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Zhao D, Liu H, Xu M, Yin C, Xiao X, Dai K. Functional carbon dots-hydrogel complex for selective antibacterial and detection applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124195. [PMID: 38547782 DOI: 10.1016/j.saa.2024.124195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The carbon dots (CDs) with excellent optical properties and their hydrogel complex are of great significance in biomedicine, healthcare and biochemical detection fields. This paper reports the preparation of green-emitting CDs (MA-CDs) through one-step hydrothermal route with citric acid as reducing agent, L-malic acid as carbon source and N-(2-hydroxyethyl)ethylenediamine as nitrogen source. To expand its application in biology, MA-CDs were coupled with vancomycin to obtain multifunctional CDs (VMA-CDs). The prepared VMA-CDs exhibit selective antibacterial behavior to Gram-positive bacteria, and it could be used as a fluorescent probe to selectively label Staphylococcus aureus (S. aureus). Moreover, thanks to the excellent optical properties of VMA-CDs, it has been used as a fluorescent sensor to detect Au3+ with detection range of 6.50 nM-21.93 μM and detection limit 3.98 nM. By introducing the fluorescence of CDs as the reference signal, and VMA-CDs as a response signal, the hydrogel (V-SP) was prepared and realized the detection of Au3+ in microfluidics with assistance of a smartphone to collect and analyze data.
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Affiliation(s)
- Dan Zhao
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China.
| | - Huan Liu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China
| | - Mengyu Xu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China
| | - Chengxin Yin
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China
| | - Xincai Xiao
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China
| | - Kang Dai
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, PR China; National Demonstration Center for Experimental Ethnopharmacology Education (South-Central Minzu University), Wuhan 430065, PR China.
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2
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Mediati DG, Dan W, Lalaouna D, Dinh H, Pokhrel A, Rowell KN, Michie KA, Stinear TP, Cain AK, Tree JJ. The 3' UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions. Cell Rep 2024; 43:114082. [PMID: 38583155 DOI: 10.1016/j.celrep.2024.114082] [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] [Received: 05/22/2023] [Revised: 01/17/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with vancomycin-intermediate S. aureus isolates. The regulatory 3' UTR of the vigR mRNA contributes to vancomycin tolerance and upregulates the autolysin IsaA. Using MS2-affinity purification coupled with RNA sequencing, we find that the vigR 3' UTR also regulates dapE, a succinyl-diaminopimelate desuccinylase required for lysine and peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the 3' UTR increased virulence, while the isaA mutant is completely attenuated in a wax moth larvae model. Sequence and structural analyses of vigR indicated that the 3' UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions that contribute sequence for the isaA interaction seed and may functionalize the 3' UTR.
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Affiliation(s)
- Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
| | - William Dan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - David Lalaouna
- Université de Strasbourg, CNRS, ARN UPR 9002, Strasbourg, France
| | - Hue Dinh
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia; School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Keiran N Rowell
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Katharine A Michie
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amy K Cain
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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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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Hu J, Han X, Ma X, Chen X, Zhou Z, Peng P, Yu Z, Hou Y, Han P, Pang L, Yang Y, Xu J, Wu W. Comparative proteomic analysis of vancomycin-sensitive and vancomycin-intermediate resistant Staphylococcus aureus. Eur J Clin Microbiol Infect Dis 2024; 43:139-153. [PMID: 37985551 DOI: 10.1007/s10096-023-04709-3] [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] [Received: 05/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
PURPOSE The extensive use of vancomycin has led to the development of Staphylococcus aureus strains with varying degrees of resistance to vancomycin. The present study aimed to explore the molecular causes of vancomycin resistance by conducting a proteomics analysis of subcellular fractions isolated from vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-sensitive S. aureus (VSSA) strains. METHODS We conducted proteomics analysis of subcellular fractions isolated from 2 isogenic S. aureus strains: strain 11 (VSSA) and strain 11Y (VISA). We used an integrated quantitative proteomics approach assisted by bioinformatics analysis, and comprehensively investigated the proteome profile. Intensive bioinformatics analysis, including protein annotation, functional classification, functional enrichment, and functional enrichment-based cluster analysis, was used to annotate quantifiable targets. RESULTS We identified 128 upregulated proteins and 21 downregulated proteins in strain 11Y as compared to strain 11. The largest group of differentially expressed proteins was composed of enzymatic proteins associated with metabolic and catalytic activity, which accounted for 32.1% and 50% of the total proteins, respectively. Some proteins were indispensable parts of the regulatory networks of S. aureus that were altered with vancomycin treatment, and these proteins were related to cell wall metabolism, cell adhesion, proteolysis, and pressure response. CONCLUSION Our proteomics study revealed regulatory proteins associated with vancomycin resistance in S. aureus. Some of these proteins were involved in the regulation of cell metabolism and function, which provides potential targets for the development of strategies to manage vancomycin resistance in S. aureus.
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Affiliation(s)
- Jian Hu
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Xinjun Han
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Xiaoxue Ma
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Xutao Chen
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Zhenping Zhou
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China
| | - Peilan Peng
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Zhao Yu
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Yongzhi Hou
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Peiru Han
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Long Pang
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Yali Yang
- Department of Medical Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, People's Republic of China
| | - Jia Xu
- Department of Medical Microbiology, Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, 110034, People's Republic of China.
| | - Wenhui Wu
- Department of Laboratory Medicine, Yixing Hospital of Traditional Chinese Medicine, Yixing, No. 128 East Yangquan Road, Yicheng Subdistrict, Yixing, 214200, Jiangsu, People's Republic of China.
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5
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Esteban-Serna S, Chu LC, Chauhan M, Raja P, Granneman S. Defining Bacterial RNA-RNA Interactomes Using CLASH. Methods Mol Biol 2024; 2741:307-345. [PMID: 38217661 DOI: 10.1007/978-1-0716-3565-0_17] [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: 01/15/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen accounting for high mortality rates among infected patients. Transcriptomic regulation by small RNAs (sRNAs) has been shown to regulate networks promoting antibiotic resistance and virulence in S. aureus. Yet, the biological role of most sRNAs during MRSA host infection remains unknown. To fill this gap, in collaboration with the lab of Jai Tree, we performed comprehensive RNA-RNA interactome analyses in MRSA using CLASH under conditions that mimic the host environment. Here we present a detailed version of this optimized CLASH (cross-linking, ligation, and sequencing of hybrids) protocol we recently developed, which has been tailored to explore the RNA interactome in S. aureus as well as other Gram-positive bacteria. Alongside, we introduce a compilation of helpful Python functions for analyzing folding energies of putative RNA-RNA interactions and streamlining sRNA and mRNA seed discovery in CLASH data. In the accompanying computational demonstration, we aim to establish a standardized strategy to evaluate the likelihood that observed chimeras arise from true RNA-RNA interactions.
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Affiliation(s)
- Sofia Esteban-Serna
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Liang-Cui Chu
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mehak Chauhan
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Pujitha Raja
- Division of Pathway and Infection Medicine, University of Edinburgh, Edinburgh, UK
| | - Sander Granneman
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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6
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Börner J, Friedrich T, Klug G. RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides. Mol Microbiol 2023; 120:874-892. [PMID: 37823424 DOI: 10.1111/mmi.15181] [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: 07/21/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
RNase III is a dsRNA-specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α-proteobacterium Rhodobacter sphaeroides. RNA-seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type-like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum-sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment-protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III-mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.
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Affiliation(s)
- Janek Börner
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Friedrich
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Giessen, Germany
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
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7
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Esteban‐Serna S, McCaughan H, Granneman S. Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes. Mol Microbiol 2023; 120:477-489. [PMID: 37165708 PMCID: PMC10952675 DOI: 10.1111/mmi.15073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
RNA-binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles in adaptive responses in microbes. A robust approach to examine protein-RNA interactions involves irradiating cells with UV light to form covalent adducts between RBPs and their cognate RNAs. Combined with RNA or protein purification, these procedures can provide global RBP censuses or transcriptomic maps for all target sequences of a single protein in living cells. The recent development of novel methods has quickly populated the RBP landscape in microorganisms. Here, we provide an overview of prominent UV cross-linking techniques which have been applied to investigate RNA interactomes in microbes. By assessing their advantages and caveats, this technical evaluation intends to guide the selection of appropriate methods and experimental design as well as to encourage the use of complementary UV-dependent techniques to inspect RNA-binding activity.
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Affiliation(s)
- Sofia Esteban‐Serna
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Hugh McCaughan
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Sander Granneman
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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8
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Broglia L, Le Rhun A, Charpentier E. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol Rev 2023; 47:fuad049. [PMID: 37656885 PMCID: PMC10503654 DOI: 10.1093/femsre/fuad049] [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: 03/23/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.
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Affiliation(s)
- Laura Broglia
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Center for Human Technologies, Istituto Italiano di Tecnologia, 16152 Genova, Italy
| | - Anaïs Le Rhun
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
- Institute for Biology, Humboldt University, D-10115 Berlin, Germany
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9
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Wu W, Pang CNI, Tree JJ, Mediati DG. Profiling the in vivo RNA interactome associated with the endoribonuclease RNase III in Staphylococcus aureus. Methods Enzymol 2023; 692:299-324. [PMID: 37925184 DOI: 10.1016/bs.mie.2023.05.001] [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: 11/06/2023]
Abstract
Regulatory small RNA (sRNA) have been extensively studied in model Gram-negative bacteria, but the functional characterisation of these post-transcriptional gene regulators in Gram-positives remains a major challenge. Our previous work in enterohaemorrhagic E. coli utilised the proximity-dependant ligation technique termed CLASH (UV-crosslinking, ligation, and sequencing of hybrids) for direct high-throughput sequencing of the regulatory sRNA-RNA interactions within the cell. Recently, we adapted the CLASH technique and demonstrated that UV-crosslinking and RNA proximity-dependant ligation can be applied to Staphylococcus aureus, which uncovered the first RNA-RNA interaction network in a Gram-positive bacterium. In this chapter, we describe modifications to the CLASH technique that were developed to capture the RNA interactome associated with the double-stranded endoribonuclease RNase III in two clinical isolates of S. aureus. To briefly summarise our CLASH methodology, regulatory RNA-RNA interactions were first UV-crosslinked in vivo to the RNase III protein and protein-RNA complexes were affinity-purified using the His6-TEV-FLAG tags. Linkers were ligated to RNase III-bound RNA during library preparation and duplexed RNA-RNA species were ligated together to form a single contiguous RNA 'hybrid'. The RNase III-RNA binding sites and RNA-RNA interactions occurring on RNase III (RNA hybrids) were then identified by paired-end sequencing technology. RNase III-CLASH represents a step towards a systems-level understanding of regulatory RNA in Gram-positive bacteria.
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Affiliation(s)
- Winton Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Chi Nam Ignatius Pang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Children's Medical Research Institute, Westmead, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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10
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RNase III-CLASH brings bacterial RNA networks into focus. Trends Microbiol 2022; 30:1125-1127. [PMID: 36184448 DOI: 10.1016/j.tim.2022.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Bacterial small RNAs have emerged as crucial regulators in complex networks controlling diverse phenotypes. Two groups, Mediati et al. and McKellar et al., have leveraged CLASH technology and the global regulatory potential of RNase III to build a rich landscape of RNA interactions in Staphylococcus aureus, revealing post-transcriptional control of virulence and new mechanistic themes for exploration.
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11
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McKellar SW, Ivanova I, Arede P, Zapf RL, Mercier N, Chu LC, Mediati DG, Pickering AC, Briaud P, Foster RG, Kudla G, Fitzgerald JR, Caldelari I, Carroll RK, Tree JJ, Granneman S. RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression. Nat Commun 2022; 13:3560. [PMID: 35732654 PMCID: PMC9217828 DOI: 10.1038/s41467-022-31173-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/03/2022] [Indexed: 01/13/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.
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Affiliation(s)
- Stuart W McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Ivayla Ivanova
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Pedro Arede
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rachel L Zapf
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Noémie Mercier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Liang-Cui Chu
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Amy C Pickering
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK
| | - Paul Briaud
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
| | - Robert G Foster
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, Scotland, UK
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA
- The Infectious and Tropical Disease Institute, Ohio University, Athens, OH, 45701, USA
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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12
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Miyakoshi M, Morita T, Kobayashi A, Berger A, Takahashi H, Gotoh Y, Hayashi T, Tanaka K. Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae. eLife 2022; 11:82411. [PMID: 36440827 PMCID: PMC9731577 DOI: 10.7554/elife.82411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glutamine synthetase (GS) is the key enzyme of nitrogen assimilation induced under nitrogen limiting conditions. The carbon skeleton of glutamate and glutamine, 2-oxoglutarate, is supplied from the TCA cycle, but how this metabolic flow is controlled in response to nitrogen availability remains unknown. We show that the expression of the E1o component of 2-oxoglutarate dehydrogenase, SucA, is repressed under nitrogen limitation in Salmonella enterica and Escherichia coli. The repression is exerted at the post-transcriptional level by an Hfq-dependent sRNA GlnZ generated from the 3'UTR of the GS-encoding glnA mRNA. Enterobacterial GlnZ variants contain a conserved seed sequence and primarily regulate sucA through base-pairing far upstream of the translation initiation region. During growth on glutamine as the nitrogen source, the glnA 3'UTR deletion mutants expressed SucA at higher levels than the S. enterica and E. coli wild-type strains, respectively. In E. coli, the transcriptional regulator Nac also participates in the repression of sucA. Lastly, this study clarifies that the release of GlnZ from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA. Thus, the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of TsukubaTsukubaJapan,Transborder Medical Research Center, University of TsukubaTsukubaJapan,International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | - Teppei Morita
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan,Graduate School of Media and Governance, Keio UniversityFujisawaJapan
| | - Asaki Kobayashi
- Transborder Medical Research Center, University of TsukubaTsukubaJapan
| | - Anna Berger
- International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | | | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of TechnologyYokohamaJapan
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