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Zhao Z, Yang T, Xiang G, Zhang S, Cai Y, Zhong G, Pu J, Shen C, Zeng J, Chen C, Huang B. A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant Klebsiella pneumoniae. Emerg Microbes Infect 2024:2366354. [PMID: 38979571 DOI: 10.1080/22221751.2024.2366354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant Klebsiella pneumoniae. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant K. pneumoniae strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted phoP through the green fluorescent protein reporter system. PhaS promoted the expression of phoP, thereby encouraging the expression of downstream genes pmrD and arnT. This upregulation of arnT promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant K. pneumoniae.
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Affiliation(s)
- Zhiwei Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tingting Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shebin Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Guosheng Zhong
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jieying Pu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Jianming Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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2
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Wu W, Huang J, Xu Z. Antibiotic influx and efflux in Pseudomonas aeruginosa: Regulation and therapeutic implications. Microb Biotechnol 2024; 17:e14487. [PMID: 38801351 PMCID: PMC11129675 DOI: 10.1111/1751-7915.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Pseudomonas aeruginosa is a notorious multidrug-resistant pathogen that poses a serious and growing threat to the worldwide public health. The expression of resistance determinants is exquisitely modulated by the abundant regulatory proteins and the intricate signal sensing and transduction systems in this pathogen. Downregulation of antibiotic influx porin proteins and upregulation of antibiotic efflux pump systems owing to mutational changes in their regulators or the presence of distinct inducing molecular signals represent two of the most efficient mechanisms that restrict intracellular antibiotic accumulation and enable P. aeruginosa to resist multiple antibiotics. Treatment of P. aeruginosa infections is extremely challenging due to the highly inducible mechanism of antibiotic resistance. This review comprehensively summarizes the regulatory networks of the major porin proteins (OprD and OprH) and efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY) that play critical roles in antibiotic influx and efflux in P. aeruginosa. It also discusses promising therapeutic approaches using safe and efficient adjuvants to enhance the efficacy of conventional antibiotics to combat multidrug-resistant P. aeruginosa by controlling the expression levels of porins and efflux pumps. This review not only highlights the complexity of the regulatory network that induces antibiotic resistance in P. aeruginosa but also provides important therapeutic implications in targeting the inducible mechanism of resistance.
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Affiliation(s)
- Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
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3
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Wu W, Pang CNI, Mediati DG, Tree JJ. The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerant Staphylococcus aureus. mSystems 2024; 9:e0097123. [PMID: 38534138 PMCID: PMC11019875 DOI: 10.1128/msystems.00971-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance is poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. To identify sRNA-mRNA interactions that regulate mRNA translation, we examined the correlation between gene transcript abundance, ribosome occupancy, and protein levels. We used the machine learning technique self-organizing maps (SOMs) to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating our clustering with sRNA-mRNA interactome data generated in vancomycin-tolerant S. aureus by RNase III-CLASH, we identified sRNAs that may be mediating translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin. We demonstrate the regulation of HPr and the cell-wall autolysin Atl. These findings suggest that RsaOI coordinates carbon metabolism and cell wall turnover during vancomycin treatment. IMPORTANCE The emergence of multidrug-resistant Staphylococcus aureus (MRSA) is a major public health concern. Current treatment is dependent on the efficacy of last-line antibiotics like vancomycin. The most common cause of vancomycin treatment failure is strains with intermediate resistance or tolerance that arise through the acqusition of a diverse repertoire of point mutations. These strains have been shown to altered small RNA (sRNA) expression in response to antibiotic treatment. Here, we have used a technique termed RNase III-CLASH to capture sRNA interactions with their target mRNAs. To understand the function of these interactions, we have looked at RNA and protein abundance for mRNAs targeted by sRNAs. Messenger RNA and protein levels are generally well correlated and we use deviations from this correlation to infer post-transcriptional regulation and the function of individual sRNA-mRNA interactions. Using this approach we identify mRNA targets of the vancomycin-induced sRNA, RsaOI, that are repressed at the translational level. We find that RsaOI represses the cell wall autolysis Atl and carbon transporter HPr suggestion a link between vancomycin treatment and suppression of cell wall turnover and carbon metabolism.
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Affiliation(s)
- Winton Wu
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
| | | | - Daniel G. Mediati
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
| | - Jai Justin Tree
- School of Biotechnology and Biomolecular Sciences, Sydney, New South Wales, Australia
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4
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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5
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Ferrara S, Bertoni G. Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa. Methods Mol Biol 2024; 2721:183-195. [PMID: 37819523 DOI: 10.1007/978-1-0716-3473-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In recent years, several genome-wide approaches based on RNA sequencing (RNA-seq) have been developed. These methods allow a comprehensive and dynamic view of the structure and function of the multi-layered RNA pathways and networks. Many of these approaches, including the promising one of single-cell transcriptome analysis, have been successfully applied to Pseudomonas aeruginosa. However, we are only at the beginning because only a few surrounding conditions have been considered. Here, we aim to illustrate the different types of approaches based on RNA-seq that will lead us in the future to a better understanding of the dynamics of RNA biology in P. aeruginosa.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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6
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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7
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Tjaden B. TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning. Genome Biol 2023; 24:276. [PMID: 38041165 PMCID: PMC10691042 DOI: 10.1186/s13059-023-03117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
Small regulatory RNAs pervade prokaryotes, with the best-studied family of these non-coding genes corresponding to trans-acting regulators that bind via base pairing to their message targets. Given the increasing frequency with which these genes are being identified, it is important that methods for illuminating their regulatory targets keep pace. Using a machine learning approach, we investigate thousands of interactions between small RNAs and their targets, and we interrogate more than a hundred features indicative of these interactions. We present a new method, TargetRNA3, for predicting targets of small RNA regulators and show that it outperforms existing approaches. TargetRNA3 is available at https://cs.wellesley.edu/~btjaden/TargetRNA3 .
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Affiliation(s)
- Brian Tjaden
- Department of Computer Science, Wellesley College, Wellesley, MA, USA.
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8
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Gebhardt MJ, Farland EA, Basu P, Macareno K, Melamed S, Dove SL. Hfq-licensed RNA-RNA interactome in Pseudomonas aeruginosa reveals a keystone sRNA. Proc Natl Acad Sci U S A 2023; 120:e2218407120. [PMID: 37285605 PMCID: PMC10214189 DOI: 10.1073/pnas.2218407120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/08/2023] [Indexed: 06/09/2023] Open
Abstract
The RNA chaperone Hfq plays important regulatory roles in many bacteria by facilitating the base pairing between small RNAs (sRNAs) and their cognate mRNA targets. In the gram-negative opportunistic pathogen Pseudomonas aeruginosa, over a hundred putative sRNAs have been identified but for most, their regulatory targets remained unknown. Using RIL-seq with Hfq in P. aeruginosa, we identified the mRNA targets for dozens of previously known and unknown sRNAs. Strikingly, hundreds of the RNA-RNA interactions we discovered involved PhrS. This sRNA was thought to mediate its effects by pairing with a single target mRNA and regulating the abundance of the transcription regulator MvfR required for the synthesis of the quorum sensing signal PQS. We present evidence that PhrS controls many transcripts by pairing with them directly and employs a two-tiered mechanism for governing PQS synthesis that involves control of an additional transcription regulator called AntR. Our findings in P. aeruginosa expand the repertoire of targets for previously known sRNAs, reveal potential regulatory targets for previously unknown sRNAs, and suggest that PhrS may be a keystone sRNA with the ability to pair with an unusually large number of transcripts in this organism.
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Affiliation(s)
- Michael J. Gebhardt
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Elizabeth A. Farland
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Pallabi Basu
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Keven Macareno
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem9112102, Israel
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA02115
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9
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Sass AM, Coenye T. The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia. mSphere 2023; 8:e0008323. [PMID: 36971554 PMCID: PMC10117139 DOI: 10.1128/msphere.00083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Regulation of porin expression in bacteria is complex and often involves small-RNA regulators. Several small-RNA regulators have been described for Burkholderia cenocepacia, and this study aimed to characterize the biological role of the conserved small RNA NcS25 and its cognate target, outer membrane protein BCAL3473. The B. cenocepacia genome carries a large number of genes encoding porins with yet-uncharacterized functions. Expression of the porin BCAL3473 is strongly repressed by NcS25 and activated by other factors, such as a LysR-type regulator and nitrogen-depleted growth conditions. The porin is involved in transport of arginine, tyrosine, tyramine, and putrescine across the outer membrane. Porin BCAL3473, with NcS25 as a major regulator, plays an important role in the nitrogen metabolism of B. cenocepacia. IMPORTANCE Burkholderia cenocepacia is a Gram-negative bacterium which causes infections in immunocompromised individuals and in people with cystic fibrosis. A low outer membrane permeability is one of the factors giving it a high level of innate resistance to antibiotics. Porins provide selective permeability for nutrients, and antibiotics can also traverse the outer membrane by this means. Knowing the properties and specificities of porin channels is therefore important for understanding resistance mechanisms and for developing new antibiotics and could help in overcoming permeability issues in antibiotic treatment.
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Affiliation(s)
- Andrea M. Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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10
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Dunham DT, Angermeyer A, Seed KD. The RNA-RNA interactome between a phage and its satellite virus reveals a small RNA that differentially regulates gene expression across both genomes. Mol Microbiol 2023; 119:515-533. [PMID: 36786209 PMCID: PMC10392615 DOI: 10.1111/mmi.15046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Satellite viruses are present across all domains of life, defined as subviral parasites that require infection by another virus for satellite progeny production. Phage satellites exhibit various regulatory mechanisms to manipulate phage gene expression to the benefit of the satellite, redirecting resources from the phage to the satellite, and often inhibiting phage progeny production. While small RNAs (sRNAs) are well documented as regulators of prokaryotic gene expression, they have not been shown to play a regulatory role in satellite-phage conflicts. Vibrio cholerae encodes the phage inducible chromosomal island-like element (PLE), a phage satellite, to defend itself against the lytic phage ICP1. Here, we use Hi-GRIL-seq to identify a complex RNA-RNA interactome between PLE and ICP1. Both inter- and intragenome RNA interactions were detected, headlined by the PLE sRNA, SviR. SviR is involved in regulating both PLE and ICP1 gene expression uniquely, decreasing ICP1 target translation and affecting PLE transcripts. The striking conservation of SviR across all known PLEs suggests the sRNA is deeply rooted in the PLE-ICP1 conflict and implicates sRNAs as unidentified regulators of gene expression in phage-satellite interactions.
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Affiliation(s)
- Drew T Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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11
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Dendooven T, Sonnleitner E, Bläsi U, Luisi BF. Translational regulation by Hfq-Crc assemblies emerges from polymorphic ribonucleoprotein folding. EMBO J 2023; 42:e111129. [PMID: 36504222 PMCID: PMC9890229 DOI: 10.15252/embj.2022111129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
The widely occurring bacterial RNA chaperone Hfq is a key factor in the post-transcriptional control of hundreds of genes in Pseudomonas aeruginosa. How this broadly acting protein can contribute to the regulatory requirements of many different genes remains puzzling. Here, we describe cryo-EM structures of higher order assemblies formed by Hfq and its partner protein Crc on control regions of different P. aeruginosa target mRNAs. Our results show that these assemblies have mRNA-specific quaternary architectures resulting from the combination of multivalent protein-protein interfaces and recognition of patterns in the RNA sequence. The structural polymorphism of these ribonucleoprotein assemblies enables selective translational repression of many different target mRNAs. This system elucidates how highly complex regulatory pathways can evolve with a minimal economy of proteinogenic components in combination with RNA sequence and fold.
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Affiliation(s)
- Tom Dendooven
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Ben F Luisi
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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12
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Transcriptome analysis of sRNA responses to four different antibiotics in Pseudomonas aeruginosa PAO1. Microb Pathog 2022; 173:105865. [DOI: 10.1016/j.micpath.2022.105865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
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13
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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14
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Holban AM, Gregoire CM, Gestal MC. Conquering the host: Bordetella spp. and Pseudomonas aeruginosa molecular regulators in lung infection. Front Microbiol 2022; 13:983149. [PMID: 36225372 PMCID: PMC9549215 DOI: 10.3389/fmicb.2022.983149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022] Open
Abstract
When bacteria sense cues from the host environment, stress responses are activated. Two component systems, sigma factors, small RNAs, ppGpp stringent response, and chaperones start coordinate the expression of virulence factors or immunomodulators to allow bacteria to respond. Although, some of these are well studied, such as the two-component systems, the contribution of other regulators, such as sigma factors or ppGpp, is increasingly gaining attention. Pseudomonas aeruginosa is the gold standard pathogen for studying the molecular mechanisms to sense and respond to environmental cues. Bordetella spp., on the other hand, is a microbial model for studying host-pathogen interactions at the molecular level. These two pathogens have the ability to colonize the lungs of patients with chronic diseases, suggesting that they have the potential to share a niche and interact. However, the molecular networks that facilitate adaptation of Bordetella spp. to cues are unclear. Here, we offer a side-by-side comparison of what is known about these diverse molecular mechanisms that bacteria utilize to counteract host immune responses, while highlighting the relatively unexplored interactions between them.
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Affiliation(s)
- Alina M. Holban
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Courtney M. Gregoire
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
| | - Monica C. Gestal
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
- *Correspondence: Monica C. Gestal, ;
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15
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Liu P, Yue C, Liu L, Gao C, Lyu Y, Deng S, Tian H, Jia X. The function of small RNA in Pseudomonas aeruginosa. PeerJ 2022; 10:e13738. [PMID: 35891650 PMCID: PMC9308961 DOI: 10.7717/peerj.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/25/2022] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies.
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Affiliation(s)
- Pei Liu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Changwu Yue
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Lihua Liu
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Can Gao
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Yuhong Lyu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Shanshan Deng
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Hongying Tian
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Xu Jia
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China,School of Basic Medical Science, Chengdu Medical College, Chengdu, Sichuan, China
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16
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Menard G, Silard C, Suriray M, Rouillon A, Augagneur Y. Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications. Int J Mol Sci 2022; 23:ijms23137346. [PMID: 35806357 PMCID: PMC9266662 DOI: 10.3390/ijms23137346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/20/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is a widespread livestock and human pathogen that colonizes diverse microenvironments within its host. Its adaptation to the environmental conditions encountered within humans relies on coordinated gene expression. This requires a sophisticated regulatory network, among which regulatory RNAs (usually called sRNAs) have emerged as key players over the last 30 years. In S. aureus, sRNAs regulate target genes at the post-transcriptional level through base–pair interactions. The functional characterization of a subset revealed that they participate in all biological processes, including virulence, metabolic adaptation, and antibiotic resistance. In this review, we report 30 years of S. aureus sRNA studies, from their discovery to the in-depth characterizations of some of them. We also discuss their actual in vivo contribution, which is still lagging behind, and their place within the complex regulatory network. These shall be key aspects to consider in order to clearly uncover their in vivo biological functions.
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Affiliation(s)
- Guillaume Menard
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Chloé Silard
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Marie Suriray
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Astrid Rouillon
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Yoann Augagneur
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
- Correspondence: ; Tel.: +33-223234631
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17
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Wang LJ, Jiang XR, Hou J, Wang CH, Chen GQ. Engineering Halomonas bluephagenesis via small regulatory RNAs. Metab Eng 2022; 73:58-69. [PMID: 35738548 DOI: 10.1016/j.ymben.2022.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/05/2022] [Accepted: 06/17/2022] [Indexed: 12/25/2022]
Abstract
Halomonas bluephagenesis, a robust and contamination-resistant microorganism has been developed as a chassis for "Next Generation Industrial Biotechnology". The non-model H. bluephagenesis requires efficient tools to fine-tune its metabolic fluxes for enhanced production phenotypes. Here we report a highly efficient gene expression regulation system (PrrF1-2-HfqPa) in H. bluephagenesis, small regulatory RNA (sRNA) PrrF1 scaffold from Pseudomonas aeruginosa and a target-binding sequence that downregulate gene expression, and its cognate P. aeruginosa Hfq (HfqPa), recruited by the scaffold to facilitate the hybridization of sRNA and the target mRNA. The PrrF1-2-HfqPa system targeting prpC in H. bluephagenesis helps increase 3-hydroxyvalerate fraction in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) to 21 mol% compared to 3.1 mol% of the control. This sRNA system repressed phaP1 and minD simultaneously, resulting in large polyhydroxybutyrate granules. Further, an sRNA library targeting 30 genes was employed for large-scale target identification to increase mevalonate production. This work expands the study on using an sRNA system not based on Escherichia coli MicC/SgrS-Hfq to repress gene expression, providing a framework to exploit new powerful genome engineering tools based on other sRNAs.
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Affiliation(s)
- Li-Juan Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China; Shandong Provincial Research Center for Bioinformatic Engineering and Technology, School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Xiao-Ran Jiang
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Jie Hou
- Shandong Provincial Research Center for Bioinformatic Engineering and Technology, School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Cong-Han Wang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technology, School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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18
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Hong J, Li X, Jiang M, Hong R. Co-expression Mechanism Analysis of Different Tachyplesin I-Resistant Strains in Pseudomonas aeruginosa Based on Transcriptome Sequencing. Front Microbiol 2022; 13:871290. [PMID: 35464984 PMCID: PMC9022664 DOI: 10.3389/fmicb.2022.871290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/10/2022] [Indexed: 11/23/2022] Open
Abstract
Tachyplesin I is a cationic antimicrobial peptide with 17 amino acids. The long-term continuous exposure to increased concentrations of tachyplesin I induced resistance in Pseudomonas aeruginosa. The global gene expression profiling of tachyplesin I–resistant P. aeruginosa strains PA-60 and PA-99 and the sensitive strain P. aeruginosa CGMCC1.2620 (PA1.2620) were conducted by transcriptome sequencing to analyze the common underlying mechanism of resistance to tachyplesin I in low- or high-resistance mutants. The co-expression patterns, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, sRNA target genes, and single-nucleotide polymorphism (SNP) change were analyzed for the co-expressed genes in this study. A total of 661 differentially co-expressed genes under treatments of PA1.2620 vs. PA-99 and PA1.2620 vs. PA-60 (HL) were divided into 12 kinds of expression patterns. GO and KEGG pathway enrichment analyses indicated that the enrichment of co-expressed genes was mainly associated with oxidoreductase activity, mismatched DNA binding, mismatch repair, RNA degradation of GO terms, aminoacyl-tRNA biosynthesis, and aminobenzoate degradation pathways, and so forth. The co-expressed resistance-related genes were mainly involved in antibiotic efflux and antibiotic inactivation. Seven co-expressed genes had SNP changes. Some co-expressed sRNAs were involved in P. aeruginosa resistance to tachyplesin I by regulating target genes and pathways related to resistance. The common resistance mechanism of P. aeruginosa among different mutants to tachyplesin I was mainly associated with the expression alteration of several genes and sRNA-regulated target genes related to resistance; few genes had base mutations. The findings of this study might provide guidance for understanding the resistance mechanism of P. aeruginosa to tachyplesin I.
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Affiliation(s)
- Jun Hong
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Xinyang Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Mengyao Jiang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Ruofei Hong
- School of International Education, Henan University of Technology, Zhengzhou, China
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19
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Ponath F, Hör J, Vogel J. An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends. FEMS Microbiol Rev 2022; 46:6564598. [PMID: 35388892 PMCID: PMC9438474 DOI: 10.1093/femsre/fuac017] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, small noncoding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs—processed 3′ end fragments of mRNAs. Several such 3′ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3′ end-derived sRNAs—their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins such as Hfq or ProQ and their functional scope, which ranges from acting as specialized regulators of single metabolic genes to constituting entire noncoding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3′ end-derived sRNAs has been vastly underestimated and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
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20
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The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages. Nat Commun 2022; 13:1258. [PMID: 35273147 PMCID: PMC8913705 DOI: 10.1038/s41467-022-28849-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 02/14/2022] [Indexed: 01/16/2023] Open
Abstract
The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa.
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21
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Matera G, Altuvia Y, Gerovac M, El Mouali Y, Margalit H, Vogel J. Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity. Mol Cell 2022; 82:629-644.e4. [PMID: 35063132 DOI: 10.1016/j.molcel.2021.12.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 10/04/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
The envelope of Gram-negative bacteria is a vital barrier that must balance protection and nutrient uptake. Small RNAs are crucial regulators of the envelope composition and function. Here, using RIL-seq to capture the Hfq-mediated RNA-RNA interactome in Salmonella enterica, we discover envelope-related riboregulators, including OppX. We show that OppX acts as an RNA sponge of MicF sRNA, a prototypical porin repressor. OppX originates from the 5' UTR of oppABCDF, encoding the major inner-membrane oligopeptide transporter, and sequesters MicF's seed region to derepress the synthesis of the porin OmpF. Intriguingly, OppX operates as a true sponge, storing MicF in an inactive complex without affecting its levels or stability. Conservation of the opp-OppX-MicF-ompF axis in related bacteria suggests that it serves an important mechanism, adjusting envelope porosity to specific transport capacity. These data also highlight the resource value of this Salmonella RNA interactome, which will aid in unraveling RNA-centric regulation in enteric pathogens.
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Affiliation(s)
- Gianluca Matera
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Milan Gerovac
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Youssef El Mouali
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany.
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22
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Wang D, Zhang X, Yin L, Liu Q, Yu Z, Xu C, Ma Z, Xia Y, Shi J, Gong Y, Bai F, Cheng Z, Wu W, Lin J, Jin Y. RplI interacts with 5’ UTR of exsA to repress its translation and type III secretion system in Pseudomonas aeruginosa. PLoS Pathog 2022; 18:e1010170. [PMID: 34986198 PMCID: PMC8730436 DOI: 10.1371/journal.ppat.1010170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/04/2021] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen capable of causing variety of infections in humans. The type III secretion system (T3SS) is a critical virulence determinant of P. aeruginosa in the host infections. Expression of the T3SS is regulated by ExsA, a master regulator that activates the expression of all known T3SS genes. Expression of the exsA gene is controlled at both transcriptional and posttranscriptional levels. Here, we screened a P. aeruginosa transposon (Tn5) insertional mutant library and found rplI, a gene coding for the ribosomal large subunit protein L9, to be a repressor for the T3SS gene expression. Combining real-time quantitative PCR (qPCR), western blotting and lacZ fusion assays, we show that RplI controls the expression of exsA at the posttranscriptional level. Further genetic experiments demonstrated that RplI mediated control of the exsA translation involves 5’ untranslated region (5’ UTR). A ribosome immunoprecipitation assay and qPCR revealed higher amounts of a 24 nt fragment from exsA mRNA being associated with ribosomes in the ΔrplI mutant. An interaction between RplI and exsA mRNA harboring its 24 nt, but not 12 nt, 5’ UTR was confirmed by RNA Gel Mobility Shift and Microscale Thermophoresis assays. Overall, this study identifies the ribosomal large subunit protein L9 as a novel T3SS repressor that inhibits ExsA translation in P. aeruginosa. Ribosomes provide all living organisms the capacity to synthesize proteins. The production of many ribosomal proteins is often controlled by an autoregulatory feedback mechanism. P. aeruginosa is an opportunistic human pathogen and its type III secretion system (T3SS) is a critical virulence determinant in host infections. In this study, by screening a Tn5 mutant library, we identified rplI, encoding ribosomal large subunit protein L9, as a novel repressor for the T3SS. Further exploring the regulatory mechanism, we found that the RplI protein interacts with the 5’ UTR (5’ untranslated region) of exsA, a gene coding for transcriptional activator of the T3SS. Such an interaction likely blocks ribosome loading on the exsA 5’ UTR, inhibiting the initiation of exsA translation. The significance of this work is in the identification of a novel repressor for the T3SS and elucidation of its molecular mechanism. Furthermore, this work provides evidence for individual ribosomal protein regulating mRNA translation beyond its autogenous feedback control.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Liwen Yin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenzhen Ma
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yushan Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuehua Gong
- Cancer Institute, the First Affiliated Hospital of China Medical University, Shenyang, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail:
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23
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Naskulwar K, Peña-Castillo L. sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction. RNA Biol 2021; 19:44-54. [PMID: 34965197 PMCID: PMC8794260 DOI: 10.1080/15476286.2021.2012058] [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: 12/02/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A key step to understand sRNAs function is to identify the mRNAs these sRNAs bind to. There are several computational methods for sRNA target prediction, and the most accurate one is CopraRNA which is based on comparative-genomics. However, species-specific sRNAs are quite common and CopraRNA cannot be used for these sRNAs. The most commonly used transcriptome-wide sRNA target prediction method and second-most-accurate method is IntaRNA. However, IntaRNA can take hours to run on a bacterial transcriptome. Here we present sRNARFTarget, a machine-learning-based method for transcriptome-wide sRNA target prediction applicable to any sRNA. We comparatively assessed the performance of sRNARFTarget, CopraRNA and IntaRNA in three bacterial species. Our results show that sRNARFTarget outperforms IntaRNA in terms of accuracy, ranking of true interacting pairs, and running time. However, CopraRNA substantially outperforms the other two programsin terms of accuracy. Thus, we suggest using CopraRNA when homolog sequences of the sRNA are available, and sRNARFTarget for transcriptome-wide prediction or for species-specific sRNAs. sRNARFTarget is available at https://github.com/BioinformaticsLabAtMUN/sRNARFTarget.
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Affiliation(s)
- Kratika Naskulwar
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Canada
| | - Lourdes Peña-Castillo
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Canada
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25
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Brinkman FSL, Winsor GL, Done RE, Filloux A, Francis VI, Goldberg JB, Greenberg EP, Han K, Hancock REW, Haney CH, Häußler S, Klockgether J, Lamont IL, Levesque RC, Lory S, Nikel PI, Porter SL, Scurlock MW, Schweizer HP, Tümmler B, Wang M, Welch M. The Pseudomonas aeruginosa whole genome sequence: A 20th anniversary celebration. Adv Microb Physiol 2021; 79:25-88. [PMID: 34836612 DOI: 10.1016/bs.ampbs.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time-including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to colonize diverse environments. A remarkable 9% of its ORFs were predicted to encode proteins with regulatory functions, providing new insight into bacterial network complexity as a function of network size. In this celebratory article, we fast forward 20 years, and examine how access to this resource has transformed our understanding of P. aeruginosa. What follows is more than a simple review or commentary; we have specifically asked some of the leaders in the field to provide personal reflections on how the PAO1 genome sequence, along with the Pseudomonas Community Annotation Project (PseudoCAP) and Pseudomonas Genome Database (pseudomonas.com), have contributed to the many exciting discoveries in this field. In addition to bringing us all up to date with the latest developments, we also ask our contributors to speculate on how the next 20 years of Pseudomonas research might pan out.
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Affiliation(s)
- Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel E Done
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Vanessa I Francis
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | | | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanne Häußler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Klockgether
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène Marchand, Faculté of Médicine, Université Laval, Québec City, QC, Canada
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Steven L Porter
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | | | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Burkhard Tümmler
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Meng Wang
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom.
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26
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Ferrara S, Carrubba R, Santoro S, Bertoni G. The Small RNA ErsA Impacts the Anaerobic Metabolism of Pseudomonas aeruginosa Through Post-Transcriptional Modulation of the Master Regulator Anr. Front Microbiol 2021; 12:691608. [PMID: 34759894 PMCID: PMC8575079 DOI: 10.3389/fmicb.2021.691608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas aeruginosa is one of the most critical opportunistic pathogens in humans, able to cause both lethal acute and chronic lung infections. In previous work, we indicated that the small RNA ErsA plays a role in the regulatory network of P. aeruginosa pathogenicity in airways infection. To give further insight into the lifestyle functions that could be either directly or indirectly regulated by ErsA during infection, we reanalyzed the categories of genes whose transcription appeared dysregulated in an ersA knock-out mutant of the P. aeruginosa PAO1 reference strain. This preliminary analysis indicated ErsA as a candidate co-modulator of denitrification and in general, the anaerobiosis response, a characteristic physiologic state of P. aeruginosa during chronic infection of the lung of cystic fibrosis (CF) patients. To explain the pattern of dysregulation of the anaerobic-lifestyle genes in the lack of ErsA, we postulated that ErsA regulation could target the expression of Anr, a well-known transcription factor that modulates a broad regulon of anoxia-responsive genes, and also Dnr, required for the transcription activation of the denitrification machinery. Our results show that ErsA positively regulates Anr expression at the post-transcriptional level while no direct ErsA-mediated regulatory effect on Dnr was observed. However, Dnr is transcriptionally downregulated in the absence of ErsA and this is consistent with the well-characterized regulatory link between Anr and Dnr. Anr regulatory function is critical for P. aeruginosa anaerobic growth, both through denitrification and fermentation of arginine. Interestingly, we found that, differently from the laboratory strain PAO1, ErsA deletion strongly impairs the anaerobic growth by both denitrification and arginine fermentation of the RP73 clinical isolate, a multi-drug resistant P. aeruginosa CF-adapted strain. This suggests that P. aeruginosa adaptation to CF lung might result in a higher dependence on ErsA for the transduction of the multiple signals to the regulatory network of key functions for survivance in such a complex environment. Together, our results suggest that ErsA takes an upper place in the regulatory network of airways infection, transducing host inputs to biofilm-related factors, as underlined in our previous reports, and to functions that allow P. aeruginosa to thrive in low-oxygen conditions.
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Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Riccardo Carrubba
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Santoro
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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27
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Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Felden B, Augagneur Y. Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens. Front Microbiol 2021; 12:719977. [PMID: 34447363 PMCID: PMC8383071 DOI: 10.3389/fmicb.2021.719977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that they go beyond the so-called cis- and trans-encoded classifications. These molecules can be derived and processed from 5' untranslated regions (UTRs), coding or non-coding sequences, and even from 3' UTRs. They usually act within the bacterial cytoplasm, but recent studies showed sRNAs in extracellular vesicles, where they influence host cell interactions. In this review, we highlight the various functions of sRNAs in bacterial pathogens, and focus on the increasing examples of widely diverse regulatory mechanisms that might compel us to reconsider what constitute the sRNA.
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Affiliation(s)
- Brice Felden
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
| | - Yoann Augagneur
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
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29
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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30
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Malecka EM, Bassani F, Dendooven T, Sonnleitner E, Rozner M, Albanese TG, Resch A, Luisi B, Woodson S, Bläsi U. Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:7075-7087. [PMID: 34139006 PMCID: PMC8266614 DOI: 10.1093/nar/gkab510] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) govern translation of numerous transcripts during carbon catabolite repression. Here, Crc was shown to enhance Hfq-mediated translational repression of several mRNAs. We have developed a single-molecule fluorescence assay to quantitatively assess the cooperation of Hfq and Crc to form a repressive complex on a RNA, encompassing the translation initiation region and the proximal coding sequence of the P. aeruginosa amiE gene. The presence of Crc did not change the amiE RNA-Hfq interaction lifetimes, whereas it changed the equilibrium towards more stable repressive complexes. This observation is in accord with Cryo-EM analyses, which showed an increased compactness of the repressive Hfq/Crc/RNA assemblies. These biophysical studies revealed how Crc protein kinetically stabilizes Hfq/RNA complexes, and how the two proteins together fold a large segment of the mRNA into a more compact translationally repressive structure. In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. Although Hfq is well-known to act with small regulatory RNAs, this study shows how Hfq can collaborate with another protein to down-regulate translation of mRNAs that become targets for the degradative machinery.
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Affiliation(s)
- Ewelina M Malecka
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Marlena Rozner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Ben Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah Woodson
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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31
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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The RNA Chaperone Hfq Participates in Persistence to Multiple Antibiotics in the Fish Pathogen Yersinia ruckeri. Microorganisms 2021; 9:microorganisms9071404. [PMID: 34209738 PMCID: PMC8308036 DOI: 10.3390/microorganisms9071404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Yersinia ruckeri causes outbreaks of enteric redmouth disease in salmon aquaculture all over the world. The transient antibiotic tolerance exhibited by bacterial persisters is commonly thought to be responsible for outbreaks; however, the molecular factors underlying this behavior have not been explored in Y. ruckeri. In this study, we investigated the participation of the RNA chaperone Hfq from Y. ruckeri in antibiotic persistence. Cultures of the hfq-knockout mutant (Δhfq) exhibited faster replication, increased ATP levels and a more reductive environment than the wild type. The growth curves of bacteria exposed to sublethal concentrations of ampicillin, oxolinic acid, ciprofloxacin and polymyxin B revealed a greater susceptibility for the Δhfq strain. The time-kill curves of bacteria treated with the antibiotics mentioned above and florfenicol, using inoculums from exponential, stationary and biofilm cultures, demonstrated that the Δhfq strain has significant defects in persister cells production. To shed more light on the role of Hfq in antibiotic persistence, we analyzed its dependence on the (p)ppGpp synthetase RelA by determining the persister cells production in the absence of the relA gene. The ΔrelA and ΔrelAΔhfq strains displayed similar defects in persister cells formation, but higher than Δhfq strain. Similarly, stationary cultures of the ΔrelA and ΔrelAΔhfq strains exhibited comparable levels of ATP but higher than that of the Δhfq strain, indicating that relA is epistatic over hfq. Taken together, our findings provide valuable information on antibiotic persistence in Y. ruckeri, shedding light on the participation of Hfq in the persistence phenomenon.
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33
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Cianciulli Sesso A, Lilić B, Amman F, Wolfinger MT, Sonnleitner E, Bläsi U. Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin. Front Microbiol 2021; 12:626715. [PMID: 33995291 PMCID: PMC8120321 DOI: 10.3389/fmicb.2021.626715] [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: 11/06/2020] [Accepted: 03/31/2021] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is notorious for its high-level resistance toward clinically used antibiotics. In fact, Pae has rendered most antimicrobials ineffective, leaving polymyxins and aminoglycosides as last resort antibiotics. Although several resistance mechanisms of Pae are known toward these drugs, a profounder knowledge of hitherto unidentified factors and pathways appears crucial to develop novel strategies to increase their efficacy. Here, we have performed for the first time transcriptome analyses and ribosome profiling in parallel with strain PA14 grown in synthetic cystic fibrosis medium upon exposure to polymyxin E (colistin) and tobramycin. This approach did not only confirm known mechanisms involved in colistin and tobramycin susceptibility but revealed also as yet unknown functions/pathways. Colistin treatment resulted primarily in an anti-oxidative stress response and in the de-regulation of the MexT and AlgU regulons, whereas exposure to tobramycin led predominantly to a rewiring of the expression of multiple amino acid catabolic genes, lower tricarboxylic acid (TCA) cycle genes, type II and VI secretion system genes and genes involved in bacterial motility and attachment, which could potentially lead to a decrease in drug uptake. Moreover, we report that the adverse effects of tobramycin on translation are countered with enhanced expression of genes involved in stalled ribosome rescue, tRNA methylation and type II toxin-antitoxin (TA) systems.
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Affiliation(s)
- Anastasia Cianciulli Sesso
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Branislav Lilić
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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34
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Toward a Comprehensive Analysis of Posttranscriptional Regulatory Networks: a New Tool for the Identification of Small RNA Regulators of Specific mRNAs. mBio 2021; 12:mBio.03608-20. [PMID: 33622723 PMCID: PMC8545128 DOI: 10.1128/mbio.03608-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of computational or experimental tools have been developed to identify targets of small RNA (sRNA) regulation. Here, we modified one of these methods, based on in vivo proximity ligation of sRNAs bound to their targets, referred to as rGRIL-seq, that can be used to capture sRNA regulators of a gene of interest. Intracellular expression of bacteriophage T4 RNA ligase leads to a covalent linking of sRNAs base-paired with mRNAs, and the chimeras are captured using oligonucleotides complementary to the mRNA, followed by sequencing. This allows the identification of known as well as novel sRNAs. We applied rGRIL-seq toward finding sRNA regulators of expression of the stress response sigma factor RpoS in Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae. In E. coli, we confirmed the regulatory role of known sRNAs and discovered a new negative regulator, asYbiE. When applied to P. aeruginosa and V. cholerae, we identified two novel sRNAs (s03661 and s0223) in P. aeruginosa and two known sRNAs (TfoR and Vcr043) in V. cholerae as direct regulators of rpoS. The use of rGRIL-seq for defining multiple posttranscriptional regulatory inputs into individual mRNAs represents a step toward a more comprehensive understanding of the workings of bacterial regulatory networks.
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35
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Wolter DJ, Scott A, Armbruster CR, Whittington D, Edgar JS, Qin X, Buccat AM, McNamara S, Blackledge M, Waalkes A, Salipante SJ, Ernst RK, Hoffman LR. Repeated isolation of an antibiotic-dependent and temperature-sensitive mutant of Pseudomonas aeruginosa from a cystic fibrosis patient. J Antimicrob Chemother 2021; 76:616-625. [PMID: 33259594 DOI: 10.1093/jac/dkaa482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/02/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacteria adapt to survive and grow in different environments. Genetic mutations that promote bacterial survival under harsh conditions can also restrict growth. The causes and consequences of these adaptations have important implications for diagnosis, pathogenesis, and therapy. OBJECTIVES We describe the isolation and characterization of an antibiotic-dependent, temperature-sensitive Pseudomonas aeruginosa mutant chronically infecting the respiratory tract of a cystic fibrosis (CF) patient, underscoring the clinical challenges bacterial adaptations can present. METHODS Respiratory samples collected from a CF patient during routine care were cultured for standard pathogens. P. aeruginosa isolates recovered from samples were analysed for in vitro growth characteristics, antibiotic susceptibility, clonality, and membrane phospholipid and lipid A composition. Genetic mutations were identified by whole genome sequencing. RESULTS P. aeruginosa isolates collected over 5 years from respiratory samples of a CF patient frequently harboured a mutation in phosphatidylserine decarboxylase (psd), encoding an enzyme responsible for phospholipid synthesis. This mutant could only grow at 37°C when in the presence of supplemented magnesium, glycerol, or, surprisingly, the antibiotic sulfamethoxazole, which the source patient had repeatedly received. Of concern, this mutant was not detectable on standard selective medium at 37°C. This growth defect correlated with alterations in membrane phospholipid and lipid A content. CONCLUSIONS A P. aeruginosa mutant chronically infecting a CF patient exhibited dependence on sulphonamides and would likely evade detection using standard clinical laboratory methods. The diagnostic and therapeutic challenges presented by this mutant highlight the complex interplay between bacterial adaptation, antibiotics, and laboratory practices, during chronic bacterial infections.
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Affiliation(s)
- Daniel J Wolter
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Seattle Children's Hospital, Seattle, WA, USA
| | - Alison Scott
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA
| | | | - Dale Whittington
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - John S Edgar
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Xuan Qin
- Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Seattle Children's Hospital, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA
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36
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A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. mBio 2021; 12:mBio.03454-20. [PMID: 33563827 PMCID: PMC8545117 DOI: 10.1128/mbio.03454-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Gram-negative rod-shaped bacterium Pseudomonas aeruginosa is not only a major cause of nosocomial infections but also serves as a model species of bacterial RNA biology. While its transcriptome architecture and posttranscriptional regulation through the RNA-binding proteins Hfq, RsmA, and RsmN have been studied in detail, global information about stable RNA-protein complexes in this human pathogen is currently lacking. Here, we implement gradient profiling by sequencing (Grad-seq) in exponentially growing P. aeruginosa cells to comprehensively predict RNA and protein complexes, based on glycerol gradient sedimentation profiles of >73% of all transcripts and ∼40% of all proteins. As to benchmarking, our global profiles readily reported complexes of stable RNAs of P. aeruginosa, including 6S RNA with RNA polymerase and associated product RNAs (pRNAs). We observe specific clusters of noncoding RNAs, which correlate with Hfq and RsmA/N, and provide a first hint that P. aeruginosa expresses a ProQ-like FinO domain-containing RNA-binding protein. To understand how biological stress may perturb cellular RNA/protein complexes, we performed Grad-seq after infection by the bacteriophage ΦKZ. This model phage, which has a well-defined transcription profile during host takeover, displayed efficient translational utilization of phage mRNAs and tRNAs, as evident from their increased cosedimentation with ribosomal subunits. Additionally, Grad-seq experimentally determines previously overlooked phage-encoded noncoding RNAs. Taken together, the Pseudomonas protein and RNA complex data provided here will pave the way to a better understanding of RNA-protein interactions during viral predation of the bacterial cell.
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Chen J, Chen Z, Yuan K, Huang Z, Mao M. Recombinant bacteriophage T4 Rnl1 impacts Streptococcus mutans biofilm formation. J Oral Microbiol 2020; 13:1860398. [PMID: 33456722 PMCID: PMC7782964 DOI: 10.1080/20002297.2020.1860398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Bacteriophage T4 RNA ligase 1 (T4 Rnl1) can be stably expressed in many bacteria and has been reported to affect the bioactivity of the host bacteria. Recently, we constructed bacteriophage T4 Rnl1 expressing system in Streptococcus mutans, a crucial biofilm-forming and dental caries-causing oral pathogen. Here, we characterized the function of recombinant bacteriophage T4 Rnl1 in biofilm formation of S. mutans. The T4 Rnl1 mutant exhibited similar growth phenotype but resulted in a significant reduction of biofilm biomass compared to wild type strain and empty plasmid carrying strain. The abnormal biofilm of the T4 Rnl1 mutant harbored loose bacterial clusters with defective production and distribution of exopolysaccharides. Moreover, the expression of several biofilm formation-associated genes was dysregulated at mRNA level in the T4 Rnl1 mutant. These results reveal that the bacteriophage T4 Rnl1 exert antibiofilm activities against the cariogenic bacterium S. mutans, which impacts the spatial organization of the exopolysaccharides and further impairs the three-dimensional biofilm architecture. These findings implicate that manipulation of bacteriophage T4 Rnl1, a biological tool used for RNA ligation, will provide a promising approach to cariogenic biofilm control.
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Affiliation(s)
- Juxiu Chen
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhanyi Chen
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keyong Yuan
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengwei Huang
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengying Mao
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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38
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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39
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The Small RNA ErsA Plays a Role in the Regulatory Network of Pseudomonas aeruginosa Pathogenicity in Airway Infections. mSphere 2020; 5:5/5/e00909-20. [PMID: 33055260 PMCID: PMC7565897 DOI: 10.1128/msphere.00909-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial small RNAs play a remarkable role in the regulation of functions involved in host-pathogen interaction. ErsA is a small RNA of Pseudomonas aeruginosa that contributes to the regulation of bacterial virulence traits such as biofilm formation and motility. Shown to take part in a regulatory circuit under the control of the envelope stress response sigma factor σ22, ErsA targets posttranscriptionally the key virulence-associated gene algC Moreover, ErsA contributes to biofilm development and motility through the posttranscriptional modulation of the transcription factor AmrZ. Intending to evaluate the regulatory relevance of ErsA in the pathogenesis of respiratory infections, we analyzed the impact of ErsA-mediated regulation on the virulence potential of P. aeruginosa and the stimulation of the inflammatory response during the infection of bronchial epithelial cells and a murine model. Furthermore, we assessed ErsA expression in a collection of P. aeruginosa clinical pulmonary isolates and investigated the link of ErsA with acquired antibiotic resistance by generating an ersA gene deletion mutant in a multidrug-resistant P. aeruginosa strain which has long been adapted in the airways of a cystic fibrosis (CF) patient. Our results show that the ErsA-mediated regulation is relevant for the P. aeruginosa pathogenicity during acute infection and contributes to the stimulation of the host inflammatory response. Besides, ErsA was able to be subjected to selective pressure for P. aeruginosa pathoadaptation and acquirement of resistance to antibiotics commonly used in clinical practice during chronic CF infections. Our findings establish the role of ErsA as an important regulatory element in the host-pathogen interaction.IMPORTANCE Pseudomonas aeruginosa is one of the most critical multidrug-resistant opportunistic pathogens in humans, able to cause both lethal acute and chronic lung infections. Thorough knowledge of the regulatory mechanisms involved in the establishment and persistence of the airways infections by P. aeruginosa remains elusive. Emerging candidates as molecular regulators of pathogenesis in P. aeruginosa are small RNAs, which act posttranscriptionally as signal transducers of host cues. Known for being involved in the regulation of biofilm formation and responsive to envelope stress response, we show that the small RNA ErsA can play regulatory roles in acute infection, stimulation of host inflammatory response, and mechanisms of acquirement of antibiotic resistance and adaptation during the chronic lung infections of cystic fibrosis patients. Elucidating the complexity of the networks regulating host-pathogen interactions is crucial to identify novel targets for future therapeutic applications.
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40
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Mediati DG, Wu S, Wu W, Tree JJ. Networks of Resistance: Small RNA Control of Antibiotic Resistance. Trends Genet 2020; 37:35-45. [PMID: 32951948 DOI: 10.1016/j.tig.2020.08.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 12/20/2022]
Abstract
The golden age of antibiotics has passed, and the threat of untreatable antimicrobial resistant infections is now a reality for many individuals. Understanding how bacteria resist antimicrobial treatment and regulate gene expression in response to antibiotics is an important step towards combating resistance. In this review we focus on a ubiquitous class of bacterial gene regulators termed regulatory small RNAs (sRNAs) and how they contribute to antimicrobial resistance and tolerance. Small RNAs have notable roles in modulating the composition of the bacterial envelope, and through these functions control intrinsic antimicrobial resistance in many human pathogens. Recent technical advances that allow profiling of the 'sRNA interactome' have revealed a complex post-transcriptional network of sRNA interactions that can be used to identify network hubs and regulatory bottlenecks. Sequence-specific inhibition of these sRNAs with programmable RNA-targeting therapeutics may present avenues for treating antimicrobial resistant pathogens or resensitizing to our current antibiotics.
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Affiliation(s)
- Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sylvania Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Winton Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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41
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Xu G, Xiao L, Wu A, Han R, Ni Y. Enhancing n-Butanol Tolerance of Escherichia coli by Overexpressing of Stress-Responsive Molecular Chaperones. Appl Biochem Biotechnol 2020; 193:257-270. [PMID: 32929579 DOI: 10.1007/s12010-020-03417-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Microbial tolerance to organic solvents is critical for efficient production of biofuels. In this study, n-butanol tolerance of Escherichia coli JM109 was improved by overexpressing of genes encoding stress-responsive small RNA-regulator, RNA chaperone, and molecular chaperone. Gene rpoS, coding for sigma S subunit of RNA polymerase, was the most efficient in improving n-butanol tolerance of E. coli. The highest OD600 and the specific growth rate of JM109/pQE80L-rpoS reached 1.692 and 0.144 h-1 respectively at 1.0% (v/v) n-butanol. Double and triple expression of molecular chaperones rpoS, secB, and groS were conducted and optimized. Recombinant strains JM109/pQE80L-secB-rpoS and JM109/pQE80L-groS-secB-rpoS exhibited the highest n-butanol tolerance, with specific growth rates of 0.164 and 0.165 h-1, respectively. Membrane integrity, potentials, and cell morphology analyses demonstrated the high viability of JM109/pQE80L-groS-secB-rpoS. This study provides guidance on employing various molecular chaperones for enhancing the tolerance of E. coli against n-butanol.
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Affiliation(s)
- Guochao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Lin Xiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Anning Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Ruizhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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42
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Janssen KH, Corley JM, Djapgne L, Cribbs JT, Voelker D, Slusher Z, Nordell R, Regulski EE, Kazmierczak BI, McMackin EW, Yahr TL. Hfq and sRNA 179 Inhibit Expression of the Pseudomonas aeruginosa cAMP-Vfr and Type III Secretion Regulons. mBio 2020; 11:e00363-20. [PMID: 32546612 PMCID: PMC7298702 DOI: 10.1128/mbio.00363-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen causing skin and soft tissue, respiratory, and bloodstream infections. The type III secretion system (T3SS) is one important virulence factor. Production of the T3SS is controlled by ExsA, a transcription factor that activates expression of the entire T3SS regulon. Global regulators including Vfr, RsmA, and Hfq also contribute to regulation of the T3SS. Vfr is a cAMP-responsive transcription factor that activates exsA transcription. RsmA, an RNA-binding protein, inversely controls expression of the T3SS and the type VI secretion system (T6SS). Hfq is an RNA chaperone that functions by stabilizing small noncoding RNAs (sRNAs) and/or facilitating base pairing between sRNAs and mRNA targets. A previous study identified sRNA 1061, which directly targets the exsA mRNA and likely inhibits ExsA synthesis. In this study, we screened an sRNA expression library and identified sRNA 179 as an Hfq-dependent inhibitor of T3SS gene expression. Further characterization revealed that sRNA 179 inhibits the synthesis of both ExsA and Vfr. The previous finding that RsmA stimulates ExsA and Vfr synthesis suggested that sRNA 179 impacts the Gac/Rsm system. Consistent with that idea, the inhibitory activity of sRNA 179 is suppressed in a mutant lacking rsmY and rsmZ, and sRNA 179 expression stimulates rsmY transcription. RsmY and RsmZ are small noncoding RNAs that sequester RsmA from target mRNAs. Our combined findings show that Hfq and sRNA 179 indirectly regulate ExsA and Vfr synthesis by reducing the available pool of RsmA, leading to reduced expression of the T3SS and cAMP-Vfr regulons.IMPORTANCE Control of gene expression by small noncoding RNA (sRNA) is well documented but underappreciated. Deep sequencing of mRNA preparations from Pseudomonas aeruginosa suggests that >500 sRNAs are generated. Few of those sRNAs have defined roles in gene expression. To address that knowledge gap, we constructed an sRNA expression library and identified sRNA 179 as a regulator of the type III secretion system (T3SS) and the cAMP-Vfr regulons. The T3SS- and cAMP-Vfr-controlled genes are critical virulence factors. Increased understanding of the signals and regulatory mechanisms that control these important factors will enhance our understanding of disease progression and reveal potential approaches for therapeutic intervention.
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Affiliation(s)
- Kayley H Janssen
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Jodi M Corley
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Louise Djapgne
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - J T Cribbs
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Deven Voelker
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Zachary Slusher
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Robert Nordell
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Elizabeth E Regulski
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Barbara I Kazmierczak
- Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Timothy L Yahr
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
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43
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Khodadadi E, Zeinalzadeh E, Taghizadeh S, Mehramouz B, Kamounah FS, Khodadadi E, Ganbarov K, Yousefi B, Bastami M, Kafil HS. Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies. Infect Drug Resist 2020; 13:1785-1806. [PMID: 32606829 PMCID: PMC7305820 DOI: 10.2147/idr.s238446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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44
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Denham EL. The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194565. [PMID: 32475775 DOI: 10.1016/j.bbagrm.2020.194565] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
In bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Sponge RNAs modulate free sRNA levels in the cell through RNA-RNA interactions that sequester ("soak up") the sRNA and/or promote degradation of the target sRNA or the sponge RNA-sRNA complex. The development of complex RNA sequencing strategies for the detection of RNA-RNA interactions has enabled identification of several sponge RNAs, as well as previously known regulatory RNAs able to act as both regulators and sponges. This review highlights techniques that have enabled the identification of these sponge RNAs, the origins of sponge RNAs and the mechanisms by which they function in the post-transcriptional network.
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Affiliation(s)
- Emma L Denham
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom.
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45
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Sonnleitner E, Pusic P, Wolfinger MT, Bläsi U. Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq. Front Microbiol 2020; 11:1001. [PMID: 32528439 PMCID: PMC7264166 DOI: 10.3389/fmicb.2020.01001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/24/2020] [Indexed: 12/29/2022] Open
Abstract
Carbapenems are often the antibiotics of choice to combat life threatening infections caused by the opportunistic human pathogen Pseudomonas aeruginosa. The outer membrane porins OprD and OpdP serve as entry ports for carbapenems. Here, we report that the RNA chaperone Hfq governs post-transcriptional regulation of the oprD and opdP genes in a distinctive manner. Hfq together with the recently described small regulatory RNAs (sRNAs) ErsA and Sr0161 is shown to mediate translational repression of oprD, whereas opdP appears not to be regulated by sRNAs. At variance, our data indicate that opdP is translationally repressed by a regulatory complex consisting of Hfq and the catabolite repression protein Crc, an assembly known to be key to carbon catabolite repression in P. aeruginosa. The regulatory RNA CrcZ, which is up-regulated during growth of P. aeruginosa on less preferred carbon sources, is known to sequester Hfq, which relieves Hfq-mediated translational repression of genes. The differential carbapenem susceptibility during growth on different carbon sources can thus be understood in light of Hfq-dependent oprD/opdP regulation and of the antagonizing function of the CrcZ RNA on Hfq regulatory complexes.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Petra Pusic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
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46
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Adams PP, Storz G. Prevalence of small base-pairing RNAs derived from diverse genomic loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194524. [PMID: 32147527 DOI: 10.1016/j.bbagrm.2020.194524] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. 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)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
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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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48
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Valli RXE, Lyng M, Kirkpatrick CL. There is no hiding if you Seq: recent breakthroughs in Pseudomonas aeruginosa research revealed by genomic and transcriptomic next-generation sequencing. J Med Microbiol 2020; 69:162-175. [PMID: 31935190 DOI: 10.1099/jmm.0.001135] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The advent of next-generation sequencing technology has revolutionized the field of prokaryotic genetics and genomics by allowing interrogation of entire genomes, transcriptomes and global transcription factor binding profiles. As more studies employing these techniques have been performed, the state of the art regarding prokaryotic gene regulation has developed from the level of individual genes to genetic regulatory networks and systems biology. When applied to bacterial pathogens, particularly valuable insights have been gained into the regulation of virulence-associated genes, their relative importance to bacterial survival in planktonic, biofilm or host infection scenarios, antimicrobial resistance and the molecular details of host-pathogen interactions. This review outlines some of the latest developments and applications of next-generation sequencing techniques that have used primarily Pseudomonas aeruginosa as a model system. We focus particularly on insights into Pseudomonas virulence and infection that have been gained from these approaches and the future directions in which this field could develop.
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Affiliation(s)
- Richard X E Valli
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Clare L Kirkpatrick
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Gestal MC, Howard LK, Dewan K, Johnson HM, Barbier M, Bryant C, Soumana IH, Rivera I, Linz B, Blas-Machado U, Harvill ET. Enhancement of immune response against Bordetella spp. by disrupting immunomodulation. Sci Rep 2019; 9:20261. [PMID: 31889098 PMCID: PMC6937331 DOI: 10.1038/s41598-019-56652-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/12/2019] [Indexed: 12/27/2022] Open
Abstract
Well-adapted pathogens must evade clearance by the host immune system and the study of how they do this has revealed myriad complex strategies and mechanisms. Classical bordetellae are very closely related subspecies that are known to modulate adaptive immunity in a variety of ways, permitting them to either persist for life or repeatedly infect the same host. Exploring the hypothesis that exposure to immune cells would cause bordetellae to induce expression of important immunomodulatory mechanisms, we identified a putative regulator of an immunomodulatory pathway. The deletion of btrS in B. bronchiseptica did not affect colonization or initial growth in the respiratory tract of mice, its natural host, but did increase activation of the inflammasome pathway, and recruitment of inflammatory cells. The mutant lacking btrS recruited many more B and T cells into the lungs, where they rapidly formed highly organized and distinctive Bronchial Associated Lymphoid Tissue (BALT) not induced by any wild type Bordetella species, and a much more rapid and strong antibody response than observed with any of these species. Immunity induced by the mutant was measurably more robust in all respiratory organs, providing completely sterilizing immunity that protected against challenge infections for many months. Moreover, the mutant induced sterilizing immunity against infection with other classical bordetellae, including B. pertussis and B. parapertussis, something the current vaccines do not provide. These findings reveal profound immunomodulation by bordetellae and demonstrate that by disrupting it much more robust protective immunity can be generated, providing a pathway to greatly improve vaccines and preventive treatments against these important pathogens.
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Affiliation(s)
- Monica C Gestal
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America.
| | - Laura K Howard
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Kalyan Dewan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Hannah M Johnson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, United States of America
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, United States of America
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, United Kingdom
| | - Illiassou Hamidou Soumana
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Israel Rivera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Bodo Linz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Uriel Blas-Machado
- Department of Pathology, Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Eric T Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America.
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50
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Lei L, Zhang B, Mao M, Chen H, Wu S, Deng Y, Yang Y, Zhou H, Hu T. Carbohydrate Metabolism Regulated by Antisense vicR RNA in Cariogenicity. J Dent Res 2019; 99:204-213. [PMID: 31821772 DOI: 10.1177/0022034519890570] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Streptococcus mutans is a major cariogenic pathogen that resides in multispecies oral microbial biofilms. The VicRK 2-component system is crucial for bacterial adaptation, virulence, and biofilm organization and contains a global and vital response regulator, VicR. Notably, we identified an antisense vicR RNA (AS vicR) associated with an adjacent RNase III–encoding ( rnc) gene that was relevant to microRNA-size small RNAs (msRNAs). Here, we report that ASvicR overexpression significantly impeded bacterial growth, biofilm exopolysaccharide synthesis, and cariogenicity in vivo. Transcriptome analysis revealed that the AS vicR RNA mainly regulated carbohydrate metabolism. In particular, overproducing AS vicR demonstrated a reduction in galactose and glucose metabolism by monosaccharide composition analysis. The results of high-performance gel permeation chromatography revealed that the water-insoluble glucans isolated from AS vicR presented much lower molecular weights. Furthermore, direct evidence showed that total RNAs were disrupted by rnc-encoded RNase III. With the coexpression of T4 RNA ligase, putative msRNA1657, which is an rnc-related messenger RNA, was verified to bind to the 5′-UTR regions of the vicR gene. Furthermore, AS vicR regulation revealed a sponge regulatory-mediated network for msRNA associated with adjacent RNase III–encoding genes. There was an increase in AS vicR transcript levels in clinical S. mutans strains from caries-free children, while the expression of AS vicR was decreased in early childhood caries patients; this outcome may be explored as a potential strategy contributing to the management of dental caries. Taken together, our findings suggest an important role of AS vicR-mediated sponge regulation in S. mutans, indicating the characterization of lactose metabolism by a vital response regulator in cariogenicity. These findings have a number of implications and have reshaped our understanding of bacterial gene regulation from its transcriptional conception to the key roles of regulatory RNAs.
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Affiliation(s)
- L. Lei
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - B. Zhang
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - M. Mao
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Endodontics, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - H. Chen
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - S. Wu
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y. Deng
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Y. Yang
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - H. Zhou
- Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - T. Hu
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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