1
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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2
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Getahun M, Abebe RB, Sendekie AK, Woldeyohanis AE, Kasahun AE. Evaluation of Antibiotics Residues in Milk and Meat Using Different Analytical Methods. Int J Anal Chem 2023; 2023:4380261. [PMID: 37424721 PMCID: PMC10328735 DOI: 10.1155/2023/4380261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023] Open
Abstract
Veterinary drugs are pharmacologically and biologically active chemical agents. At present, veterinary drugs are extensively used to prevent and treat animal diseases, to promote animal growth, and to improve the conversion rate of feed. However, the use of veterinary drugs in food-producing animals may leave residues of the parent compounds and/or their metabolites in food products resulting in harmful effects on humans. To ensure food safety, sensitive and effective analytical methods have been developing rapidly. This review describes sample extraction and cleanup methods, and different analytical techniques are used for the determination of veterinary drug residues in milk and meat. Sample extraction methods, such as solvent extraction, liquid-liquid extraction, and cleanup methods such as dispersive solid-phase extraction and immunoaffinity chromatography, were summarized. Different types of analytical methods such as microbial, immunological, biosensor, thin layer chromatography, high-performance liquid chromatography, and liquid chromatography-tandem mass spectrometry were discussed for the analysis of veterinary drug residues in animal-derived foods. Liquid chromatography-tandem mass spectrometry is the most widely used analytical technique for the determination of antibiotic drug residues. This is due to the powerful separation of LC and accurate identification of MS, and LC-MS/MS is more popular in the analysis of veterinary drug residues.
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Affiliation(s)
- Melaku Getahun
- Department of Veterinary Pharmacy, College of Veterinary Medicine and Animal Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
| | - Rahel Belete Abebe
- Department of Clinical Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
| | - Ashenafi Kibret Sendekie
- Department of Clinical Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
| | - Alem Endeshaw Woldeyohanis
- Department of Pharmaceutics and Social Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
| | - Asmamaw Emagn Kasahun
- Department of Pharmaceutics and Social Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, P.O. Box 196, Gondar, Ethiopia
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3
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Wang Y, Li S, Xue N, Wang L, Zhang X, Zhao L, Guo Y, Zhang Y, Wang M. Modulating Sensitivity of an Erythromycin Biosensor for Precise High-Throughput Screening of Strains with Different Characteristics. ACS Synth Biol 2023; 12:1761-1771. [PMID: 37198736 DOI: 10.1021/acssynbio.3c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Genetically encoded biosensors are powerful tools for product-driven high-throughput screening in synthetic biology and metabolic engineering. However, most biosensors can only properly function in a limited concentration cutoff, and the incompatible performance characteristics of biosensors will lead to false positives or failure in screening. The transcription factor (TF)-based biosensors are usually organized in modular architecture and function in a regulator-depended manner, whose performance properties can be fine-tuned by modifying the expression level of the TF. In this study, we modulated the performance characteristics, including sensitivity and operating range, of an MphR-based erythromycin biosensor by fine-adjusting regulator expression levels via ribosome-binding site (RBS) engineering and obtained a panel of biosensors with varied sensitivities by iterative fluorescence-assisted cell sorting (FACS) in Escherichia coli to accommodate different screening purposes. To exemplify their application potential, two engineered biosensors with 10-fold different sensitivities were employed in the precise high-throughput screening by microfluidic-based fluorescence-activated droplet sorting (FADS) of Saccharopolyspora erythraea mutant libraries with different starting erythromycin productions, and mutants representing as high as 6.8 folds and over 100% of production improvements were obtained starting from the wild-type strain and the high-producing industrial strain, respectively. This work demonstrated a simple strategy to engineer biosensor performance properties, which was significant to stepwise strain engineering and production improvement.
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Affiliation(s)
- Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Shixin Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ning Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xuemei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Longqian Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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4
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Rütten A, Kirchner T, Musiol-Kroll EM. Overview on Strategies and Assays for Antibiotic Discovery. Pharmaceuticals (Basel) 2022; 15:1302. [PMID: 36297414 PMCID: PMC9607151 DOI: 10.3390/ph15101302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
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Affiliation(s)
- Anika Rütten
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Teresa Kirchner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ewa Maria Musiol-Kroll
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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5
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Li Y, Reed M, Wright HT, Cropp TA, Williams GJ. Development of Genetically Encoded Biosensors for Reporting the Methyltransferase-Dependent Biosynthesis of Semisynthetic Macrolide Antibiotics. ACS Synth Biol 2021; 10:2520-2531. [PMID: 34546703 DOI: 10.1021/acssynbio.1c00151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Clarithromycin is an improved semisynthetic analogue of the naturally occurring macrolide, erythromycin. The subtle modification of a methyl group on the C-6 hydroxyl group endows the molecule with improved acid stability and results in a clinically useful antibiotic. Here, we show that the effector specificity of the biosensor protein, MphR, can be evolved to selectively recognize clarithromycin and therefore report on the production of this molecule in vivo. In addition, a crystal structure of the evolved variant reveals the molecular basis for selectivity and provides a guide for the evolution of a new metabolic function using this biosensor.
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Affiliation(s)
- Yiwei Li
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Megan Reed
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - H. Tonie Wright
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - T. Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Gavin J. Williams
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
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6
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Miller CA, Ho JM, Parks SE, Bennett MR. Macrolide Biosensor Optimization through Cellular Substrate Sequestration. ACS Synth Biol 2021; 10:258-264. [PMID: 33555859 PMCID: PMC7901672 DOI: 10.1021/acssynbio.0c00572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Developing and optimizing small-molecule biosensors is a central goal of synthetic
biology. Here we incorporate additional cellular components to improve biosensor
sensitivity by preventing target molecules from diffusing out of cells. We demonstrate
that trapping erythromycin within Escherichia coli through
phosphorylation increases the sensitivity of its biosensor (MphR) by approximately
10-fold. When combined with prior engineering efforts, our optimized biosensor can
detect erythromycin concentrations as low as 13 nM. We show that this strategy works
with a range of macrolide substrates, enabling the potential usage of our optimized
system for drug development and metabolic engineering. This strategy can be extended in
future studies to improve the sensitivity of other biosensors. Our findings further
suggest that many naturally evolved genes involved in resistance to multiple classes of
antibiotics may increase intracellular drug concentrations to modulate their own
expression, acting as a form of regulatory feedback.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Joanne M. Ho
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Sydney E. Parks
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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7
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Piroozmand F, Mohammadipanah F, Faridbod F. Emerging biosensors in detection of natural products. Synth Syst Biotechnol 2020; 5:293-303. [PMID: 32954023 PMCID: PMC7484522 DOI: 10.1016/j.synbio.2020.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 01/10/2023] Open
Abstract
Natural products (NPs) are a valuable source in the food, pharmaceutical, agricultural, environmental, and many other industrial sectors. Their beneficial properties along with their potential toxicities make the detection, determination or quantification of NPs essential for their application. The advanced instrumental methods require time-consuming sample preparation and analysis. In contrast, biosensors allow rapid detection of NPs, especially in complex media, and are the preferred choice of detection when speed and high throughput are intended. Here, we review diverse biosensors reported for the detection of NPs. The emerging approaches for improving the efficiency of biosensors, such as microfluidics, nanotechnology, and magnetic beads, are also discussed. The simultaneous use of two detection techniques is suggested as a robust strategy for precise detection of a specific NP with structural complexity in complicated matrices. The parallel detection of a variety of NPs structures or biological activities in a mixture of extract in a single detection phase is among the anticipated future advancements in this field which can be achieved using multisystem biosensors applying multiple flow cells, sensing elements, and detection mechanisms on miniaturized folded chips.
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Affiliation(s)
- Firoozeh Piroozmand
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Farnoush Faridbod
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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8
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Ye Y, Guo H, Sun X. Recent progress on cell-based biosensors for analysis of food safety and quality control. Biosens Bioelectron 2018; 126:389-404. [PMID: 30469077 DOI: 10.1016/j.bios.2018.10.039] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 10/28/2022]
Abstract
Food quality and safety has become a subject of major concern for authorities and professionals in the food supply chain. Rapid methods, particularly biosensors, have exceptional specificity and sensitivity, rapid response times, low cost, relatively compact size, and are user friendly to operate. Cell-based biosensors are portable, and provide the biological activity of the analyte suitable for an initial screening of food. In this overview, the utilization of cell-based biosensors for food safety and quality analyses, such as detecting toxins, foodborne pathogens, allergens, and evaluating toxicity and function are summarized. Our results will promote the future development of cell-based biosensors in the food field.
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Affiliation(s)
- Yongli Ye
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hongyan Guo
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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9
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Kasey CM, Zerrad M, Li Y, Cropp TA, Williams GJ. Development of Transcription Factor-Based Designer Macrolide Biosensors for Metabolic Engineering and Synthetic Biology. ACS Synth Biol 2018; 7:227-239. [PMID: 28950701 DOI: 10.1021/acssynbio.7b00287] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrolides are a large group of natural products that display broad and potent biological activities and are biosynthesized by type I polyketide synthases (PKSs) and associated enzymatic machinery. There is an urgent need to access macrolides and unnatural macrolide derivatives for drug discovery, drug manufacture, and probe development. Typically, efforts to engineer the biosynthesis of macrolides and macrolide analogues in various microbial hosts are hampered by the complexity of macrolide biosynthetic pathways and our limited ability to rationally reprogram type I PKSs and post-PKS machinery. High-throughput approaches based on synthetic biology and directed evolution could overcome this problem by testing the function of large libraries of variants. Yet, methods that can identify mutant enzymes, pathways, and strains that produce the desired macrolide target are not generally available. Here we show that the promiscuous macrolide sensing transcription factor MphR is a powerful platform for engineering variants with tailored properties. We identified variants that displayed improved sensitivity toward erythromycin, tailored the inducer specificity, and significantly improved sensitivity to macrolides that were very poor inducers of the wild-type MphR biosensor. Designer macrolide biosensors should find broad utility and enable applications related to high-throughput synthetic biology and directed evolution of macrolide biosynthesis.
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Affiliation(s)
- Christian M. Kasey
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Mounir Zerrad
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - Yiwei Li
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
| | - T. Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gavin J. Williams
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Comparative Medicine Institute, NC State University, Raleigh, North Carolina 27695, United States
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10
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The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies. ISME JOURNAL 2017; 12:885-897. [PMID: 29259290 DOI: 10.1038/s41396-017-0017-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/17/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022]
Abstract
The ecology of antibiotic resistance involves the interplay of a long natural history of antibiotic production in the environment, and the modern selection of resistance in pathogens through human use of these drugs. Important components of the resistome are intrinsic resistance genes of environmental bacteria, evolved and acquired over millennia, and their mobilization, which drives dissemination in pathogens. Understanding the dynamics and evolution of resistance across bacterial taxa is essential to address the current crisis in drug-resistant infections. Here we report the exploration of antibiotic resistance in the Paenibacillaceae prompted by our discovery of an ancient intrinsic resistome in Paenibacillus sp. LC231, recovered from the isolated Lechuguilla cave environment. Using biochemical and gene expression analysis, we have mined the resistome of the second member of the Paenibacillaceae family, Brevibacillus brevis VM4, which produces several antimicrobial secondary metabolites. Using phylogenomics, we show that Paenibacillaceae resistomes are in flux, evolve mostly independent of secondary metabolite biosynthetic diversity, and are characterized by cryptic, redundant, pseudoparalogous, and orthologous genes. We find that in contrast to pathogens, mobile genetic elements are not significantly responsible for resistome remodeling. This offers divergent modes of resistome development in pathogens and environmental bacteria.
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11
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Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories. Metab Eng 2017; 44:253-264. [PMID: 29097310 DOI: 10.1016/j.ymben.2017.10.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/17/2017] [Accepted: 10/27/2017] [Indexed: 12/12/2022]
Abstract
Malonyl-CoA is the basic building block for synthesizing a range of important compounds including fatty acids, phenylpropanoids, flavonoids and non-ribosomal polyketides. Centering around malonyl-CoA, we summarized here the various metabolic engineering strategies employed recently to regulate and control malonyl-CoA metabolism and improve cellular productivity. Effective metabolic engineering of microorganisms requires the introduction of heterologous pathways and dynamically rerouting metabolic flux towards products of interest. Transcriptional factor-based biosensors translate an internal cellular signal to a transcriptional output and drive the expression of the designed genetic/biomolecular circuits to compensate the activity loss of the engineered biosystem. Recent development of genetically-encoded malonyl-CoA sensor has stood out as a classical example to dynamically reprogram cell metabolism for various biotechnological applications. Here, we reviewed the design principles of constructing a transcriptional factor-based malonyl-CoA sensor with superior detection limit, high sensitivity and broad dynamic range. We discussed various synthetic biology strategies to remove pathway bottleneck and how genetically-encoded metabolite sensor could be deployed to improve pathway efficiency. Particularly, we emphasized that integration of malonyl-CoA sensing capability with biocatalytic function would be critical to engineer efficient microbial cell factory. Biosensors have also advanced beyond its classical function of a sensor actuator for in situ monitoring of intracellular metabolite concentration. Applications of malonyl-CoA biosensors as a sensor-invertor for negative feedback regulation of metabolic flux, a metabolic switch for oscillatory balancing of malonyl-CoA sink pathway and source pathway and a screening tool for engineering more efficient biocatalyst are also presented in this review. We envision the genetically-encoded malonyl-CoA sensor will be an indispensable tool to optimize cell metabolism and cost-competitively manufacture malonyl-CoA-derived compounds.
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12
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New methodologies in screening of antibiotic residues in animal-derived foods: Biosensors. Talanta 2017; 175:435-442. [PMID: 28842013 DOI: 10.1016/j.talanta.2017.07.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/15/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023]
Abstract
Antibiotics are leading medicine asset for fighting against microbial infection, but also one of the important causes of death worldwide. Many antibiotics used as therapeutics and growth promotion agents in animals can lead to antibiotic residues in animal-derived food which harm the health of people. Hence, it is vital to screen antibiotic residues in animal derived foods. Typical methods for screening antibiotic residues are based on microbiological growth inhibition and immunological analyses. However these two methods have some disadvantages, such as poor sensitive, lack of specificity and etc. Therefore, it is necessary to develop simple, more efficient and high sensitive screening methods of antibiotic residues. These assays have been introduced for the screening of numerous food samples. Biosensors are emerging methods, applied in screening antibiotic residues in animal-derived foods. Two types of biosensors, whole-cell based biosensors and surface plasmon resonance-based sensors have been extensively used. Their advantages include portability, small sample requirement, high sensitivity and good specificity over the traditional screening methods.
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13
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Wang Z, Beier RC, Shen J. Immunoassays for the detection of macrocyclic lactones in food matrices – A review. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Osterman IA, Komarova ES, Shiryaev DI, Korniltsev IA, Khven IM, Lukyanov DA, Tashlitsky VN, Serebryakova MV, Efremenkova OV, Ivanenkov YA, Bogdanov AA, Sergiev PV, Dontsova OA. Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors. Antimicrob Agents Chemother 2016; 60:7481-7489. [PMID: 27736765 PMCID: PMC5119032 DOI: 10.1128/aac.02117-16] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter. The gene of the far-red fluorescent protein, katushka2S, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
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Affiliation(s)
- Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry I Shiryaev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Ilya A Korniltsev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Irina M Khven
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry A Lukyanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Vadim N Tashlitsky
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Olga V Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Yan A Ivanenkov
- Moscow Institute of Physics and Technology (State University), Moscow Region, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga A Dontsova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Osterman IA, Bogdanov AA, Dontsova OA, Sergiev PV. Techniques for Screening Translation Inhibitors. Antibiotics (Basel) 2016; 5:antibiotics5030022. [PMID: 27348012 PMCID: PMC5039519 DOI: 10.3390/antibiotics5030022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 02/03/2023] Open
Abstract
The machinery of translation is one of the most common targets of antibiotics. The development and screening of new antibiotics usually proceeds by testing antimicrobial activity followed by laborious studies of the mechanism of action. High-throughput methods for new antibiotic screening based on antimicrobial activity have become routine; however, identification of molecular targets is usually a challenge. Therefore, it is highly beneficial to combine primary screening with the identification of the mechanism of action. In this review, we describe a collection of methods for screening translation inhibitors, with a special emphasis on methods which can be performed in a high-throughput manner.
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Affiliation(s)
- Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
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Rogers JK, Taylor ND, Church GM. Biosensor-based engineering of biosynthetic pathways. Curr Opin Biotechnol 2016; 42:84-91. [PMID: 26998575 DOI: 10.1016/j.copbio.2016.03.005] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/21/2016] [Accepted: 03/03/2016] [Indexed: 01/18/2023]
Abstract
Biosynthetic pathways provide an enzymatic route from inexpensive renewable resources to valuable metabolic products such as pharmaceuticals and plastics. Designing these pathways is challenging due to the complexities of biology. Advances in the design and construction of genetic variants has enabled billions of cells, each possessing a slightly different metabolic design, to be rapidly generated. However, our ability to measure the quality of these designs lags by several orders of magnitude. Recent research has enabled cells to report their own success in chemical production through the use of genetically encoded biosensors. A new engineering discipline is emerging around the creation and application of biosensors. Biosensors, implemented in selections and screens to identify productive cells, are paving the way for a new era of biotechnological progress.
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Affiliation(s)
- Jameson K Rogers
- Wyss Institute for Biologically Inspired Engineering Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Noah D Taylor
- Wyss Institute for Biologically Inspired Engineering Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA.
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Aga DS, Lenczewski M, Snow D, Muurinen J, Sallach JB, Wallace JS. Challenges in the Measurement of Antibiotics and in Evaluating Their Impacts in Agroecosystems: A Critical Review. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:407-19. [PMID: 27065387 DOI: 10.2134/jeq2015.07.0393] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Large quantities of antibiotics are used in agricultural production, resulting in their release to agroecosystems through numerous pathways, including land application of contaminated manure, runoff from manure-fertilized fields, and wastewater irrigation of croplands. Antibiotics and their transformation products (TPs) exhibit a wide range of physico-chemical and biological properties and thus present substantive analytical challenges. Advances in the measurement of these compounds in various environmental compartments (plants, manure, soil, sediment, and water) have uncovered a previously unrealized landscape of antibiotic residues. These advanced multiresidue methods, designed to measure sub-ng g concentrations in complex mixtures, remain limited by the inherent intricacy of the sample matrices and the difficultly in eliminating interferences that affect antibiotic detection. While efficient extraction methods combined with high sensitivity analysis by liquid chromatography/mass spectrometry can provide accurate quantification of antibiotics and their TPs, measured concentrations do not necessarily reflect their bioavailable fractions and effects in the environment. Consequently, there is a need to complement chemical analysis with biological assays that can provide information on bioavailability, biological activity, and effects of mixtures. Enzyme-linked immunosorbent assays (ELISA), often used as screening tools for antibiotic residues, may be useful for detecting the presence of structurally related antibiotic mixtures but not their effects. Other tools, including bioreporter assays, hold promise in measuring bioavailable antibiotics and could provide insights on their biological activity. Improved assessment of the ecological and human health risks associated with antibiotics in agroecosystems requires continued advances in analytical accuracy and sensitivity through improvements in sample preparation, instrumentation, and screening technologies.
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Franklin AM, Aga DS, Cytryn E, Durso LM, McLain JE, Pruden A, Roberts MC, Rothrock MJ, Snow DD, Watson JE, Dungan RS. Antibiotics in Agroecosystems: Introduction to the Special Section. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:377-93. [PMID: 27065385 DOI: 10.2134/jeq2016.01.0023] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper.
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Comparative study between macrolide regulatory proteins MphR(A) and MphR(E) in ligand identification and DNA binding based on the rapid in vitro detection system. Anal Bioanal Chem 2016; 408:1623-31. [PMID: 26753969 DOI: 10.1007/s00216-015-9270-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/20/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022]
Abstract
The macrolide regulatory protein MphR(A) has been widely studied and used in various aspects such as metabolism monitoring, exogenous gene expression, and in vivo and in vitro macrolide antibiotic screening. Another macrolide regulatory protein, MphR(E), has rarely been reported. In this study, in vitro ELISA-type systems were established for MphR(A) and MphR(E) to study their correlation. The reactivity of 14 macrolide antibiotics and pseudo-macrolide antibiotics was tested in the systems. The results indicated that the ligand identification spectra of MphR(A) and MphR(E) were basically consistent. The binding characteristics of MphR(A) and MphR(E) with three corresponding promoter DNA sequences were preliminarily studied. According to the ELISA-type analysis results, MphR(A) and MphR(E) have consistent DNA binding properties, which bind to A-DNA/B-DNA more easily than to C-DNA. This study has confirmed that MphR(E) can bind to the promoter DNA sequences mrx(E) and mph(E) in plasmid pRSB111, and different DNAs can affect the sensitivity of the in vitro detection systems.
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Sergiev P, Osterman I, Golovina A, Laptev I, Pletnev P, Evfratov S, Marusich E, Leonov S, Ivanenkov Y, Bogdanov A, Dontsova O. Application of reporter strains for new antibiotic screening. ACTA ACUST UNITED AC 2016; 62:117-23. [DOI: 10.18097/pbmc20166202117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Screening for new antibiotics remains an important area of biology and medical science. Indispensable for this type of research is early identification of antibiotic mechanism of action. Preferentially, it should be studied quickly and cost-effectively, on the stage of primary screening. In this review we describe an application of reporter strains for rapid classification of antibiotics by its target, without prior purification of an active compound and determination of chemical structure
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Affiliation(s)
- P.V. Sergiev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.A. Osterman
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A.Ya. Golovina
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I.G. Laptev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - P.I. Pletnev
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - S.A. Evfratov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E.I. Marusich
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - S.V. Leonov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - Ya.A. Ivanenkov
- Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow region, Russia
| | - A.A. Bogdanov
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - O.A. Dontsova
- Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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21
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Rogers JK, Guzman CD, Taylor ND, Raman S, Anderson K, Church GM. Synthetic biosensors for precise gene control and real-time monitoring of metabolites. Nucleic Acids Res 2015; 43:7648-60. [PMID: 26152303 PMCID: PMC4551912 DOI: 10.1093/nar/gkv616] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 04/20/2015] [Accepted: 06/01/2015] [Indexed: 12/19/2022] Open
Abstract
Characterization and standardization of inducible transcriptional regulators has transformed how scientists approach biology by allowing precise and tunable control of gene expression. Despite their utility, only a handful of well-characterized regulators exist, limiting the complexity of engineered biological systems. We apply a characterization pipeline to four genetically encoded sensors that respond to acrylate, glucarate, erythromycin and naringenin. We evaluate how the concentration of the inducing chemical relates to protein expression, how the extent of induction affects protein expression kinetics, and how the activation behavior of single cells relates to ensemble measurements. We show that activation of each sensor is orthogonal to the other sensors, and to other common inducible systems. We demonstrate independent control of three fluorescent proteins in a single cell, chemically defining eight unique transcriptional states. To demonstrate biosensor utility in metabolic engineering, we apply the glucarate biosensor to monitor product formation in a heterologous glucarate biosynthesis pathway and identify superior enzyme variants. Doubling the number of well-characterized inducible systems makes more complex synthetic biological circuits accessible. Characterizing sensors that transduce the intracellular concentration of valuable metabolites into fluorescent readouts enables high-throughput screening of biological catalysts and alleviates the primary bottleneck of the metabolic engineering design-build-test cycle.
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Affiliation(s)
- Jameson K Rogers
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, MA 02143, USA
| | - Christopher D Guzman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Noah D Taylor
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Srivatsan Raman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kelley Anderson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Biosensors, antibiotics and food. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 145:153-85. [PMID: 25216955 DOI: 10.1007/978-3-662-43619-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Antibiotics are medicine's leading asset for fighting microbial infection, which is one of the leading causes of death worldwide. However, the misuse of antibiotics has led to the rapid spread of antibiotic resistance among bacteria and the development of multiple resistant pathogens. Therefore, antibiotics are rapidly losing their antimicrobial value. The use of antibiotics in food production animals is strictly controlled by the European Union (EU). Veterinary use is regulated to prevent the spread of resistance. EU legislation establishes maximum residue limits for veterinary medicinal products in foodstuffs of animal origin and enforces the establishment and execution of national monitoring plans. Among samples selected for monitoring, suspected noncompliant samples are screened and then subjected to confirmatory analysis to establish the identity and concentration of the contaminant. Screening methods for antibiotic residues are typically based on microbiological growth inhibition, whereas physico-chemical methods are used for confirmatory analysis. This chapter discusses biosensors, especially whole-cell based biosensors, as emerging screening methods for antibiotic residues. Whole-cell biosensors can offer highly sensitive and specific detection of residues. Applications demonstrating quantitative analysis and specific analyte identification further improve their potential as screening methods.
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High-performance thin-layer chromatography screening of multi class antibiotics in animal food by bioluminescent bioautography and electrospray ionization mass spectrometry. J Chromatogr A 2014; 1356:249-57. [DOI: 10.1016/j.chroma.2014.06.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/12/2014] [Accepted: 06/12/2014] [Indexed: 11/22/2022]
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24
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Kotova VY, Ryzhenkova KV, Manukhov IV, Zavilgelsky GB. Inducible specific lux-biosensors for the detection of antibiotics: Construction and main parameters. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683814010074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Osterman IA, Prokhorova IV, Sysoev VO, Boykova YV, Efremenkova OV, Svetlov MS, Kolb VA, Bogdanov AA, Sergiev PV, Dontsova OA. Attenuation-based dual-fluorescent-protein reporter for screening translation inhibitors. Antimicrob Agents Chemother 2012; 56:1774-83. [PMID: 22252829 PMCID: PMC3318315 DOI: 10.1128/aac.05395-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/28/2011] [Indexed: 11/20/2022] Open
Abstract
A reporter construct was created on the basis of the transcription attenuator region of the Escherichia coli tryptophan operon. Dual-fluorescent-protein genes for red fluorescent protein and cerulean fluorescent protein were used as a sensor and internal control of gene expression. The sequence of the attenuator was modified to avoid tryptophan sensitivity while preserving sensitivity to ribosome stalling. Antimicrobial compounds which cause translation arrest at the stage of elongation induce the reporter both in liquid culture and on an agar plate. This reporter could be used for high-throughput screening of translation inhibitors.
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Affiliation(s)
- Ilya A. Osterman
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Irina V. Prokhorova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Vasily O. Sysoev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Yulia V. Boykova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Olga V. Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Maxim S. Svetlov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vyacheslav A. Kolb
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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26
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Xu X, Ying Y. Microbial Biosensors for Environmental Monitoring and Food Analysis. FOOD REVIEWS INTERNATIONAL 2011. [DOI: 10.1080/87559129.2011.563393] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hong CC, Wang CY, Peng KT, Chu IM. A microfluidic chip platform with electrochemical carbon nanotube electrodes for pre-clinical evaluation of antibiotics nanocapsules. Biosens Bioelectron 2011; 26:3620-6. [DOI: 10.1016/j.bios.2011.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/23/2011] [Accepted: 02/11/2011] [Indexed: 10/18/2022]
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28
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Huet AC, Delahaut P, Fodey T, Haughey SA, Elliott C, Weigel S. Advances in biosensor-based analysis for antimicrobial residues in foods. Trends Analyt Chem 2010. [DOI: 10.1016/j.trac.2010.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Chromatography-bioluminescence coupling reveals surprising bioactivity of inthomycin A. Anal Bioanal Chem 2010; 398:2081-8. [PMID: 20842351 DOI: 10.1007/s00216-010-4086-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 10/19/2022]
Abstract
By employing a novel technique for the direct coupling of a bacterial bioassay with chromatography, we discovered a gyrA promotor active compound in myxobacterial extracts and elucidated the structure directly without any isolation step. As a result, we identified inthomycin A as the bioactive substance. Our method is based on a whole-cell bioluminescent reporter gene assay coupled with thin-layer chromatography for primary hit detection and with liquid chromatography (LC)/mass spectrometry or LC/NMR for dereplication and structure elucidation. Previously, inthomycin A has been isolated from Streptomycetes and was associated with the inhibition of cellulose biosynthesis and herbicidal activity. Thus, our findings support the basic principle that completely different microbial phyla are able to synthesize the same natural product. Moreover, our results indicate that inthomycin A affects bacterial DNA supercoiling, which reveals an unexpected bioactivity for this compound. These results can possibly promote further investigation of the biosynthesis as well as the biological activity of inthomycins and related natural products.
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Ostash B, Ostash I, Zhu L, Kharel MK, Luzhetskyy A, Bechthold A, Walker S, Rohr J, Fedorenko V. Properties of lanK-based regulatory circuit involved in landomycin biosynthesis in Streptomyces cyanogenus S136. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410050030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Bovee TFH, Pikkemaat MG. Bioactivity-based screening of antibiotics and hormones. J Chromatogr A 2009; 1216:8035-50. [PMID: 19342055 DOI: 10.1016/j.chroma.2009.03.045] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/26/2009] [Accepted: 03/17/2009] [Indexed: 01/03/2023]
Abstract
Bioactivity-based screening methods are relatively cheap, quick and easy to use tools. Especially with respect to antimicrobial residues and compounds with hormonal activity, they form a very cost-effective alternative to physical chemical methods in large-scale surveillance and monitoring programs, where their main purpose is to identify samples that require additional chemical confirmation. A major advantage is their intrinsic capability to detect unknown compounds and new hazards. This review shows an overview of the available methods and their potential and limitations for regulatory control.
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Affiliation(s)
- T F H Bovee
- RIKILT - Institute of Food Safety, Wageningen UR, 6700 AE Wageningen, The Netherlands.
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33
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Zheng J, Sagar V, Smolinsky A, Bourke C, LaRonde-LeBlanc N, Cropp TA. Structure and function of the macrolide biosensor protein, MphR(A), with and without erythromycin. J Mol Biol 2009; 387:1250-60. [PMID: 19265703 DOI: 10.1016/j.jmb.2009.02.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/12/2009] [Accepted: 02/16/2009] [Indexed: 11/16/2022]
Abstract
The regulatory protein MphR(A) has recently seen extensive use in synthetic biological applications, such as metabolite sensing and exogenous control of gene expression. This protein negatively regulates the expression of a macrolide 2'-phosphotransferase I resistance gene (mphA) via binding to a 35-bp DNA operator upstream of the start codon and is de-repressed by the presence of erythromycin. Here, we present the refined crystal structure of the MphR(A) protein free of erythromycin and that of the MphR(A) protein with bound erythromycin at 2.00- and 1.76-A resolutions, respectively. We also studied the DNA binding properties of the protein and identified mutants of MphR(A) that are defective in gene repression and ligand binding in a cell-based reporter assay. The combination of these two structures illustrates the molecular basis of erythromycin-induced gene expression and provides a framework for additional applied uses of this protein in the isolation and engineered biosynthesis of polyketide natural products.
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Affiliation(s)
- Jianting Zheng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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34
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A review of analytical methods for the determination of aminoglycoside and macrolide residues in food matrices. Anal Chim Acta 2008; 624:1-15. [DOI: 10.1016/j.aca.2008.05.054] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 05/22/2008] [Accepted: 05/23/2008] [Indexed: 11/18/2022]
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