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Schnoor SB, Neubauer P, Gimpel M. Recent insights into the world of dual-function bacterial sRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1824. [PMID: 38039556 DOI: 10.1002/wrna.1824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/03/2023]
Abstract
Dual-function sRNAs refer to a small subgroup of small regulatory RNAs that merges base-pairing properties of antisense RNAs with peptide-encoding properties of mRNA. Both functions can be part of either same or in another metabolic pathway. Here, we want to update the knowledge of to the already known dual-function sRNAs and review the six new sRNAs found since 2017 regarding their structure, functional mechanisms, evolutionary conservation, and role in the regulation of distinct biological/physiological processes. The increasing identification of dual-function sRNAs through bioinformatics approaches, RNomics and RNA-sequencing and the associated increase in regulatory understanding will likely continue to increase at the same rate in the future. This may improve our understanding of the physiology, virulence and resistance of bacteria, as well as enable their use in technical applications. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
| | - Peter Neubauer
- Department of Bioprocess Engineering, Technische Universitat Berlin, Berlin, Germany
| | - Matthias Gimpel
- Department of Bioprocess Engineering, Technische Universitat Berlin, Berlin, Germany
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2
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The emerging role of bacterial regulatory RNAs in disease. Trends Microbiol 2022; 30:959-972. [DOI: 10.1016/j.tim.2022.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 02/02/2023]
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3
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Venkat K, Hoyos M, Haycocks JR, Cassidy L, Engelmann B, Rolle-Kampczyk U, von Bergen M, Tholey A, Grainger DC, Papenfort K. A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. EMBO J 2021; 40:e108542. [PMID: 34612526 PMCID: PMC8672173 DOI: 10.15252/embj.2021108542] [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: 04/26/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are well known to modulate gene expression by base pairing with trans‐encoded transcripts and are typically non‐coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual‐function RNAs. In this study, we discovered a dual‐function RNA from Vibrio cholerae, called VcdRP, harboring a 29 amino acid small protein (VcdP), as well as a base‐pairing sequence. Using a forward genetic screen, we identified VcdRP as a repressor of cholera toxin production and link this phenotype to the inhibition of carbon transport by the base‐pairing segment of the regulator. By contrast, we demonstrate that the VcdP small protein acts downstream of carbon transport by binding to citrate synthase (GltA), the first enzyme of the citric acid cycle. Interaction of VcdP with GltA results in increased enzyme activity and together VcdR and VcdP reroute carbon metabolism. We further show that transcription of vcdRP is repressed by CRP allowing us to provide a model in which VcdRP employs two different molecular mechanisms to synchronize central metabolism in V. cholerae.
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Affiliation(s)
- Kavyaa Venkat
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mona Hoyos
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - James Rj Haycocks
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | | | | | | | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | - David C Grainger
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
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4
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Guérin C, Lee BH, Fradet B, van Dijk E, Mirauta B, Thermes C, Bernardet JF, Repoila F, Duchaud E, Nicolas P, Rochat T. Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen. ISME COMMUNICATIONS 2021; 1:33. [PMID: 36739365 PMCID: PMC9723704 DOI: 10.1038/s43705-021-00029-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum is a freshwater pathogen that infects salmonid fish worldwide, with critical environmental and economic impact. Here, we report an extensive transcriptome analysis that established the genome map of transcription start sites and transcribed regions, predicted alternative sigma factor regulons and regulatory RNAs, and documented gene expression profiles across 32 biological conditions mimicking the pathogen life cycle. The results link genes to environmental conditions and phenotypic traits and provide insights into gene regulation, highlighting similarities with better known bacteria and original characteristics linked to the phylogenetic position and the ecological niche of the bacterium. In particular, osmolarity appears as a signal for transition between free-living and within-host programs and expression patterns of secreted proteins shed light on probable virulence factors. Further investigations showed that a newly discovered sRNA widely conserved in the genus, Rfp18, is required for precise expression of proteases. By pointing proteins and regulatory elements probably involved in host-pathogen interactions, metabolic pathways, and molecular machineries, the results suggest many directions for future research; a website is made available to facilitate their use to fill knowledge gaps on flavobacteria.
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Affiliation(s)
- Cyprien Guérin
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Bo-Hyung Lee
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Benjamin Fradet
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Erwin van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Bogdan Mirauta
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | | | - Francis Repoila
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eric Duchaud
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France.
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
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5
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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6
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Yang G, Li B, Jia L, Qiu H, Yang M, Zhu B, Xie J, Qiu S, Li P, Ma H, Song H, Wang L. A Novel sRNA in Shigella flexneri That Regulates Tolerance and Virulence Under Hyperosmotic Pressure. Front Cell Infect Microbiol 2020; 10:483. [PMID: 33042862 PMCID: PMC7526569 DOI: 10.3389/fcimb.2020.00483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023] Open
Abstract
Regulation of the environmental stress response and virulence of Shigella flexneri may involve multiple signaling pathways; however, these mechanisms are not well-defined. In bacteria, small regulatory RNAs (sRNAs) regulate bacterial growth, metabolism, virulence, and environmental stress response. Therefore, identifying novel functional sRNAs in S. flexneri could help elucidate pathogenic adaptations to host micro-environmental stresses and associated virulence. The aim of this study was to confirm the presence of an sRNA, Ssr54, in S. flexneri and to determine its functions and possible mechanism of action. Ssr54 was found to regulate tolerance and virulence under hyperosmotic pressure. Its expression was verified by qRT-PCR and Northern blotting, and its genomic position was confirmed by 5'-rapid amplification of cDNA ends. Ssr54 expression was significantly decreased (~ 80%) under hyperosmotic conditions (680 mM NaCl), and the survival rate of the Ssr54 deletion strain increased by 20% under these conditions. This suggested that Ssr54 has been selected to promote host survival under hyperosmotic conditions. Additionally, virulence assessment, including guinea pig Sereny test and competitive invasion assays in mouse lungs, revealed that Ssr54 deletion significantly decreased S. flexneri virulence. Two-dimensional gel analyses suggest that Ssr54 may modulate the expression of tolC, ompA, and treF genes, which may affect the virulence and survival of S. flexneri under osmotic pressures. Furthermore, treF expression has been shown to improve the survival of S. flexneri under osmotic pressures. These results suggest that Ssr54 has a broad range of action in S. flexneri response to hyperosmotic environmental stresses and in controlling its virulence to adapt to environmental stresses encountered during host infection.
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Affiliation(s)
- Guang Yang
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
- The 5th Medical Center of General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Boan Li
- The 5th Medical Center of General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Leili Jia
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Huaiyu Qiu
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Mingjuan Yang
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | | | - Jing Xie
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Shaofu Qiu
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Peng Li
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Hui Ma
- The 6th Medical Center of General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Hongbin Song
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Ligui Wang
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
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Abstract
Here, we describe SR7, a dual-function antisense RNA encoded on the Bacillus subtilis chromosome. This RNA was earlier described as SigB-dependent regulatory RNA S1136 and reported to reduce the amount of the small ribosomal subunit under ethanol stress. We found that the 5ʹ portion of SR7 encodes a small protein composed of 39 amino acids which we designated SR7P. It is translated from a 185 nt SigB-dependent mRNA under five different stress conditions and a longer SigB-independent RNA constitutively. About three-fold higher amounts of SR7P were detected in B. subtilis cells exposed to salt, ethanol, acid or heat stress. Co-elution experiments with SR7PC-FLAG and Far-Western blotting demonstrated that SR7P interacts with the glycolytic enzyme enolase. Enolase is a scaffolding component of the B. subtilis degradosome where it interacts with RNase Y and phosphofructokinase PfkA. We found that SR7P increases the amount of RNase Y bound to enolase without affecting PfkA. RNA does not bridge the SR7P-enolase-RNase Y interaction. In vitro-degradation assays with the known RNase Y substrates yitJ and rpsO mRNA revealed enhanced enzymatic activity of enolase-bound RNase Y in the presence of SR7P. Northern blots showed a major effect of enolase and a minor effect of SR7P on the half-life of rpsO mRNA indicating a fine-tuning role of SR7P in RNA degradation.
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Affiliation(s)
- Inam Ul Haq
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
| | - Peter Müller
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
| | - Sabine Brantl
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
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8
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Diallo I, Provost P. RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions. Int J Mol Sci 2020; 21:E1627. [PMID: 32120885 PMCID: PMC7084465 DOI: 10.3390/ijms21051627] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
Proteins have long been considered to be the most prominent factors regulating so-called invasive genes involved in host-pathogen interactions. The possible role of small non-coding RNAs (sRNAs), either intracellular, secreted or packaged in outer membrane vesicles (OMVs), remained unclear until recently. The advent of high-throughput RNA-sequencing (RNA-seq) techniques has accelerated sRNA discovery. RNA-seq radically changed the paradigm on bacterial virulence and pathogenicity to the point that sRNAs are emerging as an important, distinct class of virulence factors in both gram-positive and gram-negative bacteria. The potential of OMVs, as protectors and carriers of these functional, gene regulatory sRNAs between cells, has also provided an additional layer of complexity to the dynamic host-pathogen relationship. Using a non-exhaustive approach and through examples, this review aims to discuss the involvement of sRNAs, either free or loaded in OMVs, in the mechanisms of virulence and pathogenicity during bacterial infection. We provide a brief overview of sRNA origin and importance, and describe the classical and more recent methods of identification that have enabled their discovery, with an emphasis on the theoretical lower limit of RNA sizes considered for RNA sequencing and bioinformatics analyses.
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Affiliation(s)
| | - Patrick Provost
- CHUQ Research Center/CHUL, Department of Microbiology-Infectious Disease and Immunity, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada;
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Wang J, Jiao H, Meng J, Qiao M, Du H, He M, Ming K, Liu J, Wang D, Wu Y. Baicalin Inhibits Biofilm Formation and the Quorum-Sensing System by Regulating the MsrA Drug Efflux Pump in Staphylococcus saprophyticus. Front Microbiol 2019; 10:2800. [PMID: 31921008 PMCID: PMC6915091 DOI: 10.3389/fmicb.2019.02800] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus saprophyticus (S. saprophyticus) is one of the main pathogens that cause serious infection due to its acquisition of antibiotic resistance. The efflux pump decreases antibiotic abundance, and biofilm compromises the penetration of antibiotics. It has been reported that baicalin is a potential agent to inhibit efflux pumps, biofilm formation, and quorum-sensing systems. The purpose of this study was to investigate whether baicalin can inhibit S. saprophyticus biofilm formation and the quorum-sensing system by inhibiting the MsrA efflux pump. First, the mechanism of baicalin inhibiting efflux was investigated by the ethidium bromide (EtBr) efflux assay, measurement of ATP content, and pyruvate kinase (PK) activities. These results revealed that baicalin significantly reduced the efflux of EtBr, the ATP content, and the activity of PK. Moreover, its role in biofilm formation and the agr system was studied by crystal violet staining, confocal laser scanning microscopy, scanning electron microscopy, and real-time polymerase chain reaction. These results showed that baicalin decreased biofilm formation, inhibited bacterial aggregation, and downregulated mRNA transcription levels of the quorum-sensing system regulators agrA, agrC, RNAIII, and sarA. Correlation analysis indicated that there was a strong positive correlation between the efflux pump and biofilm formation and the agr system. We demonstrate for the first time that baicalin inhibits biofilm formation and the agr quorum-sensing system by inhibiting the efflux pump in S. saprophyticus. Therefore, baicalin is a potential therapeutic agent for S. saprophyticus biofilm-associated infections.
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Affiliation(s)
- Jinli Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Haihong Jiao
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production & Construction Corps, College of Animal Science, Tarim University, Alar, China
| | - Jinwu Meng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mingyu Qiao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hongxu Du
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Miao He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ke Ming
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiaguo Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Deyun Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yi Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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10
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Luo J, Padhi P, Jin H, Anantharam V, Zenitsky G, Wang Q, Willette AA, Kanthasamy A, Kanthasamy AG. Utilization of the CRISPR-Cas9 Gene Editing System to Dissect Neuroinflammatory and Neuropharmacological Mechanisms in Parkinson's Disease. J Neuroimmune Pharmacol 2019; 14:595-607. [PMID: 30879240 PMCID: PMC6746615 DOI: 10.1007/s11481-019-09844-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
Chronic and debilitating neurodegenerative diseases, such as Parkinson's disease (PD), impose an immense medical, emotional, and economic burden on patients and society. Due to a complex interaction between genetic and environmental risk factors, the etiology of PD remains elusive. However, the cumulative evidence emerging from clinical and experimental research over the last several decades has identified mitochondrial dysfunction, oxidative stress, neuroinflammation, and dysregulated protein degradation as the main drivers of PD neurodegeneration. The genome-editing system CRISPR (clustered regularly interspaced short palindromic repeats) has recently transformed the field of biotechnology and biomedical discovery and is poised to accelerate neurodegenerative disease research. It has been leveraged to generate PD animal models, such as Parkin, DJ-1, and PINK1 triple knockout miniature pigs. CRISPR has also allowed the deeper understanding of various PD gene interactions, as well as the identification of novel apoptotic pathways associated with neurodegenerative processes in PD. Furthermore, its application has been used to dissect neuroinflammatory pathways involved in PD pathogenesis, such as the PKCδ signaling pathway, as well as the roles of novel compensatory or protective pathways, such as Prokineticin-2 signaling. This review aims to highlight the historical milestones in the evolution of this technology and attempts to illustrate its transformative potential in unraveling disease mechanisms as well as in the development of innovative treatment strategies for PD. Graphical Abstract.
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Affiliation(s)
- Jie Luo
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Piyush Padhi
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Huajun Jin
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Vellareddy Anantharam
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Gary Zenitsky
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Qian Wang
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA
| | - Auriel A Willette
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA
| | - Arthi Kanthasamy
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Anumantha G Kanthasamy
- Parkinson's Disorder Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA.
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11
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Rosinski-Chupin I, Sauvage E, Fouet A, Poyart C, Glaser P. Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes. BMC Genomics 2019; 20:236. [PMID: 30902048 PMCID: PMC6431027 DOI: 10.1186/s12864-019-5613-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background The human pathogen Streptococcus pyogenes, or group A Streptococcus, is responsible for mild infections to life-threatening diseases. To facilitate the characterization of regulatory networks involved in the adaptation of this pathogen to its different environments and their evolution, we have determined the primary transcriptome of a serotype M1 S. pyogenes strain at single-nucleotide resolution and compared it with that of Streptococcus agalactiae, also from the pyogenic group of streptococci. Results By using a combination of differential RNA-sequencing and oriented RNA-sequencing we have identified 892 transcription start sites (TSS) and 885 promoters in the S. pyogenes M1 strain S119. 8.6% of S. pyogenes mRNAs were leaderless, among which 81% were also classified as leaderless in S. agalactiae. 26% of S. pyogenes transcript 5′ untranslated regions (UTRs) were longer than 60 nt. Conservation of long 5′ UTRs with S. agalactiae allowed us to predict new potential regulatory sequences. In addition, based on the mapping of 643 transcript ends in the S. pyogenes strain S119, we constructed an operon map of 401 monocistrons and 349 operons covering 81.5% of the genome. One hundred fifty-six operons and 254 monocistrons retained the same organization, despite multiple genomic reorganizations between S. pyogenes and S. agalactiae. Genomic reorganization was found to more often go along with variable promoter sequences and 5′ UTR lengths. Finally, we identified 117 putative regulatory RNAs, among which nine were regulated in response to magnesium concentration. Conclusions Our data provide insights into transcriptome evolution in pyogenic streptococci and will facilitate the analysis of genetic polymorphisms identified by comparative genomics in S. pyogenes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5613-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isabelle Rosinski-Chupin
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France.
| | - Elisabeth Sauvage
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
| | - Agnès Fouet
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Claire Poyart
- INSERM U1016, Institut Cochin, CNRS UMR 8104, Université Paris Descartes (UMR-S1016), Paris, France.,Centre Nationale de Référence des Streptocoques, Hôpitaux Universitaires Paris Centre, Cochin, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Resistance to Antibiotics, Institut Pasteur-APHP-Université Paris Saclay, UMR3525 CNRS, Paris, France
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12
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Raina M, King A, Bianco C, Vanderpool CK. Dual-Function RNAs. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0032-2018. [PMID: 30191807 PMCID: PMC6130917 DOI: 10.1128/microbiolspec.rwr-0032-2018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Indexed: 12/30/2022] Open
Abstract
Bacteria are known to use RNA, either as mRNAs encoding proteins or as noncoding small RNAs (sRNAs), to regulate numerous biological processes. However, a few sRNAs have two functions: they act as base-pairing RNAs and encode a small protein with additional regulatory functions. Thus, these so called "dual-function" sRNAs can serve as both a riboregulator and an mRNA. In some cases, these two functions can act independently within the same pathway, while in other cases, the base-pairing function and protein function act in different pathways. Here, we discuss the five known dual-function sRNAs-SgrS from enteric species, RNAIII and Psm-mec from Staphylococcus aureus, Pel RNA from Streptococcus pyogenes, and SR1 from Bacillus subtilis-and review their mechanisms of action and roles in regulating diverse biological processes. We also discuss the prospect of finding additional dual-function sRNAs and future challenges in studying the overlap and competition between the functions.
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Affiliation(s)
- Medha Raina
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892
| | - Alisa King
- Department of Microbiology, University of Illinois, Urbana, IL 61801
| | - Colleen Bianco
- Department of Microbiology, University of Illinois, Urbana, IL 61801
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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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Pappesch R, Warnke P, Mikkat S, Normann J, Wisniewska-Kucper A, Huschka F, Wittmann M, Khani A, Schwengers O, Oehmcke-Hecht S, Hain T, Kreikemeyer B, Patenge N. The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes. Sci Rep 2017; 7:12241. [PMID: 28947755 PMCID: PMC5613026 DOI: 10.1038/s41598-017-12507-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/12/2017] [Indexed: 11/16/2022] Open
Abstract
Small regulatory RNAs (sRNAs) play a role in the control of bacterial virulence gene expression. In this study, we investigated an sRNA that was identified in Streptococcus pyogenes (group A Streptococcus, GAS) but is conserved throughout various streptococci. In a deletion strain, expression of mga, the gene encoding the multiple virulence gene regulator, was reduced. Accordingly, transcript and proteome analyses revealed decreased expression of several Mga-activated genes. Therefore, and because the sRNA was shown to interact with the 5′ UTR of the mga transcript in a gel-shift assay, we designated it MarS for mga-activating regulatory sRNA. Down-regulation of important virulence factors, including the antiphagocytic M-protein, led to increased susceptibility of the deletion strain to phagocytosis and reduced adherence to human keratinocytes. In a mouse infection model, the marS deletion mutant showed reduced dissemination to the liver, kidney, and spleen. Additionally, deletion of marS led to increased tolerance towards oxidative stress. Our in vitro and in vivo results indicate a modulating effect of MarS on virulence gene expression and on the pathogenic potential of GAS.
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Affiliation(s)
- Roberto Pappesch
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Philipp Warnke
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, University Medicine Rostock, Rostock, Germany
| | - Jana Normann
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | | | - Franziska Huschka
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany.,Franziska Huschka, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Wittmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Afsaneh Khani
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Oliver Schwengers
- Institute for Medical Microbiology, Justus-Liebig University of Giessen, Giessen, Germany.,Institute for Medical Microbiology, Justus-Liebig University of Giessen, Giessen, Germany
| | - Sonja Oehmcke-Hecht
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Torsten Hain
- Institute for Medical Microbiology, Justus-Liebig University of Giessen, Giessen, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany.
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Gimpel M, Maiwald C, Wiedemann C, Görlach M, Brantl S. Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis. MICROBIOLOGY-SGM 2017; 163:1248-1259. [PMID: 28818119 DOI: 10.1099/mic.0.000505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Small regulatory RNAs (sRNAs) are the most prominent post-transcriptional regulators in all kingdoms of life. A few of them, e.g. SR1 from Bacillus subtilis, are dual-function sRNAs. SR1 acts as a base-pairing sRNA in arginine catabolism and as an mRNA encoding the small peptide SR1P in RNA degradation. Both functions of SR1 are highly conserved among 23 species of Bacillales. Here, we investigate the interaction between SR1P and GapA by a combination of in vivo and in vitro methods. De novo prediction of the structure of SR1P yielded five models, one of which was consistent with experimental circular dichroism spectroscopy data of a purified, synthetic peptide. Based on this model structure and a comparison between the 23 SR1P homologues, a series of SR1P mutants was constructed and analysed by Northern blotting and co-elution experiments. The known crystal structure of Geobacillus stearothermophilus GapA was used to model SR1P onto this structure. The hypothetical SR1P binding pocket, composed of two α-helices at both termini of GapA, was investigated by constructing and assaying a number of GapA mutants in the presence and absence of wild-type or mutated SR1P. Almost all residues of SR1P located in the two highly conserved motifs are implicated in the interaction with GapA. A critical lysine residue (K332) in the C-terminal α-helix 14 of GapA corroborated the predicted binding pocket.
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Affiliation(s)
- Matthias Gimpel
- Struktureinheit Genetik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.,Present address: Institut für Biotechnologie, Fachgebiet Bioverfahrenstechnik, TU Berlin, Ackerstraße 76, D-13355 Berlin, Germany
| | - Caroline Maiwald
- Struktureinheit Genetik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.,Present address: Achtrutenberg 50, D-13125 Berlin, Germany
| | - Christoph Wiedemann
- Head of Core and Core Service Protein Production, Leibniz Institute on Aging - Fritz Lipman Institute, Beutenbergstr. 11, D-07745 Jena, Germany.,Present address: Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany
| | - Matthias Görlach
- Head of Core and Core Service Protein Production, Leibniz Institute on Aging - Fritz Lipman Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Sabine Brantl
- Struktureinheit Genetik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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Lu W, Xin Z, Shida W, Jiyao L, Xin X. [Role of small noncoding RNA in the regulation of bacterial virulence]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2017; 34:433-438. [PMID: 28317367 DOI: 10.7518/hxkq.2016.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the long-term interaction between pathogens and host, the pathogens regulate the expression of related viru-lence genes to fit the host environment in response to the changes in the host microenvironment. Gene expression was believed to be controlled mainly at the level of transcription initiation by repressors or activators. Recent studies have revealed that small noncoding RNAs (sRNAs) are key regulators in bacterial pathogenesis. sRNA in bacteria is a noncoding RNA with length ranging from 50 to 500 nucleotides. Pathogens can sense the changes in the host environment and consequently regulate the expression of virulence genes by sRNAs. This condition promotes the ability of pathogens to survive within the host, which is beneficial to the invasion and pathogenicity of pathogens. In contrast to transcriptional factors, sRNA-mediated gene regu-lation makes rapid and sensitive responses to environmental cues. Many sRNAs involved in bacterial virulence and pathogenesis have been identified. These sRNAs are key components of coordinated regulation networks, playing important roles in regulating the expression of virulence genes at post-transcriptional level. This review aims to provide an overview on the molecular mechanisms and roles of sRNAs in the regulation of bacterial virulence.
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Affiliation(s)
- Wang Lu
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zheng Xin
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Wang Shida
- State Key Laboratory of Oral Diseases, Dept. of General Clinic, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Li Jiyao
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xu Xin
- State Key Laboratory of Oral Diseases, Dept. of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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17
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Zorgani MA, Camiade E, Quentin R, Lartigue MF. Editorial: Small Non-coding RNAs in Streptococci. Front Genet 2016; 7:192. [PMID: 27853466 PMCID: PMC5089985 DOI: 10.3389/fgene.2016.00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohamed A Zorgani
- ISP, Institut National De La Recherche Agronomique, Université Tours, Equipe Bactéries et Risque Materno-Foetal, UMR 1282 Tours, France
| | - Emilie Camiade
- ISP, Institut National De La Recherche Agronomique, Université Tours, Equipe Bactéries et Risque Materno-Foetal, UMR 1282 Tours, France
| | - Roland Quentin
- ISP, Institut National De La Recherche Agronomique, Université Tours, Equipe Bactéries et Risque Materno-Foetal, UMR 1282Tours, France; Centre Hospitalier Régional Universitaire de Tours, Service de Bactériologie Virologie et Hygiène HospitalièreTours, France
| | - Marie-Frédérique Lartigue
- ISP, Institut National De La Recherche Agronomique, Université Tours, Equipe Bactéries et Risque Materno-Foetal, UMR 1282Tours, France; Centre Hospitalier Régional Universitaire de Tours, Service de Bactériologie Virologie et Hygiène HospitalièreTours, France
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18
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Gimpel M, Brantl S. Dual-function small regulatory RNAs in bacteria. Mol Microbiol 2016; 103:387-397. [PMID: 27750368 DOI: 10.1111/mmi.13558] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022]
Abstract
Dual-function sRNAs are a subgroup of small regulatory RNAs that act on the one hand as base-pairing sRNAs to inhibit or activate target gene expression and on the other hand as peptide-encoding mRNAs that function either in the same or in another metabolic pathway. Here, we review and compare the five currently known and intensively characterized dual-function sRNAs with regard to their two functions, their biological role, their evolutionary conservation and their requirements for RNA chaperones. Furthermore, we summarize the data available on five potential dual-function sRNAs, whose base-pairing function is well established whereas the role of their encoded peptides has not yet been elucidated. In addition, we provide three examples for RNAs with more than one function that do not fall into the above-mentioned category. With the application of RNAseq, peptidomics and transcriptomics it can be expected that the number of dual-function sRNAs will considerably increase within the next years, thus enhancing our knowledge on the regulatory potential of these RNAs.
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Affiliation(s)
- Matthias Gimpel
- Biologisch-Pharmazeutische Fakultät, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, AG Bakteriengenetik, Philosophenweg 12, Jena, D-07743, Germany
| | - Sabine Brantl
- Biologisch-Pharmazeutische Fakultät, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, AG Bakteriengenetik, Philosophenweg 12, Jena, D-07743, Germany
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19
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Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E. RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. RNA Biol 2016; 13:177-95. [PMID: 26580233 PMCID: PMC4829319 DOI: 10.1080/15476286.2015.1110674] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
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Affiliation(s)
- Anaïs Le Rhun
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Yan Yan Beer
- b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany
| | - Johan Reimegård
- c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden
| | - Krzysztof Chylinski
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria
| | - Emmanuelle Charpentier
- a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.,b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.,e Hannover Medical School (MHH), D-30625 , Hannover , Germany.,f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany
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Azhikina TL, Ignatov DV, Salina EG, Fursov MV, Kaprelyants AS. Role of Small Noncoding RNAs in Bacterial Metabolism. BIOCHEMISTRY (MOSCOW) 2016; 80:1633-46. [PMID: 26878570 DOI: 10.1134/s0006297915130015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of prokaryotic small RNAs is one of the most important directions in modern molecular biology. In the last decade, multiple short regulatory transcripts have been found in prokaryotes, and for some of them functional roles have been elucidated. Bacterial small RNAs are implicated in the regulation of transcription and translation, and they affect mRNA stability and gene expression via different mechanisms, including changes in mRNA conformation and interaction with proteins. Most small RNAs are expressed in response to external factors, and they help bacteria to adapt to changing environmental conditions. Bacterial infections of various origins remain a serious medical problem, despite significant progress in fighting them. Discovery of mechanisms that bacteria employ to survive in infected organisms and ways to block these mechanisms is promising for finding new treatments for bacterial infections. Regulation of pathogenesis with small RNAs is an attractive example of such mechanisms. This review considers the role of bacterial small RNAs in adaptation to stress conditions. We pay special attention to the role of small RNAs in Mycobacterium tuberculosis infection, in particular during establishment and maintenance of latent infection.
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Affiliation(s)
- T L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Gimpel M, Brantl S. Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biol 2016; 13:916-26. [PMID: 27449348 PMCID: PMC5013986 DOI: 10.1080/15476286.2016.1208894] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
SR1 is a dual-function sRNA from B. subtilis that acts as a base-pairing regulatory RNA and as a peptide-encoding mRNA. Both functions of SR1 are highly conserved. Previously, we uncovered that the SR1 encoded peptide SR1P binds the glycolytic enzyme GapA resulting in stabilization of gapA mRNA. Here, we demonstrate that GapA interacts with RNases Y and J1, and this interaction was RNA-independent. About 1% of GapA molecules purified from B. subtilis carry RNase J1 and about 2% RNase Y. In contrast to the GapA/RNase Y interaction, the GapA/RNaseJ1 interaction was stronger in the presence of SR1P. GapA/SR1P-J1/Y displayed in vitro RNase activity on known RNase J1 substrates. Moreover, the RNase J1 substrate SR5 has altered half-lives in a ΔgapA strain and a Δsr1 strain, suggesting in vivo functions of the GapA/SR1P/J1 interaction. Our results demonstrate that the metabolic enzyme GapA moonlights in recruiting RNases while GapA bound SR1P promotes binding of RNase J1 and enhances its activity.
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Affiliation(s)
- Matthias Gimpel
- a AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena , Philosophenweg , Jena , Germany
| | - Sabine Brantl
- a AG Bakteriengenetik, Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena , Philosophenweg , Jena , Germany
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Spontaneous mutations in Streptococcus pyogenes isolates from streptococcal toxic shock syndrome patients play roles in virulence. Sci Rep 2016; 6:28761. [PMID: 27349341 PMCID: PMC4923885 DOI: 10.1038/srep28761] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/07/2016] [Indexed: 11/08/2022] Open
Abstract
Streptococcus pyogenes (group A Streptococcus; GAS) is a widespread human pathogen and causes streptococcal toxic shock syndrome (STSS). STSS isolates have been previously shown to have high frequency mutations in the csrS/csrR (covS/covR) and/or rgg (ropB) genes, which are negative regulators of virulence. However, these mutations were found at somewhat low frequencies in emm1-genotyped isolates, the most prevalent STSS genotype. In this study, we sought to detect causal mutations of enhanced virulence in emm1 isolates lacking mutation(s) in the csrS/csrR and rgg genes. Three mutations associated with elevated virulence were found in the sic (a virulence gene) promoter, the csrR promoter, and the rocA gene (a csrR positive regulator). In vivo contribution of the sic promoter and rocA mutations to pathogenicity and lethality was confirmed in a GAS mouse model. Frequency of the sic promoter mutation was significantly higher in STSS emm1 isolates than in non-invasive STSS isolates; the rocA gene mutation frequency was not significantly different among STSS and non-STSS isolates. STSS emm1 isolates possessed a high frequency mutation in the sic promoter. Thus, this mutation may play a role in the dynamics of virulence and STSS pathogenesis.
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The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier's life. Nature 2016; 532:432-4. [PMID: 27121823 DOI: 10.1038/532432a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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The Mechanisms of Virulence Regulation by Small Noncoding RNAs in Low GC Gram-Positive Pathogens. Int J Mol Sci 2015; 16:29797-814. [PMID: 26694351 PMCID: PMC4691137 DOI: 10.3390/ijms161226194] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/01/2015] [Accepted: 12/04/2015] [Indexed: 11/30/2022] Open
Abstract
The discovery of small noncoding regulatory RNAs (sRNAs) in bacteria has grown tremendously recently, giving new insights into gene regulation. The implementation of computational analysis and RNA sequencing has provided new tools to discover and analyze potential sRNAs. Small regulatory RNAs that act by base-pairing to target mRNAs have been found to be ubiquitous and are the most abundant class of post-transcriptional regulators in bacteria. The majority of sRNA studies has been limited to E. coli and other gram-negative bacteria. However, examples of sRNAs in gram-positive bacteria are still plentiful although the detailed gene regulation mechanisms behind them are not as well understood. Strict virulence control is critical for a pathogen’s survival and many sRNAs have been found to be involved in that process. This review outlines the targets and currently known mechanisms of trans-acting sRNAs involved in virulence regulation in various gram-positive pathogens. In addition, their shared characteristics such as CU interaction motifs, the role of Hfq, and involvement in two-component regulators, riboswitches, quorum sensing, or toxin/antitoxin systems are described.
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The Mga Regulon but Not Deoxyribonuclease Sda1 of Invasive M1T1 Group A Streptococcus Contributes to In Vivo Selection of CovRS Mutations and Resistance to Innate Immune Killing Mechanisms. Infect Immun 2015; 83:4293-303. [PMID: 26283338 DOI: 10.1128/iai.00857-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 11/20/2022] Open
Abstract
Invasive M1T1 group A Streptococcus (GAS) can have a mutation in the regulatory system CovRS, and this mutation can render strains hypervirulent. Interestingly, via mechanisms that are not well understood, the host innate immune system's neutrophils select spontaneous M1T1 GAS CovRS hypervirulent mutants, thereby enhancing the pathogen's ability to evade immune killing. It has been reported that the DNase Sda1 is critical for the resistance of M1T1 strain 5448 to killing in human blood and provides pressure for in vivo selection of CovRS mutations. We reexamined the role of Sda1 in the selection of CovRS mutations and in GAS innate immune evasion. Deletion of sda1 or all DNase genes in M1T1 strain MGAS2221 did not alter emergence of CovRS mutants during murine infection. Deletion of sda1 in strain 5448 resulted in Δsda1 mutants with (5448 Δsda1(M+) strain) and without (5448 Δsda1(M-) strain) M protein production. The 5448 Δsda1(M+) strain accumulated CovRS mutations in vivo and resisted killing in the bloodstream, whereas the 5448 Δsda1(M-) strain lost in vivo selection of CovRS mutations and was sensitive to killing. The deletion of emm and a spontaneous Mga mutation in MGAS2221 reduced and prevented in vivo selection for CovRS mutants, respectively. Thus, in contrast to previous reports, Sda1 is not critical for in vivo selection of invasive M1T1 CovRS mutants and GAS resistance to innate immune killing mechanisms. In contrast, M protein and other Mga-regulated proteins contribute to the in vivo selection of M1T1 GAS CovRS mutants. These findings advance the understanding of the progression of invasive M1T1 GAS infections.
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Patenge N, Pappesch R, Khani A, Kreikemeyer B. Genome-wide analyses of small non-coding RNAs in streptococci. Front Genet 2015; 6:189. [PMID: 26042151 PMCID: PMC4438229 DOI: 10.3389/fgene.2015.00189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
Streptococci represent a diverse group of Gram-positive bacteria, which colonize a wide range of hosts among animals and humans. Streptococcal species occur as commensal as well as pathogenic organisms. Many of the pathogenic species can cause severe, invasive infections in their hosts leading to a high morbidity and mortality. The consequence is a tremendous suffering on the part of men and livestock besides the significant financial burden in the agricultural and healthcare sectors. An environmentally stimulated and tightly controlled expression of virulence factor genes is of fundamental importance for streptococcal pathogenicity. Bacterial small non-coding RNAs (sRNAs) modulate the expression of genes involved in stress response, sugar metabolism, surface composition, and other properties that are related to bacterial virulence. Even though the regulatory character is shared by this class of RNAs, variation on the molecular level results in a high diversity of functional mechanisms. The knowledge about the role of sRNAs in streptococci is still limited, but in recent years, genome-wide screens for sRNAs have been conducted in an increasing number of species. Bioinformatics prediction approaches have been employed as well as expression analyses by classical array techniques or next generation sequencing. This review will give an overview of whole genome screens for sRNAs in streptococci with a focus on describing the different methods and comparing their outcome considering sRNA conservation among species, functional similarities, and relevance for streptococcal infection.
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Affiliation(s)
- Nadja Patenge
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Roberto Pappesch
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Afsaneh Khani
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, Hygiene and Bacteriology, Rostock University Medical Center Rostock, Germany
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Liu N, Niu G, Xie Z, Chen Z, Itzek A, Kreth J, Gillaspy A, Zeng L, Burne R, Qi F, Merritt J. The Streptococcus mutans irvA gene encodes a trans-acting riboregulatory mRNA. Mol Cell 2015; 57:179-90. [PMID: 25574948 DOI: 10.1016/j.molcel.2014.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/12/2014] [Accepted: 11/04/2014] [Indexed: 02/08/2023]
Abstract
In both prokaryotes and eukaryotes, insight into gene function is typically obtained by in silico homology searches and/or phenotypic analyses of strains bearing mutations within open reading frames. However, the studies herein illustrate how mRNA function is not limited to the expression of a cognate protein. We demonstrate that a stress-induced protein-encoding mRNA (irvA) from the dental caries pathogen Streptococcus mutans directly modulates target mRNA (gbpC) stability through seed pairing interactions. The 5' untranslated region of irvA mRNA is a trans riboregulator of gbpC and a critical activator of the DDAG stress response, whereas IrvA functions independently in the regulation of natural competence. The irvA riboregulatory domain controls GbpC production by forming irvA-gbpC hybrid mRNA duplexes that prevent gbpC degradation by an RNase J2-mediated pathway. These studies implicate a potentially ubiquitous role for typical protein-encoding mRNAs as riboregulators, which could alter current concepts in gene regulation.
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Affiliation(s)
- Nan Liu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Guoqing Niu
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhoujie Xie
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Zhiyun Chen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Andreas Itzek
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Jens Kreth
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Allison Gillaspy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA
| | - Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert Burne
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
| | - Fengxia Qi
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Justin Merritt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 71304, USA; Division of Oral Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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Kreth J, Liu N, Chen Z, Merritt J. RNA regulators of host immunity and pathogen adaptive responses in the oral cavity. Microbes Infect 2015; 17:493-504. [PMID: 25790757 DOI: 10.1016/j.micinf.2015.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 12/15/2022]
Abstract
The recent explosion of RNA-seq studies has resulted in a newfound appreciation for the importance of riboregulatory RNAs in the posttranscriptional control of eukaryotic and prokaryotic genetic networks. The current review will explore the role of trans-riboregulatory RNAs in various adaptive responses of host and pathogen in the oral cavity.
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Affiliation(s)
- Jens Kreth
- OUHSC Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA; OUHSC College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Nan Liu
- Department of Restorative Dentistry, Oregon Health and Science University, 2730 SW Moody Ave., Portland, OR, 97201-5042, USA
| | - Zhiyun Chen
- OUHSC Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science University, 2730 SW Moody Ave., Portland, OR, 97201-5042, USA.
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Brantl S. Antisense-RNA mediated control of plasmid replication - pIP501 revisited. Plasmid 2014; 78:4-16. [PMID: 25108234 DOI: 10.1016/j.plasmid.2014.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/24/2014] [Accepted: 07/26/2014] [Indexed: 02/02/2023]
Abstract
Over the past decade, a wealth of small noncoding RNAs (sRNAs) have been discovered in the genomes of almost all bacterial species, where they constitute the most abundant class of posttranscriptional regulators. These sRNAs are key-players in prokaryotic metabolism, stress response and virulence. However, the first bona-fide antisense RNAs had been found already in 1981 in plasmids, where they regulate replication or maintenance. Antisense RNAs involved in plasmid replication control - meanwhile investigated in depth for almost 35 years - employ a variety of mechanisms of action: They regulate primer maturation, inhibit translation of essential replication initiator proteins (Rep proteins) as well as leader peptides or the formation of activator pseudoknots required for efficient rep translation. Alternatively they attenuate transcription or translation of rep mRNAs. Some antisense RNAs collaborate with transcriptional repressors to ensure proper copy-number control. Here, I summarize our knowledge on replication control of the broad-host range plasmid pIP501 that was originally isolated from Streptococcus agalactiae. Plasmid pIP501 uses two copy number-control elements, RNAIII, a cis-encoded antisense RNA, and transcriptional repressor CopR. RNA III mediates transcription attenuation, a rather widespread concept that found its culmination in the recent discovery of riboswitches. A peculiarity of pIP501 is the unusual stability of RNA III, which requires a second function of CopR: CopR does not only repress transcription from the essential repR promoter, but also prevents convergent transcription between rep mRNA and RNAIII, thereby indirectly increasing the amount of RNAIII. The concerted action of these two control elements is necessary to prevent plasmid loss at dangerously low copy numbers.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
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Involvement of Enterococcus faecalis small RNAs in stress response and virulence. Infect Immun 2014; 82:3599-611. [PMID: 24914223 DOI: 10.1128/iai.01900-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Candidate small RNAs (sRNAs) have recently been identified in Enterococcus faecalis, a Gram-positive opportunistic pathogen, and six of these candidate sRNAs with unknown functions were selected for a functional study. Deletion mutants and complemented strains were constructed, and their virulence was tested. We were unable to obtain the ef0869-0870 mutant, likely due to an essential role, and the ef0820-0821 sRNA seemed not to be involved in virulence. In contrast, the mutant lacking ef0408-0409 sRNA, homologous to the RNAII component of the toxin-antitoxin system, appeared more virulent and more able to colonize mouse organs. The three other mutants showed reduced virulence. In addition, we checked the responses of these mutant strains to several stresses encountered in the gastrointestinal tract or during the infection process. In parallel, the activities of the sRNA promoters were measured using transcriptional fusion constructions. To attempt to identify the regulons of these candidate sRNAs, proteomics profiles of the mutant strains were compared with that of the wild type. This showed that the selected sRNAs controlled the expression of proteins involved in diverse cellular processes and the stress response. The combined data highlight the roles of certain candidate sRNAs in the adaptation of E. faecalis to environmental changes and in the complex transition process from a commensal to a pathogen.
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Fischer A, Kambara K, Meyer H, Stenz L, Bonetti EJ, Girard M, Lalk M, Francois P, Schrenzel J. GdpS contributes to Staphylococcus aureus biofilm formation by regulation of eDNA release. Int J Med Microbiol 2014; 304:284-99. [DOI: 10.1016/j.ijmm.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/25/2013] [Accepted: 10/27/2013] [Indexed: 11/30/2022] Open
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Michaux C, Verneuil N, Hartke A, Giard JC. Physiological roles of small RNA molecules. MICROBIOLOGY-SGM 2014; 160:1007-1019. [PMID: 24694375 DOI: 10.1099/mic.0.076208-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Unlike proteins, RNA molecules have emerged lately as key players in regulation in bacteria. Most reviews hitherto focused on the experimental and/or in silico methods used to identify genes encoding small RNAs (sRNAs) or on the diverse mechanisms of these RNA regulators to modulate expression of their targets. However, less is known about their biological functions and their implications in various physiological responses. This review aims to compile what is known presently about the diverse roles of sRNA transcripts in the regulation of metabolic processes, in different growth conditions, in adaptation to stress and in microbial pathogenesis. Several recent studies revealed that sRNA molecules are implicated in carbon metabolism and transport, amino acid metabolism or metal sensing. Moreover, regulatory RNAs participate in cellular adaptation to environmental changes, e.g. through quorum sensing systems or development of biofilms, and analyses of several sRNAs under various physiological stresses and culture conditions have already been performed. In addition, recent experiments performed with Gram-positive and Gram-negative pathogens showed that regulatory RNAs play important roles in microbial virulence and during infection. The combined results show the diversity of regulation mechanisms and physiological processes in which sRNA molecules are key actors.
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Affiliation(s)
- Charlotte Michaux
- Unité de Recherche Risques Microbiens (U2RM), Equipe Stress Virulence, Université de Caen, 14032 Caen, France
| | - Nicolas Verneuil
- Unité de Recherche Risques Microbiens (U2RM), Equipe Stress Virulence, Université de Caen, 14032 Caen, France
| | - Axel Hartke
- Unité de Recherche Risques Microbiens (U2RM), Equipe Stress Virulence, Université de Caen, 14032 Caen, France
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Abstract
Small regulatory RNAs (sRNAs) that act by base-pairing were first discovered in so-called accessory DNA elements—plasmids, phages, and transposons—where they control replication, maintenance, and transposition. Since 2001, a huge body of work has been performed to predict and identify sRNAs in a multitude of bacterial genomes. The majority of chromosome-encoded sRNAs have been investigated in E. coli and other Gram-negative bacteria. However, during the past five years an increasing number of sRNAs were found in Gram-positive bacteria. Here, we outline our current knowledge on chromosome-encoded sRNAs from low-GC Gram-positive species that act by base-pairing, i.e., an antisense mechanism. We will focus on sRNAs with known targets and defined regulatory mechanisms with special emphasis on Bacillus subtilis.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena; Biologisch-Pharmazeutische Fakultät; AG Bakteriengenetik; Philosophenweg 12; Jena, Germany
| | - Reinhold Brückner
- Mikrobiologie; TU Kaiserslautern; Paul-Ehrlich-Str. 23; D-67663 Kaiserslautern, Germany
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36
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Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lécrivain AL, Bzdrenga J, Koonin EV, Charpentier E. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 2013; 42:2577-90. [PMID: 24270795 PMCID: PMC3936727 DOI: 10.1093/nar/gkt1074] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool.
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Affiliation(s)
- Ines Fonfara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå S-90187, Sweden, Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig D-38124, Germany, Deptartment of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna A-1030, Austria, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and Hannover Medical School, Hannover D-30625, Germany
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Zhou Y, Hanks TS, Feng W, Li J, Liu G, Liu M, Lei B. The sagA/pel locus does not regulate the expression of the M protein of the M1T1 lineage of group A Streptococcus. Virulence 2013; 4:698-706. [PMID: 24121654 DOI: 10.4161/viru.26413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Altered expression of Group A Streptococcus (GAS) virulence factors, including the M protein, can result as a consequence of spontaneous genetic changes that occur during laboratory and animal passage. Occurrence of such secondary mutations during targeted gene deletion could confound the interpretation of effects attributable to the function of the gene being investigated. Contradicting reports on whether the sagA/pel locus regulates the M protein-encoding emm might be due to inconsistent occurrence of mutations unrelated with sagA. This study examined the possibility that altered emm expression observed in association with sagA/pel deletion mutants is artifactual. sagA deletion mutants (MGAS2221ΔsagA) of M1T1 isolate MGAS2221 obtained using liquid broth for GAS growth during the deletion process had diminished emm transcription and no detectable M protein production. In contrast, a ΔsagA mutant of another closely genetically related M1T1 isolate had normal emm expression. The sagB gene does not regulate emm; however, one of three MGAS2221ΔsagB mutants had diminished emm expression. The emm regulator mga was downregulated in these M protein expression-negative strains. These results argue that sagA deletion does not directly cause the downregulation of emm expression. Indeed, two MGAS2221ΔsagA mutants obtained using agar plates for GAS growth during the deletion process both had normal emm expression. We conclude that the sagA/pel locus does not regulate emm expression in the M1T1 lineage and provide a protocol for targeted gene deletion that we find less prone to the generation of mutants exhibiting downregulation in emm expression.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Agricultural Microbiology; College of Veterinary Medicine; Huazhong Agricultural University; Wuhan, P.R. China; Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Tracey S Hanks
- Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Wenchao Feng
- Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology; College of Veterinary Medicine; Huazhong Agricultural University; Wuhan, P.R. China; Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Guanghui Liu
- Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Mengyao Liu
- Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
| | - Benfang Lei
- Department of Immunology and Infectious Diseases; Montana State University; Bozeman, MT USA
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Abstract
Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in computational prediction, we employed a combination of three different computational algorithms (sRNAPredict, eQRNA and RNAz). A total of 45 candidates were chosen based on the computational analysis, and their transcription was analyzed by reverse-transcriptase PCR and Northern blot. Through this process, we discovered 7 putative novel trans-acting sRNAs. Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals. Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis. This study provides a significant resource for future study of small RNAs and their roles in physiology and pathogenesis of S. pyogenes.
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Park SH, Butcher BG, Anderson Z, Pellegrini N, Bao Z, D’Amico K, Filiatrault MJ. Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. MICROBIOLOGY-SGM 2012; 159:296-306. [PMID: 23258266 PMCID: PMC3709562 DOI: 10.1099/mic.0.063826-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacteria contain small non-coding RNAs (ncRNAs) that are responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae pv. tomato DC3000, P16, was investigated. We determined that RpoS regulates the expression of P16. We found that deletion of P16 results in increased sensitivity to hydrogen peroxide compared to the wild-type strain, suggesting that P16 plays a role in the bacteria’s susceptibility to oxidative stress. Additionally the P16 mutant displayed enhanced resistance to heat stress. Our findings provide new information on the regulation and role of this ncRNA in P. syringae.
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Affiliation(s)
- So Hae Park
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bronwyn G. Butcher
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zoe Anderson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nola Pellegrini
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Katherine D’Amico
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Melanie J. Filiatrault
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
- Plant–Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
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Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J, Boisguérin V, Hartsch T, Hain T, Kreikemeyer B. Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays. BMC Genomics 2012; 13:550. [PMID: 23062031 PMCID: PMC3542284 DOI: 10.1186/1471-2164-13-550] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/10/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria to identify sRNA regulators. Many sRNAs are well characterized, including their target mRNAs and mode of action. In comparison, little is known about sRNAs in Gram-positive pathogens. In this study, we identified novel sRNAs in the exclusively human pathogen Streptococcus pyogenes M49 (Group A Streptococcus, GAS M49), employing a whole genome intergenic tiling array approach. GAS is an important pathogen that causes diseases ranging from mild superficial infections of the skin and mucous membranes of the naso-pharynx, to severe toxic and invasive diseases. RESULTS We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of these, 42 were novel. Some of the newly-identified sRNAs belonged to one of the common non-coding RNA families described in the Rfam database. Comparison of the results of our screen with the outcome of two recently published bioinformatics tools showed a low level of overlap between putative sRNA genes. Previously, 40 potential sRNAs have been reported to be expressed in a GAS M1T1 serotype, as detected by a whole genome intergenic tiling array approach. Our screen detected 12 putative sRNA genes that were expressed in both strains. Twenty sRNA candidates appeared to be regulated in a medium-dependent fashion, while eight sRNA genes were regulated throughout growth in chemically defined medium. Expression of candidate genes was verified by reverse transcriptase-qPCR. For a subset of sRNAs, the transcriptional start was determined by 5' rapid amplification of cDNA ends-PCR (RACE-PCR) analysis. CONCLUSIONS In accord with the results of previous studies, we found little overlap between different screening methods, which underlines the fact that a comprehensive analysis of sRNAs expressed by a given organism requires the complementary use of different methods and the investigation of several environmental conditions. Despite a high conservation of sRNA genes within streptococci, the expression of sRNAs appears to be strain specific.
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Affiliation(s)
- Nadja Patenge
- Institute of Medical Microbiology and Hospital Hygiene, University of Rostock, Schillingallee 70, 18057, Rostock, Germany
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Gimpel M, Preis H, Barth E, Gramzow L, Brantl S. SR1--a small RNA with two remarkably conserved functions. Nucleic Acids Res 2012; 40:11659-72. [PMID: 23034808 PMCID: PMC3526287 DOI: 10.1093/nar/gks895] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that—despite divergent primary sequences—the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.
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Affiliation(s)
- Matthias Gimpel
- AG Bakteriengenetik, Lehrstuhl für Mikrobiologie und Mikrobengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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42
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Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI, Rosch JW. Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 2012; 8:e1002788. [PMID: 22807675 PMCID: PMC3395615 DOI: 10.1371/journal.ppat.1002788] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/22/2012] [Indexed: 01/10/2023] Open
Abstract
Small noncoding RNAs (sRNAs) play important roles in gene regulation in both prokaryotes and eukaryotes. Thus far, no sRNA has been assigned a definitive role in virulence in the major human pathogen Streptococcus pneumoniae. Based on the potential coding capacity of intergenic regions, we hypothesized that the pneumococcus produces many sRNAs and that they would play an important role in pathogenesis. We describe the application of whole-genome transcriptional sequencing to systematically identify the sRNAs of Streptococcus pneumoniae. Using this approach, we have identified 89 putative sRNAs, 56 of which are newly identified. Furthermore, using targeted genetic approaches and Tn-seq transposon screening, we demonstrate that many of the identified sRNAs have important global and niche-specific roles in virulence. These data constitute the most comprehensive analysis of pneumococcal sRNAs and provide the first evidence of the extensive roles of sRNAs in pneumococcal pathogenesis.
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Affiliation(s)
- Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Tim van Opijnen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jianmin Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Caroline Obert
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Yong-Dong Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Robert Carter
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Daniel J. McGoldrick
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Granger Ridout
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Andrew Camilli
- Howard Hughes Medical Institute and Tufts University School of Medicine, Department of Molecular Biology and Microbiology, Boston, Massachusetts, United States of America
| | - Elaine I. Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
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Brantl S. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiol 2012; 7:853-71. [DOI: 10.2217/fmb.12.59] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
sRNAs that act by base pairing were first discovered in plasmids, phages and transposons, where they control replication, maintenance and transposition. Since 2001, however, computational searches were applied that led to the discovery of a plethora of sRNAs in bacterial chromosomes. Whereas the majority of these chromsome-encoded sRNAs have been investigated in Escherichia coli, Salmonella and other Gram-negative bacteria, only a few well-studied examples are known from Gram-positive bacteria. Here, the author summarizes our current knowledge on plasmid- and chromosome-encoded sRNAs from Gram-positive species, thereby focusing on regulatory mechanisms used by these RNAs and their biological role in complex networks. Furthermore, regulatory factors that control the expression of these RNAs will be discussed and differences between sRNAs from Gram-positive and Gram-negative bacteria highlighted. The main emphasis of this review is on sRNAs that act by base pairing (i.e., by an antisense mechanism). Thereby, both plasmid-encoded and chromosome-encoded sRNAs will be considered.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany
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Synergistic effects of streptolysin S and streptococcal pyrogenic exotoxin B on the mouse model of group A streptococcal infection. Med Microbiol Immunol 2012; 201:357-69. [PMID: 22610375 DOI: 10.1007/s00430-012-0241-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 05/03/2012] [Indexed: 02/01/2023]
Abstract
Streptococcus pyogenes is a group A streptococcus (GAS) and an important human pathogen that causes a variety of diseases. Streptococcal pyrogenic exotoxin B (SPE B) and streptolysin S (SLS) are important virulence factors involved in GAS infection, but it is not clear which one is more virulent. Using an air pouch infection model, the wild-type strain NZ131, its isogenic mutants, and complementary mutants were used to examine the effects of SPE B and SLS on GAS infection. The results of the skin lesion and mouse mortality assays showed that although SPE B and SLS had a synergistic effect on GAS infection, SPE B played a more important role in local tissue damage while SLS had a more prominent effect on mouse mortality. Surveys of the exudates from the air pouch revealed that the expression of inflammatory cytokines was significantly inhibited in the sagB/speB-double-mutant JM4-infected mice. Furthermore, in vivo and in vitro studies showed that the isogenic mutant strains were more susceptible to the immune cell killing than the wild-type strain and that the sagB/speB-double-mutant JM4 was the most sensitive among these strains. Moreover, infection with the sagB/speB-double-mutant JM4 strain caused the least amount of macrophage apoptosis compared to infection with the wild-type NZ131 and the other complementary strains, which express only SPE B or SLS or both. Taken together, these results indicate that both SPE B and SLS contributed to GAS evasion from immune cell killing, local tissue damage, and mouse mortality.
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Patenge N, Fiedler T, Kreikemeyer B. Common regulators of virulence in streptococci. Curr Top Microbiol Immunol 2012; 368:111-53. [PMID: 23242855 DOI: 10.1007/82_2012_295] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Streptococcal species are a diverse group of bacteria which can be found in animals and humans. Their interactions with host organisms can vary from commensal to pathogenic. Many of the pathogenic species are causative agents of severe, invasive infections in their hosts, accounting for a high burden of morbidity and mortality, associated with high economic costs in industry and health care. Among them, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus pneumoniae, and Streptococcus suis are discussed here. An environmentally stimulated and tightly controlled expression of their virulence factors is of utmost importance for their pathogenic potential. Thus, the most universal and widespread regulators from the classes of stand-alone transcriptional regulators, two-component signal transduction systems (TCS), eukaryotic-like serine/threonine kinases, and small noncoding RNAs are the topic of this chapter. The regulatory levels are reviewed with respect to function, activity, and their role in pathogenesis. Understanding of and interfering with transcriptional regulation mechanisms and networks is a promising basis for the development of novel anti-infective therapies.
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Affiliation(s)
- Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057 Rostock, Germany
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Abstract
UNLABELLED In bacteria, RNAs regulate gene expression and function via several mechanisms. An RNA may pair with complementary sequences in a target RNA to impact transcription, translation, or degradation of the target. Control of conjugation of pCF10, a pheromone response plasmid of Enterococcus faecalis, is a well-characterized system that serves as a model for the regulation of gene expression in bacteria by intercellular signaling. The prgQ operon, whose products mediate conjugation, is negatively regulated by two products of the prgX operon, Anti-Q, a small RNA, and PrgX, the transcriptional repressor of the prgQ promoter. Here we show that Qs, an RNA from the 5' end of the prgQ operon, represses expression of PrgX by targeting prgX mRNA for cleavage by RNase III. Our results demonstrate that the prgQ and prgX operons each use RNAs to negatively regulate gene expression from the opposing operon by different mechanisms. Such reciprocal regulation between two operons using RNAs has not been previously demonstrated. Furthermore, these results show that Qs is an unusually versatile RNA, serving three separate functions in the regulation of conjugation. Understanding the potential versatility of RNAs and their various roles in gene regulatory networks will allow us to better understand how cells regulate complex behavior. IMPORTANCE Bacteria use RNA to regulate gene expression by a variety of mechanisms. The prgQ and prgX operons of pCF10, a conjugative plasmid of Enterococcus faecalis, have been shown to negatively regulate one another by a variety of mechanisms. One of these mechanisms involves Anti-Q, a small RNA from the prgX operon that prevents gene expression from the prgQ operon. In this work, we find that Qs, an RNA from the prgQ operon, negatively regulates gene expression from the prgX operon. These findings have a number of implications. (i) The Anti-Q and Qs RNAs act by different mechanisms, highlighting the variety of ways in which bacteria can regulate gene expression using RNAs. (ii) Reciprocal regulation between operons mediated by small RNAs has not been previously described, deepening our understanding of how bacteria regulate complex behavior. (iii) Additional roles for Qs have been described, demonstrating the versatility of this RNA.
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Identification and Role of Regulatory Non-Coding RNAs in Listeria monocytogenes. Int J Mol Sci 2011; 12:5070-9. [PMID: 21954346 PMCID: PMC3179153 DOI: 10.3390/ijms12085070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 07/15/2011] [Accepted: 08/08/2011] [Indexed: 11/16/2022] Open
Abstract
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- and trans-acting regulatory RNAs, including sRNAs, asRNAs, untranslated regions (UTR) and riboswitches. As a result, we obtained a more comprehensive view on the complexity and plasticity of the prokaryotic genome biology. Listeria monocytogenes was utilized as a model system for intracellular pathogenic bacteria in several studies, which revealed the presence of about 180 regulatory RNAs in the listerial genome. A regulatory role of non-coding RNAs in survival, virulence and adaptation mechanisms of L. monocytogenes was confirmed in subsequent experiments, thus, providing insight into a multifaceted modulatory function of RNA/mRNA interference. In this review, we discuss the identification of regulatory RNAs by high-throughput techniques and in their functional role in L. monocytogenes.
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Molloy EM, Cotter PD, Hill C, Mitchell DA, Ross RP. Streptolysin S-like virulence factors: the continuing sagA. Nat Rev Microbiol 2011; 9:670-81. [PMID: 21822292 DOI: 10.1038/nrmicro2624] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Streptolysin S (SLS) is a potent cytolytic toxin and virulence factor that is produced by nearly all Streptococcus pyogenes strains. Despite a 100-year history of research on this toxin, it has only recently been established that SLS is just one of an extended family of post-translationally modified virulence factors (the SLS-like peptides) that are produced by some streptococci and other Gram-positive pathogens, such as Listeria monocytogenes and Clostridium botulinum. In this Review, we describe the identification, genetics, biochemistry and various functions of SLS. We also discuss the shared features of the virulence-associated SLS-like peptides, as well as their place within the rapidly expanding family of thiazole/oxazole-modified microcins (TOMMs).
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Affiliation(s)
- Evelyn M Molloy
- Department of Microbiology, University College Cork, Cork, Ireland
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Carroll RK, Musser JM. From transcription to activation: how group A streptococcus, the flesh-eating pathogen, regulates SpeB cysteine protease production. Mol Microbiol 2011; 81:588-601. [PMID: 21707787 DOI: 10.1111/j.1365-2958.2011.07709.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Streptococcal pyrogenic exotoxin B (SpeB) is a protease secreted by group A streptococci and known to degrade a wide range of host and GAS proteins in vitro. Although the role of SpeB in GAS infection is debated, recent evidence has conclusively demonstrated that SpeB is critical for the pathogenesis of severe invasive disease caused by GAS. Genetic inactivation of the speB gene results in significantly decreased virulence in a necrotizing fasciitis model of infection. Production of fully active SpeB by GAS is extremely complex. Following transcription and translation the SpeB protein is secreted as an inactive zymogen, which is autocatalytically processed through a series of intermediates to form an active protease. Each step from transcription to protease activation is tightly controlled and regulated by the bacterial cell reflecting the critical role played by this virulence factor in GAS infection. Here we review the molecular aspects of SpeB production by GAS from transcription to activation and the multiple layers of control involved.
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Affiliation(s)
- Ronan K Carroll
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, TX 77030, USA
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Mraheil MA, Billion A, Kuenne C, Pischimarov J, Kreikemeyer B, Engelmann S, Hartke A, Giard JC, Rupnik M, Vorwerk S, Beier M, Retey J, Hartsch T, Jacob A, Cemič F, Hemberger J, Chakraborty T, Hain T. Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application. Microb Biotechnol 2011; 3:658-76. [PMID: 21255362 PMCID: PMC3815340 DOI: 10.1111/j.1751-7915.2010.00171.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the recent years, the number of drug- and multi-drug-resistant microbial strains has increased rapidly. Therefore, the need to identify innovative approaches for development of novel anti-infectives and new therapeutic targets is of high priority in global health care. The detection of small RNAs (sRNAs) in bacteria has attracted considerable attention as an emerging class of new gene expression regulators. Several experimental technologies to predict sRNA have been established for the Gram-negative model organism Escherichia coli. In many respects, sRNA screens in this model system have set a blueprint for the global and functional identification of sRNAs for Gram-positive microbes, but the functional role of sRNAs in colonization and pathogenicity for Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis and Clostridium difficile is almost completely unknown. Here, we report the current knowledge about the sRNAs of these socioeconomically relevant Gram-positive pathogens, overview the state-of-the-art high-throughput sRNA screening methods and summarize bioinformatics approaches for genome-wide sRNA identification and target prediction. Finally, we discuss the use of modified peptide nucleic acids (PNAs) as a novel tool to inactivate potential sRNA and their applications in rapid and specific detection of pathogenic bacteria.
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Affiliation(s)
- Mobarak A Mraheil
- Institute of Medical Microbiology, Justus-Liebig-University, Frankfurter Strasse 107, 35392 Giessen, Germany
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