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Grenga L, Little RH, Malone JG. Quick change: post-transcriptional regulation in Pseudomonas. FEMS Microbiol Lett 2018; 364:3866594. [PMID: 28605536 PMCID: PMC5812540 DOI: 10.1093/femsle/fnx125] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/09/2017] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas species have evolved dynamic and intricate regulatory networks to fine-tune gene expression, with complex regulation occurring at every stage in the processing of genetic information. This approach enables Pseudomonas to generate precise individual responses to the environment in order to improve their fitness and resource economy. The weak correlations we observe between RNA and protein abundance highlight the significant regulatory contribution of a series of intersecting post-transcriptional pathways, influencing mRNA stability, translational activity and ribosome function, to Pseudomonas environmental responses. This review examines our current understanding of three major post-transcriptional regulatory systems in Pseudomonas spp.; Gac/Rsm, Hfq and RimK, and presents an overview of new research frontiers, emerging genome-wide methodologies, and their potential for the study of global regulatory responses in Pseudomonas.
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Affiliation(s)
- Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.,University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Richard H Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jacob G Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.,University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Molecular basis of binding between the global post-transcriptional regulator CsrA and the T3SS chaperone CesT. Nat Commun 2018; 9:1196. [PMID: 29567971 PMCID: PMC5864733 DOI: 10.1038/s41467-018-03625-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/01/2018] [Indexed: 02/05/2023] Open
Abstract
The T3SS chaperone CesT is recently shown to interact with the post-transcriptional regulator CsrA to modulate post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. The molecular basis of the CesT/CsrA binding, however, remains elusive. Here, we show that CesT and CsrA both created two ligand binding sites in their homodimers, forming irregular multimeric complexes in solution. Through construction of a recombinant CsrA-dimer (Re-CsrA) that contains a single CesT binding site, the atomic binding features between CesT and CsrA are delineated via the structure of the CesT/Re-CsrA complex. In contrast to a previously reported N-terminally swapped dimer-form, CesT adopts a dimeric architecture with a swapped C-terminal helix for CsrA engagement. In CsrA, CesT binds to a surface patch that extensively overlaps with its mRNA binding site. The binding mode therefore justifies a mechanism of CsrA-modulation by CesT via competitive inhibition of the CsrA/mRNA interactions. CesT is a type III secretion system chaperone that interacts with the post-transcriptional regulator CsrA, which is important for the modulation of post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. Here the authors present the structure of the CsrA/CesT complex and propose a mechanism for CsrA-modulation by CesT.
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Regulation of host–pathogen interactions via the post-transcriptional Csr/Rsm system. Curr Opin Microbiol 2018; 41:58-67. [DOI: 10.1016/j.mib.2017.11.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022]
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Liu W, Li M, Jiao L, Wang P, Yan Y. PmrA/PmrB Two-Component System Regulation of lipA Expression in Pseudomonas aeruginosa PAO1. Front Microbiol 2018; 8:2690. [PMID: 29379484 PMCID: PMC5775262 DOI: 10.3389/fmicb.2017.02690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/26/2017] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas lipases are well-studied, but few studies have examined the mechanisms of lipase expression regulation. As a global regulatory protein, PmrA controls the expression of multiple genes such as the Dot/Icm apparatus, eukaryotic-like proteins, and secreted effectors. In this study, the effect of PmrA on expression of the lipase lipA in Pseudomonas aeruginosa PAO1 was investigated by knocking out or overexpressing pmrA, rsmY, and rsmA. PmrA regulated the expression of lipA at both the transcriptional and translational level although translation was the pivotal regulatory mechanism for lipA expression. PmrA also regulated the expression of rsmY. Using gel mobility shift assay and pmrA/rsmY double gene knock-out model, we showed that PmrA directly bound to the promoter sequence of rsmY to regulate lipA expression. Translation of lipA was activated by the PmrA/PmrB system via RsmA. Specifically, the Shine-Dalgarno (SD) sequence located at lipA mRNA was overlapped through combination between RsmA and the AGAUGA sequence, subsequently blocking the 30S ribosomal subunit to the SD sequence, leading to translational inhibition of lipA. Transcriptional repression of RsmY initiated translation of lipA through negative translational regulation of rsmA. In conclusion, this study demonstrated that in P. aeruginosa PAO1, PmrA mainly regulated rsmY expression at a translational level to influence lipA expression. RsmY primarily activated lipA translation via negative translational regulation of rsmA.
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Affiliation(s)
- Wu Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Menggang Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liangcheng Jiao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengbo Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Michel E, Duss O, Allain FHT. An Integrated Cell-Free Assay to Study Translation Regulation by Small Bacterial Noncoding RNAs. Methods Mol Biol 2018; 1737:177-195. [PMID: 29484594 DOI: 10.1007/978-1-4939-7634-8_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Posttranscriptional regulation of gene expression by small noncoding RNAs (sRNAs) is an important control mechanism that modulates bacterial metabolism, motility, and pathogenesis. Using the bacterial carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) system, we here describe an E. coli-based cell-free translation assay that allows a quantitative analysis of translation regulation by ncRNAs and their corresponding translation repressor proteins. The assay quantifies the translation of chloramphenicol acetyltransferase in cell-free expression reactions that contain defined amounts of ncRNA and repressor protein. We demonstrate our protocol with a comparative translation activation analysis of the RsmX, RsmY, and RsmZ sRNAs from Pseudomonas protegens, which reveals a superior efficacy of RsmZ over RsmX and RsmY.
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Affiliation(s)
- Erich Michel
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Olivier Duss
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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Ren X, Zeng R, Tortorella M, Wang J, Wang C. Structural Insight into Inhibition of CsrA-RNA Interaction Revealed by Docking, Molecular Dynamics and Free Energy Calculations. Sci Rep 2017; 7:14934. [PMID: 29097778 PMCID: PMC5668361 DOI: 10.1038/s41598-017-14916-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
The carbon storage regulator A (CsrA) and its homologs play an important role in coordinating the expression of bacterial virulence factors required for successful host infection. In addition, bacterial pathogens with deficiency of CsrA are typically attenuated for virulence. In 2016, the first series of small-molecule inhibitors of CsrA-RNA interaction were identified, which were found to achieve the CsrA-RNA inhibition by binding to the CsrA, without interfering with the RNA. However, the binding mechanism of these inhibitors of CsrA is not known. Herein, we applied molecular docking, molecular dynamics and binding free energy calculations to investigate the binding mode of inhibitors to CsrA. We found that the G11(RNA)-binding site is the most important binding site for CsrA inhibitors. An inhibitor with the proper size range can bind to that site and form a stable complex. We also found that inhibitors with larger size ranges bind to the entire CsrA-RNA interface, but have loose binding. However, this loose binding still resulted in inhibitory activity. The calculated binding free energy from MM/GBSA has a good correlation with the derived experimental binding energy, which might be used as a tool to further select CsrA inhibitors after a first-round of high-throughput virtual screening.
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Affiliation(s)
- Xiaodong Ren
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, 550002, P.R. China
| | - Rui Zeng
- College of Pharmacy, Southwest University for Nationalities, Chengdu, 610041, P.R. China
| | - Micky Tortorella
- Guangzhou Institute of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, 510530, P.R. China
| | - Jinming Wang
- Guangzhou Institute of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, 510530, P.R. China
| | - Changwei Wang
- Guangzhou Institute of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, Guangdong, 510530, P.R. China.
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Circuitry Linking the Global Csr- and σ E-Dependent Cell Envelope Stress Response Systems. J Bacteriol 2017; 199:JB.00484-17. [PMID: 28924029 DOI: 10.1128/jb.00484-17] [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: 08/04/2017] [Accepted: 09/08/2017] [Indexed: 01/23/2023] Open
Abstract
CsrA of Escherichia coli is an RNA-binding protein that globally regulates a wide variety of cellular processes and behaviors, including carbon metabolism, motility, biofilm formation, and the stringent response. CsrB and CsrC are small RNAs (sRNAs) that sequester CsrA, thereby preventing CsrA-mRNA interaction. RpoE (σE) is the extracytoplasmic stress response sigma factor of E. coli Previous RNA sequencing (RNA-seq) studies identified rpoE mRNA as a CsrA target. Here, we explored the regulation of rpoE by CsrA and found that CsrA represses rpoE translation. Gel mobility shift, footprint, and toeprint studies identified three CsrA binding sites in the rpoE leader transcript, one of which overlaps the rpoE Shine-Dalgarno (SD) sequence, while another overlaps the rpoE translation initiation codon. Coupled in vitro transcription-translation experiments showed that CsrA represses rpoE translation by binding to these sites. We further demonstrate that σE indirectly activates the transcription of csrB and csrC, leading to increased sequestration of CsrA, such that repression of rpoE by CsrA is reduced. We propose that the Csr system fine-tunes the σE-dependent cell envelope stress response. We also identified a 51-amino-acid coding sequence whose stop codon overlaps the rpoE start codon and demonstrate that rpoE is translationally coupled with this upstream open reading frame (ORF51). The loss of coupling reduces rpoE translation by more than 50%. Identification of a translationally coupled ORF upstream of rpoE suggests that this previously unannotated protein may participate in the cell envelope stress response. In keeping with existing nomenclature, we named ORF51 rseD, resulting in an operon arrangement of rseD-rpoE-rseA-rseB-rseC IMPORTANCE CsrA posttranscriptionally represses genes required for bacterial stress responses, including the stringent response, catabolite repression, and the RpoS (σS)-mediated general stress response. We show that CsrA represses the translation of rpoE, encoding the extracytoplasmic stress response sigma factor, and that σE indirectly activates the transcription of csrB and csrC, resulting in reciprocal regulation of these two global regulatory systems. These findings suggest that extracytoplasmic stress leads to derepression of rpoE translation by CsrA, and CsrA-mediated repression helps reset RpoE abundance to prestress levels once envelope damage is repaired. The discovery of an ORF, rseD, translationally coupled with rpoE adds further complexity to translational control of rpoE.
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Sobrero PM, Muzlera A, Frescura J, Jofré E, Valverde C. A matter of hierarchy: activation of orfamide production by the post-transcriptional Gac-Rsm cascade of Pseudomonas protegens CHA0 through expression upregulation of the two dedicated transcriptional regulators. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:599-611. [PMID: 28703431 DOI: 10.1111/1758-2229.12566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
In this work, we surveyed the genome of P. protegens CHA0 in order to identify novel mRNAs possibly under the control of the Gac-Rsm cascade that might, for their part, serve to elucidate as-yet-unknown functions involved in the biocontrol of plant pathogens and/or in cellular processes required for fitness in natural environments. In view of the experimental evidence from former studies on the Gac-Rsm cascade, we developed a computational screen supported by a combination of sequence, structural and evolutionary constraints that led to a dataset of 43 potential novel mRNA targets. We then confirmed several mRNA targets experimentally and next focused on two of the respective genes that are physically linked to the orfamide biosynthetic gene cluster and whose predicted open-reading frames resembled cognate LuxR-type transcriptional regulators of cyclic lipopeptide clusters in related pseudomonads. In this report, we demonstrate that in strain CHA0, orfamide production is stringently dependent on a functional Gac-Rsm cascade and that both mRNAs encoding transcriptional regulatory proteins are under direct translational control of the RsmA/E proteins. Our results have thus revealed a hierarchical control over the expression of orfamide biosynthetic genes with the final transcriptional control subordinated to the global Gac-Rsm post-transcriptional regulatory system.
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Affiliation(s)
- Patricio Martín Sobrero
- CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo. Roque Sáenz Peña 352, Bernal B1876BXD, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Andrés Muzlera
- CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo. Roque Sáenz Peña 352, Bernal B1876BXD, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Julieta Frescura
- CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo. Roque Sáenz Peña 352, Bernal B1876BXD, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Edgardo Jofré
- CONICET, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Departmento de Ciencias Naturales. Ruta Nacional 36 Km 601, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina
| | - Claudio Valverde
- CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo. Roque Sáenz Peña 352, Bernal B1876BXD, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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Huertas‐Rosales Ó, Romero M, Heeb S, Espinosa‐Urgel M, Cámara M, Ramos‐González MI. The Pseudomonas putida CsrA/RsmA homologues negatively affect c-di-GMP pools and biofilm formation through the GGDEF/EAL response regulator CfcR. Environ Microbiol 2017; 19:3551-3566. [PMID: 28677348 PMCID: PMC6849547 DOI: 10.1111/1462-2920.13848] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 11/30/2022]
Abstract
Expression of cfcR, encoding the only GGDEF/EAL response regulator in Pseudomonas putida, is transcriptionally regulated by RpoS, ANR and FleQ, and the functionality of CfcR as a diguanylate cyclase requires the multisensor CHASE3/GAF hybrid histidine kinase named CfcA. Here an additional level of cfcR control, operating post-transcriptionally via the RNA-binding proteins RsmA, RsmE and RsmI, is unraveled. Specific binding of the three proteins to an Rsm-binding motif (5'CANGGANG3') encompassing the translational start codon of cfcR was confirmed. Although RsmA exhibited the highest binding affinity to the cfcR transcript, single deletions of rsmA, rsmE or rsmI caused minor derepression in CfcR translation compared to a ΔrsmIEA triple mutant. RsmA also showed a negative impact on c-di-GMP levels in a double mutant ΔrsmIE through the control of cfcR, which is responsible for most of the free c-di-GMP during stationary phase in static conditions. In addition, a CfcR-dependent c-di-GMP boost was observed during this stage in ΔrsmIEA confirming the negative effect of Rsm proteins on CfcR translation and explaining the increased biofilm formation in this mutant compared to the wild type. Overall, these results suggest that CfcR is a key player in biofilm formation regulation by the Rsm proteins in P. putida.
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Affiliation(s)
- Óscar Huertas‐Rosales
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICProfesor Albareda, 1, Granada 18008Spain
| | - Manuel Romero
- Centre for Biomolecular Sciences, School of Life SciencesUniversity of NottinghamNottingham NG7 2RDUK
| | - Stephan Heeb
- Centre for Biomolecular Sciences, School of Life SciencesUniversity of NottinghamNottingham NG7 2RDUK
| | - Manuel Espinosa‐Urgel
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICProfesor Albareda, 1, Granada 18008Spain
| | - Miguel Cámara
- Centre for Biomolecular Sciences, School of Life SciencesUniversity of NottinghamNottingham NG7 2RDUK
| | - María Isabel Ramos‐González
- Department of Environmental ProtectionEstación Experimental del Zaidín, CSICProfesor Albareda, 1, Granada 18008Spain
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Translational Repression of the RpoS Antiadapter IraD by CsrA Is Mediated via Translational Coupling to a Short Upstream Open Reading Frame. mBio 2017; 8:mBio.01355-17. [PMID: 28851853 PMCID: PMC5574718 DOI: 10.1128/mbio.01355-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CsrA is a global regulatory RNA binding protein that has important roles in regulating carbon metabolism, motility, biofilm formation, and numerous other cellular processes. IraD functions as an antiadapter protein that inhibits RssB-mediated degradation of RpoS, the general stress response and stationary-phase sigma factor of Escherichia coli. Here we identified a novel mechanism in which CsrA represses iraD translation via translational coupling. Expression studies with quantitative reverse transcriptase PCR, Western blotting, and lacZ fusions demonstrated that CsrA represses iraD expression. Gel mobility shift, footprint, and toeprint studies identified four CsrA binding sites in the iraD leader transcript, all of which are far upstream of the iraD ribosome binding site. Computational modeling and RNA structure mapping identified an RNA structure that sequesters the iraD Shine-Dalgarno (SD) sequence. Three open reading frames (ORFs), all of which are translated, were identified in the iraD leader region. Two of these ORFs do not affect iraD expression. However, the translation initiation region of the third ORF contains three of the CsrA binding sites, one of which overlaps its SD sequence. Furthermore, the ORF stop codon overlaps the iraD start codon, a sequence arrangement indicative of translational coupling. In vivo expression and in vitro translation studies with wild-type and mutant reporter fusions demonstrated that bound CsrA directly represses translation initiation of this ORF. We further established that CsrA-dependent repression of iraD translation occurs entirely via translational coupling with this ORF, leading to accelerated iraD mRNA decay. CsrA posttranscriptionally represses gene expression associated with stationary-phase bacterial growth, often in opposition to the transcriptional effects of the stationary-phase sigma factor RpoS. We show that CsrA employs a novel regulatory mechanism to repress translation of iraD, which encodes an antiadapter protein that protects RpoS against proteolysis. CsrA binds to four sites in the iraD leader transcript but does not directly occlude ribosome binding to the iraD SD sequence. Instead, CsrA represses translation of a short open reading frame encoded upstream of iraD, causing repression of iraD translation via translational coupling. This finding offers a novel mechanism of gene regulation by the global regulator CsrA, and since RpoS can activate csrA transcription, this also highlights a new negative-feedback loop within the complex Csr and RpoS circuitry.
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The Pseudomonas aeruginosa Two-Component Regulator AlgR Directly Activates rsmA Expression in a Phosphorylation-Independent Manner. J Bacteriol 2017; 199:JB.00048-17. [PMID: 28320883 DOI: 10.1128/jb.00048-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/13/2017] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa is an important pathogen of the immunocompromised, causing both acute and chronic infections. In cystic fibrosis (CF) patients, P. aeruginosa causes chronic disease. The impressive sensory network of P. aeruginosa allows the bacterium to sense and respond to a variety of stimuli found in diverse environments. Transcriptional regulators, including alternative sigma factors and response regulators, integrate signals changing gene expression, allowing P. aeruginosa to cause infection. The two-component transcriptional regulator AlgR is important in P. aeruginosa pathogenesis in both acute and chronic infections. In chronic infections, AlgR and the alternative sigma factor AlgU activate the genes responsible for alginate production. Previous work demonstrated that AlgU controls rsmA expression. RsmA is a posttranscriptional regulator that is antagonized by two small RNAs, RsmY and RsmZ. In this work, we demonstrate that AlgR directly activates rsmA expression from the same promoter as AlgU. In addition, phosphorylation was not necessary for AlgR activation of rsmA using algR and algZ mutant strains. AlgU and AlgR appear to affect the antagonizing small RNAs rsmY and rsmZ indirectly. RsmA was active in a mucA22 mutant strain using leader fusions of two RsmA targets, tssA1 and hcnA AlgU and AlgR were necessary for posttranscriptional regulation of tssA1 and hcnA Altogether, our work demonstrates that the alginate regulators AlgU and AlgR are important in the control of the RsmA posttranscriptional regulatory system. These findings suggest that RsmA plays an unknown role in mucoid strains due to AlgU and AlgR activities.IMPORTANCE P. aeruginosa infections are difficult to treat and frequently cause significant mortality in CF patients. Understanding the mechanisms of persistence is important. Our work has demonstrated that the alginate regulatory system also significantly impacts the posttranscriptional regulator system RsmA/Y/Z. We demonstrate that AlgR directly activates rsmA expression, and this impacts the RsmA regulon. This leads to the possibility that the RsmA/Y/Z system plays a role in helping P. aeruginosa persist during chronic infection. In addition, this furthers our understanding of the reach of the alginate regulators AlgU and AlgR.
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Fakhry CT, Kulkarni P, Chen P, Kulkarni R, Zarringhalam K. Prediction of bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach. BMC Genomics 2017; 18:645. [PMID: 28830349 PMCID: PMC5568370 DOI: 10.1186/s12864-017-4057-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Small RNAs (sRNAs) constitute an important class of post-transcriptional regulators that control critical cellular processes in bacteria. Recent research using high-throughput transcriptomic approaches has led to a dramatic increase in the discovery of bacterial sRNAs. However, it is generally believed that the currently identified sRNAs constitute a limited subset of the bacterial sRNA repertoire. In several cases, sRNAs belonging to a specific class are already known and the challenge is to identify additional sRNAs belonging to the same class. In such cases, machine-learning approaches can be used to predict novel sRNAs in a given class. METHODS In this work, we develop novel bioinformatics approaches that integrate sequence and structure-based features to train machine-learning models for the discovery of bacterial sRNAs. We show that features derived from recurrent structural motifs in the ensemble of low energy secondary structures can distinguish the RNA classes with high accuracy. RESULTS We apply this approach to predict new members in two broad classes of bacterial small RNAs: 1) sRNAs that bind to the RNA-binding protein RsmA/CsrA in diverse bacterial species and 2) sRNAs regulated by the master regulator of virulence, ToxT, in Vibrio cholerae. CONCLUSION The involvement of sRNAs in bacterial adaptation to changing environments is an increasingly recurring theme in current research in microbiology. It is likely that future research, combining experimental and computational approaches, will discover many more examples of sRNAs as components of critical regulatory pathways in bacteria. We have developed a novel approach for prediction of small RNA regulators in important bacterial pathways. This approach can be applied to specific classes of sRNAs for which several members have been identified and the challenge is to identify additional sRNAs.
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Affiliation(s)
- Carl Tony Fakhry
- Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125 MA USA
| | - Prajna Kulkarni
- Department of Physics, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125 MA USA
| | - Ping Chen
- Department of Engineering, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125 MA USA
| | - Rahul Kulkarni
- Department of Physics, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125 MA USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125 MA USA
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Wang Z, Huang X, Liu Y, Yang G, Liu Y, Zhang X. GacS/GacA activates pyoluteorin biosynthesis through Gac/Rsm-RsmE cascade and RsmA/RsmE-driven feedback loop inPseudomonas protegensH78. Mol Microbiol 2017; 105:968-985. [DOI: 10.1111/mmi.13749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Yujie Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Guohuan Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Yang Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai China
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Sahr T, Rusniok C, Impens F, Oliva G, Sismeiro O, Coppée JY, Buchrieser C. The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system. PLoS Genet 2017; 13:e1006629. [PMID: 28212376 PMCID: PMC5338858 DOI: 10.1371/journal.pgen.1006629] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 03/06/2017] [Accepted: 02/09/2017] [Indexed: 01/09/2023] Open
Abstract
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA co-immunoprecipitation followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs. Further analyses revealed that CsrA exhibits a dual regulatory role in virulence as it affects the expression of the regulators FleQ, LqsR, LetE and RpoS but it also directly regulates the timely expression of over 40 Dot/Icm substrates. CsrA controls its own expression and the stringent response through a regulatory feedback loop as evidenced by its binding to RelA-mRNA and links it to quorum sensing and motility. CsrA is a central player in the carbon, amino acid, fatty acid metabolism and energy transfer and directly affects the biosynthesis of cofactors, vitamins and secondary metabolites. We describe the first L. pneumophila riboswitch, a thiamine pyrophosphate riboswitch whose regulatory impact is fine-tuned by CsrA, and identified a unique regulatory mode of CsrA, the active stabilization of RNA anti-terminator conformations inside a coding sequence preventing Rho-dependent termination of the gap operon through transcriptional polarity effects. This allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Thus the L. pneumophila genome has evolved to acclimate at least five different modes of regulation by CsrA giving it a truly unique position in its life cycle. The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. Here, we have used deep sequencing of RNA enriched by co-immunoprecipitation with epitope-tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 479 mRNAs or non-coding RNAs to be targets of CsrA. Among those major regulators including FleQ, the regulator of flagella expression, LqsR, the regulator of quorum sensing and RpoS implicated in stress response were identified. The expression of over 40 type IV secreted effector proteins important for intracellular survival and virulence are under the control of CsrA. Combined with transcriptomics, whole shotgun proteomics of a wild type and a CsrA mutant strain and functional analyses of several CsrA-targeted RNAs we identified the first riboswitch in L. pneumophila, a thiamine pyrophosphate riboswitch, and discovered a new mode of regulation by CsrA that allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Our results further underline the indispensable role of CsrA in the life cycle of L. pneumophila and provide new insights into its regulatory roles and mechanisms.
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Affiliation(s)
- Tobias Sahr
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France
- CNRS UMR 3525, Paris, France
| | - Christophe Rusniok
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France
- CNRS UMR 3525, Paris, France
| | - Francis Impens
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Inserm U604, INRA Unité sous-contrat, Paris, France
- VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Giulia Oliva
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France
- CNRS UMR 3525, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France
- CNRS UMR 3525, Paris, France
- * E-mail:
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Katsowich N, Elbaz N, Pal RR, Mills E, Kobi S, Kahan T, Rosenshine I. Host cell attachment elicits posttranscriptional regulation in infecting enteropathogenic bacteria. Science 2017; 355:735-739. [DOI: 10.1126/science.aah4886] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/19/2017] [Indexed: 01/04/2023]
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Ancona V, Lee JH, Zhao Y. The RNA-binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora. Sci Rep 2016; 6:37195. [PMID: 27845410 PMCID: PMC5109040 DOI: 10.1038/srep37195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022] Open
Abstract
The GacS/GacA two-component system (also called GrrS/GrrA) is a global regulatory system which is highly conserved among gamma-proteobacteria. This system positively regulates non-coding small regulatory RNA csrB, which in turn binds to the RNA-binding protein CsrA. However, how GacS/GacA-Csr system regulates virulence traits in E. amylovora remains unknown. Results from mutant characterization showed that the csrB mutant was hypermotile, produced higher amount of exopolysaccharide amylovoran, and had increased expression of type III secretion (T3SS) genes in vitro. In contrast, the csrA mutant exhibited complete opposite phenotypes, including non-motile, reduced amylovoran production and expression of T3SS genes. Furthermore, the csrA mutant did not induce hypersensitive response on tobacco or cause disease on immature pear fruits, indicating that CsrA is a positive regulator of virulence factors. These findings demonstrated that CsrA plays a critical role in E. amylovora virulence and suggested that negative regulation of virulence by GacS/GacA acts through csrB sRNA, which binds to CsrA and neutralizes its positive effect on T3SS gene expression, flagellar formation and amylovoran production. Future research will be focused on determining the molecular mechanism underlying the positive regulation of virulence traits by CsrA.
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Affiliation(s)
- Veronica Ancona
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urban 61801, USA
| | - Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urban 61801, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urban 61801, USA
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Primary and Secondary Sequence Structure Requirements for Recognition and Discrimination of Target RNAs by Pseudomonas aeruginosa RsmA and RsmF. J Bacteriol 2016; 198:2458-69. [PMID: 27381913 DOI: 10.1128/jb.00343-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/27/2016] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED CsrA family RNA-binding proteins are widely distributed in bacteria and regulate gene expression at the posttranscriptional level. Pseudomonas aeruginosa has a canonical member of the CsrA family (RsmA) and a novel, structurally distinct variant (RsmF). To better understand RsmF binding properties, we performed parallel systematic evolution of ligands by exponential enrichment (SELEX) experiments for RsmA and RsmF. The initial target library consisted of 62-nucleotide (nt) RNA transcripts with central cores randomized at 15 sequential positions. Most targets selected by RsmA and RsmF were the expected size and shared a common consensus sequence (CANGGAYG) that was positioned in a hexaloop region of the stem-loop structure. RsmA and RsmF also selected for longer targets (≥96 nt) that were likely generated by rare PCR errors. Most of the long targets contained two consensus-binding sites. Representative short (single consensus site) and long (two consensus sites) targets were tested for RsmA and RsmF binding. Whereas RsmA bound the short targets with high affinity, RsmF was unable to bind the same targets. RsmA and RsmF both bound the long targets. Mutation of either consensus GGA site in the long targets reduced or eliminated RsmF binding, suggesting a requirement for two tandem binding sites. Conversely, RsmA bound long targets containing only a single GGA site with unaltered affinity. The RsmF requirement for two binding sites was confirmed with tssA1, an in vivo regulatory target of RsmA and RsmF. Our findings suggest that RsmF binding requires two GGA-containing sites, while RsmA binding requirements are less stringent. IMPORTANCE The CsrA family of RNA-binding proteins is widely conserved in bacteria and plays important roles in the posttranscriptional regulation of protein synthesis. P. aeruginosa has two CsrA proteins, RsmA and RsmF. Although RsmA and RsmF share a few RNA targets, RsmF is unable to bind to other targets recognized by RsmA. The goal of the present study was to better understand the basis for differential binding by RsmF. Our data indicate that RsmF binding requires target RNAs with two consensus-binding sites, while RsmA recognizes targets with just a single binding site. This information should prove useful to future efforts to define the RsmF regulon and its contribution to P. aeruginosa physiology and virulence.
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Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein. Proc Natl Acad Sci U S A 2016; 113:10168-73. [PMID: 27551070 DOI: 10.1073/pnas.1602425113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Regulation of translation is critical for maintaining cellular protein levels, and thus protein homeostasis. The conserved RNA-binding protein CsrA (also called RsmA; for carbon storage regulator and regulator of secondary metabolism, respectively; hereafter called CsrA) represents a well-characterized example of regulation at the level of translation initiation in bacteria. Binding of a CsrA homodimer to the 5'UTR of an mRNA occludes the Shine-Dalgarno sequence, blocking ribosome access for translation. Small noncoding RNAs (sRNAs) can competitively antagonize CsrA activity by a well-understood mechanism. However, the regulation of CsrA by the protein FliW is just emerging. FliW antagonizes the CsrA-dependent repression of translation of the flagellar filament protein, flagellin. Crystal structures of the FliW monomer reveal a novel, minimal β-barrel-like fold. Structural analysis of the CsrA/FliW heterotetramer shows that FliW interacts with a C-terminal extension of CsrA. In contrast to the competitive regulation of CsrA by sRNAs, FliW allosterically antagonizes CsrA in a noncompetitive manner by excluding the 5'UTR from the CsrA-RNA binding site. Our phylogenetic analysis shows that the FliW-mediated regulation of CsrA regulation is the ancestral state in flagellated bacteria. We thus demonstrate fundamental mechanistic differences in the regulation of CsrA by sRNA in comparison with an ancient regulatory protein.
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FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism. Proc Natl Acad Sci U S A 2016; 113:9870-5. [PMID: 27516547 DOI: 10.1073/pnas.1602455113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CsrA (carbon storage regulator A) is a widely distributed bacterial RNA binding protein that regulates translation initiation and mRNA stability of target transcripts. In γ-proteobacteria, CsrA activity is competitively antagonized by one or more small RNAs (sRNAs) containing multiple CsrA binding sites, but CsrA in bacteria outside the γ-proteobacteria is antagonized by a protein called FliW. Here we show that FliW of Bacillus subtilis does not bind to the same residues of CsrA required for RNA binding. Instead, CsrA mutants resistant to FliW antagonism (crw) altered residues of CsrA on an allosteric surface of previously unattributed function. Some crw mutants abolished CsrA-FliW binding, but others did not, suggesting that FliW and RNA interaction is not mutually exclusive. We conclude that FliW inhibits CsrA by a noncompetitive mechanism that differs dramatically from the well-established sRNA inhibitors. FliW is highly conserved with CsrA in bacteria, appears to be the ancestral form of CsrA regulation, and represents a widespread noncompetitive mechanism of CsrA control.
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RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions. BMC Microbiol 2016; 16:155. [PMID: 27430253 PMCID: PMC4950607 DOI: 10.1186/s12866-016-0771-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-sequencing (RNA-seq) to detect sRNAs differentially expressed in Pseudomonas aeruginosa biofilm versus planktonic state. RESULTS A computational algorithm was devised to detect and categorize sRNAs into 5 types: intergenic, intragenic, 5'-UTR, 3'-UTR, and antisense. Here we report a novel RsmY/RsmZ-type sRNA, termed RsmW, in P. aeruginosa up-transcribed in biofilm versus planktonic growth. RNA-Seq, 5'-RACE and Mfold predictions suggest RsmW has a secondary structure with 3 of 7 GGA motifs located on outer stem loops. Northern blot revealed two RsmW binding bands of 400 and 120 bases, suggesting RsmW is derived from the 3'-UTR of the upstream hypothetical gene, PA4570. RsmW expression is elevated in late stationary versus logarithmic growth phase in PB minimal media, at higher temperatures (37 °C versus 28 °C), and in both gacA and rhlR transposon mutants versus wild-type. RsmW specifically binds to RsmA protein in vitro and restores biofilm production and reduces swarming in an rsmY/rsmZ double mutant. PA4570 weakly resembles an RsmA/RsmN homolog having 49 % and 51 % similarity, and 16 % and 17 % identity to RsmA and RsmN amino acid sequences, respectively. PA4570 was unable to restore biofilm and swarming phenotypes in ΔrsmA deficient strains. CONCLUSION Collectively, our study reveals an interesting theme regarding another sRNA regulator of the Rsm system and further unravels the complexities regulating adaptive responses for Pseudomonas species.
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Meyer MM. The role of mRNA structure in bacterial translational regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27301829 DOI: 10.1002/wrna.1370] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/08/2023]
Abstract
The characteristics of bacterial messenger RNAs (mRNAs) that influence translation efficiency provide many convenient handles for regulation of gene expression, especially when coupled with the processes of transcription termination and mRNA degradation. An mRNA's structure, especially near the site of initiation, has profound consequences for how readily it is translated. This property allows bacterial gene expression to be altered by changes to mRNA structure induced by temperature, or interactions with a wide variety of cellular components including small molecules, other RNAs (such as sRNAs and tRNAs), and RNA-binding proteins. This review discusses the links between mRNA structure and translation efficiency, and how mRNA structure is manipulated by conditions and signals within the cell to regulate gene expression. The range of RNA regulators discussed follows a continuum from very complex tertiary structures such as riboswitch aptamers and ribosomal protein-binding sites to thermosensors and mRNA:sRNA interactions that involve only base-pairing interactions. Furthermore, the high degrees of diversity observed for both mRNA structures and the mechanisms by which inhibition of translation occur have significant consequences for understanding the evolution of bacterial translational regulation. WIREs RNA 2017, 8:e1370. doi: 10.1002/wrna.1370 For further resources related to this article, please visit the WIREs website.
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Pseudomonas aeruginosa AlgU Contributes to Posttranscriptional Activity by Increasing rsmA Expression in a mucA22 Strain. J Bacteriol 2016; 198:1812-1826. [PMID: 27091153 DOI: 10.1128/jb.00133-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/12/2016] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Pseudomonas aeruginosa thrives in multiple environments and is capable of causing life-threatening infections in immunocompromised patients. RsmA is a posttranscriptional regulator that controls virulence factor production and biofilm formation. In this study, we investigated the expression and activity of rsmA and the protein that it encodes, RsmA, in P. aeruginosa mucA mutant strains, which are common in chronic infections. We determined that AlgU regulates a previously unknown rsmA promoter in P. aeruginosa Western blot analysis confirmed that AlgU controls rsmA expression in both a laboratory strain and a clinical isolate. RNase protection assays confirmed the presence of two rsmA transcripts and suggest that RpoS and AlgU regulate rsmA expression. Due to the increased amounts of RsmA in mucA mutant strains, a translational leader fusion of the RsmA target, tssA1, was constructed and tested in mucA, algU, retS, gacA, and rsmA mutant backgrounds to examine posttranscriptional activity. From these studies, we determined that RsmA is active in mucA22 mutants, suggesting a role for RsmA in mucA mutant strains. Taken together, we have demonstrated that AlgU controls rsmA transcription and is responsible for RsmA activity in mucA mutant strains. We propose that RsmA is active in P. aeruginosa mucA mutant strains and that RsmA also plays a role in chronic infections. IMPORTANCE P. aeruginosa causes severe infections in immunocompromised patients. The posttranscriptional regulator RsmA is known to control virulence and biofilm formation. We identify a new rsmA promoter and determine that AlgU is important in the control of rsmA expression. Mutant mucA strains that are considered mucoid were used to confirm increased rsmA expression from the AlgU promoter. We demonstrate, for the first time, that there is RsmA activity in mucoid P. aeruginosa strains. Our work suggests that RsmA may play a role during chronic infections as well as acute infections.
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Discovery of the first small-molecule CsrA-RNA interaction inhibitors using biophysical screening technologies. Future Med Chem 2016; 8:931-47. [PMID: 27253623 DOI: 10.4155/fmc-2016-0033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM CsrA is a global post-transcriptional regulator protein affecting mRNA translation and/or stability. Widespread among bacteria, it is essential for their full virulence and thus represents a promising anti-infective drug target. Therefore, we aimed at the discovery of CsrA-RNA interaction inhibitors. Results & methodology: We followed two strategies: a screening of small molecules (A) and an RNA ligand-based approach (B). Using surface plasmon resonance-based binding and fluorescence polarization-based competition assays, (A) yielded seven small-molecule inhibitors, among them MM14 (IC50 of 4 µM). (B) resulted in RNA-based inhibitor GGARNA (IC50 of 113 µM). CONCLUSION The first small-molecule inhibitors of the CsrA-RNA interaction were discovered exhibiting micromolar affinities. These hits represent tools to investigate the effects of CsrA-RNA interaction inhibition on bacterial virulence.
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Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
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EL CIRCUITO REGULATORIO BARA/UVRY-CSRA EN ESCHERICHIA COLI Y SUS HOMÓLOGOS EN LAS γ-PROTEOBACTERIAS. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2016. [DOI: 10.1016/j.recqb.2016.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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CsrA Participates in a PNPase Autoregulatory Mechanism by Selectively Repressing Translation of pnp Transcripts That Have Been Previously Processed by RNase III and PNPase. J Bacteriol 2015; 197:3751-9. [PMID: 26438818 DOI: 10.1128/jb.00721-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/28/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Csr is a conserved global regulatory system that represses or activates gene expression posttranscriptionally. CsrA of Escherichia coli is a homodimeric RNA binding protein that regulates transcription elongation, translation initiation, and mRNA stability by binding to the 5' untranslated leader or initial coding sequence of target transcripts. pnp mRNA, encoding the 3' to 5' exoribonuclease polynucleotide phosphorylase (PNPase), was previously identified as a CsrA target by transcriptome sequencing (RNA-seq). Previous studies also showed that RNase III and PNPase participate in a pnp autoregulatory mechanism in which RNase III cleavage of the untranslated leader, followed by PNPase degradation of the resulting 5' fragment, leads to pnp repression by an undefined translational repression mechanism. Here we demonstrate that CsrA binds to two sites in pnp leader RNA but only after the transcript is fully processed by RNase III and PNPase. In the absence of processing, both of the binding sites are sequestered in an RNA secondary structure, which prevents CsrA binding. The CsrA dimer bridges the upstream high-affinity site to the downstream site that overlaps the pnp Shine-Dalgarno sequence such that bound CsrA causes strong repression of pnp translation. CsrA-mediated translational repression also leads to a small increase in the pnp mRNA decay rate. Although CsrA has been shown to regulate translation and mRNA stability of numerous genes in a variety of organisms, this is the first example in which prior mRNA processing is required for CsrA-mediated regulation. IMPORTANCE CsrA protein represses translation of numerous mRNA targets, typically by binding to multiple sites in the untranslated leader region preceding the coding sequence. We found that CsrA represses translation of pnp by binding to two sites in the pnp leader transcript but only after it is processed by RNase III and PNPase. Processing by these two ribonucleases alters the mRNA secondary structure such that it becomes accessible to the ribosome for translation as well as to CsrA. As one of the CsrA binding sites overlaps the pnp ribosome binding site, bound CsrA prevents ribosome binding. This is the first example in which regulation by CsrA requires prior mRNA processing and should link pnp expression to conditions affecting CsrA activity.
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Foxall RL, Ballok AE, Avitabile A, Whistler CA. Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA. BMC Microbiol 2015; 15:180. [PMID: 26376921 PMCID: PMC4573307 DOI: 10.1186/s12866-015-0509-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 08/17/2015] [Indexed: 11/25/2022] Open
Abstract
Background Symbiosis defective GacA-mutant derivatives of Vibrio fischeri are growth impaired thereby creating a selective advantage for growth-enhanced spontaneous suppressors. Suppressors were isolated and characterized for effects of the mutations on gacA-mutant defects of growth, siderophore activity and luminescence. The mutations were identified by targeted and whole genome sequencing. Results Most mutations that restored multiple phenotypes were non-null mutations that mapped to conserved domains in or altered expression of CsrA, a post-transcriptional regulator that mediates GacA effects in a number of bacterial species. These represent an array of unique mutations compared to those that have been described previously. Different substitutions at the same amino acid residue were identified allowing comparisons of effects such as at the R6 residue, which conferred relative differences in luminescence and siderophore levels. The screen revealed residues not previously identified as critical for function including a single native alanine. Most csrA mutations enhanced luminescence more than siderophore activity, which was especially evident for mutations predicted to reduce the amount of CsrA. Although CsrA mutations compensate for many known GacA mutant defects, not all CsrA suppressors restore symbiotic colonization. Phenotypes of a suppressor allele of ihfA that encodes one subunit of the integration host factor (IHF) heteroduplex indicated the protein represses siderophore and activates luminescence in a GacA-independent manner. Conclusions In addition to its established role in regulation of central metabolism, the CsrA regulator represses luminescence and siderophore as an intermediate of the GacA regulatory hierachy. Siderophore regulation was less sensitive to stoichiometry of CsrA consistent with higher affinity for the targets of this trait. The lack of CsrA null-mutant recovery implied these mutations do not enhance fitness of gacA mutants and alluded to this gene being conditionally essential. This study also suggests a role for IHF in the GacA-CsrB-CsrA regulatory cascade by potentially assisting with the binding of repressors of siderohphore and activators of luminescence. As many phosphorelay proteins reduce fitness when mutated, the documented instability used in this screen also highlights a potentially universal and underappreciated problem that, if not identified and strategically avoided, could introduce confounding variability during experimental study of these regulatory pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0509-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Randi L Foxall
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824, USA. .,Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, USA.
| | - Alicia E Ballok
- Gradaute Program in Genetics, University of New Hampshire, Durham, USA. .,Current address: Department of Surgery, Massachusetts General Hospital and Department of Microbiology and Immunobiology, Harvard Medical School, Durham, USA.
| | - Ashley Avitabile
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824, USA.
| | - Cheryl A Whistler
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824, USA. .,Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, USA.
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Andresen L, Frolova J, Põllumaa L, Mäe A. Dual role of RsmA in the coordinated regulation of expression of virulence genes in Pectobacterium wasabiae strain SCC3193. MICROBIOLOGY-SGM 2015; 161:2079-86. [PMID: 26306750 DOI: 10.1099/mic.0.000159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The CsrA/RsmA family of post-transcriptional regulators in bacteria is involved in regulating many cellular processes, including pathogenesis. Using a bioinformatics approach, we identified an RsmA binding motif, A(N)GGA, in the Shine-Dalgarno regions of 901 genes. Among these genes with the predicted RsmA binding motif, 358 were regulated by RsmA according to our previously published gene expression profiling analysis (WT vs rsmA negative mutant; Kõiv et al., 2013). A small subset of the predicted targets known to be important as virulence factors was selected for experimental validation. RNA footprint analyses demonstrated that RsmA binds specifically to the ANGGA motif in the 5'UTR sequences of celV1, pehA, pelB, pel2 and prtW. RsmA-dependent regulation of these five genes was examined in vivo using plasmid-borne translational and transcriptional fusions with a reporter gusA gene. They were all affected negatively by RsmA. However, we demonstrated that whereas the overall effect of RsmA on celV1 and prtW was determined on both the translational and transcriptional level, expression of pectinolytic enzyme genes (pehA, pel2 and pelB) was affected mainly on the level of transcription in tested conditions. In summary, these data indicate that RsmA controls virulence by integration of its regulatory activities at various levels.
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Affiliation(s)
- Liis Andresen
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Jekaterina Frolova
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Lee Põllumaa
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Andres Mäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
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Abstract
UNLABELLED ToxR is a major virulence gene regulator in Vibrio cholerae. Although constitutively expressed under many laboratory conditions, our previous work demonstrated that the level of ToxR increases significantly when cells are grown in the presence of the 4 amino acids asparagine, arginine, glutamate, and serine (NRES). We show here that the increase in ToxR production in response to NRES requires the Var/Csr global regulatory circuit. The VarS/VarA two-component system controls the amount of active CsrA, a small RNA-binding protein involved in the regulation of a wide range of cellular processes. Our data show that a varA mutant, which is expected to overproduce active CsrA, had elevated levels of ToxR in the absence of the NRES stimulus. Conversely, specific amino acid substitutions in CsrA were associated with defects in ToxR production in response to NRES. These data indicate that CsrA is a positive regulator of ToxR levels. Unlike previously described effects of CsrA on virulence gene regulation, the effects of CsrA on ToxR were not mediated through quorum sensing and HapR. CsrA is likely essential in V. cholerae, since a complete deletion of csrA was not possible; however, point mutations in CsrA were tolerated well. The CsrA Arg6His mutant had wild-type growth in vitro but was severely attenuated in the infant mouse model of V. cholerae infection, showing that CsrA is critical for pathogenesis. This study has broad implications for our understanding of how V. cholerae integrates its response to environmental cues with the regulation of important virulence genes. IMPORTANCE In order to colonize the human host, Vibrio cholerae must sense and respond to environmental signals to ensure appropriate expression of genes required for pathogenesis. Uncovering how V. cholerae senses its environment and activates its virulence gene repertoire is critical for our understanding of how V. cholerae transitions from its natural aquatic habitat to the human host. Here we demonstrate a previously unknown link between the global regulator CsrA and the major V. cholerae virulence gene regulator ToxR. The role of CsrA in the cell is to receive input from the environment and coordinate an appropriate cellular response. By linking environmental sensing to the ToxR regulon, CsrA effectively acts as a switch that controls pathogenesis in response to specific signals. We demonstrate that CsrA is critical for virulence in the infant mouse model of V. cholerae infection, consistent with its role as an in vivo regulator of virulence gene expression.
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80
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Vakulskas CA, Potts AH, Babitzke P, Ahmer BMM, Romeo T. Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev 2015; 79:193-224. [PMID: 25833324 PMCID: PMC4394879 DOI: 10.1128/mmbr.00052-14] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5' untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.
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Affiliation(s)
- Christopher A Vakulskas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Anastasia H Potts
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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81
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Brantl S, Jahn N. sRNAs in bacterial type I and type III toxin-antitoxin systems. FEMS Microbiol Rev 2015; 39:413-27. [PMID: 25808661 DOI: 10.1093/femsre/fuv003] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 01/17/2023] Open
Abstract
Toxin-antitoxin (TA) loci consist of two genes: a stable toxin whose overexpression kills the cell or causes growth stasis and an unstable antitoxin that neutralizes the toxin action. Currently, five TA systems are known. Here, we review type I and type III systems in which the antitoxins are regulatory RNAs. Type I antitoxins act by a base-pairing mechanism on toxin mRNAs. By contrast, type III antitoxins are RNA pseudoknots that bind their cognate toxins directly in an RNA-protein interaction. Whereas for a number of plasmid-encoded systems detailed information on structural requirements, kinetics of interaction with their targets and regulatory mechanisms employed by the antitoxin RNAs is available, the investigation of chromosomal systems is still in its infancy. Here, we summarize our current knowledge on that topic. Furthermore, we compare factors and conditions that induce antitoxins or toxins and different mechanisms of toxin action. Finally, we discuss biological roles for chromosome-encoded TA systems.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
| | - Natalie Jahn
- AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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82
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Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
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83
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Takeuchi K, Noda N, Katayose Y, Mukai Y, Numa H, Yamada K, Someya N. Rhizoxin analogs contribute to the biocontrol activity of a newly isolated pseudomonas strain. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:333-42. [PMID: 25496595 DOI: 10.1094/mpmi-09-14-0294-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two strains of Pseudomonas sp., Os17 and St29, were newly isolated from the rhizosphere of rice and potato, respectively, by screening for 2,4-diacetylphloroglucinol producers. These strains were found to be the same species and were the closest to but different from Pseudomonas protegens among the sequenced pseudomonads, based on 16S ribosomal RNA gene and whole-genome analyses. Strain Os17 was as effective a biocontrol agent as reported for P. protegens Cab57, whereas strain St29 was less effective. The whole-genome sequences of these strains were obtained: the genomes are organized into a single circular chromosome with 6,885,464 bp, 63.5% G+C content, and 6,195 coding sequences for strain Os17; and with 6,833,117 bp, 63.3% G+C content, and 6,217 coding sequences for strain St29. Comparative genome analysis of these strains revealed that the complete rhizoxin analog biosynthesis gene cluster (approximately 79 kb) found in the Os17 genome was absent from the St29 genome. In an rzxB mutant, which lacks the polyketide synthase essential for the production of rhizoxin analogs, the growth inhibition activity against fungal and oomycete pathogens and the plant protection efficacy were attenuated compared with those of wild-type Os17. These findings suggest that rhizoxin analogs are important biocontrol factors of this strain.
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84
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Gardner PP, Eldai H. Annotating RNA motifs in sequences and alignments. Nucleic Acids Res 2015; 43:691-8. [PMID: 25520192 PMCID: PMC4333381 DOI: 10.1093/nar/gku1327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 11/30/2014] [Accepted: 12/05/2014] [Indexed: 11/21/2022] Open
Abstract
RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam.
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Affiliation(s)
- Paul P Gardner
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Hisham Eldai
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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85
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Tan Y, Liu ZY, Liu Z, Zheng HJ, Li FL. Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain. MOLECULAR BIOSYSTEMS 2015; 11:1434-42. [DOI: 10.1039/c4mb00600c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.
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Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zhen Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics
- Chinese National Human Genome Center at Shanghai
- Shanghai 201203
- China
| | - Fu-Li Li
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
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86
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Effects of the global regulator CsrA on the BarA/UvrY two-component signaling system. J Bacteriol 2014; 197:983-91. [PMID: 25535275 DOI: 10.1128/jb.02325-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The hybrid sensor kinase BarA and its cognate response regulator UvrY, members of the two-component signal transduction family, activate transcription of CsrB and CsrC noncoding RNAs. These two small RNAs act by sequestering the RNA binding protein CsrA, which posttranscriptionally regulates translation and/or stability of its target mRNAs. Here, we provide evidence that CsrA positively affects, although indirectly, uvrY expression, at both the transcriptional and translational levels. We also demonstrate that CsrA is required for properly switching BarA from its phosphatase to its kinase activity. Thus, the existence of a feedback loop mechanism that involves the Csr and BarA/UvrY global regulatory systems is exposed.
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87
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Heroven AK, Böhme K, Dersch P. The Csr/Rsm system of Yersinia and related pathogens. RNA Biol 2014; 9:379-91. [DOI: 10.4161/rna.19333] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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88
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The two-component GacS-GacA system activates lipA translation by RsmE but not RsmA in Pseudomonas protegens Pf-5. Appl Environ Microbiol 2014; 80:6627-37. [PMID: 25128345 DOI: 10.1128/aem.02184-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Pseudomonas spp., the Gac-Rsm signal transduction system is required for the production of lipases. The current model assumes that the system induces lipase gene transcription mediated through the quorum-sensing (QS) system. However, there are no reports of a QS system based upon N-acyl homoserine lactones or the regulation of lipase gene expression in Pseudomonas protegens. In this study, we investigated the regulatory mechanism acting on lipA expression activated by the Gac-Rsm system in P. protegens Pf-5 through deletion and overexpression of gacA, overexpression of rsmA or rsmE, expression of various lacZ fusions, reverse transcription-PCR analysis, and determination of whole-cell lipase activity. The results demonstrated that the GacS-GacA (GacS/A) system activates lipA expression at both the transcriptional and the translational levels but that the translational level is the key regulatory pathway. Further results showed that the activation of lipA translation by the GacS/A system is mediated through RsmE, which inhibits lipA translation by binding to the ACAAGGAUGU sequence overlapping the Shine-Dalgarno (SD) sequence of lipA mRNA to hinder the access of the 30S ribosomal subunit to the SD sequence. Moreover, the GacS/A system promotes lipA transcription through the mediation of RsmA inhibiting lipA transcription via an unknown pathway. Besides the transcriptional repression, RsmA mainly activates lipA translation by negatively regulating rsmE translation. In summary, in P. protegens Pf-5, the Gac-RsmE system mainly and directly activates lipA translation and the Gac-RsmA system indirectly enhances lipA transcription.
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89
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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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90
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Ito M, Nomura K, Sugimoto H, Watanabe T, Suzuki K. Identification of a Csr system in Serratia marcescens 2170. J GEN APPL MICROBIOL 2014; 60:79-88. [PMID: 24859866 DOI: 10.2323/jgam.60.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The carbon storage regulator (Csr) global regulatory system is conserved in many eubacteria and coordinates the expression of various genes that facilitate adaptation during the major physiological growth phase. The Csr system in Escherichia coli comprises an RNA-binding protein, CsrA; small non-coding RNAs, CsrB and CsrC; and a decay factor for small RNAs, CsrD. In this study, we identified the Csr system in Serratia marcescens 2170. S. marcescens CsrA was 97% identical to E. coli CsrA. CsrB and CsrC RNAs had typical stem-loop structures, including a GGA motif that is the CsrA binding site. CsrD was composed of N-terminal two times transmembrane region and HAMP-like, GGDEF, and EAL domains. Overexpression of S. marcescens csr genes complemented the phenotype of E. coli csr mutants. S. marcescens CsrD affected the decay of CsrB and CsrC RNAs in E. coli. These results suggest that the Csr system in S. marcescens is composed of an RNA-binding protein, two Csr small RNAs, and a decay factor for Csr small RNAs.
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Affiliation(s)
- Manabu Ito
- Graduate School of Science and Technology, Niigata University
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91
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Duss O, Yulikov M, Jeschke G, Allain FHT. EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes. Nat Commun 2014; 5:3669. [PMID: 24828280 DOI: 10.1038/ncomms4669] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 03/14/2014] [Indexed: 12/18/2022] Open
Abstract
High-resolution structural information on RNA and its functionally important complexes with proteins is dramatically underrepresented compared with proteins but is urgently needed for understanding cellular processes at the molecular and atomic level. Here we present an EPR-based protocol to help solving large RNA and protein-RNA complex structures in solution by providing long-range distance constraints between rigid fragments. Using enzymatic ligation of smaller RNA fragments, large doubly spin-labelled RNAs can be obtained permitting the acquisition of long distance distributions (>80 Å) within a large protein-RNA complex. Using a simple and fast calculation in torsion angle space of the spin-label distributions with the program CYANA, we can derive simple distance constraints between the spin labels and use them together with short-range distance restraints derived from NMR to determine the structure of a 70 kDa protein-RNA complex composed of three subcomplexes.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Maxim Yulikov
- Institute for Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Gunnar Jeschke
- Institute for Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
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92
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Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FHT. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature 2014; 509:588-92. [DOI: 10.1038/nature13271] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 03/24/2014] [Indexed: 01/01/2023]
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93
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Kulkarni PR, Jia T, Kuehne SA, Kerkering TM, Morris ER, Searle MS, Heeb S, Rao J, Kulkarni RV. A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa. Nucleic Acids Res 2014; 42:6811-25. [PMID: 24782516 PMCID: PMC4066749 DOI: 10.1093/nar/gku309] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA_TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA. We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins.
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Affiliation(s)
- Prajna R Kulkarni
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Tao Jia
- Social Cognitive Networks Academic Research Center, and Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Sarah A Kuehne
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Thomas M Kerkering
- Section of Infectious Diseases, Carilion Clinic/Virginia Tech Carilion School of Medicine/Jefferson College of Health Sciences, Roanoke, VA 24013, USA
| | - Elizabeth R Morris
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Mark S Searle
- School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stephan Heeb
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jayasimha Rao
- Section of Infectious Diseases, Carilion Clinic/Virginia Tech Carilion School of Medicine/Jefferson College of Health Sciences, Roanoke, VA 24013, USA
| | - Rahul V Kulkarni
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
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94
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Abstract
Microbes commonly live in dense surface-attached communities where cells layer on top of one another such that only those at the edges have unimpeded access to limiting nutrients and space. Theory predicts that this simple spatial effect, akin to plants competing for light in a forest, generates strong natural selection on microbial phenotypes. However, we require direct empirical tests of the importance of this spatial structuring. Here we show that spontaneous mutants repeatedly arise, push their way to the surface, and dominate colonies of the bacterium Pseudomonas fluorescens Pf0-1. Microscopy and modeling suggests that these mutants use secretions to expand and push themselves up to the growth surface to gain the best access to oxygen. Physically mixing the cells in the colony, or introducing space limitations, largely removes the mutant's advantage, showing a key link between fitness and the ability of the cells to position themselves in the colony. We next follow over 500 independent adaptation events and show that all occur through mutation of a single repressor of secretions, RsmE, but that the mutants differ in competitiveness. This process allows us to map the genetic basis of their adaptation at high molecular resolution and we show how evolutionary competitiveness is explained by the specific effects of each mutation. By combining population level and molecular analyses, we demonstrate how living in dense microbial communities can generate strong natural selection to reach the growing edge.
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95
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Andrade MO, Farah CS, Wang N. The post-transcriptional regulator rsmA/csrA activates T3SS by stabilizing the 5' UTR of hrpG, the master regulator of hrp/hrc genes, in Xanthomonas. PLoS Pathog 2014; 10:e1003945. [PMID: 24586158 PMCID: PMC3937308 DOI: 10.1371/journal.ppat.1003945] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/09/2014] [Indexed: 11/28/2022] Open
Abstract
The RsmA/CsrA family of the post-transcriptional regulators of bacteria is involved in the regulation of many cellular processes, including pathogenesis. In this study, we demonstrated that rsmA not only is required for the full virulence of the phytopathogenic bacterium Xanthomonas citri subsp. citri (XCC) but also contributes to triggering the hypersensitive response (HR) in non-host plants. Deletion of rsmA resulted in significantly reduced virulence in the host plant sweet orange and a delayed and weakened HR in the non-host plant Nicotiana benthamiana. Microarray, quantitative reverse-transcription PCR, western-blotting, and GUS assays indicated that RsmA regulates the expression of the type 3 secretion system (T3SS) at both transcriptional and post-transcriptional levels. The regulation of T3SS by RsmA is a universal phenomenon in T3SS-containing bacteria, but the specific mechanism seems to depend on the interaction between a particular bacterium and its hosts. For Xanthomonads, the mechanism by which RsmA activates T3SS remains unknown. Here, we show that RsmA activates the expression of T3SS-encoding hrp/hrc genes by directly binding to the 5′ untranslated region (UTR) of hrpG, the master regulator of the hrp/hrc genes in XCC. RsmA stabilizes hrpG mRNA, leading to increased accumulation of HrpG proteins and subsequently, the activation of hrp/hrc genes. The activation of the hrp/hrc genes by RsmA via HrpG was further supported by the observation that ectopic overexpression of hrpG in an rsmA mutant restored its ability to cause disease in host plants and trigger HR in non-host plants. RsmA also stabilizes the transcripts of another T3SS-associated hrpD operon by directly binding to the 5′ UTR region. Taken together, these data revealed that RsmA primarily activates T3SS by acting as a positive regulator of hrpG and that this regulation is critical to the pathogenicity of XCC. Pathogenic bacteria demonstrate sophisticated capacity to regulate gene expression to meet requirements of living in different environmental niches, including in the hosts. The activation of the Type 3 secretion system (T3SS) genes in response to the host enviroment is under the control of several factors, such as the post-transcriptional regulator RsmA/CsrA. Here, we show that RsmA contributes to the pathogenicity of Xanthomonas citri in host plants and the HR-triggering activity in non-host plants by regulating the expression of T3SS-encoding hrp/hrc genes. RsmA directly interacts with the 5′ UTRs of hrpG and hrpD mRNAs, which leads to increased HrpG protein levels by stabilizing the hrpG transcript. Further, overexpression of hrpG in an rsmA mutant restored its pathogenicity and ability to cause HR. The deletion of rsmA did not affect the phosphorylation of HrpG, which is also required for T3SS activation. This work provides mechanistic insights for the first time into RsmA-mediated regulation of T3SS gene expression by acting as a positive regulator of hrpG at the post-transcription level.
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Affiliation(s)
- Maxuel O. Andrade
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Chuck S. Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, Lake Alfred, Florida, United States of America
- * E-mail:
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96
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Duss O, Michel E, Diarra dit Konté N, Schubert M, Allain FHT. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition. Nucleic Acids Res 2014; 42:5332-46. [PMID: 24561806 PMCID: PMC4005645 DOI: 10.1093/nar/gku141] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.
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Affiliation(s)
- Olivier Duss
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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97
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98
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The ribonucleoprotein Csr network. Int J Mol Sci 2013; 14:22117-31. [PMID: 24217225 PMCID: PMC3856055 DOI: 10.3390/ijms141122117] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/21/2013] [Accepted: 10/28/2013] [Indexed: 11/16/2022] Open
Abstract
Ribonucleoprotein complexes are essential regulatory components in bacteria. In this review, we focus on the carbon storage regulator (Csr) network, which is well conserved in the bacterial world. This regulatory network is composed of the CsrA master regulator, its targets and regulators. CsrA binds to mRNA targets and regulates translation either negatively or positively. Binding to small non-coding RNAs controls activity of this protein. Expression of these regulators is tightly regulated at the level of transcription and stability by various global regulators (RNAses, two-component systems, alarmone). We discuss the implications of these complex regulations in bacterial adaptation.
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99
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An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2013; 110:15055-60. [PMID: 23980177 DOI: 10.1073/pnas.1307217110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Members of the CsrA family of prokaryotic mRNA-binding proteins alter the translation and/or stability of transcripts needed for numerous global physiological processes. The previously described CsrA family member in Pseudomonas aeruginosa (RsmA) plays a central role in determining infection modality by reciprocally regulating processes associated with acute (type III secretion and motility) and chronic (type VI secretion and biofilm formation) infection. Here we describe a second, structurally distinct RsmA homolog in P. aeruginosa (RsmF) that has an overlapping yet unique regulatory role. RsmF deviates from the canonical 5 β-strand and carboxyl-terminal α-helix topology of all other CsrA proteins by having the α-helix internally positioned. Despite striking changes in topology, RsmF adopts a tertiary structure similar to other CsrA family members and binds a subset of RsmA mRNA targets, suggesting that RsmF activity is mediated through a conserved mechanism of RNA recognition. Whereas deletion of rsmF alone had little effect on RsmA-regulated processes, strains lacking both rsmA and rsmF exhibited enhanced RsmA phenotypes for markers of both type III and type VI secretion systems. In addition, simultaneous deletion of rsmA and rsmF resulted in superior biofilm formation relative to the wild-type or rsmA strains. We show that RsmF translation is derepressed in an rsmA mutant and demonstrate that RsmA specifically binds to rsmF mRNA in vitro, creating a global hierarchical regulatory cascade that operates at the posttranscriptional level.
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100
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Morris ER, Hall G, Li C, Heeb S, Kulkarni RV, Lovelock L, Silistre H, Messina M, Cámara M, Emsley J, Williams P, Searle MS. Structural rearrangement in an RsmA/CsrA ortholog of Pseudomonas aeruginosa creates a dimeric RNA-binding protein, RsmN. Structure 2013; 21:1659-71. [PMID: 23954502 PMCID: PMC3791407 DOI: 10.1016/j.str.2013.07.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/11/2013] [Accepted: 07/14/2013] [Indexed: 12/20/2022]
Abstract
In bacteria, the highly conserved RsmA/CsrA family of RNA-binding proteins functions as global posttranscriptional regulators acting on mRNA translation and stability. Through phenotypic complementation of an rsmA mutant in Pseudomonas aeruginosa, we discovered a family member, termed RsmN. Elucidation of the RsmN crystal structure and that of the complex with a hairpin from the sRNA, RsmZ, reveals a uniquely inserted α helix, which redirects the polypeptide chain to form a distinctly different protein fold to the domain-swapped dimeric structure of RsmA homologs. The overall β sheet structure required for RNA recognition is, however, preserved with compensatory sequence and structure differences, allowing the RsmN dimer to target binding motifs in both structured hairpin loops and flexible disordered RNAs. Phylogenetic analysis indicates that, although RsmN appears unique to P. aeruginosa, homologous proteins with the inserted α helix are more widespread and arose as a consequence of a gene duplication event. Phenotypic complementation identifies a CsrA/RsmA family member from P. aeruginosa Crystallography reveals a dimeric fold for RsmN The RsmN complex was solved with a hairpin motif from the noncoding sRNA RsmZ-2 Details of binding affinity and specificity with target RNA 5′-ANGGAN motifs are revealed
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Affiliation(s)
- Elizabeth R Morris
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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