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Krohmaly KI, Freishtat RJ, Hahn AL. Bioinformatic and experimental methods to identify and validate bacterial RNA-human RNA interactions. J Investig Med 2023; 71:23-31. [PMID: 36162901 DOI: 10.1136/jim-2022-002509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/21/2023]
Abstract
Ample evidence supports the importance of the microbiota on human health and disease. Recent studies suggest that extracellular vesicles are an important means of bacterial-host communication, in part via the transport of small RNAs (sRNAs). Bacterial sRNAs have been shown to co-precipitate with human and mouse RNA-induced silencing complex, hinting that some may regulate gene expression as eukaryotic microRNAs do. Bioinformatic tools, including those that can incorporate an sRNA's secondary structure, can be used to predict interactions between bacterial sRNAs and human messenger RNAs (mRNAs). Validation of these potential interactions using reproducible experimental methods is essential to move the field forward. This review will cover the evidence of interspecies communication via sRNAs, bioinformatic tools currently available to identify potential bacterial sRNA-host (specifically, human) mRNA interactions, and experimental methods to identify and validate those interactions.
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Affiliation(s)
- Kylie I Krohmaly
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Division of Emergency Medicine, Children's National Hospital, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Andrea L Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, District of Columbia, USA.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA.,Division of Infectious Diseases, Children's National Hospital, Washington, District of Columbia, USA
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2
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A Reverse Genetic Approach for Studying sRNAs in Chlamydia trachomatis. mBio 2022; 13:e0086422. [PMID: 35726915 PMCID: PMC9426522 DOI: 10.1128/mbio.00864-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
sRNAs are noncoding transcripts that play critical roles in posttranscriptional regulation in prokaryotes. In the intracellular bacterium Chlamydia, sRNAs have been identified, but functional studies have been limited to an E. coli heterologous system. We have developed an inducible sRNA overexpression system in Chlamydia trachomatis and used it to screen putative sRNAs for effects on the Chlamydia developmental cycle, which involves conversion between replicating (RB) and infectious (EB) chlamydial forms. Overexpression of 4 of 13 C. trachomatis sRNAs decreased production of infectious EBs. We performed detailed characterization of CtrR3 and CtrR7, the two sRNAs that caused the largest progeny defects in our screen. By quantifying chlamydial number and infectious progeny, and by visualizing chlamydial forms using electron microscopy, we showed that overexpression of CtrR3 prevented RB-to-EB conversion, whereas CtrR7 overexpression blocked bacterial replication. We also describe a workflow that allowed us to identify the mRNA targets of CtrR3 in Chlamydia. We first used MS2 aptamer affinity purification coupled with RNA sequencing as an unbiased approach to isolate interacting mRNAs. We then prioritized candidates based on sequence complementarity to the CtrR3 target recognition sequence, which we had identified with bioinformatic and mutational analyses. Finally, we tested putative targets with translational fusion assays in E. coli and C. trachomatis. Using this integrated approach, we provide experimental evidence that YtgB and CTL0389 are mRNA targets of CtrR3 in Chlamydia. These findings demonstrate how our C. trachomatis sRNA overexpression system can be used to investigate the functions and mRNA targets of chlamydial sRNAs.
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Talank N, Morad H, Barabadi H, Mojab F, Amidi S, Kobarfard F, Mahjoub MA, Jounaki K, Mohammadi N, Salehi G, Ashrafizadeh M, Mostafavi E. Bioengineering of green-synthesized silver nanoparticles: In vitro physicochemical, antibacterial, biofilm inhibitory, anticoagulant, and antioxidant performance. Talanta 2022; 243:123374. [DOI: 10.1016/j.talanta.2022.123374] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023]
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4
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Le Huyen KB, Gonzalez CD, Pascreau G, Bordeau V, Cattoir V, Liu W, Bouloc P, Felden B, Chabelskaya S. A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity. Nucleic Acids Res 2021; 49:10644-10656. [PMID: 34554192 PMCID: PMC8501977 DOI: 10.1093/nar/gkab782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 01/17/2023] Open
Abstract
Staphylococcus aureus is an opportunistic human and animal pathogen with an arsenal of virulence factors that are tightly regulated during bacterial infection. The latter is achieved through a sophisticated network of regulatory proteins and regulatory RNAs. Here, we describe the involvement of a novel prophage-carried small regulatory S. aureus RNA, SprY, in the control of virulence genes. An MS2-affinity purification assay reveals that SprY forms a complex in vivo with RNAIII, a major regulator of S. aureus virulence genes. SprY binds to the 13th stem-loop of RNAIII, a key functional region involved in the repression of multiple mRNA targets. mRNAs encoding the repressor of toxins Rot and the extracellular complement binding protein Ecb are among the targets whose expression is increased by SprY binding to RNAIII. Moreover, SprY decreases S. aureus hemolytic activity and virulence. Our results indicate that SprY titrates RNAIII activity by targeting a specific stem loop. Thus, we demonstrate that a prophage-encoded sRNA reduces the pathogenicity of S. aureus through RNA sponge activity.
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Affiliation(s)
- Kim Boi Le Huyen
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | | | - Gaëtan Pascreau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Valérie Bordeau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Vincent Cattoir
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Wenfeng Liu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Brice Felden
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Svetlana Chabelskaya
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
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5
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Shiluli C, Achok C, Nyaswa P, Ogwai S, Aroko A, Obila J, Koigi G, Ridhwana M, Okwayo B, Wanjiru D, Lukeba L, Ryckaert E, Van Durme A, Walschaerts V, De Preter V. Antimicrobial sensitivity patterns of Staphylococcus species isolated from mobile phones and implications in the health sector. BMC Res Notes 2021; 14:1. [PMID: 33407799 PMCID: PMC7788780 DOI: 10.1186/s13104-020-05413-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Objectives The aim of this research was to determine drug sensitivity profiles of Staphylococcus species isolated from mobile phones of students in Microbiology and Biomedical Laboratory Sciences from UZIMA University, Kisumu (Kenya) and the University Colleges Leuven-Limburg, Leuven (Belgium), respectively. Results All mobile phones (16/16, 100%) had gram-positive bacteria. 3/8 (37.5%) mobile devices had Staphylococcus aureus. 2/3 (67%) Staphylococcus aureus strains were resistant to ampicillin, oxacillin, ceftazidime, vancomycin and amoxicillin. Guidelines for disinfection of mobile phones need to be developed urgently to stop transmission of resistant bacteria.
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Affiliation(s)
- Clement Shiluli
- Department of Microbiology, UZIMA University, Kisumu, Kenya.
| | - Caroly Achok
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - Philip Nyaswa
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - Susan Ogwai
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - Arthur Aroko
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - James Obila
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - George Koigi
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | | | - Bildad Okwayo
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - Dorcas Wanjiru
- Department of Microbiology, UZIMA University, Kisumu, Kenya
| | - Linda Lukeba
- Department of Health, University Colleges Leuven-Limburg (UCLL), Leuven, Belgium
| | - Eline Ryckaert
- Department of Health, University Colleges Leuven-Limburg (UCLL), Leuven, Belgium
| | - Arne Van Durme
- Department of Health, University Colleges Leuven-Limburg (UCLL), Leuven, Belgium
| | - Verena Walschaerts
- Department of Health, University Colleges Leuven-Limburg (UCLL), Leuven, Belgium
| | - Vicky De Preter
- Department of Health, University Colleges Leuven-Limburg (UCLL), Leuven, Belgium
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Desgranges E, Caldelari I, Marzi S, Lalaouna D. Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194506. [PMID: 32068131 DOI: 10.1016/j.bbagrm.2020.194506] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation to various perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated the identification and characterization of sRNAs (length, structure and expression conditions) and their RNA targets in several bacteria. Nevertheless, it could be very difficult for non-experts to understand the advantages and drawbacks related to each offered option and, consequently, to make an informed choice. Therefore, the main goal of this review is to provide a guide to navigate through the twists and turns of high-throughput RNA sequencing technologies, with a specific focus on those applied to the study of sRNAs. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Emma Desgranges
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - David Lalaouna
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France.
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Lalaouna D, Baude J, Wu Z, Tomasini A, Chicher J, Marzi S, Vandenesch F, Romby P, Caldelari I, Moreau K. RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation. Nucleic Acids Res 2019; 47:9871-9887. [PMID: 31504767 PMCID: PMC6765141 DOI: 10.1093/nar/gkz728] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/22/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023] Open
Abstract
The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5′ end while its 3′ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3′UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.
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Affiliation(s)
- David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Jessica Baude
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Lyon1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Arnaud Tomasini
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg-Esplanade, IBMC-CNRS, Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Lyon1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France.,Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Lyon1, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France
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Desgranges E, Bronesky D, Corvaglia A, François P, Caballero C, Prado L, Toledo-Arana A, Lasa I, Moreau K, Vandenesch F, Marzi S, Romby P, Caldelari I. RsaI, un ARN régulateur aux multiples facettes, module le métabolisme du pathogène opportuniste Staphylococcus aureus. Med Sci (Paris) 2019; 35:1221-1223. [DOI: 10.1051/medsci/2019235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Georg J, Lalaouna D, Hou S, Lott SC, Caldelari I, Marzi S, Hess WR, Romby P. The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs. Mol Microbiol 2019; 113:603-612. [PMID: 31705780 PMCID: PMC7154689 DOI: 10.1111/mmi.14420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022]
Abstract
Trans‐acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post‐transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNAs targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB, and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more details. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA‐dependent regulatory networks is now attainable.
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Affiliation(s)
- Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - David Lalaouna
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Shengwei Hou
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Steffen C Lott
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, Strasbourg, France
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