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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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2
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Mishra RAK, Muthukaliannan GK, Rathinasabapathi P. Effects of Flavonoids and Antibiotics Combination on Preformed Biofilms and Small RNA of Staphylococcus aureus. Indian J Microbiol 2023; 63:307-316. [PMID: 37781018 PMCID: PMC10533456 DOI: 10.1007/s12088-023-01086-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/24/2023] [Indexed: 10/03/2023] Open
Abstract
Antibiotic resistance of Staphylococcus aureus has considerably increased among non-clinical or asymptomatic individuals. The formation of biofilms denies antimicrobial access to its targets present on the surface and inside the cell. The present study tested the effect of the combination of flavonoids and antibiotics over the preformed biofilms of S. aureus. The eradication of the preformed biofilms was analyzed using the crystal violet method. It has shown that 2500 µg mL-1 Rutin and 100 µg mL-1 Erythromycin (MIC Concentration) combination efficiently reduced the growth of the cells, which were adhered to the surfaces forming the biofilms. Fluorescence microscopic analysis indicated that the Rutin and Erythromycin (MIC value) combinations could eradicate the preformed biofilm cells more efficiently than other combinations. We found that the flavonoids and antibiotics with MIC concentration show a significant effect over the preformed biofilms cells of S. aureus. In addition, the semi-quantitative real-time PCR analysis for the sRNAs under the treatment of Rutin and Erythromycin combinations showed that few small RNAs expression (SprF, SprG, ArtR, Teg49, Teg41, and RNAIII) are getting downregulated upon the treatment; but again recovers with the incubation time interval increases. Combinations have a significant effect on Teg49 where there is a very faint intensity of the band, but for other small RNAs, there is an irregular pattern on the gel image. It has been concluded that at the initial period of incubation, the combinations have an effect on all the sRNAs but once the incubation increases, the effects have been slowly decreasing. It has been concluded that the combination has been able to reduce the doubling time of S. aureus upon treatment. Whereas, the small RNAs used in the study can be further evaluated for expression profiling through qRT-PCT. Graphical abstract
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Affiliation(s)
- Rudra Awdhesh Kumar Mishra
- School of Biosciences and Technology, Vellore Institute of Technology, Katpadi, Vellore, 632014 India
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | | | - Pasupathi Rathinasabapathi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
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Wang M, Liang Y, Li F, Shen S, Huang X, Sun Y. Enhancement of biological denitrification by the addition of novel sRNA Pda200 under antibiotic pressure. BIORESOURCE TECHNOLOGY 2022; 365:128113. [PMID: 36252762 DOI: 10.1016/j.biortech.2022.128113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Paracoccus denitrificans can adapt to complex environmental changes and sRNAs play crucial roles during this process. This work aim to identify antibiotic-induced sRNA that regulated denitrification and explored its potential for functional enhancement of this process. Target prediction indicated complementary base pairing between the denitrifying gene nosZ and the sRNA Pda200. Anaerobic culture of P. denitrificans ATCC 19367 in the presence of florfenicol (FF) resulted in significant decreases in nosZ and Pda200 gene expression (p < 0.01). Two additional denitrifiers isolated from contaminated sediment were co-cultured with ATCC 19367 to generate a consortium. And an inducible Pda200 expression strain was also added. The results revealed that Pda200 significantly enhanced napA, napB and norB expression in different types of denitrifiers under FF condition (p < 0.05 ∼ 0.001). This study identified the sRNA Pda200 as a novel positive regulator of denitrification, which may realize the efficient treatment of antibiotic-contaminated wastewater by microbial agents.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China; Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Fulin Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Shuqing Shen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Xinyu Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China.
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Perlaza-Jiménez L, Tan KS, Piper SJ, Johnson RM, Bamert RS, Stubenrauch CJ, Wright A, Lupton D, Lithgow T, Belousoff MJ. A Structurally Characterized Staphylococcus aureus Evolutionary Escape Route from Treatment with the Antibiotic Linezolid. Microbiol Spectr 2022; 10:e0058322. [PMID: 35736238 PMCID: PMC9431193 DOI: 10.1128/spectrum.00583-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the oxazolidinone family, of which linezolid is the first member to see regular use in the clinic. Here, we report a short time scale selection experiment in which strains of MRSA were subjected to linezolid treatment. Clonal isolates which had evolved a linezolid-resistant phenotype were characterized by whole-genome sequencing. Linezolid-resistant mutants were identified which had accumulated mutations in the ribosomal protein uL3. Multiple clones which had two mutations in uL3 exhibited resistance to linezolid, 2-fold higher than the clinical breakpoint. Ribosomes from this strain were isolated and subjected to single-particle cryo-electron microscopic analysis and compared to the ribosomes from the parent strain. We found that the mutations in uL3 lead to a rearrangement of a loop that makes contact with Helix 90, propagating a structural change over 15 Å away. This distal change swings nucleotide U2504 into the binding site of the antibiotic, causing linezolid resistance. IMPORTANCE Antibiotic resistance poses a critical problem to human health and decreases the utility of these lifesaving drugs. Of particular concern is the "superbug" methicillin-resistant Staphylococcus aureus (MRSA), for which treatment of infection requires the use of last-line antibiotics, including linezolid. In this paper, we characterize the atomic rearrangements which the ribosome, the target of linezolid, undergoes during its evolutionary journey toward becoming drug resistant. Using cryo-electron microscopy, we describe a particular molecular mechanism which MRSA uses to become resistant to linezolid.
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Affiliation(s)
- Laura Perlaza-Jiménez
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Kher-Shing Tan
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sarah J. Piper
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Rachel M. Johnson
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Rebecca S. Bamert
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Christopher J. Stubenrauch
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Alexander Wright
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - David Lupton
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Matthew J. Belousoff
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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5
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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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Wang M, Zhou T, Liang Y, Li G, Sun Y. Response characteristics of nirS-type denitrifier Paracoccus denitrificans under florfenicol stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 219:112355. [PMID: 34049225 DOI: 10.1016/j.ecoenv.2021.112355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Florfenicol (FF) is widely used in aquaculture and can interfere with denitrification when released into natural ecosystems. The aim of this study was to analyze the response characteristics of nirS-type denitrifier Paracoccus denitrificans under FF stress and further mine antibiotic-responsive factors in aquatic environment. Phenotypic analysis revealed that FF delayed the nitrate removal with a maximum inhibition value of 82.4% at exponential growth phase, leading to nitrite accumulation reached to 21.9-fold and biofilm biomass decreased by ~38.6%, which were due to the lower bacterial population count (P < 0.01). RNA-seq transcriptome analyses indicated that FF treatment decreased the expression of nirS, norB, nosD and nosZ genes that encoded enzymes required for NO2- to N2 conversion from 1.02- to 2.21-fold (P < 0.001). Furthermore, gene associated with the flagellar system FlgL was also down-regulated by 1.03-fold (P < 0.001). Moreover, 10 confirmed sRNAs were significantly induced, which regulated a wide range of metabolic pathways and protein expression. Interestingly, different bacteria contained the same sRNAs means that sRNAs can spread between them. Overall, this study suggests that the denitrification of nirS-type denitrifiers can be hampered widely by FF and the key sRNAs have great potential to be antibiotic-responsive factors.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Tong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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7
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Joshi B, Singh B, Nadeem A, Askarian F, Wai SN, Johannessen M, Hegstad K. Transcriptome Profiling of Staphylococcus aureus Associated Extracellular Vesicles Reveals Presence of Small RNA-Cargo. Front Mol Biosci 2021; 7:566207. [PMID: 33521050 PMCID: PMC7838569 DOI: 10.3389/fmolb.2020.566207] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial extracellular vesicles (EVs) have a vital role in bacterial pathogenesis. However, to date, the small RNA-cargo of EVs released by the opportunistic pathogen Staphylococcus aureus has not been characterized. Here, we shed light on the association of small RNAs with EVs secreted by S. aureus MSSA476 cultured in iron-depleted bacteriologic media supplemented with a subinhibitory dosage of vancomycin to mimic infection condition. Confocal microscopy analysis on intact RNase-treated EVs indicated that RNA is associated with EV particles. Transcriptomic followed by bioinformatics analysis of EV-associated RNA revealed the presence of potential gene regulatory small RNAs and high levels of tRNAs. Among the EV-associated enriched small RNAs were SsrA, RsaC and RNAIII. Our finding invites new insights into the potential role of EV-associated RNA as a modulator of host-pathogen interaction.
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Affiliation(s)
- Bishnu Joshi
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Aftab Nadeem
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fatemeh Askarian
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sun Nyunt Wai
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mona Johannessen
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North-Norway, Tromsø, Norway
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