channel is specific for chitooligosaccharides. This report describes the biophysical nature of sugar-channel interactions and the kinetics of sugar association and dissociation. Titrating EcChiP with chitohexaose resulted in protein fluorescence enhancement in a concentration-dependent manner, yielding a binding constant of 2.9 × 105 m-1, consistent with the value of 2.5 × 105 m-1 obtained from isothermal titration microcalorimetry. Analysis of the integrated heat change suggested that the binding process was endothermic and driven by entropy. Single-channel recordings confirmed the voltage dependence of the penetration of chitohexaose molecules into and their release from EcChiP. Once inside the pore, the sugar release rate (koff) from the affinity site increased with elevated voltage, regardless of the side of sugar addition. Our findings revealed distinct thermodynamic and kinetic features of the activity of sugar-specific EcChiP and advance our knowledge of the physiological possibility of chitin utilization by non-chitinolytic bacteria.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and
| | - Albert Schulte
- the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science and .,the Center of Excellence in Advanced Functional Materials, Suranaree University of Technology Nakhon Ratchasima 30000, Thailand and
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11
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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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12
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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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13
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Qian Z, Trostel A, Lewis DEA, Lee SJ, He X, Stringer AM, Wade JT, Schneider TD, Durfee T, Adhya S. Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli. Front Mol Biosci 2016; 3:74. [PMID: 27900321 PMCID: PMC5110547 DOI: 10.3389/fmolb.2016.00074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022] Open
Abstract
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors. Surprisingly, we detect regulation of 158 transcripts by GalR, with few regulated genes being associated with a nearby GalR binding site. Based on our earlier observation of long-range interactions between distally bound GalR dimers, we propose that GalR indirectly regulates the transcription of many genes by inducing large-scale restructuring of the chromosome.
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Affiliation(s)
- Zhong Qian
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Andrei Trostel
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Dale E A Lewis
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Sang Jun Lee
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, Korea
| | - Ximiao He
- Laboratory of Metabolism, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health Albany, NY, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of HealthAlbany, NY, USA; Department of Biomedical Sciences, School of Public Health, University of AlbanyAlbany, NY, USA
| | - Thomas D Schneider
- Gene Regulation and Chromosome Biology Laboratory, National Institutes of Health, National Cancer Institute, Center for Cancer Research Frederick, MD, USA
| | | | - Sankar Adhya
- Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA
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14
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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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15
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Soysa HSM, Suginta W. Identification and Functional Characterization of a Novel OprD-like Chitin Uptake Channel in Non-chitinolytic Bacteria. J Biol Chem 2016; 291:13622-33. [PMID: 27226611 DOI: 10.1074/jbc.m116.728881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Chitoporin from the chitinolytic marine Vibrio has been characterized as a trimeric OmpC-like channel responsible for effective chitin uptake. In this study we describe the identification and characterization of a novel OprD-like chitoporin (so-called EcChiP) from Escherichia coli The gene was identified, cloned, and functionally expressed in the Omp-deficient E. coli BL21 (Omp8) Rosetta strain. On size exclusion chromatography, EcChiP had an apparent native molecular mass of 50 kDa, as predicted by amino acid sequencing and mass analysis, confirming that the protein is a monomer. Black lipid membrane reconstitution demonstrated that EcChiP could readily form stable, monomeric channels in artificial phospholipid membranes, with an average single channel conductance of 0.55 ± 0.01 nanosiemens and a slight preference for cations. Single EcChiP channels showed strong specificity, interacting with long chain chitooligosaccharides but not with maltooligosaccharides. Liposome swelling assays indicated the bulk permeation of neutral monosaccharides and showed the size exclusion limit of EcChiP to be ∼200-300 Da for small permeants that pass through by general diffusion while allowing long chain chitooligosaccharides to pass through by a facilitated diffusion process. Taking E. coli as a model, we offer the first evidence that non-chitinolytic bacteria can activate a quiescent ChiP gene to express a functional chitoporin, enabling them to take up chitooligosaccharides for metabolism as an immediate source of energy.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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16
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Bonocora RP, Smith C, Lapierre P, Wade JT. Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. PLoS Genet 2015; 11:e1005552. [PMID: 26425847 PMCID: PMC4591121 DOI: 10.1371/journal.pgen.1005552] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/03/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs. Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription. There are two families of σ factor: σ70 and σ54. Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences, in association with RNA polymerase, in a transcriptionally inactive state. We have determined positions in the Escherichia coli genome that are bound by σ54, the archetypal member of the σ54 family. Surprisingly, we identified 135 binding sites for σ54, a huge increase over the number of previously described sites. Our data suggest that there are more than 250 σ54 sites in total. Strikingly, most σ54 binding sites are located inside genes, whereas only one intragenic σ54 binding site has previously been described. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved in other bacterial species. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this notion, we identify three σ54 promoters in E. coli that are located inside genes but drive transcription of unusual mRNAs for the neighboring genes.
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Affiliation(s)
- Richard P. Bonocora
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail:
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Knopp M, Andersson DI. Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins. Mol Biol Evol 2015; 32:3252-63. [DOI: 10.1093/molbev/msv195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella. Proc Natl Acad Sci U S A 2015; 112:E4772-81. [PMID: 26307765 DOI: 10.1073/pnas.1507825112] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.
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Plumbridge J. Regulation of the Utilization of Amino Sugars by Escherichia coli and Bacillus subtilis: Same Genes, Different Control. J Mol Microbiol Biotechnol 2015; 25:154-67. [DOI: 10.1159/000369583] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Amino sugars are dual-purpose compounds in bacteria: they are essential components of the outer wall peptidoglycan (PG) and the outer membrane of Gram-negative bacteria and, in addition, when supplied exogenously their catabolism contributes valuable supplies of energy, carbon and nitrogen to the cell. The enzymes for both the synthesis and degradation of glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) are highly conserved but during evolution have become subject to different regulatory regimes. <i>Escherichia coli</i> grows more rapidly using GlcNAc as a carbon source than with GlcN. On the other hand, <i>Bacillus subtilis,</i> but not other <i>Bacilli</i> tested, grows more efficiently on GlcN than GlcNAc. The more rapid growth on this sugar is associated with the presence of a second, GlcN-specific operon, which is unique to this species. A single locus is associated with the genes for catabolism of GlcNAc and GlcN in <i>E. coli,</i> although they enter the cell via different transporters. In <i>E. coli</i> the amino sugar transport and catabolic genes have also been requisitioned as part of the PG recycling process. Although PG recycling likely occurs in <i>B. subtilis,</i> it appears to have different characteristics.
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Lalaouna D, Carrier MC, Massé E. The shock absorber: preventing sRNA transcriptional noise. Cell Cycle 2015; 14:2539-40. [PMID: 26066059 DOI: 10.1080/15384101.2015.1060771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- David Lalaouna
- a Department of Biochemistry ; RNA Group; Université de Sherbrooke ; Sherbrooke , QC Canada
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21
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Miyakoshi M, Chao Y, Vogel J. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J 2015; 34:1478-92. [PMID: 25630703 PMCID: PMC4474525 DOI: 10.15252/embj.201490546] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022] Open
Abstract
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
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Affiliation(s)
- Masatoshi Miyakoshi
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Yanjie Chao
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
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22
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A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise. Mol Cell 2015; 58:393-405. [DOI: 10.1016/j.molcel.2015.03.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
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Papenfort K, Vanderpool CK. Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 2015; 39:362-78. [PMID: 25934124 DOI: 10.1093/femsre/fuv016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA Department of Biology I, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Liu N, Niu G, Xie Z, Chen Z, Itzek A, Kreth J, Gillaspy A, Zeng L, Burne R, Qi F, Merritt J. The Streptococcus mutans irvA gene encodes a trans-acting riboregulatory mRNA. Mol Cell 2015; 57:179-90. [PMID: 25574948 DOI: 10.1016/j.molcel.2014.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/12/2014] [Accepted: 11/04/2014] [Indexed: 02/08/2023]
Abstract
In both prokaryotes and eukaryotes, insight into gene function is typically obtained by in silico homology searches and/or phenotypic analyses of strains bearing mutations within open reading frames. However, the studies herein illustrate how mRNA function is not limited to the expression of a cognate protein. We demonstrate that a stress-induced protein-encoding mRNA (irvA) from the dental caries pathogen Streptococcus mutans directly modulates target mRNA (gbpC) stability through seed pairing interactions. The 5' untranslated region of irvA mRNA is a trans riboregulator of gbpC and a critical activator of the DDAG stress response, whereas IrvA functions independently in the regulation of natural competence. The irvA riboregulatory domain controls GbpC production by forming irvA-gbpC hybrid mRNA duplexes that prevent gbpC degradation by an RNase J2-mediated pathway. These studies implicate a potentially ubiquitous role for typical protein-encoding mRNAs as riboregulators, which could alter current concepts in gene regulation.
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Affiliation(s)
- Nan Liu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Guoqing Niu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhoujie Xie
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhiyun Chen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Andreas Itzek
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Jens Kreth
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Allison Gillaspy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert Burne
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Fengxia Qi
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Justin Merritt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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25
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Feng L, Rutherford ST, Papenfort K, Bagert JD, van Kessel JC, Tirrell DA, Wingreen NS, Bassler BL. A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics. Cell 2015; 160:228-40. [PMID: 25579683 DOI: 10.1016/j.cell.2014.11.051] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/20/2014] [Accepted: 11/14/2014] [Indexed: 12/18/2022]
Abstract
Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response.
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Affiliation(s)
- Lihui Feng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Steven T Rutherford
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - John D Bagert
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Julia C van Kessel
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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26
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Papenfort K, Vogel J. Small RNA functions in carbon metabolism and virulence of enteric pathogens. Front Cell Infect Microbiol 2014; 4:91. [PMID: 25077072 PMCID: PMC4098024 DOI: 10.3389/fcimb.2014.00091] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Enteric pathogens often cycle between virulent and saprophytic lifestyles. To endure these frequent changes in nutrient availability and composition bacteria possess an arsenal of regulatory and metabolic genes allowing rapid adaptation and high flexibility. While numerous proteins have been characterized with regard to metabolic control in pathogenic bacteria, small non-coding RNAs have emerged as additional regulators of metabolism. Recent advances in sequencing technology have vastly increased the number of candidate regulatory RNAs and several of them have been found to act at the interface of bacterial metabolism and virulence factor expression. Importantly, studying these riboregulators has not only provided insight into their metabolic control functions but also revealed new mechanisms of post-transcriptional gene control. This review will focus on the recent advances in this area of host-microbe interaction and discuss how regulatory small RNAs may help coordinate metabolism and virulence of enteric pathogens.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University Princeton, NJ, USA
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg Würzburg, Germany
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27
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Figueroa-Bossi N, Schwartz A, Guillemardet B, D'Heygère F, Bossi L, Boudvillain M. RNA remodeling by bacterial global regulator CsrA promotes Rho-dependent transcription termination. Genes Dev 2014; 28:1239-51. [PMID: 24888591 PMCID: PMC4052769 DOI: 10.1101/gad.240192.114] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
RNA-binding protein CsrA is a key regulator of a variety of cellular process in bacteria, including biofilm formation. Figueroa-Bossi et al. uncover a novel gene regulatory mechanism through which CsrA inhibits translation initiation. CsrA binding to the 5′ UTR of E. coli pgA mRNA—involved in biofilm formation—unfolds a secondary structure that sequesters an entry site for termination factor Rho, resulting in the premature stop of transcription. CsrA-induced transcription termination thus marks the switch from the sessile to the planktonic lifestyle. RNA-binding protein CsrA is a key regulator of a variety of cellular processes in bacteria, including carbon and stationary phase metabolism, biofilm formation, quorum sensing, and virulence gene expression in pathogens. CsrA binds to bipartite sequence elements at or near the ribosome loading site in messenger RNA (mRNA), most often inhibiting translation initiation. Here we describe an alternative novel mechanism through which CsrA achieves negative regulation. We show that CsrA binding to the upstream portion of the 5′ untranslated region of Escherichia coli pgaA mRNA—encoding a polysaccharide adhesin export protein—unfolds a secondary structure that sequesters an entry site for transcription termination factor Rho, resulting in the premature stop of transcription. These findings establish a new paradigm for bacterial gene regulation in which remodeling of the nascent transcript by a regulatory protein promotes Rho-dependent transcription attenuation.
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Affiliation(s)
- Nara Figueroa-Bossi
- CNRS UPR3404, Centre de Génétique Moléculaire, Gif-sur-Yvette 91198, France, affilié à l'Université Paris Sud XI, Orsay 91405, France
| | - Annie Schwartz
- CNRS UPR4301, Centre de Biophysique Moléculaire, Orléans 45071, France, affilié à l'Université d'Orléans, Orléans 45100, France
| | - Benoit Guillemardet
- CNRS UPR3404, Centre de Génétique Moléculaire, Gif-sur-Yvette 91198, France, affilié à l'Université Paris Sud XI, Orsay 91405, France
| | - François D'Heygère
- CNRS UPR4301, Centre de Biophysique Moléculaire, Orléans 45071, France, affilié à l'Université d'Orléans, Orléans 45100, France
| | - Lionello Bossi
- CNRS UPR3404, Centre de Génétique Moléculaire, Gif-sur-Yvette 91198, France, affilié à l'Université Paris Sud XI, Orsay 91405, France
| | - Marc Boudvillain
- CNRS UPR4301, Centre de Biophysique Moléculaire, Orléans 45071, France, affilié à l'Université d'Orléans, Orléans 45100, France
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28
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Göpel Y, Görke B. Lies and deception in bacterial gene regulation: the roles of nucleic acid decoys. Mol Microbiol 2014; 92:641-7. [PMID: 24707963 DOI: 10.1111/mmi.12604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2014] [Indexed: 12/24/2022]
Abstract
Bacteria use intricately interconnected mechanisms acting at the transcriptional and post-transcriptional level to adjust gene expression to their needs. An intriguing example found in the chitosugar utilization systems of Escherichia coli and Salmonella is uncovered in a study by Plumbridge and colleagues. Three transcription factors (TFs), a small regulatory RNA (sRNA) and a sRNA trap cooperate to set thresholds and dynamics in regulation of chitosugar utilization. Specifically, under inducing conditions a decoy site on the polycistronic chitobiose (chbBCARFG) mRNA sequesters sRNA ChiX, which represses synthesis of the separately encoded chitoporin ChiP. Base-pairing of ChiX with its decoy has no role for the chb genes themselves when the mRNA is in excess. In the absence of substrate, however, this base-pairing tightly represses chbC encoding a subunit of the chitosugar transporter. Thus, one and the same sRNA/mRNA interaction serves different regulatory functions under different environmental conditions. The employment of RNA decoys to control the activities of post-transcriptional regulators themselves is an increasingly recognized mechanism in gene regulation. Another observation in the current study highlights the possibility that decoy sites might even exist on the DNA controlling the availability of TFs for their target promoters.
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Affiliation(s)
- Yvonne Göpel
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, 1030, Vienna, Austria
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