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Liu X, Ahmad S, Ma J, Wang D, Tang J. Comparative study on the toxic effects of secondary nanoplastics from biodegradable and conventional plastics on Streptomyces coelicolor M145. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132343. [PMID: 37639795 DOI: 10.1016/j.jhazmat.2023.132343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Because of the excellent properties, plastics have been widely used in the past decades and caused serious environmental issues. As an excellent substitute for conventional plastics, the biodegradable plastics have attracted increasing attention. However, biodegradable plastics may produce more micro/nanoplastics in the short time compared with conventional plastics, and cause more serious ecological risks. In this study, the short-term toxicity of nanoplastics released from biodegradable and conventional plastics on Streptomyces coelicolor M145 was investigated. After 30 days of degradation, the biodegradable microplastics, polylactic acid (PLA) and polyhydroxyalkanoates (PHA) released more secondary nanoplastics than conventional microplastics, polystyrene (PS). After exposure, PLA and PHA nanoplastics showed significant toxicity to M145. The survival rate of M145 cells was 16.1% after treatment with PLA nanoplastics for 7 days (PLA-7). The toxicity of PHA was lower than that of PLA. This might have been due to the agglomeration of PHA nanoplastics in the solution. Compared with the controls, the PS secondary nanoplastics showed no significant toxicity to M145. After the treatment, the production of antibiotics, actinorhodin (ACT) and undecylprodigiosin (RED), significantly increased. The yields of ACT and RED reached their maximum values after treatment with PLA-7, which were 4.2-fold and 2.1-fold higher than those of the controls, respectively. The addition of biodegradable nanoplastics significantly increased the expression of these key pathway-specific regulatory genes, leading to increased antibiotic production. This study provides toxicological insights into the impacts of conventional and biodegradable microplastics on S. coelicolor.
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Affiliation(s)
- Xiaomei Liu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China; MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shakeel Ahmad
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jingkang Ma
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Dan Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jingchun Tang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Nag A, Mehra S. Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator. Appl Microbiol Biotechnol 2022; 106:2175-2190. [PMID: 35194656 DOI: 10.1007/s00253-022-11837-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/05/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
Overexpression of efflux pumps represents a key mechanism of resistance in bacteria. Soil bacteria such as Streptomyces harbour a vast array of efflux genes that are transcriptionally silent under laboratory conditions. However, dissemination of many of these genes into clinical pathogens via horizontal gene transfer results in conferring resistance to multiple drugs. In this study, we have identified the role of a MFS transporter, SCO3366 from Streptomyces coelicolor, in governing multidrug resistance. Overexpression and knockout studies revealed that SCO3366 provides resistance to several structurally unrelated drugs including ciprofloxacin, chloramphenicol, rifampicin and EtBr, with rifampicin being the major substrate. Beyond multidrug resistance, SCO3366 was efficient in providing tolerance towards oxidative stress. A combinatorial mechanism of increased oxidative stress tolerance decreased intracellular drug levels and decreased permeability act synergistically to provide resistance towards rifampicin. Shedding light on the regulation of SCO3366, we find the pump to be directly regulated by the TetR regulator SCO3367 in a negative manner and the repression was found to be relieved in presence of different compounds recognized as substrates of SCO3366. KEY POINTS: • First reported rifampicin efflux pump in Streptomyces coelicolor • Resistance to rifampicin is the result of a synergistic action of increased efflux with increased oxidative stress tolerance and decreased permeability, which can potentially arise in clinically relevant bacteria • SCO3366-SCO3367 to be a novel system that operates to protect the bacteria under varied environmental stress conditions.
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Affiliation(s)
- Ankita Nag
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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Unique physiological and genetic features of ofloxacin-resistant Streptomyces mutants. Appl Environ Microbiol 2021; 88:e0232721. [PMID: 34936843 DOI: 10.1128/aem.02327-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New antimicrobial agents are urgently needed to combat the emergence and spread of multidrug-resistant bacteria. Activating the cryptic biosynthetic gene clusters for actinomycete secondary metabolites can provide essential clues for research into new antimicrobial agents. An effective method for this purpose is based on drug resistance selection. This report describes interesting results for drug resistance selection using antibiotics that target DNA replication can effectively potentiate secondary metabolite production by actinomycetes. Ofloxacin-resistant mutants were isolated from five different streptomycetes. Ofloxacin is an antibiotic that binds to DNA complexes and type II topoisomerase, causing double-stranded breaks in bacterial chromosomes. Physiological and genetic characterization of the mutants revealed that the development of ofloxacin resistance in streptomycetes leads to the emergence of various types of secondary metabolite-overproducing strains. In Streptomyces coelicolor A3(2), ofloxacin-resistant mutants that overproduced actinorhodin, undecylprodigiosin, or carotenoid were identified. Also, an ofloxacin-resistant mutant that overproduces methylenomycin A, whose biosynthetic gene cluster is located on the endogenous plasmid, SCP1, was isolated. These observations indicate that ofloxacin resistance might activate biosynthetic genes on both chromosomes and on endogenous plasmids. We also identified the mutations that are probably involved in the phenotype of ofloxacin resistance and secondary metabolite overproduction in S. coelicolor A3(2). Furthermore, we observed an interesting phenomenon in which several ofloxacin-resistant mutants overproduced antibiotics in the presence of ofloxacin. Based on these results, we present the unique physiological and genetic characteristics of ofloxacin-resistant Streptomyces mutants and discuss the importance and potential development of the new findings. IMPORTANCE The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, there are now fewer effective antimicrobials available. Due to the depleted antibiotic pipeline, pandemic outbreaks caused by antimicrobial-resistant bacteria are deeply concerned, and the development of new antibiotics is now an urgent issue. Promising sources of antimicrobial agents include cryptic biosynthetic gene clusters for secondary metabolites in streptomycetes and rare actinomycetes. This study's significance is an unprecedented activation method to accelerate drug discovery research on a global scale. The technique developed in this study could allow for simultaneous drug discovery in different countries, maximizing the world's microbial resources.
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Sridhar S, Forrest S, Pickard D, Cormie C, Lees EA, Thomson NR, Dougan G, Baker S. Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium. mBio 2021; 12:e0109321. [PMID: 34154399 PMCID: PMC8262899 DOI: 10.1128/mbio.01093-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global health crisis, which has been fueled by the sustained use of certain classes of antimicrobials, including fluoroquinolones. While the genetic mutations responsible for decreased fluoroquinolone (ciprofloxacin) susceptibility are known, the implications of ciprofloxacin exposure on bacterial growth, survival, and interactions with host cells are not well described. Aiming to understand the influence of inhibitory concentrations of ciprofloxacin in vitro, we subjected three clinical isolates of Salmonella enterica serovar Typhimurium to differing concentrations of ciprofloxacin, dependent on their MICs, and assessed the impact on bacterial growth, morphology, and transcription. We further investigated the differential morphology and transcription that occurred following ciprofloxacin exposure and measured the ability of ciprofloxacin-treated bacteria to invade and replicate in host cells. We found that ciprofloxacin-exposed S. Typhimurium is able to recover from inhibitory concentrations of ciprofloxacin and that the drug induces specific morphological and transcriptional signatures associated with the bacterial SOS response, DNA repair, and intracellular survival. In addition, ciprofloxacin-treated S. Typhimurium has increased capacity for intracellular replication in comparison to that of untreated organisms. These data suggest that S. Typhimurium undergoes an adaptive response under ciprofloxacin perturbation that promotes cellular survival, a consequence that may justify more measured use of ciprofloxacin for Salmonella infections. The combination of multiple experimental approaches provides new insights into the collateral effects that ciprofloxacin and other antimicrobials have on invasive bacterial pathogens. IMPORTANCE Antimicrobial resistance is a critical concern in global health. In particular, there is rising resistance to fluoroquinolones, such as ciprofloxacin, a first-line antimicrobial for many Gram-negative pathogens. We investigated the adaptive response of clinical isolates of Salmonella enterica serovar Typhimurium to ciprofloxacin, finding that the bacteria adapt in short timespans to high concentrations of ciprofloxacin in a way that promotes intracellular survival during early infection. Importantly, by studying three clinically relevant isolates, we were able to show that individual isolates respond differently to ciprofloxacin and that for each isolate, there was a heterogeneous response under ciprofloxacin treatment. The heterogeneity that arises from ciprofloxacin exposure may drive survival and proliferation of Salmonella during treatment and lead to drug resistance.
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Affiliation(s)
- Sushmita Sridhar
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sally Forrest
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Derek Pickard
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Claire Cormie
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Emily A. Lees
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
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A Major Facilitator Superfamily (MFS) Efflux Pump, SCO4121, from Streptomyces coelicolor with Roles in Multidrug Resistance and Oxidative Stress Tolerance and Its Regulation by a MarR Regulator. Appl Environ Microbiol 2021; 87:AEM.02238-20. [PMID: 33483304 DOI: 10.1128/aem.02238-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Overexpression of efflux pumps is one of the major determinants of resistance in bacteria. Streptomyces species harbor a large array of efflux pumps that are transcriptionally silenced under laboratory conditions. However, their dissemination results in multidrug resistance in different clinical pathogens. In this study, we have identified an efflux pump from Streptomyces coelicolor, SCO4121, belonging to the major facilitator superfamily (MFS) family of transporters and characterized its role in antibiotic resistance. SCO4121 provided resistance to multiple dissimilar drugs upon overexpression in both native and heterologous hosts. Further, deletion of SCO4121 resulted in increased sensitivity toward ciprofloxacin and chloramphenicol, suggesting the pump to be a major transporter of these substrates. Apart from providing multidrug resistance, SCO4121 imparted increased tolerance against the strong oxidant HOCl. In wild-type Streptomyces coelicolor cells, these drugs were found to transcriptionally regulate the pump in a concentration-dependent manner. Additionally, we identified SCO4122, a MarR regulator that positively regulates SCO4121 in response to various drugs and the oxidant HOCl. Thus, through these studies we present the multiple roles of SCO4121 in S. coelicolor and highlight the intricate mechanisms via which it is regulated in response to antibiotics and oxidative stress.IMPORTANCE One of the key mechanisms of drug resistance in bacteria is overexpression of efflux pumps. Streptomyces species are a reservoir of a large number of efflux pumps, potentially to provide resistance to both endogenous and nonendogenous antibiotics. While many of these pumps are not expressed under standard laboratory conditions, they result in resistance to multiple drugs when spread to other bacterial pathogens through horizontal gene transfer. In this study, we have identified a widely conserved efflux pump SCO4121 from Streptomyces coelicolor with roles in both multidrug resistance and oxidative stress tolerance. We also report the presence of an adjacent MarR regulator, SCO4122, which positively regulates SCO4121 in the presence of diverse substrates in a redox-responsive manner. This study highlights that soil bacteria such as Streptomyces can reveal novel mechanisms of antibiotic resistance that may potentially emerge in clinically important bacteria.
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Dai X, Bai Y, Zhang Y, Ma Z, Li J, Sun H, Zhang X. Protonation-Activity Relationship of Bioinspired Ionizable Glycomimetics for the Growth Inhibition of Bacteria. ACS APPLIED BIO MATERIALS 2020; 3:3868-3879. [PMID: 35025257 DOI: 10.1021/acsabm.0c00424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Variations in physiological parameters (i.e., pH, redox potential, and ions) for distinct types of diseases make them attractive targets. Ionizable groups capable of pH-dependent charge conversion impart pH-switchable materials under acid condition through the protonation effect, which stimulates the emergence of various pH-inspired materials. However, it is confusing to distinguish preferable groups for high-efficiency drug-delivery vehicles attributing to the lack of perceiving the relationship between protonation and activity. Herein, we developed a series of bioinspired ionizable glycomimetics responses to the ambient variation from physiological environment (pH 7.4) to bacterial infectious acidic microenvironment (pH 6.0) to explore the protonation-activity relationship of various ionizable groups. The nanoparticles are coated with bacterial adhesion molecules galactose and fucose to target Pseudomonas aeruginosa. Moreover, the particle cores were composed of ionizable polymers responding to acidic microenvironment changes and entrapped antibiotic payload. Ionizable glyconanoparticles targeted bacteria and local cues as triggers to transfer payloads in on-demand patterns for the inhibition of bacteria-related infection. Significantly, we find that the nanoparticles with the pH-sensitive block of ionizable poly(2-(diisopropylamino)ethyl methacrylate) (pDPA) exhibit predominant bacterial adhesion and killing and growth inhibition of biofilm in acid environment (pH 6.0) due to the ionizable polymer protonation effect with more positive charge cooperated with the lectin-targeted effect of polysaccharide causing a huge bacterial aggregation and a highly favorable germicidal effect. The nanoparticles with poly(2-(hexamethyleneimino)ethyl methacrylate) (pHMEMA) have suboptimal antibacterial activity but advanced protonation at pH 6.3 compared to pDPA at 6.1, suggesting its selection as an applicable pH-switchable group for a slightly higher acid microenvironment like tumor (pH 6.9-6.5) because of the efficient performance after protonation than at deprotonation. On the other hand, the glycomimetic containing poly(2-(dibutylamino)ethyl methacrylate) (pDBA) as a pH-sensitive moiety displayed weak antimicrobial activity and superior stability before protonation (pH 4.7), which make it possible to prevent premature drug leakage, suggesting that pDBA is a good candidate to be applied to construct pH-sensitive drug-delivery carriers for the treatment of bacteria-related infection with a low acidic microenvironment. Overall, the structure-activity relationship of ionizable glycomimetics for the inhibition of bacteria signifies not only the development of a drug-delivery system but also the mechanism-dependent treatment of nanomedicine for infectious diseases.
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Affiliation(s)
- Xijuan Dai
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yayun Bai
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yufei Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhuang Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jie Li
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Haonan Sun
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xinge Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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Liu X, Tang J, Wang L, Liu R. Synergistic toxic effects of ball-milled biochar and copper oxide nanoparticles on Streptomyces coelicolor M145. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137582. [PMID: 32146398 DOI: 10.1016/j.scitotenv.2020.137582] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/16/2020] [Accepted: 02/24/2020] [Indexed: 05/24/2023]
Abstract
The toxic effects of multi-nanomaterial systems are receiving increasing attention owing to their inevitable release of various nanomaterials. Knowledge of the bioavailability of the new carbon material ball-milled biochar (BMB) and its synergistic toxicity with metal oxide nanoparticles in bacteria is currently limited. In this study, the interactions of BMB with copper oxide nanoparticles (CuO NPs) and their synergistic toxicity towards Streptomyces coelicolor M145 were analyzed. Results showed that the cytotoxicity, ROS level and permeability of cells changed greatly with the pyrolysis temperatures of biochar and the concentrations of CuO NPs. The greatest cytotoxicity (up to 63.1%) was achieved by adding 20 mg/L CuO NPs to BMB700. The ROS level and cell permeability of this treatment was also the highest, about 4.2 folds and 2.9 folds greater than that of control, respectively. The combination of 10 mg/L BMB700 with 10 mg/L CuO NPs can maximize production of antibiotics, with the yield of undecylprodigiosin (RED) and actinorhodin (ACT) 3.0 times and 4.2 times higher than that in the control, respectively, and the change trend of related genes was consistent with that of antibiotics production. Mechanism analysis showed that the different adsorption capacity of BMB of different pyrolysis temperatures on copper ions played a vital role in the synergistic toxicity, and the increase in cell membrane permeability caused by cell collisions with particles was also an important reason for cytotoxicity. Overall, the synergistic toxicity of BMB with other NPs varies the pyrolysis temperatures, when considering the synergistic toxicity of these materials, the preparation conditions need to be taken into account so as to assess their environmental risks more accurately. On the other hand, this research may provide a new approach for the antibiotic industry to increase its output.
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Affiliation(s)
- Xiaomei Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Lan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, China
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8
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McLean TC, Lo R, Tschowri N, Hoskisson PA, Al Bassam MM, Hutchings MI, Som NF. Sensing and responding to diverse extracellular signals: an updated analysis of the sensor kinases and response regulators of Streptomyces species. MICROBIOLOGY-SGM 2020; 165:929-952. [PMID: 31334697 DOI: 10.1099/mic.0.000817] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Streptomyces venezuelae is a Gram-positive, filamentous actinomycete with a complex developmental life cycle. Genomic analysis revealed that S. venezuelae encodes a large number of two-component systems (TCSs): these consist of a membrane-bound sensor kinase (SK) and a cognate response regulator (RR). These proteins act together to detect and respond to diverse extracellular signals. Some of these systems have been shown to regulate antimicrobial biosynthesis in Streptomyces species, making them very attractive to researchers. The ability of S. venezuelae to sporulate in both liquid and solid cultures has made it an increasingly popular model organism in which to study these industrially and medically important bacteria. Bioinformatic analysis identified 58 TCS operons in S. venezuelae with an additional 27 orphan SK and 18 orphan RR genes. A broader approach identified 15 of the 58 encoded TCSs to be highly conserved in 93 Streptomyces species for which high-quality and complete genome sequences are available. This review attempts to unify the current work on TCS in the streptomycetes, with an emphasis on S. venezuelae.
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Affiliation(s)
- Thomas C McLean
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Rebecca Lo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Natalia Tschowri
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Mahmoud M Al Bassam
- Department of Paediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Nicolle F Som
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK. The Transcription Unit Architecture of Streptomyces lividans TK24. Front Microbiol 2019; 10:2074. [PMID: 31555254 PMCID: PMC6742748 DOI: 10.3389/fmicb.2019.02074] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/22/2019] [Indexed: 12/15/2022] Open
Abstract
Streptomyces lividans is an attractive host for production of heterologous proteins and secondary metabolites of other Streptomyces species. To fully harness the industrial potential of S. lividans, understanding its metabolism and genetic regulatory elements is essential. This study aimed to determine its transcription unit (TU) architecture and elucidate its diverse regulatory elements, including promoters, ribosome binding sites, 5′-untranslated regions, and transcription terminators. Total 1,978 transcription start sites and 1,640 transcript 3′-end positions were identified, which were integrated to determine 1,300 TUs, consistent with transcriptomic profiles. The conserved promoter sequences were found as 5′-TANNNT and 5′-TGAC, representing the −10 and −35 elements, respectively. Analysis of transcript 3′-end positions revealed the presence of distinctive terminator sequences and the RNA stem structure responsible for the determination of the 3′-boundary of a transcript. Functionally related genes are likely to be regulated simultaneously by using similar promoters and being transcribed as a poly-cistronic TU. Poly-cistronic TUs were further processed or alternatively transcribed into multiple TUs to fine-regulate individual genes in response to environmental conditions. The TU information and regulatory elements identified will serve as invaluable resources for understanding the complex regulatory mechanisms of S. lividans and to elevate its industrial potential.
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Affiliation(s)
- Yongjae Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yujin Jeong
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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10
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Mechanism of CuO nano-particles on stimulating production of actinorhodin in Streptomyces coelicolor by transcriptional analysis. Sci Rep 2019; 9:11253. [PMID: 31375702 PMCID: PMC6677739 DOI: 10.1038/s41598-019-46833-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022] Open
Abstract
In this research, antibiotic-producing bacteria, Streptomyces coelicolor (S. coelicolor) M145, was exposed to copper oxide (CuO) particles to investigate the effects of nano-particles (NPs) on antibiotic production. Results showed that a higher yield of antibiotics was obtained with smaller particle sizes of CuO NPs. When exposed to 10 mg/L of 40 nm CuO NPs, the maximum amount of actinorhodin (ACT) obtained was 2.6 mg/L after 144 h, which was 2.0-fold greater than that of control. However, the process was inhibited when the concentration of CuO NPs was increased to higher than 20 mg/L. Transcriptome analysis showed that all the genes involved in the ACT cluster were significantly up-regulated after exposure to 10 mg/L NPs, which could be the direct cause of the increase of ACT production. Additionally, some genes related to the generation of acetyl-coA were up-regulated. In this way, CuO NPs led to an increase of secondary metabolites. The mechanism related to these changes indicated that nano-particle‒induced ROS and Cu2+ played synergetic roles in promoting ACT biosynthesis. This is a first report suggesting that CuO NPs had a significant effect on antibiotic production, which will be helpful in understanding the mechanism of antibiotic production in nature.
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Lian X, Wang X, Liu X, Xia J, Fang L, Sun J, Liao X, Liu Y. oqxAB-Positive IncHI2 Plasmid pHXY0908 Increase Salmonella enterica Serotype Typhimurium Strains Tolerance to Ciprofloxacin. Front Cell Infect Microbiol 2019; 9:242. [PMID: 31334135 PMCID: PMC6617520 DOI: 10.3389/fcimb.2019.00242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/18/2019] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serotype Typhimurium is a major global food-borne pathogen and causes life-threatening infections. Although the resistance mechanisms to fluoroquinolones in S. Typhimurium had been well-defined, tolerance to fluoroquinolones and the associated mechanism for this are obscure. In the current work, we investigated an oqxAB-positive plasmid pHXY0908 and analyzed its role in S. Typhimurium tolerance to ciprofloxacin using time-kill, transcriptome sequencing and real-time PCR. S. Typhimurium ATCC14028 could survive under lethal concentrations of ciprofloxacin after acquiring plasmid pHXY0908. Transcriptome sequence analysis showed the chromosomal genes were systematically regulated after acquiring this plasmid suggesting an interaction between chromosome and plasmid. Additionally, the chromosomal efflux pump genes acrB, acrA, tolC, and yceE were up-regulated after acquiring plasmid pHXY0908 suggesting that these efflux pumps may contribute to the survival of ATCC14028 exposed to the lethal concentrations of ciprofloxacin. In conclusion, this is the first known report demonstrating that an IncHI2 type plasmid harboring oqxAB could assist S. Typhimurium survival under lethal concentrations of ciprofloxacin.
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Affiliation(s)
- Xinlei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jing Xia
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Liangxing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Yahong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
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12
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Liu X, Tang J, Wang L, Giesy JP. Al 2O 3 nanoparticles promote secretion of antibiotics in Streptomyces coelicolor by regulating gene expression through the nano effect. CHEMOSPHERE 2019; 226:687-695. [PMID: 30959453 DOI: 10.1016/j.chemosphere.2019.03.156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Toxic effects of nanoparticles (NPs) on microorganisms have attracted substantial attention; however, there are few reports on whether NPs can affect the secondary metabolism of microbes. To investigate the toxic effects of Al2O3 NPs on cell growth and antibiotic secretion, Streptomyces coelicolor M145 was exposed to Al2O3 NPs with diameters of 30 and 80 nm and bulk Al2O3 at concentrations up to 1000 mg/L. The results indicated that differences in the toxicity of Al2O3 NPs were related to the particle size. In treatment with Al2O3 NPs, the maximum yields of undecylprodigiosin (RED) and actinorhodin (ACT) were 3.7- and 4.6-fold greater than that of the control, respectively, and the initial time of antibiotic production was much shorter. ROS quenching experiment by N-acetylcysteine (NAC) confirmed that ROS were responsible for the increased RED production. From 0 to 72 h, ROS had a significant impact on ACT production; however, after 72 h, the ROS content began to decrease until it disappeared. During ongoing exposure (0-144 h), ACT production continued to increase, indicating that in addition to ROS, nano effect of Al2O3 NPs also played roles in this process. Transcriptional analysis demonstrated that Al2O3 NPs could increase the expression levels of antibiotic biosynthetic genes and two-component systems (TCSs) and inhibit the expression levels of primary metabolic pathways. This study provides a new perspective for understanding the mechanisms of antibiotic production in nature and reveals important implications for exploring other uses of NPs in biomedical applications or regulation of antibiotics in nature.
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Affiliation(s)
- Xiaomei Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
| | - Lan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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13
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Briffotaux J, Liu S, Gicquel B. Genome-Wide Transcriptional Responses of Mycobacterium to Antibiotics. Front Microbiol 2019; 10:249. [PMID: 30842759 PMCID: PMC6391361 DOI: 10.3389/fmicb.2019.00249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Antibiotics can stimulate or depress gene expression in bacteria. The analysis of transcriptional responses of Mycobacterium to antimycobacterial compounds has improved our understanding of the mode of action of various drug classes and the efficacy and effect of such compounds on the global metabolism of Mycobacterium. This approach can provide new insights for known antibiotics, for example those currently used for tuberculosis treatment, as well as help to identify the mode of action and predict the targets of new compounds identified by whole-cell screening assays. In addition, changes in gene expression profiles after antimycobacterial treatment can provide information about the adaptive ability of bacteria to escape the effects of antibiotics and allow monitoring of the physiology of the bacteria during treatment. Genome-wide expression profiling also makes it possible to pinpoint genes differentially expressed between drug sensitive Mycobacterium and multidrug-resistant clinical isolates. Finally, genes involved in adaptive responses and drug tolerance could become new targets for improving the efficacy of existing antibiotics.
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Affiliation(s)
- Julien Briffotaux
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shengyuan Liu
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Brigitte Gicquel
- Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.,Emerging Bacterial Pathogens Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,Mycobacterial Genetics Unit, Institut Pasteur, Paris, France
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14
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Read N, Howlett R, Smith MCM. An operon encoding enzymes for synthesis of a putative extracellular carbohydrate attenuates acquired vancomycin resistance in Streptomyces coelicolor. MICROBIOLOGY-SGM 2019; 165:208-223. [PMID: 30632959 DOI: 10.1099/mic.0.000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Actinomycete bacteria use polyprenol phosphate mannose as a lipid-linked sugar donor for extra-cytoplasmic glycosyl transferases that transfer mannose to cell envelope polymers, including glycoproteins and glycolipids. Strains of Streptomyces coelicolor with mutations in the gene ppm1, encoding polyprenol phosphate mannose synthase, and in pmt, encoding a protein O-mannosyltransferase, are resistant to phage ϕC31 and have greatly increased susceptibility to some antibiotics, including vancomycin. In this work, second-site suppressors of the vancomycin susceptibility were isolated. The suppressor strains fell into two groups. Group 1 strains had increased resistance to vancomycin, teicoplanin and β-lactams, and had mutations in the two-component sensor regulator system encoded by vanSR, leading to upegulation of the vanSRJKHAX cluster. Group 2 strains only had increased resistance to vancomycin and these mostly had mutations in sco2592 or sco2593, genes that are derepressed in the presence of phosphate and are likely to be required for the synthesis of a phosphate-containing extracellular polymer. In some suppressor strains the increased resistance was only observed in media with limited phosphate (mimicking the phenotype of wild-type S. coelicolor), but two strains, DT3017_R21 (ppm1-vanR-) and DT3017_R15 (ppm1- sco2593-), retained resistance on media with high phosphate content. These results support the view that vancomycin resistance in S. coelicolor is a trade-off between mechanisms that confer resistance and at least one that interferes with resistance mediated through the sco2594-sco2593-sco2592 operon.
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15
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Patkari M, Kumbhar C, Nag A, Mehra S. Distinct transcriptomic response of S. coelicolor to ciprofloxacin in a nutrient-rich environment. Appl Microbiol Biotechnol 2018; 102:10623-10643. [PMID: 30327831 DOI: 10.1007/s00253-018-9398-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/07/2023]
Abstract
With the rising threat of anti-microbial resistance (AMR), there is an urgent need to enhance efficacy of existing antibiotics. Understanding the myriad mechanisms through which bacteria evade these drugs would be of immense value to designing novel strategies against them. Streptomyces coelicolor A3(2) M145 belongs to the actinomyctes species that are responsible for more than two-thirds of antibiotics. This group of bacteria therefore encodes for various mechanisms that can resist both endogenous and non-endogenous antibiotics. In an earlier study, we had studied the transcriptomic response of these bacteria to ciprofloxacin, when cultured in a minimal media. In this work, we investigate why the minimum inhibitory concentration of the drug increases by fourfold when the bacteria are grown in a nutrient-rich media. Through transcriptomic, biochemical, and microscopic studies, we show that S. coelicolor responds to ciprofloxacin in a concentration-dependent manner. While, sub-inhibitory concentration of the drug primarily causes oxidative stress, the inhibitory concentration of ciprofloxacin evokes a more severe genome-wide response in the cell, which ranges from the familiar upregulation of the SOS response and DNA repair pathways to the widespread alterations in the central metabolism pathway to accommodate the increased needs of nucleotides and other precursors. Further, the upregulation of peptidoglycan synthesis genes, along with microscopy images, suggest alterations in the cell morphology to increase fitness of the bacteria during the antibiotic stress. The data also points to the enhanced efflux activity in cells cultured in rich media that contributes significantly towards reducing intracellular drug concentration and thus promotes survival.
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Affiliation(s)
- Minal Patkari
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | - Ankita Nag
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, IIT Bombay, Powai, 400076, India.
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16
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Domínguez Á, Muñoz E, López MC, Cordero M, Martínez JP, Viñas M. Transcriptomics as a tool to discover new antibacterial targets. Biotechnol Lett 2017; 39:819-828. [PMID: 28289911 DOI: 10.1007/s10529-017-2319-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/07/2017] [Indexed: 12/20/2022]
Abstract
The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.
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Affiliation(s)
- Ángel Domínguez
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain.
| | - Elisa Muñoz
- Department of Cell Biology & Pathology, Universidad de Salamanca, Salamanca, Spain
| | - M Carmen López
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain
| | - Miguel Cordero
- Department of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - José Pedro Martínez
- Department of Microbiology & Ecology, Universitat de Valencia/Estudi General (UVEG), Valencia, Spain
| | - Miguel Viñas
- Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
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17
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Lubitz D, Wendisch VF. Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum. BMC Microbiol 2016; 16:235. [PMID: 27717325 PMCID: PMC5055667 DOI: 10.1186/s12866-016-0857-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum is a well-studied bacterium which naturally overproduces glutamate when induced by an elicitor. Glutamate production is accompanied by decreased 2-oxoglutatate dehydrogenase activity. Elicitors of glutamate production by C. glutamicum analyzed to molecular detail target the cell envelope. RESULTS Ciprofloxacin, an inhibitor of bacterial DNA gyrase and topoisomerase IV, was shown to inhibit growth of C. glutamicum wild type with concomitant excretion of glutamate. Enzyme assays showed that 2-oxoglutarate dehydrogenase activity was decreased due to ciprofloxacin addition. Transcriptome analysis revealed that this inhibitor of DNA gyrase increased RNA levels of genes involved in DNA synthesis, repair and modification. Glutamate production triggered by ciprofloxacin led to glutamate titers of up to 37 ± 1 mM and a substrate specific glutamate yield of 0.13 g/g. Even in the absence of the putative glutamate exporter gene yggB, ciprofloxacin effectively triggered glutamate production. When C. glutamicum wild type was cultivated under nitrogen-limiting conditions, 2-oxoglutarate rather than glutamate was produced as consequence of exposure to ciprofloxacin. Recombinant C. glutamicum strains overproducing lysine, arginine, ornithine, and putrescine, respectively, secreted glutamate instead of the desired amino acid when exposed to ciprofloxacin. CONCLUSIONS Ciprofloxacin induced DNA synthesis and repair genes, reduced 2-oxoglutarate dehydrogenase activity and elicited glutamate production by C. glutamicum. Production of 2-oxoglutarate could be triggered by ciprofloxacin under nitrogen-limiting conditions.
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Affiliation(s)
- Dorit Lubitz
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.
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18
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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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