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Han Y, Xiong Y, Wang M, Wang J, Song T, Yu J, Hu J, Zhao Z, Li M, Li Y, Chen Y. Small RNA-regulated expression of efflux pump affects tigecycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae. Microbiol Res 2024; 287:127825. [PMID: 39047663 DOI: 10.1016/j.micres.2024.127825] [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: 09/18/2023] [Revised: 12/22/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
Tigecycline and the newly Food and Drug Administration-approved tetracyclines, including eravacycline and omadacycline, are regarded as last-resort treatments for multidrug-resistant Enterobacterales. However, tigecycline resistance in Klebsiella pneumoniae has increased, especially the underlying mechanism of heteroresistance is unclear. This study aimed to elucidate the mechanisms underlying tigecycline resistance and heteroresistance in clinical K. pneumoniae isolates. A total of 153 clinical K. pneumoniae isolates were collected, and identified 15 tigecycline-resistant and three tigecycline-heteroresistant isolates using broth microdilution and population analysis profile methods, respectively. Total RNAs from K. pneumoniae ATCC13883 and the laboratory-induced tigecycline-resistant strain were extracted and sequenced on an Illumina platform. Differentially expressed genes and regulatory small RNAs (sRNAs) were analyzed and validated in clinical isolates of K. pneumoniae using quantitative real-time PCR. RNA sequencing results showed that mdtABC efflux pump genes were significantly upregulated in the tigecycline-resistant strains. Overexpression of mdtABC was observed in a clinical K. pneumoniae isolate, which increased tigecycline minimum inhibitory concentrations (MICs) and was involved in tigecycline heteroresistance. Sequencing analysis of sRNA demonstrated that candidate sRNA-120 directly interacted with the mdtABC operon and was downregulated in tigecycline-resistant strains. We generated an sRNA-120 deletion mutation strain and a complemented strain of K. pneumoniae. The sRNA-120 deletion strain displayed increased mRNA levels of mdtA, mdtB, and mdtC and an increase in MICs of tigecycline. The complemented strain of sRNA-120 restored the mRNA levels of these genes and the susceptibility to tigecycline. RNA antisense purification and parallel reaction monitoring mass spectrometry were performed to verify the interactions between sRNA-120 and mdtABC. Collectively, our study highlights that the post-transcriptional repression of mdtABC through sRNA-120 may provide an additional layer of efflux pump gene expression control, which is important for resistance and heteroresistance in clinical K. pneumoniae isolates.
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Affiliation(s)
- Yuqiao Han
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Yilin Xiong
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Mengyao Wang
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Jia Wang
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Tao Song
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Jing Yu
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Jia Hu
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Zinan Zhao
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Ming Li
- Department of Microecology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China
| | - Ying Li
- Department of Clinical Laboratory, Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Yang Chen
- Department of Biotechnology, College of Basic Medical Science, Dalian Medical University, Dalian 116044, China; Liaoning Provincial Core Lab of Medical Molecular Biology, Dalian Medical University, Dalian 116044, China.
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Li L, Gao Y, Wang L, Lu F, Ji Q, Zhang Y, Yang S, Cheng P, Sun F, Qu S. The effects of NDM-5 on Escherichia coli and the screening of interacting proteins. Front Microbiol 2024; 15:1328572. [PMID: 38348193 PMCID: PMC10861311 DOI: 10.3389/fmicb.2024.1328572] [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: 10/27/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (E. coli) strains are widely distributed and spreading rapidly, creating significant challenges for clinical therapeutics. NDM-5, a novel mutant of New Delhi Metallo-β-Lactamase-1 (NDM-1), exhibits high hydrolase activity toward carbapenems. Since the genetic backgrounds of clinically isolated carbapenem-resistant E. coli are heterogeneous, it is difficult to accurately evaluate the impact of blaNDM-5 on antibiotic resistance. Herein, E. coli BL21 was transformed with a plasmid harboring blaNDM-5, and the resultant strain was named BL21 (pET-28a-blaNDM-5). Consistent with the findings of previous studies, the introduction of exogenous blaNDM-5 resulted in markedly greater resistance of E. coli to multiple β-lactam antibiotics. Compared with BL21 (pET-28a), BL21 (pET-28a-blaNDM-5) exhibited reduced motility but a significant increase in biofilm formation capacity. Furthermore, transcriptome sequencing was conducted to compare the transcriptional differences between BL21 (pET-28a) and BL21 (pET-28a-blaNDM-5). A total of 461 differentially expressed genes were identified, including those related to antibiotic resistance, such as genes associated with the active efflux system (yddA, mcbR and emrY), pili (csgC, csgF and fimD), biofilm formation (csgD, csgB and ecpR) and antioxidant processes (nuoG). Finally, the pGS21a plasmid harboring blaNDM-5 was transformed into E. coli Rosetta2, after which the expression of the NDM-5 protein was induced using isopropyl-β-D-thiogalactoside (IPTG). Using glutathione-S-transferase (GST) pull-down assays, total proteins from E. coli were scanned to screen out 82 proteins that potentially interacted with NDM-5. Our findings provide new insight into the identified proteins to identify potential antibiotic targets and design novel inhibitors of carbapenem-resistant bacteria.
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Affiliation(s)
- Lin Li
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Yiming Gao
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Longbo Wang
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Fang Lu
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qianyu Ji
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yanfang Zhang
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Shuo Yang
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ping Cheng
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Feifei Sun
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Shaoqi Qu
- Pharmacology and Toxicology Laboratory, Animal-Derived Food Safety Innovation Team, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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Gao L, Ma X. Transcriptome Analysis of Acinetobacter baumannii in Rapid Response to Subinhibitory Concentration of Minocycline. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16095. [PMID: 36498165 PMCID: PMC9741440 DOI: 10.3390/ijerph192316095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The increasing emergence of multidrug-resistant Acinetobacter baumannii brings great threats to public health. Minocycline is a kind of semisynthetic derivative of the antibacterial drug tetracycline and is often used to treat infections caused by multidrug-resistant A. baumannii with other antibiotics. However, minocycline-resistant A. baumannii appears constantly. To rapidly explore the response of A. baumannii to minocycline stress, RNA-seq was carried out to compare the difference in the transcriptome of A. baumannii ATCC19606 in the presence or absence of minocycline. The results showed that 25 genes were differentially expressed, including 10 downregulated genes and 15 upregulated genes, and 24 sRNA were upregulated and 24 were downregulated based on the filter criteria (Log2FC > 1 or <−1 and FDR < 0.05). RtcB family protein and ABC transporter ATP-binding protein were upregulated by 2.6- and 11.3-fold, and molecular chaperone GroES, chaperonin GroL, class C beta-lactamase ADC-158, amino acid ABC transporter permease, and APC family permease were downregulated by at least two-fold in the presence of half-MIC minocycline. The differentially expressed genes are mainly involved in the stress response, the GroES/GroEL chaperonin system, and transport metabolic pathways. sRNA 1248 was significantly upregulated, and sRNA 1767, 5182, and 6984 were downregulated in a rapid response to minocycline. These results provide insights into the adaptive mechanism of A. baumannii to minocycline.
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Affiliation(s)
- Lili Gao
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaochun Ma
- Experimental Animal Center, Zunyi Medical University, Zunyi 563003, China
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Marin C, Martín-Maldonado B, Cerdà-Cuéllar M, Sevilla-Navarro S, Lorenzo-Rebenaque L, Montoro-Dasi L, Manzanares A, Ayats T, Mencía-Gutiérrez A, Jordá J, González F, Rojo-Solís C, Barros C, García-Párraga D, Vega S. Antimicrobial Resistant Salmonella in Chelonians: Assessing Its Potential Risk in Zoological Institutions in Spain. Vet Sci 2022; 9:vetsci9060264. [PMID: 35737316 PMCID: PMC9230454 DOI: 10.3390/vetsci9060264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 11/27/2022] Open
Abstract
Salmonella is mostly noted as a food-borne pathogen, but contact with chelonians has also been reported as a source of infection. Moreover, high levels of antimicrobial resistance (AMR) have been reported in Salmonella isolated from wild and captive reptiles. The aim of this study was to assess the occurrence of Salmonella AMR carriage by chelonians admitted to two zoological institutions in Spain, characterizing the isolates to assess the Salmonella AMR epidemiology in wildlife. To this end, 152 chelonians from nine species were sampled upon their arrival at the zoological nuclei. Salmonella identification was based on ISO 6579-1:2017 (Annex D), isolates were serotyped and their AMR analysed according to the EU Decision 2013/652. Moreover, the genetic relationship of the isolates was assessed by pulsed-field gel electrophoresis (PFGE). Results showed 19% (29/152) of the chelonians positive to Salmonella, all of them tortoises. For all isolates, 69% (20/29) were resistant and 34% (10/29) multidrug-resistant (MDR) strains. PFGE clustered isolates according to the serovar, confirming a low genetic diversity. In conclusion, this study shows a high presence of MDR Salmonella strains in tortoises at their entry into zoological nuclei. This condition highlights the need to establish Salmonella detection protocols for the entry of animals into these centres.
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Affiliation(s)
- Clara Marin
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
- Grupo Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), 28220 Majadahonda, Spain; (B.M.-M.); (A.M.-G.); (F.G.)
- Correspondence:
| | - Bárbara Martín-Maldonado
- Grupo Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), 28220 Majadahonda, Spain; (B.M.-M.); (A.M.-G.); (F.G.)
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), 28220 Majadahonda, Spain
- Deparment of Veterinary Medicine, School of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain
| | - Marta Cerdà-Cuéllar
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain; (M.C.-C.); (A.M.); (T.A.)
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Sandra Sevilla-Navarro
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), 12539 Les Alqueries, Spain
| | - Laura Lorenzo-Rebenaque
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
| | - Laura Montoro-Dasi
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
| | - Alicia Manzanares
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain; (M.C.-C.); (A.M.); (T.A.)
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Teresa Ayats
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain; (M.C.-C.); (A.M.); (T.A.)
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Aida Mencía-Gutiérrez
- Grupo Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), 28220 Majadahonda, Spain; (B.M.-M.); (A.M.-G.); (F.G.)
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), 28220 Majadahonda, Spain
| | - Jaume Jordá
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
| | - Fernando González
- Grupo Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), 28220 Majadahonda, Spain; (B.M.-M.); (A.M.-G.); (F.G.)
- Grupo de Rehabilitación de la Fauna Autóctona y su Hábitat (GREFA), 28220 Majadahonda, Spain
| | - Carlos Rojo-Solís
- Oceanogràfic Veterinary Services, Avanqua Oceanogàfic S.L., C/Eduardo Primo Yúfera (Científic) nº1B, 46013 Valencia, Spain; (C.R.-S.); (C.B.); (D.G.-P.)
| | - Carlos Barros
- Oceanogràfic Veterinary Services, Avanqua Oceanogàfic S.L., C/Eduardo Primo Yúfera (Científic) nº1B, 46013 Valencia, Spain; (C.R.-S.); (C.B.); (D.G.-P.)
| | - Daniel García-Párraga
- Oceanogràfic Veterinary Services, Avanqua Oceanogàfic S.L., C/Eduardo Primo Yúfera (Científic) nº1B, 46013 Valencia, Spain; (C.R.-S.); (C.B.); (D.G.-P.)
| | - Santiago Vega
- Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Alfara del Patriarca, Spain; (S.S.-N.); (L.L.-R.); (L.M.-D.); (J.J.); (S.V.)
- Grupo Estudio de la Medicina y Conservación de la Fauna Silvestre (GEMAS), 28220 Majadahonda, Spain; (B.M.-M.); (A.M.-G.); (F.G.)
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An Outer Membrane Protein YiaD Contributes to Adaptive Resistance of Meropenem in Acinetobacter baumannii. Microbiol Spectr 2022; 10:e0017322. [PMID: 35377216 PMCID: PMC9045393 DOI: 10.1128/spectrum.00173-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Acinetobacter baumannii is an important nosocomial pathogen that can develop various resistance mechanisms to many antibiotics. However, little is known about how it evolves from an antibiotic sensitive to a resistant phenotype. In this study, we investigated the transition of outer membrane proteins (OMPs) under antibiotic stress and identified YiaD as an OMP marker involved in the development of adaptive resistance to meropenem (MEM) in A. baumannii. Following stimulation of a carbapenem-sensitive strain AB5116 with sub-MIC of MEM, yiaD showed significantly decreased expression, and this decrease continued with prolonged stimulation for 8 h. The downregulation of yiaD was not only observed in clinically sensitive strains but also in 45 carbapenem-resistant isolates that produced the β-lactamases TEM and OXA-23. However, the extent of the reduction of yiaD expression in resistant strains was less than that in sensitive strains. Lack of yiaD resulted in a 4-fold increase in the MIC of AB5116 to MEM. The same level of depressed susceptibility induced by yiaD deletion was observed in both a growth curve test and a survival rate assay. Moreover, the colony shape became enlarged and irregular after loss of yiaD, and the biofilm formation ability of A. baumannii was influenced by YiaD. These results suggest that YiaD could respond to the stimulus of MEM in A. baumannii with a downregulation trend that kept pace with the prolonged stimulation time, indicating that it participates in various routes to benefit MEM resistance evolution in both carbapenem-sensitive and -resistant A. baumannii strains. IMPORTANCEAcinetobacter baumannii can develop various resistance mechanisms to carbapenems. However, the factors involved in the evolutionary process that leads from transition to the sensitive to resistant phenotype are not clear. The outer membrane protein YiaD of A. baumannii was downregulated under the stress of meropenem (MEM), and its expression level was continuously reduced with prolonged stimulation time. The downregulation of yiaD was not only observed in sensitive strains but also in carbapenem-resistant isolates producing the β-lactamases TEM and OXA-23. However, the extent of yiaD reduction was less in resistant strains than in sensitive strains. Lack of yiaD resulted in an increased MEM MIC, enlarged and irregular colonies, and decreased biofilm formation ability. These results suggest that YiaD responds to MEM stimulus in A. baumannii and participates in the adaptive resistance of MEM in both carbapenem-sensitive and -resistant strains.
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Abstract
Transcription of DNA into RNA is crucial to life, and understanding RNA polymerase (RNAP) function has received considerable attention. In contrast, how the nascent RNA folds into structures that impact transcription itself and regulate gene expression remains poorly understood. Here, we combine single-molecule Förster resonance energy transfer and site-specific fluorescent labelling of transcripts within native complexes to enable real-time cotranscriptional folding studies of a metabolite-sensing riboswitch from Escherichia coli. By monitoring the folding of riboswitches stalled at RNAP pausing sites and during active elongation, we reveal a crucial role for RNAP, which directs RNA folding to allow thiamin pyrophosphate sensing within a precise, transcriptional hotspot. Our approach offers a unique opportunity to unveil cotranscriptional processes in eukaryotic and bacterial systems. Cotranscriptional RNA folding is crucial for the timely control of biological processes, but because of its transient nature, its study has remained challenging. While single-molecule Förster resonance energy transfer (smFRET) is unique to investigate transient RNA structures, its application to cotranscriptional studies has been limited to nonnative systems lacking RNA polymerase (RNAP)–dependent features, which are crucial for gene regulation. Here, we present an approach that enables site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes. By monitoring Escherichia coli nascent riboswitches, we reveal an inverse relationship between elongation speed and metabolite-sensing efficiency and show that pause sites upstream of the translation start codon delimit a sequence hotspot for metabolite sensing during transcription. Furthermore, we demonstrate a crucial role of the bacterial RNAP actively delaying the formation, within the hotspot sequence, of competing structures precluding metabolite binding. Our approach allows the investigation of cotranscriptional regulatory mechanisms in bacterial and eukaryotic elongation complexes.
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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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Sun Y, Meng L, Zhang Y, Zhao D, Lin Y. The Application of Nucleic Acids and Nucleic Acid Materials in Antimicrobial Research. Curr Stem Cell Res Ther 2021; 16:66-73. [PMID: 32436832 DOI: 10.2174/1574888x15666200521084417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/16/2020] [Accepted: 02/26/2020] [Indexed: 02/08/2023]
Abstract
Due to the misuse of antibiotics, multiple drug-resistant pathogenic bacteria have increasingly emerged. This has increased the difficulty of treatment as these bacteria directly affect public health by diminishing the potency of existing antibiotics. Developing alternative therapeutic strategies is the urgent need to reduce the mortality and morbidity related to drug-resistant bacterial infections. In the past 10 to 20 years, nanomedicines have been widely studied and applied as an antibacterial agent. They have become a novel tool for fighting resistant bacteria. The most common innovative substances, metal and metal oxide nanoparticles (NPs), have been widely reported. Until recently, DNA nanostructures were used alone or functionalized with specific DNA sequences by many scholars for antimicrobial purposes which were alternatively selected as therapy for severe bacterial infections. These are a potential candidate for treatments and have a considerable role in killing antibiotic-resistant bacteria. This review involves the dimensions of multidrug resistance and the mechanism of bacteria developing drug resistance. The importance of this article is that we summarized the current study of nano-materials based on nucleic acids in antimicrobial use. Meanwhile, the current progress and the present obstacles for their antibacterial and therapeutic use and special function of stem cells in this field are also discussed.
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Affiliation(s)
- Yue Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lingxian Meng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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10
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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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11
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Maertens L, Leys N, Matroule JY, Van Houdt R. The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper. Genes (Basel) 2020; 11:E1049. [PMID: 32899882 PMCID: PMC7563307 DOI: 10.3390/genes11091049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.
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Affiliation(s)
- Laurens Maertens
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium;
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium;
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
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12
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Melior H, Maaß S, Li S, Förstner KU, Azarderakhsh S, Varadarajan AR, Stötzel M, Elhossary M, Barth-Weber S, Ahrens CH, Becher D, Evguenieva-Hackenberg E. The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. mBio 2020; 11:e01027-20. [PMID: 32546623 PMCID: PMC7298713 DOI: 10.1128/mbio.01027-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/07/2020] [Indexed: 11/20/2022] Open
Abstract
Bacterial ribosome-dependent attenuators are widespread posttranscriptional regulators. They harbor small upstream open reading frames (uORFs) encoding leader peptides, for which no functions in trans are known yet. In the plant symbiont Sinorhizobium meliloti, the tryptophan biosynthesis gene trpE(G) is preceded by the uORF trpL and is regulated by transcription attenuation according to tryptophan availability. However, trpLE(G) transcription is initiated independently of the tryptophan level in S. meliloti, thereby ensuring a largely tryptophan-independent production of the leader peptide peTrpL. Here, we provide evidence for a tryptophan-independent role of peTrpL in trans We found that peTrpL increases the resistance toward tetracycline, erythromycin, chloramphenicol, and the flavonoid genistein, which are substrates of the major multidrug efflux pump SmeAB. Coimmunoprecipitation with a FLAG-peTrpL suggested smeR mRNA, which encodes the transcription repressor of smeABR, as a peptide target. Indeed, upon antibiotic exposure, smeR mRNA was destabilized and smeA stabilized in a peTrpL-dependent manner, showing that peTrpL acts in the differential regulation of smeABR Furthermore, smeR mRNA was coimmunoprecipitated with peTrpL in antibiotic-dependent ribonucleoprotein (ARNP) complexes, which, in addition, contained an antibiotic-induced antisense RNA complementary to smeRIn vitro ARNP reconstitution revealed that the above-mentioned antibiotics and genistein directly support complex formation. A specific region of the antisense RNA was identified as a seed region for ARNP assembly in vitro Altogether, our data show that peTrpL is involved in a mechanism for direct utilization of antimicrobial compounds in posttranscriptional regulation of multiresistance genes. Importantly, this role of peTrpL in resistance is conserved in other AlphaproteobacteriaIMPORTANCE Leader peptides encoded by transcription attenuators are widespread small proteins that are considered nonfunctional in trans We found that the leader peptide peTrpL of the soil-dwelling plant symbiont Sinorhizobium meliloti is required for differential, posttranscriptional regulation of a multidrug resistance operon upon antibiotic exposure. Multiresistance achieved by efflux of different antimicrobial compounds ensures survival and competitiveness in nature and is important from both evolutionary and medical points of view. We show that the leader peptide forms antibiotic- and flavonoid-dependent ribonucleoprotein complexes (ARNPs) for destabilization of smeR mRNA encoding the transcription repressor of the major multidrug resistance operon. The seed region for ARNP assembly was localized in an antisense RNA, whose transcription is induced by antimicrobial compounds. The discovery of ARNP complexes as new players in multiresistance regulation opens new perspectives in understanding bacterial physiology and evolution and potentially provides new targets for antibacterial control.
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Affiliation(s)
- Hendrik Melior
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Sandra Maaß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Siqi Li
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Konrad U Förstner
- ZB MED-Information Centre for Life Sciences, University of Cologne, Cologne, Germany
| | - Saina Azarderakhsh
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | | | - Maximilian Stötzel
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Muhammad Elhossary
- ZB MED-Information Centre for Life Sciences, University of Cologne, Cologne, Germany
| | - Susanne Barth-Weber
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Christian H Ahrens
- Agroscope & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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13
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Abstract
Bacterial regulatory RNAs are key players in adaptation to changing environmental conditions and response to diverse cellular stresses. However, while regulatory RNAs of bacterial pathogens have been intensely studied under defined conditions in vitro, characterization of their role during the infection of eukaryotic host organisms is lagging behind. This review summarizes our current understanding of the contribution of the different classes of regulatory RNAs and RNA-binding proteins to bacterial virulence and illustrates their role in infection by reviewing the mechanisms of some prominent representatives of each class. Emerging technologies are described that bear great potential for global, unbiased studies of virulence-related RNAs in bacterial model and nonmodel pathogens in the future. The review concludes by deducing common principles of RNA-mediated gene expression control of virulence programs in different pathogens, and by defining important open questions for upcoming research in the field.
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14
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Abstract
Noncoding RNAs (ncRNAs) regulating virulence have been identified in most pathogens. This review discusses RNA-mediated mechanisms exploited by bacterial pathogens to successfully infect and colonize their hosts. It discusses the most representative RNA-mediated regulatory mechanisms employed by two intracellular [Listeria monocytogenes and Salmonella enterica serovar Typhimurium (S. Typhimurium)] and two extracellular (Vibrio cholerae and Staphylococcus aureus) bacterial pathogens. We review the RNA-mediated regulators (e.g., thermosensors, riboswitches, cis- and trans-encoded RNAs) used for adaptation to the specific niches colonized by these bacteria (intestine, blood, or the intracellular environment, for example) in the framework of the specific pathophysiological aspects of the diseases caused by these microorganisms. A critical discussion of the newest findings in the field of bacterial ncRNAs shows how examples in model pathogens could pave the way for the discovery of new mechanisms in other medically important bacterial pathogens.
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Affiliation(s)
- Juan J Quereda
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France; , .,Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France.,Institut National de la Recherche Agronomique, USC2020, Paris F-75015, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France; , .,Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France.,Institut National de la Recherche Agronomique, USC2020, Paris F-75015, France
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15
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Biological and regulatory roles of acid-induced small RNA RyeC in Salmonella Typhimurium. Biochimie 2018; 150:48-56. [PMID: 29730297 DOI: 10.1016/j.biochi.2018.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/01/2018] [Indexed: 12/23/2022]
Abstract
Salmonella Typhimurium is an enteric pathogen that has evolved masterful strategies to enable survival under stress conditions both within and outside a host. The acid tolerance response (ATR) is one such mechanism that enhances the viability of acid adapted bacteria to lethal pH levels. While numerous studies exist on the protein coding components of this response, there is very little data on the roles of small RNAs (sRNAs). These non-coding RNA molecules have recently been shown to play roles as regulators of bacterial stress response and virulence pathways. They function through complementary base pairing interactions with target mRNAs and affect their translation and/or stability. There are also a few that directly bind to proteins by mimicking their respective targets. Here, we identify several sRNAs expressed during the ATR of S. Typhimurium and characterize one highly induced candidate, RyeC. Further, we identify ptsI as a trans-encoded target that is directly regulated by this sRNA. From a functional perspective, over-expression of RyeC in Salmonella produced a general attenuation of several in vitro phenotypes including acid survival, motility, adhesion and invasion of epithelial cell lines as well as replication within macrophages. Together, this study highlights the diverse roles played by sRNAs in acid tolerance and virulence of S. Typhimurium.
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16
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Abstract
The extensive use of antibiotics has resulted in a situation where multidrug-resistant pathogens have become a severe menace to human health worldwide. A deeper understanding of the principles used by pathogens to adapt to, respond to, and resist antibiotics would pave the road to the discovery of drugs with novel mechanisms. For bacteria, antibiotics represent clinically relevant stresses that induce protective responses. The recent implication of regulatory RNAs (small RNAs [sRNAs]) in antibiotic response and resistance in several bacterial pathogens suggests that they should be considered innovative drug targets. This minireview discusses sRNA-mediated mechanisms exploited by bacterial pathogens to fight against antibiotics. A critical discussion of the newest findings in the field is provided, with emphasis on the implication of sRNAs in major mechanisms leading to antibiotic resistance, including drug uptake, active drug efflux, drug target modifications, biofilms, cell walls, and lipopolysaccharide (LPS) biosynthesis. Of interest is the lack of knowledge about sRNAs implicated in Gram-positive compared to Gram-negative bacterial resistance.
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17
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Chan H, Ho J, Liu X, Zhang L, Wong SH, Chan MT, Wu WK. Potential and use of bacterial small RNAs to combat drug resistance: a systematic review. Infect Drug Resist 2017; 10:521-532. [PMID: 29290689 PMCID: PMC5736357 DOI: 10.2147/idr.s148444] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Over the decades, new antibacterial agents have been developed in an attempt to combat drug resistance, but they remain unsuccessful. Recently, a novel class of bacterial gene expression regulators, bacterial small RNAs (sRNAs), has received increasing attention toward their involvement in antibiotic resistance. This systematic review aimed to discuss the potential of these small molecules as antibacterial drug targets. Methods Two investigators performed a comprehensive search of MEDLINE, EmBase, and ISI Web of Knowledge from inception to October 2016, without restriction on language. We included all in vitro and in vivo studies investigating the role of bacterial sRNA in antibiotic resistance. Risk of bias of the included studies was assessed by a modified guideline of Systematic Review Center for Laboratory Animal Experimentation (SYRCLE). Results Initial search yielded 432 articles. After exclusion of non-original articles, 20 were included in this review. Of these, all studies examined bacterial-type strains only. There were neither relevant in vivo nor clinical studies. The SYRCLE scores ranged from to 5 to 7, with an average of 5.9. This implies a moderate risk of bias. sRNAs influenced the antibiotics susceptibility through modulation of gene expression relevant to efflux pumps, cell wall synthesis, and membrane proteins. Conclusion Preclinical studies on bacterial-type strains suggest that modulation of sRNAs could enhance bacterial susceptibility to antibiotics. Further studies on clinical isolates and in vivo models are needed to elucidate the therapeutic value of sRNA modulation on treatment of multidrug-resistant bacterial infection.
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Affiliation(s)
- Hung Chan
- Department of Anesthesia and Intensive Care
| | - Jeffery Ho
- Department of Anesthesia and Intensive Care
| | | | - Lin Zhang
- Department of Anesthesia and Intensive Care.,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences.,School of Biomedical Sciences, Faculty of Medicine
| | - Sunny Hei Wong
- State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences.,Department of Medicine and Therapeutics, the Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - William Kk Wu
- Department of Anesthesia and Intensive Care.,State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences
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18
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Stamatopoulou V, Apostolidi M, Li S, Lamprinou K, Papakyriakou A, Zhang J, Stathopoulos C. Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors. Nucleic Acids Res 2017; 45:10242-10258. [PMID: 28973457 PMCID: PMC5622331 DOI: 10.1093/nar/gkx663] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/18/2017] [Indexed: 11/14/2022] Open
Abstract
Recently, it was discovered that exposure to mainstream antibiotics activate numerous bacterial riboregulators that control antibiotic resistance genes including metabolite-binding riboswitches and other transcription attenuators. However, the effects of commonly used antibiotics, many of which exhibit RNA-binding properties, on the widespread T-box riboswitches, remain unknown. In Staphylococcus aureus, a species-specific glyS T-box controls the supply of glycine for both ribosomal translation and cell wall synthesis, making it a promising target for next-generation antimicrobials. Here, we report that specific protein synthesis inhibitors could either significantly increase T-box-mediated transcription antitermination, while other compounds could suppress it, both in vitro and in vivo. In-line probing of the full-length T-box combined with molecular modelling and docking analyses suggest that the antibiotics that promote transcription antitermination stabilize the T-box:tRNA complex through binding specific positions on stem I and the Staphylococcal-specific stem Sa. By contrast, the antibiotics that attenuate T-box transcription bind to other positions on stem I and do not interact with stem Sa. Taken together, our results reveal that the transcription of essential genes controlled by T-box riboswitches can be directly modulated by commonly used protein synthesis inhibitors. These findings accentuate the regulatory complexities of bacterial response to antimicrobials that involve multiple riboregulators.
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Affiliation(s)
| | - Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
| | - Katerina Lamprinou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
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19
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French S, Ellis MJ, Coutts BE, Brown ED. Chemical genomics reveals mechanistic hypotheses for uncharacterized bioactive molecules in bacteria. Curr Opin Microbiol 2017; 39:42-47. [PMID: 28957731 DOI: 10.1016/j.mib.2017.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 01/24/2023]
Abstract
In an effort to combat the perpetual emergence of new antibiotic-resistant human pathogens, research in industry and academe aims to find new means of controlling infection. The discovery of new antimicrobial chemicals is not the bottleneck in an era where high-throughput screening rapidly uncovers new bioactive compounds. Rather, the rate-limiting step in antimicrobial discovery pipelines is identifying mechanisms of action (MOA) of bioactive molecules produced by these increasingly large-scale efforts. Chemical genomics has proven to be of high value in providing mechanistic hypotheses for novel bioactive chemical matter. Several techniques fall under this blanket term, including interactions with deletion or transposon libraries, fluorescent or luminescent reporter library profiles, or deep sequencing approaches. Each of these provide unique and complementary outputs, and have high value in generating target lists for chemical screens, or assisting in downstream MOA discovery. We review here the broad usefulness of this technique to aid in MOA determination, to identify targets for new lead molecules, and to expand our mechanistic understanding of existing drugs.
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Affiliation(s)
- Shawn French
- Department of Biochemistry and Biomedical Sciences and Michael G DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Michael J Ellis
- Department of Biochemistry and Biomedical Sciences and Michael G DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Brittney E Coutts
- Department of Biochemistry and Biomedical Sciences and Michael G DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences and Michael G DeGroote Institute for Infectious Disease Research, McMaster University, Canada.
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20
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Dersch P, Khan MA, Mühlen S, Görke B. Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets. Front Microbiol 2017; 8:803. [PMID: 28529506 PMCID: PMC5418344 DOI: 10.3389/fmicb.2017.00803] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/23/2023] Open
Abstract
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins. Bacteria respond with extensive changes of their sRNA repertoire to antibiotics. Each antibiotic generates a unique sRNA profile possibly causing downstream effects that may help to overcome the antibiotic challenge. In consequence, regulatory RNAs including sRNAs and their protein interaction partners such as Hfq may prove useful as targets for antimicrobial chemotherapy. Indeed, several compounds have been developed that kill bacteria by mimicking ligands for riboswitches controlling essential genes, demonstrating that regulatory RNA elements are druggable targets. Drugs acting on sRNAs are considered for combined therapies to treat infections. In this review, we address how regulatory RNAs respond to and establish resistance to antibiotics in bacteria. Approaches to target RNAs involved in intrinsic antibiotic resistance or virulence for chemotherapy will be discussed.
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Affiliation(s)
- Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection ResearchBraunschweig, Germany
| | - Muna A Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Sabrina Mühlen
- Department of Molecular Infection Biology, Helmholtz Centre for Infection ResearchBraunschweig, Germany
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
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21
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Molina-Santiago C, Daddaoua A, Gómez-Lozano M, Udaondo Z, Molin S, Ramos JL. Differential transcriptional response to antibiotics by Pseudomonas putida DOT-T1E. Environ Microbiol 2015; 17:3251-62. [PMID: 25581266 DOI: 10.1111/1462-2920.12775] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/26/2014] [Accepted: 01/06/2014] [Indexed: 11/29/2022]
Abstract
Multi-drug resistant bacteria are a major threat to humanity, especially because the current battery of known antibiotics is not sufficient to combat infections produced by these microbes. Therefore, the study of how current antibiotics act and how bacteria defend themselves against antibiotics is of critical importance. Pseudomonas putida DOT-T1E exhibits an impressive array of RND efflux pumps, which confer this microorganism high resistance to organic solvents and antibiotics that would kill most other microorganisms. We have chosen DOT-T1E as a model microbe to study the microbial responses to a wide battery of antibiotics (chloramphenicol, rifampicin, tetracycline, ciprofloxacin, ampicillin, kanamycin, spectinomycin and gentamicin). Ribonucleic acid sequencing (RNA)-seq analyses revealed that each antibiotic provokes a unique transcriptional response profile in DOT-T1E. While many of the genes identified were related to known antibiotic targets, others were unrelated or encoded hypothetical proteins. These results indicate that our knowledge of antibiotic resistance mechanisms is still partial. We also identified 138 new small RNAs (sRNAs) in DOT-T1E, dramatically adding to the 16 that have been previously described. Importantly, our results reveal that a correlation exists between the expression of messenger RNA and sRNA, indicating that some of these sRNAs are likely involved in fine tuning the expression of antibiotic resistance genes. Taken together, these findings open new frontiers in the fight against multi-drug resistant bacteria and point to the potential use of sRNAs as novel antimicrobial targets.
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Affiliation(s)
- Carlos Molina-Santiago
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, Granada, E-18008, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, Granada, E-18008, Spain
| | - María Gómez-Lozano
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Zulema Udaondo
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, Granada, E-18008, Spain
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Juan-Luis Ramos
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, Granada, E-18008, Spain
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22
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Lalaouna D, Eyraud A, Chabelskaya S, Felden B, Massé E. Regulatory RNAs involved in bacterial antibiotic resistance. PLoS Pathog 2014; 10:e1004299. [PMID: 25166280 PMCID: PMC4148430 DOI: 10.1371/journal.ppat.1004299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- David Lalaouna
- Department of Biochemistry, RNA group, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Alex Eyraud
- Université de Rennes, Inserm U835 Biochimie Pharmaceutique, Rennes, France
| | | | - Brice Felden
- Université de Rennes, Inserm U835 Biochimie Pharmaceutique, Rennes, France
- * E-mail: (BF); (EM)
| | - Eric Massé
- Department of Biochemistry, RNA group, University of Sherbrooke, Sherbrooke, Quebec, Canada
- * E-mail: (BF); (EM)
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23
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Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Front Cell Infect Microbiol 2014; 4:96. [PMID: 25105095 PMCID: PMC4109619 DOI: 10.3389/fcimb.2014.00096] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.
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Affiliation(s)
- Katie Haning
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
| | - Seung Hee Cho
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at AustinAustin, TX, USA
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at AustinAustin, TX, USA
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24
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Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure. Antimicrob Agents Chemother 2013; 57:3864-74. [PMID: 23733475 DOI: 10.1128/aac.00263-13] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The critical role of noncoding small RNAs (sRNAs) in the bacterial response to changing conditions is increasingly recognized. However, a specific role for sRNAs during antibiotic exposure has not been investigated in Staphylococcus aureus. Here, we used Illumina RNA-Seq to examine the sRNA response of multiresistant sequence type 239 (ST239) S. aureus after exposure to four antibiotics (vancomycin, linezolid, ceftobiprole, and tigecycline) representing the major classes of antimicrobials used to treat methicillin-resistant S. aureus (MRSA) infections. We identified 409 potential sRNAs and then compared global sRNA and mRNA expression profiles at 2 and 6 h, without antibiotic exposure and after exposure to each antibiotic, for a vancomycin-susceptible strain (JKD6009) and a vancomycin-intermediate strain (JKD6008). Exploration of this data set by multivariate analysis using a novel implementation of nonnegative matrix factorization (NMF) revealed very different responses for mRNA and sRNA. Where mRNA responses clustered with strain or growth phase conditions, the sRNA responses were predominantly linked to antibiotic exposure, including sRNA responses that were specific for particular antibiotics. A remarkable feature of the antimicrobial response was the prominence of antisense sRNAs to genes encoding proteins involved in protein synthesis and ribosomal function. This study has defined a large sRNA repertoire in epidemic ST239 MRSA and shown for the first time that a subset of sRNAs are part of a coordinated transcriptional response to specific antimicrobial exposures in S. aureus. These data provide a framework for interrogating the role of staphylococcal sRNAs in antimicrobial resistance and exploring new avenues for sRNA-based antimicrobial therapies.
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