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He M, Yin S, Huang X, Li Y, Li B, Gong T, Liu Q. Insights into the regulatory role of bacterial sncRNA and its extracellular delivery via OMVs. Appl Microbiol Biotechnol 2024; 108:29. [PMID: 38159117 DOI: 10.1007/s00253-023-12855-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
Small noncoding RNAs (sncRNAs) play important regulatory roles in bacterial physiological processes and host-pathogen interactions. Meanwhile, bacterial outer membrane vesicles (OMVs), as naturally secreted outer membrane structures, play a vital role in the interaction between bacteria and their living environment, including the host environment. However, most current studies focus on the biological functions of sncRNAs in bacteria or hosts, while neglecting the roles and regulatory mechanisms of the OMVs that encapsulate these sncRNAs. Therefore, this review aims to summarize the intracellular regulatory roles of bacterial sncRNAs in promoting pathogen survival by regulating virulence, modulating bacterial drug resistance, and regulating iron metabolism, and their extracellular regulatory function for influencing host immunity through host-pathogen interactions. Additionally, we introduce the key role played by OMVs, which serve as important cargoes in bacterial sncRNA-host interactions. We propose emerging pathways of sncRNA action to further discuss the mode of host-pathogen interactions, highlighting that the inhibition of sncRNA delivery by OMVs may prevent the occurrence of infection to some extent. Hence, this review lays the foundation for future prophylactic treatments against bacterial infections and strategies for addressing bacterial drug resistance. KEY POINTS: •sncRNAs have intracellular and extracellular regulatory functions in bacterial physiological processes and host-pathogen interactions. •OMVs are potential mediators between bacterial sncRNAs and host cells. •OMVs encapsulating sncRNAs have more potential biological functions.
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Affiliation(s)
- Mengdan He
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Shuanshuan Yin
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Xinlei Huang
- Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yi Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Biaoxian Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Qiong Liu
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China.
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2
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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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3
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Ponath F, Zhu Y, Vogel J. Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E-dependent small RNA with unusual mRNA activation activity. mBio 2024; 15:e0353623. [PMID: 38436569 PMCID: PMC11005410 DOI: 10.1128/mbio.03536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
The oral commensal Fusobacterium nucleatum can spread to extra-oral sites, where it is associated with diverse pathologies, including pre-term birth and cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of the RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that F. nucleatum harbors a global stress response governed by the extracytoplasmic function sigma factor, σE, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σE-dependent sRNAs, we comprehensively mapped the 5' and 3' ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156-nucleotide sRNA previously misannotated as the 5' untranslated region (UTR) of ylmH. FoxJ is tightly controlled by σE and activated by the same stress conditions as is FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from other σE-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5' and 3' UTRs in F. nucleatum and expands our understanding of the σE response in this evolutionarily distant bacterium.IMPORTANCEThe oral microbe Fusobacterium nucleatum can colonize secondary sites, including cancer tissue, and likely deploys complex regulatory systems to adapt to these new environments. These systems are largely unknown, partly due to the phylogenetic distance of F. nucleatum to other model organisms. Previously, we identified a global stress response mediated by σE that displays functional conservation with the envelope stress response in Proteobacteria, comprising a coding and noncoding regulatory arm. Through global identification of transcriptional start and stop sites, we uncovered the small RNA (sRNA) FoxJ as a novel component of the noncoding arm of the σE response in F. nucleatum. Together with its companion sRNA FoxI, FoxJ post-transcriptionally modulates the synthesis of envelope proteins, revealing a conserved function for σE-dependent sRNAs between Fusobacteriota and Proteobacteria. Moreover, FoxJ activates the gene expression for several targets, which is a mode of regulation previously unseen in the noncoding arm of the σE response.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Rep 2023; 42:113571. [PMID: 38096053 PMCID: PMC10853860 DOI: 10.1016/j.celrep.2023.113571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine. These spermidine-sensing riboswitch variants are associated with genes whose protein products are directly involved in the production of spermidine and other polyamines. Biochemical and genetic assays demonstrate that representatives of this riboswitch class robustly function as genetic "off" switches, wherein spermidine binding causes premature transcription termination to suppress the expression of polyamine biosynthetic genes. These findings confirm the existence of natural spermidine-sensing riboswitches in bacteria and expand the list of variant riboswitch classes that have adapted to bind different ligands.
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Affiliation(s)
- Hubert Salvail
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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5
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Abstract
Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.
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Affiliation(s)
- Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany;
- Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel;
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Ruddell B, Hassall A, Moss WN, Sahin O, Plummer PJ, Zhang Q, Kreuder AJ. Direct interaction of small non-coding RNAs CjNC140 and CjNC110 optimizes expression of key pathogenic phenotypes of Campylobacter jejuni. mBio 2023; 14:e0083323. [PMID: 37409826 PMCID: PMC10470494 DOI: 10.1128/mbio.00833-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 07/07/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are important players in modulating gene expression in bacterial pathogens, but their functions are largely undetermined in Campylobacter jejuni, an important cause of foodborne gastroenteritis in humans. In this study, we elucidated the functions of sRNA CjNC140 and its interaction with CjNC110, a previously characterized sRNA involved in the regulation of several virulence phenotypes of C. jejuni. Inactivation of CjNC140 increased motility, autoagglutination, L-methionine concentration, autoinducer-2 production, hydrogen peroxide resistance, and early chicken colonization, indicating a primarily inhibitory role of CjNC140 for these phenotypes. Apart from motility, all these effects directly contrasted the previously demonstrated positive regulation by CjNC110, suggesting that CjNC110 and CjNC140 operate in an opposite manner to modulate physiologic processes in C. jejuni. RNAseq and northern blotting further demonstrated that expression of CjNC140 increased in the absence of CjNC110, while expression of CjNC110 decreased in the absence of CjNC140, suggesting a possibility of their direct interaction. Indeed, electrophoretic mobility shift assay demonstrated a direct binding between the two sRNAs via GA- (CjNC110) and CU- (CjNC140) rich stem-loops. Additionally, RNAseq and follow-up experiments identified that CjNC140 positively regulates p19, which encodes a key iron uptake transporter in Campylobacter. Furthermore, computational analysis revealed both CjNC140 and CjNC110 are highly conserved in C. jejuni, and the predicted secondary structures support CjNC140 as a functional homolog of the iron regulatory sRNA, RyhB. These findings establish CjNC140 and CjNC110 as a key checks-and- balances mechanism in maintaining homeostasis of gene expression and optimizing phenotypes critical for C. jejuni pathobiology. IMPORTANCE Gene regulation is critical to all aspects of pathogenesis of bacterial disease, and small non-coding RNAs (sRNAs) represent a new frontier in gene regulation of bacteria. In Campylobacter jejuni, the role of sRNAs remains largely unexplored. Here, we investigate the role of two highly conserved sRNAs, CjNC110 and CjNC140, and demonstrate that CjNC140 displays a primarily inhibitory role in contrast to a primarily activating role for CjNC110 for several key virulence-associated phenotypes. Our results also revealed that the sRNA regulatory pathway is intertwined with the iron uptake system, another virulence mechanism critical for in vivo colonization. These findings open a new direction for understanding C. jejuni pathobiology and identify potential targets for intervention for this major foodborne pathogen.
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Affiliation(s)
- Brandon Ruddell
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), Iowa State University Research Park, Ames, Iowa, USA
| | - Alan Hassall
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Walter N. Moss
- The Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Orhan Sahin
- National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), Iowa State University Research Park, Ames, Iowa, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Paul J. Plummer
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), Iowa State University Research Park, Ames, Iowa, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), Iowa State University Research Park, Ames, Iowa, USA
| | - Amanda J. Kreuder
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- National Institute of Antimicrobial Resistance Research and Education (NIAMRRE), Iowa State University Research Park, Ames, Iowa, USA
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7
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Carrier MC, Lalaouna D, Massé E. Hfq protein and GcvB small RNA tailoring of oppA target mRNA to levels allowing translation activation by MicF small RNA in Escherichia coli. RNA Biol 2023; 20:59-76. [PMID: 36860088 PMCID: PMC9988348 DOI: 10.1080/15476286.2023.2179582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Traffic of molecules across the bacterial membrane mainly relies on porins and transporters, whose expression must adapt to environmental conditions. To ensure bacterial fitness, synthesis and assembly of functional porins and transporters are regulated through a plethora of mechanisms. Among them, small regulatory RNAs (sRNAs) are known to be powerful post-transcriptional regulators. In Escherichia coli, the MicF sRNA is known to regulate only four targets, a very narrow targetome for a sRNA responding to various stresses, such as membrane stress, osmotic shock, or thermal shock. Using an in vivo pull-down assay combined with high-throughput RNA sequencing, we sought to identify new targets of MicF to better understand its role in the maintenance of cellular homoeostasis. Here, we report the first positively regulated target of MicF, the oppA mRNA. The OppA protein is the periplasmic component of the Opp ATP-binding cassette (ABC) oligopeptide transporter and regulates the import of short peptides, some of them bactericides. Mechanistic studies suggest that oppA translation is activated by MicF through a mechanism of action involving facilitated access to a translation-enhancing region in oppA 5'UTR. Intriguingly, MicF activation of oppA translation depends on cross-regulation by negative trans-acting effectors, the GcvB sRNA and the RNA chaperone protein Hfq.
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Affiliation(s)
- Marie-Claude Carrier
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - David Lalaouna
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Massé
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Majumder R, Ghosh S, Das A, Singh MK, Samanta S, Saha A, Saha RP. Prokaryotic ncRNAs: Master regulators of gene expression. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100136. [PMID: 36568271 PMCID: PMC9780080 DOI: 10.1016/j.crphar.2022.100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, but is an important modulator of gene regulation too in all these domains. In this review, we discussed various aspects of ncRNA biology, especially their role in bacteria. The last two decades of scientific research have proved that this molecule plays an important role in the modulation of various regulatory pathways in bacteria including the adaptive immune system and gene regulation. It is also very surprising to note that this small molecule is also employed in various processes related to the pathogenicity of virulent microorganisms.
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Affiliation(s)
- Rajib Majumder
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Sanmitra Ghosh
- Department of Biological Sciences, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Arpita Das
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Manoj Kumar Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
| | - Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, 700126, India,Corresponding authors.
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Mahendran G, Jayasinghe OT, Thavakumaran D, Arachchilage GM, Silva GN. Key players in regulatory RNA realm of bacteria. Biochem Biophys Rep 2022; 30:101276. [PMID: 35592614 PMCID: PMC9111926 DOI: 10.1016/j.bbrep.2022.101276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network. The three major classes of prokaryotic ncRNAs and their characterized mechanisms of operation in gene regulation. sRNAs emerging as major players in global gene regulatory networks. Riboswitch mediated gene control mechanisms through on/off switches in response to ligand binding. RNA thermo sensors for temperature-dependent gene expression. Therapeutic importance of ncRNAs and computational approaches involved in the discovery of ncRNAs.
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Affiliation(s)
- Gowthami Mahendran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Oshadhi T. Jayasinghe
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dhanushika Thavakumaran
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, 46556, USA
| | - Gayan Mirihana Arachchilage
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA
- PTC Therapeutics Inc, South Plainfield, NJ, 07080, USA
| | - Gayathri N. Silva
- Department of Chemistry, University of Colombo, Colombo, Sri Lanka
- Corresponding author.
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10
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Trouillon J, Han K, Attrée I, Lory S. The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages. Nat Commun 2022; 13:1258. [PMID: 35273147 PMCID: PMC8913705 DOI: 10.1038/s41467-022-28849-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 02/14/2022] [Indexed: 01/16/2023] Open
Abstract
The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Ina Attrée
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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11
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Liu L, Wang W, Wu S, Gao H. Recent Advances in the Siderophore Biology of Shewanella. Front Microbiol 2022; 13:823758. [PMID: 35250939 PMCID: PMC8891985 DOI: 10.3389/fmicb.2022.823758] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the abundance of iron in nature, iron acquisition is a challenge for life in general because the element mostly exists in the extremely insoluble ferric (Fe3+) form in oxic environments. To overcome this, microbes have evolved multiple iron uptake strategies, a common one of which is through the secretion of siderophores, which are iron-chelating metabolites generated endogenously. Siderophore-mediated iron transport, a standby when default iron transport routes are abolished under iron rich conditions, is essential under iron starvation conditions. While there has been a wealth of knowledge about the molecular basis of siderophore synthesis, uptake and regulation in model bacteria, we still know surprisingly little about siderophore biology in diverse environmental microbes. Shewanella represent a group of γ-proteobacteria capable of respiring a variety of organic and inorganic substrates, including iron ores. This respiratory process relies on a large number of iron proteins, c-type cytochromes in particular. Thus, iron plays an essential and special role in physiology of Shewanella. In addition, these bacteria use a single siderophore biosynthetic system to produce an array of macrocyclic dihydroxamate siderophores, some of which show particular biological activities. In this review, we first outline current understanding of siderophore synthesis, uptake and regulation in model bacteria, and subsequently discuss the siderophore biology in Shewanella.
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Affiliation(s)
- Lulu Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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12
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Barsheshet M, Fisher S, Margalit H. Inferring the contribution of small RNAs to changes in gene expression in response to stress. NAR Genom Bioinform 2022; 4:lqac015. [PMID: 35261974 PMCID: PMC8896160 DOI: 10.1093/nargab/lqac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
A main strategy of bacteria adapting to environmental changes is the remodeling of their transcriptome. Changes in the transcript levels of specific genes are due to combined effects of various regulators, including small RNAs (sRNAs). sRNAs are post-transcriptional regulators of gene expression that mainly control translation, but also directly and indirectly affect the levels of their target transcripts. Yet, the relative contribution of an sRNA to the total change in the transcript level of a gene upon an environmental change has not been assessed. We present a design of differential gene expression analysis by RNA-seq that allows extracting the contribution of an sRNA to the total change in the transcript level of each gene in response to an environmental change by fitting a linear model to the data. We exemplify this for the sRNA RyhB in cells growing under iron limitation and show a variation among genes in the relative contribution of RyhB to the change in their transcript level upon iron limitation, from subtle to very substantial. Extracting the relative contribution of an sRNA to the total change in expression of genes is important for understanding the integration of regulation by sRNAs with other regulatory mechanisms in the cell.
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Affiliation(s)
- Meshi Barsheshet
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shira Fisher
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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13
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Salvail H, Choi J, Groisman EA. Differential synthesis of novel small protein times Salmonella virulence program. PLoS Genet 2022; 18:e1010074. [PMID: 35245279 PMCID: PMC8896665 DOI: 10.1371/journal.pgen.1010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Gene organization in operons enables concerted transcription of functionally related genes and efficient control of cellular processes. Typically, an operon is transcribed as a polycistronic mRNA that is translated into corresponding proteins. Here, we identify a bicistronic operon transcribed as two mRNAs, yet only one allows translation of both genes. We establish that the novel gene ugtS forms an operon with virulence gene ugtL, an activator of the master virulence regulatory system PhoP/PhoQ in Salmonella enterica serovar Typhimurium. Only the longer ugtSugtL mRNA carries the ugtS ribosome binding site and therefore allows ugtS translation. Inside macrophages, the ugtSugtL mRNA species allowing translation of both genes is produced hours before that allowing translation solely of ugtL. The small protein UgtS controls the kinetics of PhoP phosphorylation by antagonizing UgtL activity, preventing premature activation of a critical virulence program. Moreover, S. enterica serovars that infect cold-blooded animals lack ugtS. Our results establish how foreign gene control of ancestral regulators enables pathogens to time their virulence programs. Pathogens must express their virulence genes at precisely the right time to cause disease. Here, we identify a novel small protein that governs a critical virulence program in the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). We establish that the novel small protein UgtS prevents the virulence protein UgtL from activating the master virulence regulator PhoP inside macrophages. S. Typhimurium produces two ugtSugtL mRNAs, but only one of them allows ugtS translation. The absence of ugtS from S. enterica serovars that infect cold-blooded animals raises the possibility of UgtS playing a regulatory role during infection of warm-blooded animals. Our findings establish how a horizontally acquired bicistron enables pathogens to time their virulence programs by controlling ancestral regulators.
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Affiliation(s)
- Hubert Salvail
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Microbial Sciences Institute, West Haven, Connecticut, United States of America
- * E-mail:
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14
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Lee KW, Wen Y, Park NY, Kim KS. Quorum sensing and iron-dependent coordinated control of autoinducer-2 production via small RNA RyhB in Vibrio vulnificus. Sci Rep 2022; 12:831. [PMID: 35039556 PMCID: PMC8764119 DOI: 10.1038/s41598-021-04757-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Roles for the non-coding small RNA RyhB in quorum-sensing and iron-dependent gene modulation in the human pathogen V. vulnificus were assessed in this study. Both the quorum sensing master regulator SmcR and the Fur-iron complex were observed to bind to the region upstream of the non-coding small RNA RyhB gene to repress expression, which suggests that RyhB is associated with both quorum-sensing and iron-dependent signaling in this pathogen. We found that expression of LuxS, which is responsible for the biosynthesis of autoinducer-2 (AI-2), was higher in wild type than in a ryhB-deletion isotype. RyhB binds directly to the 5′-UTR (untranslated region) of the luxS transcript to form a heteroduplex, which not only stabilizes luxS mRNA but also disrupts the secondary structure that normally obscures the translational start codon and thereby allows translation of LuxS to begin. The binding of RyhB to luxS mRNA requires the chaperone protein Hfq, which stabilizes RyhB. These results demonstrate that the small RNA RyhB is a key element associated with feedback control of AI-2 production, and that it inhibits quorum-sensing signaling in an iron-dependent manner. This study, taken together with previous studies, shows that iron availability and cell density signals are funneled to SmcR and RyhB, and that these regulators coordinate cognate signal pathways that result in the proper balance of protein expression in response to environmental conditions.
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Affiliation(s)
- Keun-Woo Lee
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea
| | - Yancheng Wen
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer Research Center for Molecular Medicine, Fujian Medical University, Fuzhou, Fujian, People's Republic of China
| | - Na-Young Park
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea
| | - Kun-Soo Kim
- Department of Life Sciences, Sogang University, Baekbeom-Ro, Mapo-Gu, Seoul, 121-742, Korea.
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15
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London LY, Aubee JI, Nurse J, Thompson KM. Post-Transcriptional Regulation of RseA by Small RNAs RyhB and FnrS in Escherichia coli. Front Mol Biosci 2021; 8:668613. [PMID: 34805264 PMCID: PMC8595263 DOI: 10.3389/fmolb.2021.668613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
RseA is the critical central regulator of the σE-dependent stress response in E. coli and other related bacteria. The synthesis of RseA is controlled at the transcriptional level by several promoters and transcriptional regulators, including σE itself at two σE-dependent promoters: rpoEP and rseAP3. The presence of these two independent polycistrons encoding rseA is potentially redundant. We hypothesized that post-transcriptional control of the rseAP3 transcript was necessary to overcome this redundancy. However, to date, nothing is known about the post-transcriptional control of the rseAP3 transcript. We executed a targeted genetic screen to identify small RNA regulators of the rseAP3 transcript and identified RyhB and FnrS as small RNA activators of the RseA P3 transcript. Through genetic analysis, we confirmed that a direct interaction occurs between RyhB and RseA. We also identified sequences within the 5′ untranslated region (UTR) of RseA that were inhibitory for RseA expression. Point mutations predicted to prevent an interaction between RyhB and RseA resulted in increased RseA expression. Taken together, this suggests that the 5’ UTR of the RseAP3 transcript prevents optimal expression of RseA, preventing redundancy due to RseA expression from the σE-dependent rpoEP, and this is overcome by the stimulatory activity of RyhB and FnrS.
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Affiliation(s)
- Laricca Y London
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL, United States
| | - Joseph I Aubee
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States
| | - Jalisa Nurse
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States.,Department of Biology, Howard University, Washington, DC, United States
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States
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16
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Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli. Noncoding RNA 2021; 7:ncrna7040064. [PMID: 34698252 PMCID: PMC8544716 DOI: 10.3390/ncrna7040064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/03/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.
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17
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Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F, Moreno R. Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region. Nucleic Acids Res 2021; 49:9211-9228. [PMID: 34379788 PMCID: PMC8450116 DOI: 10.1093/nar/gkab672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Insertion sequences (ISs) are mobile genetic elements that only carry the information required for their own transposition. Pseudomonas putida KT2440, a model bacterium, has seven copies of an IS called ISPpu9 inserted into repetitive extragenic palindromic sequences. This work shows that the gene for ISPpu9 transposase, tnp, is regulated by two small RNAs (sRNAs) named Asr9 and Ssr9, which are encoded upstream and downstream of tnp, respectively. The tnp mRNA has a long 5′-untranslated region (5′-UTR) that can fold into a secondary structure that likely includes the ribosome-binding site (RBS). Mutations weakening this structure increased tnp mRNA translation. Asr9, an antisense sRNA complementary to the 5′-UTR, was shown to be very stable. Eliminating Asr9 considerably reduced tnp mRNA translation, suggesting that it helps to unfold this secondary structure, exposing the RBS. Ectopic overproduction of Asr9 increased the transposition frequency of a new ISPpu9 entering the cell by conjugation, suggesting improved tnp expression. Ssr9 has significant complementarity to Asr9 and annealed to it in vitro forming an RNA duplex; this would sequester it and possibly facilitate its degradation. Thus, the antisense Asr9 sRNA likely facilitates tnp expression, improving transposition, while Ssr9 might counteract Asr9, keeping tnp expression low.
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Affiliation(s)
- Guillermo Gómez-García
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Angel Ruiz-Enamorado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Luis Yuste
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
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18
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Djapgne L, Oglesby AG. Impacts of Small RNAs and Their Chaperones on Bacterial Pathogenicity. Front Cell Infect Microbiol 2021; 11:604511. [PMID: 34322396 PMCID: PMC8311930 DOI: 10.3389/fcimb.2021.604511] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are critical post-transcriptional regulators that exert broad effects on cell physiology. One class of sRNAs, referred to as trans-acting sRNAs, base-pairs with mRNAs to cause changes in their stability or translation. Another class of sRNAs sequesters RNA-binding proteins that in turn modulate mRNA expression. RNA chaperones play key roles in these regulatory events by promoting base-pairing of sRNAs to mRNAs, increasing the stability of sRNAs, inducing conformational changes on mRNA targets upon binding, or by titrating sRNAs away from their primary targets. In pathogenic bacteria, sRNAs and their chaperones exert broad impacts on both cell physiology and virulence, highlighting the central role of these systems in pathogenesis. This review provides an overview of the growing number and roles of these chaperone proteins in sRNA regulation, highlighting how these proteins contribute to bacterial pathogenesis.
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Affiliation(s)
- Louise Djapgne
- Department of Chemistry, Georgetown College, Washington, DC, United States
| | - Amanda G Oglesby
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, United States
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19
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Jabbour N, Lartigue MF. An Inventory of CiaR-Dependent Small Regulatory RNAs in Streptococci. Front Microbiol 2021; 12:669396. [PMID: 34113330 PMCID: PMC8186281 DOI: 10.3389/fmicb.2021.669396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteria adapt to the different environments encountered by rapid and tightly controlled regulations involving complex networks. A first line of control is transcriptional with regulators such as two-component systems (TCSs) that respond to physical and chemical perturbations. It is followed by posttranscriptional regulations in which small regulatory RNAs (sRNAs) may affect RNA translation. Streptococci are opportunistic pathogens for humans and farm animals. The TCS CiaRH is highly conserved among this genus and crucial in bacterial survival under stressful conditions. In several streptococcal species, some sRNAs belong to the CiaRH regulon and are called csRNAs for cia-dependent sRNAs. In this review, we start by focusing on the Streptococcus species harboring a CiaRH TCS. Then the role of CiaRH in streptococcal pathogenesis is discussed in the context of recent studies. Finally, we give an overview of csRNAs and their functions in Streptococci with a focus on their importance in bacterial adaptation and virulence.
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Affiliation(s)
| | - Marie-Frédérique Lartigue
- Université de Tours, INRAE, ISP, Tours, France.,Centre Hospitalier Universitaire de Tours, Service de Bactériologie, Virologie, et Hygiène Hospitalière, Tours, France
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20
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Positive regulation of Type III secretion effectors and virulence by RyhB paralogs in Salmonella enterica serovar Enteritidis. Vet Res 2021; 52:44. [PMID: 33691799 PMCID: PMC7944605 DOI: 10.1186/s13567-021-00915-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Small non-coding RNA RyhB is a key regulator of iron homeostasis in bacteria by sensing iron availability in the environment. Although RyhB is known to influence bacterial virulence by interacting with iron metabolism related regulators, its interaction with virulence genes, especially the Type III secretion system (T3SS), has not been reported. Here, we demonstrate that two RyhB paralogs of Salmonella enterica serovar Enteritidis upregulate Type III secretion system (T3SS) effectors, and consequently affect Salmonella invasion into intestinal epithelial cells. Specifically, we found that RyhB-1 modulate Salmonella response to stress condition of iron deficiency and hypoxia, and stress in simulated intestinal environment (SIE). Under SIE culture conditions, both RyhB-1 and RyhB-2 are drastically induced and directly upregulate the expression of T3SS effector gene sipA by interacting with its 5′ untranslated region (5′ UTR) via an incomplete base-pairing mechanism. In addition, the RyhB paralogs upregulate the expression of T3SS effector gene sopE. By regulating the invasion-related genes, RyhBs in turn affect the ability of S. Enteritidis to adhere to and invade into intestinal epithelial cells. Our findings provide evidence that RyhBs function as critical virulence factors by directly regulating virulence-related gene expression. Thus, inhibition of RyhBs may be a potential strategy to attenuate Salmonella.
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21
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Li S, Liang C, Liu G, Jin JM, Tao Y, Tang SY. De Novo Biosynthesis of Chlorogenic Acid Using an Artificial Microbial Community. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2816-2825. [PMID: 33629856 DOI: 10.1021/acs.jafc.0c07588] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineering an artificial microbial community for natural product production is a promising strategy. As mono- and dual-culture systems only gave non-detectable or minimal chlorogenic acid (CGA) biosynthesis, here, a polyculture of three recombinant Escherichia coli strains, acting as biosynthetic modules of caffeic acid (CA), quinic acid (QA), and CGA, was designed and used for de novo CGA biosynthesis. An influx transporter of 3-dehydroshikimic acid (DHS)/shikimic acid (SA), ShiA, was introduced into the QA module-a DHS auxotroph. The QA module proportion in the polyculture and CGA production were found to be dependent on ShiA expression, providing an alternative approach for controlling microbial community composition. The polyculture strategy avoids metabolic flux competition in the biosynthesis of two CGA precursors, CA and QA, and allows production improvement by balancing module proportions. The performance of this polyculture approach was superior to that of previously reported approaches of de novo CGA production.
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Affiliation(s)
- Shizhong Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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22
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Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. eLife 2021; 10:64207. [PMID: 33616037 PMCID: PMC7987339 DOI: 10.7554/elife.64207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face. Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes. The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs. Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.
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Affiliation(s)
- Seongjin Park
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Emily M Heideman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Muhammad S Azam
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Matthew A Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
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23
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Sy BM, Tree JJ. Small RNA Regulation of Virulence in Pathogenic Escherichia coli. Front Cell Infect Microbiol 2021; 10:622202. [PMID: 33585289 PMCID: PMC7873438 DOI: 10.3389/fcimb.2020.622202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
Enteric and extraintestinal pathotypes of Escherichia coli utilize a wide range of virulence factors to colonize niches within the human body. During infection, virulence factors such as adhesins, secretions systems, or toxins require precise regulation and coordination to ensure appropriate expression. Additionally, the bacteria navigate rapidly changing environments with fluctuations in pH, temperature, and nutrient levels. Enteric pathogens utilize sophisticated, interleaved systems of transcriptional and post-transcriptional regulation to sense and respond to these changes and modulate virulence gene expression. Regulatory small RNAs and RNA-binding proteins play critical roles in the post-transcriptional regulation of virulence. In this review we discuss how the mosaic genomes of Escherichia coli pathotypes utilize small RNA regulation to adapt to their niche and become successful human pathogens.
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Affiliation(s)
- Brandon M Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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24
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Saoud J, Carrier MC, Massé É, Faucher SP. The small regulatory RNA Lpr10 regulates the expression of RpoS in Legionella pneumophila. Mol Microbiol 2020; 115:789-806. [PMID: 33191583 DOI: 10.1111/mmi.14644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Legionella pneumophila (Lp) is a waterborne bacterium able to infect human alveolar macrophages, causing Legionnaires' disease. Lp can survive for several months in water, while searching for host cells to grow in, such as ciliates and amoeba. In Lp, the sigma factor RpoS is essential for survival in water. A previous transcriptomic study showed that RpoS positively regulates the small regulatory RNA Lpr10. In the present study, deletion of lpr10 results in an increased survival of Lp in water. Microarray analysis and RT-qPCR revealed that Lpr10 negatively regulates the expression of RpoS in the postexponential phase. Electrophoretic mobility shift assay and in-line probing showed that Lpr10 binds to a region upstream of the previously identified transcription start sites (TSS) of rpoS. A third putative transcription start site was identified by primer extension analysis, upstream of the Lpr10 binding site. In addition, nlpD TSS produces a polycistronic mRNA including the downstream gene rpoS, indicating a fourth TSS for rpoS. Our results suggest that the transcripts from the third and fourth TSS are negatively regulated by the Lpr10 sRNA. Therefore, we propose that Lpr10 is involved in a negative regulatory feedback loop to maintain expression of RpoS to an optimal level.
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Affiliation(s)
- Joseph Saoud
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Marie-Claude Carrier
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Éric Massé
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, QC, Canada
| | - Sébastien P Faucher
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
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Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLoS Genet 2020; 16:e1009065. [PMID: 33112851 PMCID: PMC7592755 DOI: 10.1371/journal.pgen.1009065] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behaves as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n = 7), E. fergusonii (n = 5), Escherichia clades (n = 32) and E. coli (n = 326), tested in a mouse model of sepsis. We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We confirmed the association in vivo by deleting key genes of the HPI in E. coli strains in two phylogenetic backgrounds. We then searched for correlations between virulence, iron capture systems and in vitro growth in a subset of E. coli strains (N = 186) previously phenotyped across growth conditions, including antibiotics and other chemical and physical stressors. We found that virulence and iron capture systems are positively correlated with growth in the presence of numerous antibiotics, probably due to co-selection of virulence and resistance. We also found negative correlations between virulence, iron uptake systems and growth in the presence of specific antibiotics (i.e. cefsulodin and tobramycin), which hints at potential “collateral sensitivities” associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia. Bacterial isolates belonging to the genus Escherichia can be human commensals but also opportunistic pathogens, with the ability to cause extra-intestinal infection. There is therefore the need to identify the genetic elements that favour extra-intestinal virulence, so that virulent bacterial isolates can be identified through genome analysis and potential treatment strategies be developed. To reduce the influence of host variability on virulence, we have used a mouse model of sepsis to characterize the virulence of 370 strains belonging to the genus Escherichia, for which whole genome sequences were also available. We have used a statistical approach called Genome-Wide Association Study (GWAS) to show how the presence of genes that encode for iron scavenging are significantly associated with the propensity of a bacterial isolate to cause extra-intestinal infections. Taking advantage of previously generated growth data on a subset of the strains and its correlation to virulence we generated hypothesis on the relationship between iron scavenging and growth in the presence of various antimicrobials, which could have implications for developing new treatment strategies.
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Affiliation(s)
- Marco Galardini
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
- * E-mail: (MG); (ED)
| | | | | | - Bede Busby
- Genome Biology Unit, EMBL, Heidelberg, Germany
| | - Sara Dion
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Germany
| | - Pedro Beltrao
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Erick Denamur
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
- * E-mail: (MG); (ED)
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26
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Salvail H, Groisman EA. The phosphorelay BarA/SirA activates the non-cognate regulator RcsB in Salmonella enterica. PLoS Genet 2020; 16:e1008722. [PMID: 32392214 PMCID: PMC7241856 DOI: 10.1371/journal.pgen.1008722] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/21/2020] [Accepted: 03/18/2020] [Indexed: 11/18/2022] Open
Abstract
To survive an environmental stress, organisms must detect the stress and mount an appropriate response. One way that bacteria do so is by phosphorelay systems that respond to a stress by activating a regulator that modifies gene expression. To ensure an appropriate response, a given regulator is typically activated solely by its cognate phosphorelay protein(s). However, we now report that the regulator RcsB is activated by both cognate and non-cognate phosphorelay proteins, depending on the condition experienced by the bacterium Salmonella enterica serovar Typhimurium. The RcsC and RcsD proteins form a phosphorelay that activates their cognate regulator RcsB in response to outer membrane stress and cell wall perturbations, conditions Salmonella experiences during infection. Surprisingly, the non-cognate phosphorelay protein BarA activates RcsB during logarithmic growth in Luria-Bertani medium in three ways. That is, BarA’s cognate regulator SirA promotes transcription of the rcsDB operon; the SirA-dependent regulatory RNAs CsrB and CsrC further increase RcsB-activated gene transcription; and BarA activates RcsB independently of the RcsC, RcsD, and SirA proteins. Activation of a regulator by multiple sensors broadens the spectrum of environments in which a set of genes is expressed without evolving binding sites for different regulators at each of these genes. The phosphorelay is a form of signal transduction used by organisms in all three domains of life. Typically, a phosphorelay consists of sensor proteins that respond to specific signals by activating a cognate regulatory protein that alters gene expression. Phosphorelays exhibit specificity towards their cognate regulators, thereby ensuring that any changes in gene expression help an organism cope with the experienced stress (and not with an unrelated stress). However, we now report that the regulator RcsB is activated by both cognate and non-cognate phosphorelay proteins in the bacterium Salmonella enterica serovar Typhimurium. The phosphorelay proteins RcsC and RcsD activate RcsB upon cell envelope perturbations, whereas the non-cognate phosphorelay protein BarA activates RcsB during rapid growth in Luria-Bertani medium. Our findings establish that BarA controls gene expression via both its cognate regulator SirA and the non-cognate regulator RcsB. In addition, they demonstrate that RcsB controls gene expression in response to multiple signals detected by the RcsC, RcsD, and BarA proteins.
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Affiliation(s)
- Hubert Salvail
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Microbial Sciences Institute, West Haven, Connecticut, United States of America
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Microbial Sciences Institute, West Haven, Connecticut, United States of America
- * E-mail:
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27
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Hör J, Matera G, Vogel J, Gottesman S, Storz G. Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0030-2019. [PMID: 32213244 PMCID: PMC7112153 DOI: 10.1128/ecosalplus.esp-0030-2019] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 12/20/2022]
Abstract
The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Gianluca Matera
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892
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28
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Jordan MR, Wang J, Capdevila DA, Giedroc DP. Multi-metal nutrient restriction and crosstalk in metallostasis systems in microbial pathogens. Curr Opin Microbiol 2020; 55:17-25. [PMID: 32062305 DOI: 10.1016/j.mib.2020.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/26/2022]
Abstract
Transition metals from manganese to zinc function as catalytic and structural cofactors for an amazing diversity of proteins and enzymes, and thus are essential for all forms of life. During infection, inflammatory host proteins limit the accessibility of multiple transition metals to invading pathogens in a process termed nutritional immunity. In order to respond to host-mediated metal starvation, bacteria employ both protein and RNA-based mechanisms to sense prevailing transition metal concentrations that collectively regulate systems-level strategies to maintain cellular metallostasis. In this review, we discuss a number of recent advances in our understanding of how bacteria orchestrate the adaptive response to host-mediated multi-metal restriction, highlighting crosstalk among these regulatory systems.
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Affiliation(s)
- Matthew R Jordan
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States
| | - Jiefei Wang
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - David P Giedroc
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States.
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29
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Hou B, Yang X, Xia H, Wu H, Ye J, Zhang H. sRNA EsrE Is Transcriptionally Regulated by the Ferric Uptake Regulator Fur in Escherichia coli. J Microbiol Biotechnol 2020; 30:127-135. [PMID: 31693839 PMCID: PMC9728176 DOI: 10.4014/jmb.1907.07026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Small RNAs (sRNAs) are widespread and play major roles in regulation circuits in bacteria. Previously, we have demonstrated that transcription of esrE is under the control of its own promoter. However, the regulatory elements involved in EsrE sRNA expression are still unknown. In this study, we found that different cis-regulatory elements exist in the promoter region of esrE. We then screened and analyzed seven potential corresponding trans-regulatory elements by using pull-down assays based on DNA affinity chromatography. Among these candidate regulators, we investigated the relationship between the ferric uptake regulator (Fur) and the EsrE sRNA. Electrophoresis mobility shift assays (EMSAs) and β-galactosidase activity assays demonstrated that Fur can bind to the promoter region of esrE, and positively regulate EsrE sRNA expression in the presence of Fe2+.
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Affiliation(s)
- Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China,Department of Applied Biology, East China University of Science and Technology, Shanghai, P.R. China
| | - Xichen Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China
| | - Hui Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China,Department of Applied Biology, East China University of Science and Technology, Shanghai, P.R. China,Corresponding authors H.W. Phone: +86-021-64252507 Fax: +86-021-64252507 E-mail:
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China,Department of Applied Biology, East China University of Science and Technology, Shanghai, P.R. China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, P.R. China,Department of Applied Biology, East China University of Science and Technology, Shanghai, P.R. China,H.Z. Phone: +86-021-64252507 Fax: +86-012-64252507 E-mail:
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30
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A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans. Biomolecules 2019; 10:biom10010022. [PMID: 31877996 PMCID: PMC7022480 DOI: 10.3390/biom10010022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022] Open
Abstract
Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.
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31
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Georg J, Lalaouna D, Hou S, Lott SC, Caldelari I, Marzi S, Hess WR, Romby P. The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs. Mol Microbiol 2019; 113:603-612. [PMID: 31705780 PMCID: PMC7154689 DOI: 10.1111/mmi.14420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022]
Abstract
Trans‐acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post‐transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNAs targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB, and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more details. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA‐dependent regulatory networks is now attainable.
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Affiliation(s)
- Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - David Lalaouna
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Shengwei Hou
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Steffen C Lott
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
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32
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Chiaruttini C, Guillier M. On the role of mRNA secondary structure in bacterial translation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1579. [PMID: 31760691 DOI: 10.1002/wrna.1579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/07/2022]
Abstract
Messenger RNA (mRNA) is no longer considered as a mere informational molecule whose sole function is to convey the genetic information specified by DNA to the ribosome. Beyond this primary function, mRNA also contains additional instructions that influence the way and the extent to which this message is translated by the ribosome into protein(s). Indeed, owing to its intrinsic propensity to quickly and dynamically fold and form higher order structures, mRNA exhibits a second layer of structural information specified by the sequence itself. Besides influencing transcription and mRNA stability, this additional information also affects translation, and more precisely the frequency of translation initiation, the choice of open reading frame by recoding, the elongation speed, and the folding of the nascent protein. Many studies in bacteria have shown that mRNA secondary structure participates to the rapid adaptation of these versatile organisms to changing environmental conditions by efficiently tuning translation in response to diverse signals, such as the presence of ligands, regulatory proteins, or small RNAs. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation.
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33
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Chauvier A, Nadon JF, Grondin JP, Lamontagne AM, Lafontaine DA. Role of a hairpin-stabilized pause in the Escherichia coli thiC riboswitch function. RNA Biol 2019; 16:1066-1073. [PMID: 31081713 PMCID: PMC6602414 DOI: 10.1080/15476286.2019.1616354] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022] Open
Abstract
Transcriptional pauses have been reported in bacterial riboswitches and, in some cases, their specific positioning has been shown to be important for gene regulation. Here, we show that a hairpin structure in the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch is involved in transcriptional pausing and ligand sensitivity. Using in vitro transcription kinetic experiments, we show that all three major transcriptional pauses in the thiC riboswitch are affected by NusA, a transcriptional factor known to stimulate hairpin-stabilized pauses. Using a truncated region of the riboswitch, we isolated the hairpin structure responsible for stabilization of the most upstream pause. Destabilization of this structure led to a weaker pause and a decreased NusA effect. In the context of the full-length riboswitch, this same mutation also led to a weaker pause, as well as a decreased TPP binding affinity. Our work suggests that RNA structures involved in transcriptional pausing in riboswitches are important for ligand sensitivity, most likely by increasing the time allowed to the ligand for binding to the riboswitch.
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Affiliation(s)
- Adrien Chauvier
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jean-François Nadon
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jonathan P. Grondin
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Marie Lamontagne
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Daniel A. Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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34
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Proteomic Analysis of the Pseudomonas aeruginosa Iron Starvation Response Reveals PrrF Small Regulatory RNA-Dependent Iron Regulation of Twitching Motility, Amino Acid Metabolism, and Zinc Homeostasis Proteins. J Bacteriol 2019; 201:JB.00754-18. [PMID: 30962354 DOI: 10.1128/jb.00754-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/31/2019] [Indexed: 12/16/2022] Open
Abstract
Iron is a critical nutrient for most microbial pathogens, and the immune system exploits this requirement by sequestering iron. The opportunistic pathogen Pseudomonas aeruginosa exhibits a high requirement for iron yet an exquisite ability to overcome iron deprivation during infection. Upon iron starvation, P. aeruginosa induces the expression of several high-affinity iron acquisition systems, as well as the PrrF small regulatory RNAs (sRNAs) that mediate an iron-sparing response. Here, we used liquid chromatography-tandem mass spectrometry to conduct proteomics of the iron starvation response of P. aeruginosa Iron starvation increased levels of multiple proteins involved in amino acid catabolism, providing the capacity for iron-independent entry of carbons into the tricarboxylic acid (TCA) cycle. Proteins involved in sulfur assimilation and cysteine biosynthesis were reduced upon iron starvation, while proteins involved in iron-sulfur cluster biogenesis were increased, highlighting the central role of iron in P. aeruginosa metabolism. Iron starvation also resulted in changes in the expression of several zinc-responsive proteins and increased levels of twitching motility proteins. Subsequent analyses provided evidence for the regulation of many of these proteins via posttranscriptional regulatory events, some of which are dependent upon the PrrF sRNAs. Moreover, we showed that iron-regulated twitching motility is partially dependent upon the prrF locus, highlighting a novel link between the PrrF sRNAs and motility. These findings add to the known impacts of iron starvation in P. aeruginosa and outline potentially novel roles for the PrrF sRNAs in iron homeostasis and pathogenesis.IMPORTANCE Iron is central for growth and metabolism of almost all microbial pathogens, and as such, this element is sequestered by the host innate immune system to restrict microbial growth. Here, we used label-free proteomics to investigate the Pseudomonas aeruginosa iron starvation response, revealing a broad landscape of metabolic and metal homeostasis changes that have not previously been described. We further provide evidence that many of these processes, including twitching motility, are regulated through the iron-responsive PrrF small regulatory RNAs. As such, this study demonstrates the power of proteomics for defining stress responses of microbial pathogens.
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35
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Assis NG, Ribeiro RA, da Silva LG, Vicente AM, Hug I, Marques MV. Identification of Hfq-binding RNAs in Caulobacter crescentus. RNA Biol 2019; 16:719-726. [PMID: 30870072 DOI: 10.1080/15476286.2019.1593091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium Caulobacter crescentus, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.
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Affiliation(s)
- Nadine G Assis
- a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil
| | - Rodolfo A Ribeiro
- a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil
| | - Larissa G da Silva
- a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil
| | - Alexandre M Vicente
- a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil
| | - Isabelle Hug
- b Biozentrum , University of Basel , Basel , Switzerland
| | - Marilis V Marques
- a Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , São Paulo , Brazil
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36
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Grüll MP, Massé E. Mimicry, deception and competition: The life of competing endogenous RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1525. [PMID: 30761752 DOI: 10.1002/wrna.1525] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets. While some ceRNAs seem to be expressed constitutively, others are intricately regulated according to environmental conditions. The outcome of ceRNA binding to a sRNA reaches beyond simple sequestration. Various effects observed on sRNA functions extend from reducing transcriptional noise to promote RNA turnover. Here, we present a historical perspective of the discovery of ceRNAs in eukaryotic organisms and mainly focus on the synthesis and function of select, well-described, ceRNAs in bacterial cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Marc P Grüll
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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37
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Lalaouna D, Eyraud A, Devinck A, Prévost K, Massé E. GcvB small RNA uses two distinct seed regions to regulate an extensive targetome. Mol Microbiol 2018; 111:473-486. [PMID: 30447071 DOI: 10.1111/mmi.14168] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 01/01/2023]
Abstract
GcvB small RNA is described as post-transcriptional regulator of 1-2% of all mRNAs in Escherichia coli and Salmonella Typhimurium. At least 24 GcvB:mRNA interactions have been validated in vivo, establishing the largest characterized sRNA targetome. By performing MS2-affinity purification coupled with RNA sequencing (MAPS) technology, we identified seven additional mRNAs negatively regulated by GcvB in E. coli. Contrary to the vast majority of previously known targets, which pair to the well-conserved GcvB R1 region, we validated four mRNAs targeted by GcvB R3 region. This indicates that base-pairing through R3 seed sequence seems relatively common. We also noticed unusual GcvB pairing sites in the coding sequence of two target mRNAs. One of these target mRNAs has a pairing site displaying a unique ACA motif, suggesting that GcvB could hijack a translational enhancer element. The second target mRNA is likely regulated via an active RNase E-mediated mRNA degradation mechanism. Remarkably, we confirmed the importance of the sRNA sponge SroC in the fine-tuning control of GcvB activity in function of growth conditions such as growth phase and nutrient availability.
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Affiliation(s)
- David Lalaouna
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Alex Eyraud
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Aurélie Devinck
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Karine Prévost
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Luo ZW, Kim WJ, Lee SY. Metabolic Engineering of Escherichia coli for Efficient Production of 2-Pyrone-4,6-dicarboxylic Acid from Glucose. ACS Synth Biol 2018; 7:2296-2307. [PMID: 30096230 DOI: 10.1021/acssynbio.8b00281] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudoaromatic dicarboxylic acid and is a promising biobased building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthetic pathway for PDC production from glucose was suggested by in silico metabolic flux simulation. This best pathway employs a single-step biosynthetic route to protocatechuic acid (PCA), a metabolic precursor for PDC biosynthesis. On the basis of the selected PDC biosynthetic pathway, a shikimate dehydrogenase (encoded by aroE)-deficient E. coli strain was engineered by introducing heterologous genes of different microbial origin encoding enzymes responsible for converting 3-dehydroshikimate (DHS) to PDC, which allowed de novo biosynthesis of PDC from glucose. Next, production of PDC was further improved by applying stepwise rational metabolic engineering strategies. These include elimination of feedback inhibition on 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (encoded by aroG) by overexpressing a feedback-resistant variant, enhancement of the precursor phosphoenolpyruvate supply by changing the native promoter of the ppsA gene with the strong trc promoter, and reducing accumulation of the major byproduct DHS by overexpression of a DHS importer (encoded by shiA). Furthermore, cofactor (NADP+/NADPH) utilization was manipulated through genetic modifications of the E. coli soluble pyridine nucleotide transhydrogenase (encoded by sthA), and the resultant impact on PDC production was investigated. Fed-batch fermentation of the final engineered E. coli strain allowed production of 16.72 g/L of PDC from glucose with the yield and productivity of 0.201 g/g and 0.172 g/L/h, respectively, representing the highest PDC production performance indices reported to date.
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Affiliation(s)
- Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
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After the Fact(or): Posttranscriptional Gene Regulation in Enterohemorrhagic Escherichia coli O157:H7. J Bacteriol 2018; 200:JB.00228-18. [PMID: 29967119 DOI: 10.1128/jb.00228-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To adapt to ever-changing environments, pathogens quickly alter gene expression. This can occur through transcriptional, posttranscriptional, or posttranslational regulation. Historically, transcriptional regulation has been thoroughly studied to understand pathogen niche adaptation, whereas posttranscriptional and posttranslational gene regulation has only relatively recently been appreciated to play a central role in bacterial pathogenesis. Posttranscriptional regulation may involve chaperones, nucleases, and/or noncoding small RNAs (sRNAs) and typically controls gene expression by altering the stability and/or translation of the target mRNA. In this review, we highlight the global importance of posttranscriptional regulation to enterohemorrhagic Escherichia coli (EHEC) gene expression and discuss specific mechanisms of how EHEC regulates expression of virulence factors critical to host colonization and disease progression. The low infectious dose of this intestinal pathogen suggests that EHEC is particularly well adapted to respond to the host environment.
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40
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Abstract
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.
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Abstract
ABSTRACT
While iron is essential to sustain growth, its excess can be detrimental to the cell by generating highly toxic reactive oxygen species. Regulation of iron homeostasis thus plays a vital role in almost all living organisms. During the last 15 years, the small RNA (sRNA) RyhB has been shown to be a key actor of iron homeostasis regulation in bacteria. Through multiple molecular mechanisms, RyhB represses expendable iron-utilizing proteins, promotes siderophore production, and coordinates Fe-S cluster cofactor biogenesis, thereby establishing a so-called iron-sparing response. In this review, we will summarize knowledge on how sRNAs control iron homeostasis mainly through studies on RyhB in
Escherichia coli
. The parallel roles and modes of action of other sRNAs in different bacteria will also be described. Finally, we will discuss what questions remain to be answered concerning this important stress response regulation by sRNAs.
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Kong HK, Liu X, Lo WU, Pan Q, Law COK, Chan TF, Ho PL, Lau TCK. Identification of Plasmid-Encoded sRNAs in a blaNDM-1-Harboring Multidrug-Resistance Plasmid pNDM-HK in Enterobacteriaceae. Front Microbiol 2018; 9:532. [PMID: 29636732 PMCID: PMC5880898 DOI: 10.3389/fmicb.2018.00532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/08/2018] [Indexed: 01/15/2023] Open
Abstract
Small RNAs (sRNAs) play significant roles in regulating gene expression post-transcriptionally in response to environmental changes in bacteria. In this work, we identified and characterized six novel sRNAs from an emerging multidrug-resistance (MDR) plasmid pNDM-HK, a New Delhi metallo-β-lactamase 1 gene (blaNDM−1)-carrying IncL/M plasmid that has caused worldwide threat in recent years. These sRNAs are located at different regions of pNDM-HK, such as replication, stability, and variable regions. Moreover, one of the plasmid-encoded sRNAs (NDM-sR3) functions in an Hfq-dependent manner and possibly plays roles in the fitness of pNDM-HK carrying bacteria. In addition, we attempted to construct the phylogenetic tree based on these novel sRNAs and surprisingly, the sRNA-phylogenetic tree provided significant information about the evolutionary pathway of pNDM-HK, including possible gene acquisition and insertion from relevant plasmids. Moreover, the sRNA-phylogenetic tree can specifically cluster the IncM2 type and distinguish it from other IncL/M subtypes. In summary, this is the first study to systematically identify and characterize sRNAs from clinically-isolated MDR plasmids. We believe that these newly found sRNAs could lead to further understanding and new directions to study the evolution and dissemination of the clinically MDR bacterial plasmids.
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Affiliation(s)
- Hoi-Kuan Kong
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xuan Liu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Wai U Lo
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Qing Pan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Carmen O K Law
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ting F Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Pak L Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Terrence C K Lau
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
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Azam MS, Vanderpool CK. Translational regulation by bacterial small RNAs via an unusual Hfq-dependent mechanism. Nucleic Acids Res 2018; 46:2585-2599. [PMID: 29294046 PMCID: PMC5861419 DOI: 10.1093/nar/gkx1286] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 12/08/2017] [Accepted: 12/21/2017] [Indexed: 01/06/2023] Open
Abstract
In bacteria, the canonical mechanism of translational repression by small RNAs (sRNAs) involves sRNA-mRNA base pairing that occludes the ribosome binding site (RBS), directly preventing translation. In this mechanism, the sRNA is the direct regulator, while the RNA chaperone Hfq plays a supporting role by stabilizing the sRNA. There are a few examples where the sRNA does not directly interfere with ribosome binding, yet translation of the target mRNA is still inhibited. Mechanistically, this non-canonical regulation by sRNAs is poorly understood. Our previous work demonstrated repression of the mannose transporter manX mRNA by the sRNA SgrS, but the regulatory mechanism was unknown. Here, we report that manX translation is controlled by a molecular role-reversal mechanism where Hfq, not the sRNA, is the direct repressor. Hfq binding adjacent to the manX RBS is required for sRNA-mediated translational repression. Translation of manX is also regulated by another sRNA, DicF, via the same non-canonical Hfq-dependent mechanism. Our results suggest that the sRNAs recruit Hfq to its binding site or stabilize the mRNA-Hfq complex. This work adds to the growing number of examples of diverse mechanisms of translational regulation by sRNAs in bacteria.
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Affiliation(s)
- Muhammad S Azam
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Tien M, Fiebig A, Crosson S. Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival. eLife 2018. [PMID: 29537368 PMCID: PMC5869019 DOI: 10.7554/elife.33684] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells adapt to shifts in their environment by remodeling transcription. Measuring changes in transcription at the genome scale is now routine, but defining the functional significance of individual genes within large gene expression datasets remains a major challenge. We applied a network-based algorithm to interrogate publicly available gene expression data to predict genes that serve major functional roles in Caulobacter crescentus stress survival. This approach identified GsrN, a conserved small RNA that is directly activated by the general stress sigma factor, σT, and functions as a potent post-transcriptional regulator of survival across distinct conditions including osmotic and oxidative stress. Under hydrogen peroxide stress, GsrN protects cells by base pairing with the leader of katG mRNA and activating expression of KatG catalase/peroxidase protein. We conclude that GsrN convenes a post-transcriptional layer of gene expression that serves a central functional role in Caulobacter stress physiology.
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Affiliation(s)
- Matthew Tien
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Department of Microbiology, University of Chicago, Chicago, United States
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45
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Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms. Gene 2018; 656:60-72. [PMID: 29501814 DOI: 10.1016/j.gene.2018.02.068] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/19/2018] [Accepted: 02/27/2018] [Indexed: 11/23/2022]
Abstract
Small RNAs (sRNAs) in bacteria have evolved with diverse mechanisms to balance their target gene expression in response to changes in the environment. Accumulating studies on bacterial regulatory processes firmly established that sRNAs modulate their target gene expression generally at the posttranscriptional level. Identification of large number of sRNAs by advanced technologies, like deep sequencing, tilling microarray, indicates the existence of a plethora of distinctive sRNA-mediated regulatory mechanisms in bacteria. Types of the novel mechanisms are increasing with the discovery of new sRNAs. Complementary base pairing between sRNAs and target RNAs assisted by RNA chaperones like Hfq and ProQ, in many occasions, to regulate the cognate gene expression is prevalent in sRNA mechanisms. sRNAs, in most studied cases, can directly base pair with target mRNA to remodel its expression. Base pairing can happen either in the untranslated regions or in the coding regions of mRNA to activate/repress its translation. sRNAs also act as target mimic to titrate away different regulatory RNAs from its target. Other mechanism includes the sequestration of regulatory proteins, especially transcription factors, by sRNAs. Numerous sRNAs, following analogous mechanism, are widespread in bacteria, and thus, has drawn immense attention for the development of RNA-based technologies. Nevertheless, typical sRNA mechanisms are also discovered to be confined in some bacteria. Analysis of the sRNA mechanisms unravels their existence in both the single step processes and the complex regulatory networks with a global effect on cell physiology. This review deals with the diverse array of mechanisms, which sRNAs follow to maintain bacterial lifestyle.
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46
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Falcone M, Ferrara S, Rossi E, Johansen HK, Molin S, Bertoni G. The Small RNA ErsA of Pseudomonas aeruginosa Contributes to Biofilm Development and Motility through Post-transcriptional Modulation of AmrZ. Front Microbiol 2018; 9:238. [PMID: 29497413 PMCID: PMC5819304 DOI: 10.3389/fmicb.2018.00238] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
The small RNA ErsA of Pseudomonas aeruginosa was previously suggested to be involved in biofilm formation via negative post-transcriptional regulation of the algC gene that encodes the virulence-associated enzyme AlgC, which provides sugar precursors for the synthesis of several polysaccharides. In this study, we show that a knock-out ersA mutant strain forms a flat and uniform biofilm, not characterized by mushroom-multicellular structures typical of a mature biofilm. Conversely, the knock-out mutant strain showed enhanced swarming and twitching motilities. To assess the influence of ErsA on the P. aeruginosa transcriptome, we performed RNA-seq experiments comparing the knock-out mutant with the wild-type. More than 160 genes were found differentially expressed in the knock-out mutant. Parts of these genes, important for biofilm formation and motility regulation, are known to belong also to the AmrZ transcriptional regulator regulon. Here, we show that ErsA binds in vitro and positively regulates amrZ mRNA at post-transcriptional level in vivo suggesting an interesting contribution of the ErsA-amrZ mRNA interaction in biofilm development at several regulatory levels.
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Affiliation(s)
- Marilena Falcone
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Helle K Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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Leistra AN, Amador P, Buvanendiran A, Moon-Walker A, Contreras LM. Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility. ACS Synth Biol 2017; 6:2228-2240. [PMID: 28796489 DOI: 10.1021/acssynbio.7b00185] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering. We then modularly recombine the selected substructures, differentially representing those of presumed high or low functional contribution, to build a library of 21 CsrB variants. Using fluorescent translational reporter assays, we demonstrate that the CsrB variants achieve a 5-fold gradient of control of well-characterized Csr network targets. Interestingly, results suggest that less conserved local structures within long, multisubstrate sRNAs may represent better targets for rational engineering than their well-conserved counterparts. Lastly, mapping the impact of sRNA variants on a signature Csr network phenotype indicates the potential of this approach for tuning the activity of global sRNA regulators in the context of metabolic engineering applications.
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Affiliation(s)
- Abigail N. Leistra
- McKetta
Department of Chemical Engineering, University of Texas at Austin, 200
E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Paul Amador
- Microbiology
Graduate Program, University of Texas at Austin, 100 E. 24th Street
Stop A6500, Austin, Texas 78712, United States
| | - Aishwarya Buvanendiran
- Biological
Sciences Program College of Natural Sciences, University of Texas at Austin, 120 Inner Campus Drive Stop G2500, Austin, Texas 78712, United States
| | - Alex Moon-Walker
- Biological
Sciences Program College of Natural Sciences, University of Texas at Austin, 120 Inner Campus Drive Stop G2500, Austin, Texas 78712, United States
| | - Lydia M. Contreras
- McKetta
Department of Chemical Engineering, University of Texas at Austin, 200
E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
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48
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Dynamics of translation can determine the spatial organization of membrane-bound proteins and their mRNA. Proc Natl Acad Sci U S A 2017; 114:13424-13429. [PMID: 29203677 PMCID: PMC5754755 DOI: 10.1073/pnas.1700941114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most macromolecules that are homogeneously distributed in the bacterial cell, mRNAs that encode inner-membrane proteins can be concentrated near the inner membrane. Cotranslational insertion of the nascent peptide into the membrane brings the translating ribosome and the mRNA close to the membrane. This suggests that kinetic properties of translation can determine the spatial organization of these mRNAs and proteins, which can be modulated through posttranscriptional regulation. Here we use a simple stochastic model of translation to characterize the effect of mRNA properties on the dynamics and statistics of its spatial distribution. We show that a combination of the rate of translation initiation, the availability of secretory apparatuses, and the composition of the coding region determines the abundance of mRNAs near the membrane, as well as their residence time. We propose that the spatiotemporal dynamics of mRNAs can give rise to protein clusters on the membrane and determine their size distribution.
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49
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Ghosh S, Dureja C, Khatri I, Subramanian S, Raychaudhuri S, Ghosh S. Identification of novel small RNAs in Burkholderia cenocepacia KC-01 expressed under iron limitation and oxidative stress conditions. MICROBIOLOGY-SGM 2017; 163:1924-1936. [PMID: 29099689 DOI: 10.1099/mic.0.000566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Small RNA (sRNA)-mediated regulation of gene expression is a major tool to understand bacterial responses to environmental changes. In particular, pathogenic bacteria employ sRNAs to adapt to the host environment and establish infection. Members of the Burkholderia cepacia complex, normally present in soil microbiota, cause nosocomial lung infection especially in hospitalized cystic fibrosis patients. We sequenced the draft genome of Burkholderia cenocepacia KC-01, isolated from the coastal saline soil, and identified several potential sRNAs in silico. Expression of seven small RNAs (Bc_KC_sr1-7) was subsequently confirmed. Two sRNAs (Bc_KC_sr1 and Bc_KC_sr2) were upregulated in response to iron depletion by 2,2'-bipyridyl and another two (Bc_KC_sr3 and Bc_KC_sr4) responded to the presence of 60 µM H2O2 in the culture media. Bc_Kc_sr5, 6 and 7 remained unchanged under these conditions. Expression of Bc_KC_sr2, 3 and 4 also altered with a change in temperature and incubation time. A search in the Rfam and BSRD databases identified Bc_Kc_sr4 as candidate738 in B. pseudomallei D286 and assigned Bc_Kc_sr5 and 6 as tmRNA and 6S RNA, respectively. The novel sRNAs were conserved in Burkholderiaceae but did not have any homologue in other genera. Bc_KC_sr1 and 4 were transcribed independently while the rest were part of the 3' UTR of their upstream genes. TargetRNA2 predicted that these sRNAs could target a host of cellular messages with very high stringency. Intriguingly, regions surrounding the translation initiation site for several enzymes involved in Fe-S cluster and siderophore biosynthesis, ROS homeostasis, porins, transcription and translation regulators, were among the suggested putative binding sites for these sRNAs.
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Affiliation(s)
- Suparna Ghosh
- Department of Microbiology, University of Calcutta, Kolkata 700 019, India
| | - Chetna Dureja
- CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Indu Khatri
- CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | | | | | - Sagarmoy Ghosh
- Department of Microbiology, University of Calcutta, Kolkata 700 019, India
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50
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Impact of bacterial sRNAs in stress responses. Biochem Soc Trans 2017; 45:1203-1212. [PMID: 29101308 PMCID: PMC5730939 DOI: 10.1042/bst20160363] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/11/2022]
Abstract
Bacterial life is harsh and involves numerous environmental and internal challenges that are perceived as stresses. Consequently, adequate responses to survive, cope with, and counteract stress conditions have evolved. In the last few decades, a class of small, non-coding RNAs (sRNAs) has been shown to be involved as key players in stress responses. This review will discuss — primarily from an enterobacterial perspective — selected stress response pathways that involve antisense-type sRNAs. These include themes of how bacteria deal with severe envelope stress, threats of DNA damage, problems with poisoning due to toxic sugar intermediates, issues of iron homeostasis, and nutrient limitation/starvation. The examples discussed highlight how stress relief can be achieved, and how sRNAs act mechanistically in regulatory circuits. For some cases, we will propose scenarios that may suggest why contributions from post-transcriptional control by sRNAs, rather than transcriptional control alone, appear to be a beneficial and universally selected feature.
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