1
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Bookout T, Shideler S, Cooper E, Goff K, Headley JV, Gieg LM, Lewenza S. Construction of Whole Cell Bacterial Biosensors as an Alternative Environmental Monitoring Technology to Detect Naphthenic Acids in Oil Sands Process-Affected Water. ACS Synth Biol 2024. [PMID: 39312753 DOI: 10.1021/acssynbio.4c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids (NA) in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were the atuAR promoters from a naphthenic acid degradation operon and upstream TetR regulator, the marR operon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptional lux reporter plasmids that were introduced into a tailings pond-derived Pseudomonas species. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner to simple, acyclic, and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 and 15 mg/L. The atuA and marR promoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.
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Affiliation(s)
- Tyson Bookout
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Steve Shideler
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Evan Cooper
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Kira Goff
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - John V Headley
- Environment and Climate Change Canada, National Hydrology Research Centre, Saskatoon, Saskatchewan, Canada S7N 3H5
| | - Lisa M Gieg
- Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Shawn Lewenza
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada T9S 3A3
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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2
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Mendoza ASG, Acosta MFM, Sánchez JAM, Vázquez LEC. Principles and challenges of whole cell microbial biosensors in the food industry. J Food Sci 2024. [PMID: 39175184 DOI: 10.1111/1750-3841.17294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Whole cell microbial biosensors (WCMB) are mostly genetically modified microorganisms used to detect target molecules as indicators of biological and chemical contaminants as well as in the identification of compounds of interest in the food industry. The specificity and sensitivity of these biosensors are achieved through the design of genetic circuits that make use of genetic sequences such as promoters, terminators, genes encoding regulatory proteins or reporter proteins, among others. Despite the advances of WCMBs for their application, significant challenges are faced, such as cell stability, regulatory restrictions, and the need to optimize response times so that they can be a competitive detection tool in the market. This review explores the technological progress, potential and limitations of WCMBs in the food industry, starting by reviewing the operating principles of biosensors. The importance of selecting appropriate chassis cells and the integration of recognition elements and transducers to maximize their effectiveness in the detection of contaminants and compounds of interest in the food industry is highlighted.
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Affiliation(s)
- América Selene Gaona Mendoza
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - María Fernanda Mendoza Acosta
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - Julio Armando Massange Sánchez
- Plant Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco A.C. (CIATEJ), Guadalajara, Mexico
| | - Luz Edith Casados Vázquez
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- CONAHCyT-University of Guanajuato, Guanajuato, México
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3
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Pham C, Nasr MA, Skarina T, Di Leo R, Kwan DH, Martin VJJ, Stogios PJ, Mahadevan R, Savchenko A. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors. FEBS J 2024; 291:3481-3498. [PMID: 38696354 DOI: 10.1111/febs.17149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- The Institute of Biomedical Engineering, University of Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Canada
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4
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Huo X, Zhou Z, Liu H, Wang G, Shi K. A PadR family transcriptional repressor regulates the transcription of chromate efflux transporter in Enterobacter sp. Z1. J Microbiol 2024; 62:355-365. [PMID: 38587592 DOI: 10.1007/s12275-024-00117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 04/09/2024]
Abstract
Chromium is a prevalent toxic heavy metal, and chromate [Cr(VI)] exhibits high mutagenicity and carcinogenicity. The presence of the Cr(VI) efflux protein ChrA has been identified in strains exhibiting resistance to Cr(VI). Nevertheless, certain strains of bacteria that are resistant to Cr(VI) lack the presence of ChrB, a known regulatory factor. Here, a PadR family transcriptional repressor, ChrN, has been identified as a regulator in the response of Enterobacter sp. Z1(CCTCC NO: M 2019147) to Cr(VI). The chrN gene is cotranscribed with the chrA gene, and the transcriptional expression of this operon is induced by Cr(VI). The binding capacity of the ChrN protein to Cr(VI) was demonstrated by both the tryptophan fluorescence assay and Ni-NTA purification assay. The interaction between ChrN and the chrAN operon promoter was validated by reporter gene assay and electrophoretic mobility shift assay. Mutation of the conserved histidine residues His14 and His50 resulted in loss of ChrN binding with the promoter of the chrAN operon. This observation implies that these residues are crucial for establishing a DNA-binding site. These findings demonstrate that ChrN functions as a transcriptional repressor, modulating the cellular response of strain Z1 to Cr(VI) exposure.
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Affiliation(s)
- Xueqi Huo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zijie Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, Shandong Province, People's Republic of China
| | - Gejiao Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Kaixiang Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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5
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He N, Wei Q, Li Y, Hu S, Xian Y, Yang M, Wu P, Lu Z, Zhang G. A sensitive, portable, and smartphone-based whole-cell biosensor device for salicylic acid monitoring. Biosens Bioelectron 2024; 257:116329. [PMID: 38677023 DOI: 10.1016/j.bios.2024.116329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/14/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Considerable effort has been invested in developing salicylic acid (SA) biosensors for various application purposes. Here, by engineering the sensing modules and host cell chassis, we have gradually optimized the NahR-Psal/Pr-based SA biosensor, increasing the sensitivity and maximum output by 17.2-fold and 9.4-fold, respectively, and improving the detection limit by 800-fold, from 80 μM to 0.1 μM. A portable SA sensing device was constructed by embedding a gelatin-based hydrogel containing an optimized biosensor into the perforations of tape adhered to glass slide, which allowed good determination of SA in the range of 0.1 μM-10 μM. Then, we developed a customized smartphone App to measure the fluorescence intensity of each perforation and automatically calculate the corresponding SA concentration so that we could detect SA concentrations in real cosmetic samples. We anticipate that this smartphone-based imaging biosensor, with its compact size, higher sensitivity, cost-effectiveness, and easy data transfer, will be useful for long-term monitoring of SA.
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Affiliation(s)
- Nisha He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China
| | - Qin Wei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China
| | - Yiwen Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China
| | - Shantong Hu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yufan Xian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Mo Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China
| | - Pan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China
| | - Zhenghui Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China.
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan,430062, Hubei, China; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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6
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Sahu S, Ramachandran S, Bandyopadhyaya R, Anand R. Biosensing of multiple aromatic xenobiotics in water by in-house fabricated prototype device. Biosens Bioelectron 2024; 250:116077. [PMID: 38308941 DOI: 10.1016/j.bios.2024.116077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/05/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Portable, low-cost, and accurate monitoring of hazardous mono-aromatic pollutants, such as phenol or benzene group of compounds in water is a challenging task due to the lack of suitable detectable functional groups and complex matrix of environmental samples. Here, we use a series of protein-based biosensing recognition scaffolds to enable specific detection of several mono-aromatic classes of xenobiotics. The biosensor is tuned to perform in intricate environmental conditions and is interfaced with an in-house manufactured, multi-channel device (AroTrack) capable of direct and sensitive detection of several of these aromatic contaminants, such as phenol, benzene, and 2,3-dimethylphenol (2,3-DMP) in the low ppb range (10-200 ppb). The efficiency of the prototype device was benchmarked in both simulated wastewater and real environmental samples comprising 10 times higher isostructural aromatic pollutants or ions. It was established that AroTrack is reliable for environmental sample testing with a high degree of reproducibility and efficiency comparable to that of modern spectrophotometers (<5 % error). The battery-operated device costs less than $50 to fabricate and this low cost makes it effective to be implemented in rural and low-income settings which suggests immense field deployable potential.
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Affiliation(s)
- Subhankar Sahu
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shankar Ramachandran
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Rajdip Bandyopadhyaya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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7
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Kim Y, Jeon Y, Jang G, Kim BG, Yoon Y. A novel Escherichia coli cell-based bioreporter for quantification of salicylic acid in cosmetics. Appl Microbiol Biotechnol 2024; 108:148. [PMID: 38240881 PMCID: PMC10799119 DOI: 10.1007/s00253-024-13006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/22/2024]
Abstract
Transcription factor-based bioreporters have been extensively studied for monitoring and detecting environmental toxicants. In Escherichia coli, the multiple antibiotic resistance regulator (MarR) induces transcription upon binding to salicylic acid (SA). We generated SA-specific E. coli cell-based bioreporters utilizing the operator region of the mar operon and MarR as components of the reporter and sensing domains, respectively. Although bioreporters based on endogenous MarR and wild-type E. coli cells responded to SA, their sensitivity and selectivity were insufficient for practical sample monitoring. To improve these parameters, we genetically engineered host strains for optimal MarR expression, which enhanced the sensitivity of the biosensor to micromolar quantities of SA with increased selectivity. Under the optimized experimental conditions, the biosensor could quantify SA in environmental samples. For validation, the SA concentration in artificially contaminated SA-containing cosmetic samples was determined using the developed biosensor. Reliability assessment by comparing the concentrations determined using LC-MS/MS revealed > 90% accuracy of the bioreporters. Although bioreporters are not considered standard tools for environmental monitoring, bacterial cell-based bioreporters may serve as alternative tools owing to their affordability and simplicity. The SA biosensor developed in this study can potentially be a valuable tool for monitoring SA in environmental systems. KEY POINTS: • SA-responsive bioreporter is generated by employing mar operon system in E. coli • SA specificity and selectivity were enhanced by genetic/biochemical engineering • The novel bioreporter would be valuable for SA monitoring in environmental systems.
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Affiliation(s)
- Yeonhong Kim
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yangwon Jeon
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bong-Gyu Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea.
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8
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Sahu S, Kumar L, Das S, Gupta D, Anand R. Ultrasensitive detection of aromatic water pollutants through protein immobilization driven organic electrochemical transistors. Chem Sci 2024; 15:710-719. [PMID: 38179533 PMCID: PMC10762727 DOI: 10.1039/d3sc03509c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/03/2023] [Indexed: 01/06/2024] Open
Abstract
Xenobiotic aromatic water pollutants pose an extreme threat to environmental sustainability. Due to the lack of detectable functional groups in these compounds and scarcity of selective bio-recognition scaffolds, easy-to-use sensing strategies capable of on-site detection remain unavailable. Herein, to address this lacune, we entail a strategy that combines biosensor scaffolds with organic electronics to create a compact device for environmental aromatic pollution monitoring. As proof of principle, a sensor module capable of rapid, economic, reliable, and ultrasensitive detection of phenol down to 2 ppb (0.02 μM) was designed wherein biosensing protein MopR was coupled with an organic electrochemical transistor (OECT). For effective interfacing of the sensing scaffold MopR, graphene oxide (GO) nanosheets were optimized as a host immobilization matrix. The MopR-GO immobilized sensor module was subsequently substituted as the gate electrode with PEDOT:PSS serving as an organic semiconductor material. The resulting OECT sensor provided a favourable microenvironment for protein activity, maintaining high specificity. Exclusive phenol detection with minimal loss of sensitivity (<5% error) could be achieved in both complex pollutant mixtures and real environmental samples. This fabrication strategy that amalgamates biological biosensors with organic electronics harnesses the potential to achieve detection of a host of emerging pollutants.
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Affiliation(s)
- Subhankar Sahu
- Department of Chemistry, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Lokesh Kumar
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Sumita Das
- Department of Chemistry, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Dipti Gupta
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay Powai Mumbai 400076 India
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9
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Asemoloye MD, Marchisio MA. Allosteric-Regulation-Based DNA Circuits in Saccharomyces cerevisiae to Detect Organic Acids and Monitor Hydrocarbon Metabolism In Vitro. Methods Mol Biol 2024; 2760:77-94. [PMID: 38468083 DOI: 10.1007/978-1-0716-3658-9_5] [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: 03/13/2024]
Abstract
We show the engineering of prokaryotic-transcription-factor-based biosensing devices in Saccharomyces cerevisiae cells for an in vitro detection of common hydrocarbon intermediates/metabolites and potentially, for monitoring of the metabolism of carbon compounds. We employed the bacterial receptor proteins MarR (multiple antibiotic-resistant receptor) and PdhR (pyruvate dehydrogenase-complex regulator) to detect benzoate/salicylate and pyruvate, respectively. The yeast-enhanced green fluorescence protein (yEGFP) was adopted as an output signal. Indeed, the engineered yeast strains showed a strong and dynamic fluorescent output signal in the presence of the input chemicals ranging from 2 fM up to 5 mM. In addition, we describe how to make use of these strains to assess over time the metabolism of complex hydrocarbon compounds due to the hydrocarbon-degrading fungus Trichoderma harzianum (KY488463).
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10
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Baugh AC, Momany C, Neidle EL. Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators. Annu Rev Microbiol 2023; 77:317-339. [PMID: 37285554 DOI: 10.1146/annurev-micro-050323-040543] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor-activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.
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Affiliation(s)
- Alyssa C Baugh
- Department of Microbiology, University of Georgia, Athens, Georgia, USA;
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, Georgia, USA;
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11
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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12
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Bhat S, Banerjee A, Alagesan S. AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS OMEGA 2023; 8:26806-26815. [PMID: 37546622 PMCID: PMC10399174 DOI: 10.1021/acsomega.3c01164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Isoprene is a valuable platform chemical, which is produced by engineered microorganisms, albeit in low quantities. The amount of isoprene produced is usually measured by gas chromatography, which can be time-consuming and expensive. Alternatively, biosensors have evolved as a powerful tool for real-time high-throughput screening and monitoring of product synthesis. The AraC-pBAD-inducible system has been widely studied, evolved, and engineered to develop biosensors for small molecules. In our preliminary studies, the AraC-pBAD system was mildly induced at higher isoprene concentrations when arabinose was also available. Hence, in the present study, we designed and constructed a synthetic biosensor based on the AraC-pBAD system, wherein the ligand-binding domain of AraC was replaced with IsoA. On introducing this chimeric AraC-IsoA (AcIa) transcription factor with the native PBAD promoter system regulating rfp gene expression, fluorescence output was observed only when wild-type Escherichia coli cells were induced with both isoprene and arabinose. The biosensor sensitivity and dynamic range were further enhanced by removing operator sequences and by substituting the native promoter (PAraC) with the strong tac promoter (Ptac). The chimeric sensor did not work in AraC knockout strains; however, functionality was restored by reintroducing AraC. Hence, AraC is essential for the functioning of our biosensor, while AcIa provides enhanced sensitivity and specificity for isoprene. However, insights into how AraC-AcIa interacts and the possible working mechanism remain to be explored. This study provides a prototype for developing chimeric AraC-based biosensors with proteins devoid of known dimerizing domains and opens a new avenue for further study and exploration.
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13
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Sun S, Peng K, Sun S, Wang M, Shao Y, Li L, Xiang J, Sedjoah RCAA, Xin Z. Engineering Modular and Highly Sensitive Cell-Based Biosensors for Aromatic Contaminant Monitoring and High-Throughput Enzyme Screening. ACS Synth Biol 2023; 12:877-891. [PMID: 36821745 DOI: 10.1021/acssynbio.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Although a variety of whole-cell-based biosensors have been developed for different applications in recent years, most cannot meet practical requirements due to insufficient sensing performance. Here, we constructed two sets of modular genetic circuits by serial and parallel modes capable of significantly amplifying the input/output signal in Escherichia coli. The biosensors are engineered using σ54-dependent phenol-responsive regulator DmpR as a sensor and enhanced green fluorescent protein as a reporter. Cells harboring serial and parallel genetic circuits displayed nearly 9- and 16-fold higher sensitivity than the general circuit. The genetic circuits enabled rapid detection of six phenolic contaminants in 12 h and showed the low limit of detection of 2.5 and 2.2 ppb for benzopyrene (BaP) and tetracycline (Tet), with a broad detection range of 0.01-1 and 0.005-5 μM, respectively. Furthermore, the positive rate was as high as 73% when the biosensor was applied to screen intracellular enzymes with ester-hydrolysis activity from soil metagenomic libraries using phenyl acetate as a phenolic substrate. Several novel enzymes were isolated, identified, and biochemically characterized, including serine peptidases and alkaline phosphatase family protein/metalloenzyme. Consequently, this study provides a new signal amplification method for cell-based biosensors that can be widely applied to environmental contaminant assessment and screening of intracellular enzymes.
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Affiliation(s)
- Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Kailin Peng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Sen Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Mengxi Wang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiahui Xiang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rita-Cindy Aye-Ayire Sedjoah
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
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14
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Tellechea-Luzardo J, Martín Lázaro H, Moreno López R, Carbonell P. Sensbio: an online server for biosensor design. BMC Bioinformatics 2023; 24:71. [PMID: 36855083 PMCID: PMC9972687 DOI: 10.1186/s12859-023-05201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Allosteric transcription factor (aTF) based biosensors can be used to engineer genetic circuits for a wide range of applications. The literature and online databases contain hundreds of experimentally validated molecule-TF pairs; however, the knowledge is scattered and often incomplete. Additionally, compared to the number of compounds that can be produced in living systems, those with known associated TF-compound interactions are low. For these reasons, new tools that help researchers find new possible TF-ligand pairs are called for. In this work, we present Sensbio, a computational tool that through similarity comparison against a TF-ligand reference database, is able to identify putative transcription factors that can be activated by a given input molecule. In addition to the collection of algorithms, an online application has also been developed, together with a predictive model created to find new possible matches based on machine learning.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- grid.157927.f0000 0004 1770 5832Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022 Valencia, Spain
| | - Hèctor Martín Lázaro
- grid.157927.f0000 0004 1770 5832Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022 Valencia, Spain
| | - Raúl Moreno López
- grid.157927.f0000 0004 1770 5832Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022 Valencia, Spain
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022, Valencia, Spain. .,Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, 46980, Paterna, Spain.
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15
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Tellechea-Luzardo J, Stiebritz MT, Carbonell P. Transcription factor-based biosensors for screening and dynamic regulation. Front Bioeng Biotechnol 2023; 11:1118702. [PMID: 36814719 PMCID: PMC9939652 DOI: 10.3389/fbioe.2023.1118702] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Advances in synthetic biology and genetic engineering are bringing into the spotlight a wide range of bio-based applications that demand better sensing and control of biological behaviours. Transcription factor (TF)-based biosensors are promising tools that can be used to detect several types of chemical compounds and elicit a response according to the desired application. However, the wider use of this type of device is still hindered by several challenges, which can be addressed by increasing the current metabolite-activated transcription factor knowledge base, developing better methods to identify new transcription factors, and improving the overall workflow for the design of novel biosensor circuits. These improvements are particularly important in the bioproduction field, where researchers need better biosensor-based approaches for screening production-strains and precise dynamic regulation strategies. In this work, we summarize what is currently known about transcription factor-based biosensors, discuss recent experimental and computational approaches targeted at their modification and improvement, and suggest possible future research directions based on two applications: bioproduction screening and dynamic regulation of genetic circuits.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Martin T. Stiebritz
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
- Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, Paterna, Spain
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16
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Opel F, Itzenhäuser MA, Wehner I, Lupacchini S, Lauterbach L, Lenz O, Klähn S. Toward a synthetic hydrogen sensor in cyanobacteria: Functional production of an oxygen-tolerant regulatory hydrogenase in Synechocystis sp. PCC 6803. Front Microbiol 2023; 14:1122078. [PMID: 37032909 PMCID: PMC10073562 DOI: 10.3389/fmicb.2023.1122078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/22/2023] [Indexed: 04/11/2023] Open
Abstract
Cyanobacteria have raised great interest in biotechnology, e.g., for the sustainable production of molecular hydrogen (H2) using electrons from water oxidation. However, this is hampered by various constraints. For example, H2-producing enzymes compete with primary metabolism for electrons and are usually inhibited by molecular oxygen (O2). In addition, there are a number of other constraints, some of which are unknown, requiring unbiased screening and systematic engineering approaches to improve the H2 yield. Here, we introduced the regulatory [NiFe]-hydrogenase (RH) of Cupriavidus necator (formerly Ralstonia eutropha) H16 into the cyanobacterial model strain Synechocystis sp. PCC 6803. In its natural host, the RH serves as a molecular H2 sensor initiating a signal cascade to express hydrogenase-related genes when no additional energy source other than H2 is available. Unlike most hydrogenases, the C. necator enzymes are O2-tolerant, allowing their efficient utilization in an oxygenic phototroph. Similar to C. necator, the RH produced in Synechocystis showed distinct H2 oxidation activity, confirming that it can be properly matured and assembled under photoautotrophic, i.e., oxygen-evolving conditions. Although the functional H2-sensing cascade has not yet been established in Synechocystis yet, we utilized the associated two-component system consisting of a histidine kinase and a response regulator to drive and modulate the expression of a superfolder gfp gene in Escherichia coli. This demonstrates that all components of the H2-dependent signal cascade can be functionally implemented in heterologous hosts. Thus, this work provides the basis for the development of an intrinsic H2 biosensor within a cyanobacterial cell that could be used to probe the effects of random mutagenesis and systematically identify promising genetic configurations to enable continuous and high-yield production of H2 via oxygenic photosynthesis.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | | | - Isabel Wehner
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Sara Lupacchini
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lars Lauterbach
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, Aachen, Germany
| | - Oliver Lenz
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- *Correspondence: Stephan Klähn,
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17
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Jeon Y, Lee Y, Kim Y, Park C, Choi H, Jang G, Yoon Y. Development of novel Escherichia coli cell-based biosensors to monitor Mn(II) in environmental systems. Front Microbiol 2022; 13:1051926. [PMID: 36601404 PMCID: PMC9806134 DOI: 10.3389/fmicb.2022.1051926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli uses manganese [Mn(II)] as an essential trace element; thus, it has a genetic system that regulates cellular Mn(II) levels. Several genes in the mnt-operon of E. coli respond to intercellular Mn(II) levels, and transcription is regulated by a transcription factor (MntR) that interacts with Mn(II). This study aimed to develop Mn(II)-sensing biosensors based on mnt-operon genetic systems. Additionally, the properties of biosensors developed based on the promoter regions of mntS, mntH, and mntP were investigated. MntR represses the transcription of MntS and MntH after binding with Mn(II), while it induces MntP transcription. Thus, Mn(II) biosensors that decrease and increase signals could be obtained by fusing the promoter regions of mntS/mntH and mntP, with egfp encoding an enhanced green fluorescent protein. However, only the biosensor-based mntS:egfp responded to Mn(II) exposure. Further, E. coli harboring P mntS :egfp showed a concentration-dependent decrease in fluorescence signals. To enhance the sensitivity of the biosensor toward Mn(II), E. coli containing a deleted MntP gene that encodes Mn(II) exporter, was used as a host cell for biosensor development. The sensitivity toward Mn(II) increased by two times on using E. coli-mntP, and the biosensor could quantify 0.01-10 μM of Mn(II). Further, the applicability of Mn(II) in artificially contaminated water samples was quantified and showed >95% accuracy. The newly developed Mn(II) biosensors could detect and quantify the residual Mn(II) from mancozeb in soil samples, with the quantification accuracy being approximately 90%. To the best of our knowledge, this is the first Mn (II)-specific bacterial cell-based biosensor that serves as a valuable tool for monitoring and assessing the risks of Mn(II) in environmental systems.
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Affiliation(s)
- Yangwon Jeon
- Department of Environmental Health Science, Konkuk University, Seoul, Republic of Korea
| | - Yejin Lee
- Department of Environmental Health Science, Konkuk University, Seoul, Republic of Korea
| | - Yeonhong Kim
- Department of Environmental Health Science, Konkuk University, Seoul, Republic of Korea
| | - Chanhee Park
- Department of Environmental Health Science, Konkuk University, Seoul, Republic of Korea
| | - Hoon Choi
- Department of Life and Environmental Sciences, Wonkwang University, Iksan, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul, Republic of Korea
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18
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Xu X, Xu R, Hou S, Kang Z, Lü C, Wang Q, Zhang W, Wang X, Xu P, Gao C, Ma C. A Selective Fluorescent l-Lactate Biosensor Based on an l-Lactate-Specific Transcription Regulator and Förster Resonance Energy Transfer. BIOSENSORS 2022; 12:1111. [PMID: 36551077 PMCID: PMC9775004 DOI: 10.3390/bios12121111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Selective detection of l-lactate levels in foods, clinical, and bacterial fermentation samples has drawn intensive attention. Many fluorescent biosensors based on non-stereoselective recognition elements have been developed for lactate detection. Herein, the allosteric transcription factor STLldR from Salmonella enterica serovar Typhimurium LT2 was identified to be stereo-selectively respond to l-lactate. Then, STLldR was combined with Förster resonance energy transfer (FRET) to construct a fluorescent l-lactate biosensor FILLac. FILLac was further optimized by truncating the N- and C-terminal amino acids of STLldR between cyan and yellow fluorescent proteins. The optimized biosensor FILLac10N0C exhibited a maximum emission ratio change (ΔRmax) of 33.47 ± 1.91%, an apparent dissociation constant (Kd) of 6.33 ± 0.79 μM, and a limit of detection of 0.68 μM. FILLac10N0C was applied in 96-well microplates to detect l-lactate in bacterial fermentation samples and commercial foods such as Jiaosu and yogurt. The quantitation results of FILLac10N0C exhibited good agreement with that of a commercial l-lactate biosensor SBA-40D bioanalyzer. Thus, the biosensor FILLac10N0C compatible with high-throughput detection may be a potential choice for quantitation of l-lactate in different biological samples.
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Affiliation(s)
- Xianzhi Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Rong Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Shuang Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhaoqi Kang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen Zhang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Xia Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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19
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Abstract
Chemical biosensors are an increasingly ubiquitous part of our lives. Beyond enzyme-coupled assays, recent synthetic biology advances now allow us to hijack more complex biosensing systems to respond to difficult to detect analytes, such as chemical small molecules. Here, we briefly overview recent advances in the biosensing of small molecules, including nucleic acid aptamers, allosteric transcription factors, and two-component systems. We then look more closely at a recently developed chemical sensing system, G protein-coupled receptor (GPCR)-based sensors. Finally, we consider the chemical sensing capabilities of the largest GPCR subfamily, olfactory receptors (ORs). We examine ORs' role in nature, their potential as a biomedical target, and their ability to detect compounds not amenable for detection using other biological scaffolds. We conclude by evaluating the current challenges, opportunities, and future applications of GPCR- and OR-based sensors.
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Affiliation(s)
- Amisha Patel
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Pamela Peralta-Yahya
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States,School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States,E-mail:
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20
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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21
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Transcription Factor-Based Biosensors for Detecting Pathogens. BIOSENSORS 2022; 12:bios12070470. [PMID: 35884273 PMCID: PMC9312912 DOI: 10.3390/bios12070470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 12/23/2022]
Abstract
Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.
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22
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Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci 2022; 13:6715-6731. [PMID: 35756504 PMCID: PMC9172442 DOI: 10.1039/d1sc06921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University Boston MA 02215 USA .,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629 F-33600 Pessac France .,University Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 F-33400 Talence France
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University Boston MA 02215 USA
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology, Boston UniversityBostonMA 02118USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | | | | | - Allison M. Dennis
- Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| | - James E. Galagan
- Department of Microbiology, Boston UniversityBostonMA 02118USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston UniversityBostonMA 02215USA,Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
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23
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The structure-function relationship of bacterial transcriptional regulators as a target for enhanced biodegradation of aromatic hydrocarbons. Microbiol Res 2022; 262:127087. [DOI: 10.1016/j.micres.2022.127087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022]
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24
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Sankar K, Baer R, Grazon C, Sabatelle RC, Lecommandoux S, Klapperich CM, Galagan JE, Grinstaff MW. An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone. ACS Sens 2022; 7:1132-1137. [PMID: 35412319 PMCID: PMC9985479 DOI: 10.1021/acssensors.2c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.
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Affiliation(s)
- Karthika Sankar
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - R Baer
- Department of Microbiology, Boston University, Boston, MA 02215, USA
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France.,University Bordeaux, Institut des Sciences Moléculaires (CNRS UMR 5255), 33405 Talence, France
| | - Robert C. Sabatelle
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Catherine M. Klapperich
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James E. Galagan
- Department of Microbiology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
| | - Mark W. Grinstaff
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
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25
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Nasr M, Timmins LR, Martin VJJ, Kwan DH. A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers. ACS Synth Biol 2022; 11:1692-1698. [PMID: 35316041 PMCID: PMC9017570 DOI: 10.1021/acssynbio.2c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 12/26/2022]
Abstract
Allosteric transcription factor (aTF) biosensors are valuable tools for engineering microbes toward a multitude of applications in metabolic engineering, biotechnology, and synthetic biology. One of the challenges toward constructing functional and diverse biosensors in engineered microbes is the limited toolbox of identified and characterized aTFs. To overcome this, extensive bioprospecting of aTFs from sequencing databases, as well as aTF ligand-specificity engineering are essential in order to realize their full potential as biosensors for novel applications. In this work, using the TetR-family repressor CmeR from Campylobacter jejuni, we construct aTF genetic circuits that function as salicylate biosensors in the model organisms Escherichia coli and Saccharomyces cerevisiae. In addition to salicylate, we demonstrate the responsiveness of CmeR-regulated promoters to multiple aromatic and indole inducers. This relaxed ligand specificity of CmeR makes it a useful tool for detecting molecules in many metabolic engineering applications, as well as a good target for directed evolution to engineer proteins that are able to detect new and diverse chemistries.
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Affiliation(s)
- Mohamed
A. Nasr
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Logan R. Timmins
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
| | - David H. Kwan
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
- Department
of Chemistry and Biochemistry, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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26
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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27
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Transition of Dephospho-DctD to the Transcriptionally Active State via Interaction with Dephospho-IIA
Glc. mBio 2022; 13:e0383921. [PMID: 35311533 PMCID: PMC9040800 DOI: 10.1128/mbio.03839-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs), biofilm-maturing components of Vibrio vulnificus, are abundantly produced when the expression of two major EPS gene clusters is activated by an enhancer-binding transcription factor, DctD2, whose expression and phosphorylation are induced by dicarboxylic acids. Surprisingly, when glucose was supplied to V. vulnificus, similar levels of expression of these clusters occurred, even in the absence of dicarboxylic acids. This glucose-dependent activation was also mediated by DctD2, whose expression was sequentially activated by the transcription regulator NtrC. Most DctD2 in cells grown without dicarboxylic acids was present in a dephosphorylated state, known as the transcriptionally inactive form. However, in the presence of glucose, a dephosphorylated component of the glucose-specific phosphotransferase system, d-IIAGlc, interacted with dephosphorylated DctD2 (d-DctD2). While d-DctD2 did not show any affinity to a DNA fragment containing the DctD-binding sequences, the complex of d-DctD2 and d-IIAGlc exhibited specific and efficient DNA binding, similar to the phosphorylated DctD2. The d-DctD2-mediated activation of the EPS gene clusters’ expression was not fully achieved in cells grown with mannose. Furthermore, the degrees of expression of the clusters under glycerol were less than those under mannose. This was caused by an antagonistic and competitive effect of GlpK, whose expression was increased by glycerol, in forming a complex with d-DctD2 by d-IIAGlc. The data demonstrate a novel regulatory pathway for V. vulnificus EPS biosynthesis and biofilm maturation in the presence of glucose, which is mediated by d-DctD2 through its transition to the transcriptionally active state by interacting with available d-IIAGlc.
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28
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Mahas A, Wang Q, Marsic T, Mahfouz MM. Development of Cas12a-Based Cell-Free Small-Molecule Biosensors via Allosteric Regulation of CRISPR Array Expression. Anal Chem 2022; 94:4617-4626. [PMID: 35266687 PMCID: PMC8943526 DOI: 10.1021/acs.analchem.1c04332] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Cell-free biosensors
can detect various molecules, thus promising
to transform the landscape of diagnostics. Here, we developed a simple,
rapid, sensitive, and field-deployable small-molecule detection platform
based on allosteric transcription factor (aTF)-regulated expression
of a clustered regularly interspaced short palindromic repeats (CRISPR)
array coupled to Cas12a activity. To this end, we engineered an expression
cassette harboring a T7 promoter, an aTF binding sequence, a Cas12a
CRISPR array, and protospacer adjacent motif-flanked Cas12a target
sequences. In the presence of the ligand, dissociation of the aTF
allows transcription of the CRISPR array; this leads to activation
of Cas12a collateral activity, which cleaves a single-stranded DNA
linker to free a quenched fluorophore, resulting in a rapid, significant
increase of fluorescence. As a proof of concept, we used TetR as the
aTF to detect different tetracycline antibiotics with high sensitivity
and specificity and a simple, hand-held visualizer to develop a fluorescence-based
visual readout. We also adapted a mobile phone application to further
simplify the interpretation of the results. Finally, we showed that
the reagents could be lyophilized to facilitate storage and distribution.
This detection platform represents a valuable addition to the toolbox
of cell-free, CRISPR-based biosensors, with great potential for in-field
deployment to detect non-nucleic acid small molecules.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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29
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Femerling G, Gama-Castro S, Lara P, Ledezma-Tejeida D, Tierrafría VH, Muñiz-Rascado L, Bonavides-Martínez C, Collado-Vides J. Sensory Systems and Transcriptional Regulation in Escherichia coli. Front Bioeng Biotechnol 2022; 10:823240. [PMID: 35237580 PMCID: PMC8882922 DOI: 10.3389/fbioe.2022.823240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation. Escherichia coli K-12 is the bacterium model for which the largest number of regulatory systems and its sensing capabilities have been studied in detail at the molecular level. In this special issue focused on biomolecular sensing systems, we offer an overview of the transcriptional regulatory corpus of knowledge for E. coli that has been gathered in our database, RegulonDB, from the perspective of sensing regulatory systems. Thus, we start with the beginning of the information flux, which is the signal's chemical or physical elements detected by the cell as changes in the environment; these signals are internally transduced to transcription factors and alter their conformation. Signals transduced to effectors bind allosterically to transcription factors, and this defines the dominant sensing mechanism in E. coli. We offer an updated list of the repertoire of known allosteric effectors, as well as a list of the currently known different mechanisms of this sensing capability. Our previous definition of elementary genetic sensory-response units, GENSOR units for short, that integrate signals, transport, gene regulation, and the biochemical response of the regulated gene products of a given transcriptional factor fit perfectly with the purpose of this overview. We summarize the functional heterogeneity of their response, based on our updated collection of GENSORs, and we use them to identify the expected feedback as part of their response. Finally, we address the question of multiple sensing in the regulatory network of E. coli. This overview introduces the architecture of sensing and regulation of native components in E.coli K-12, which might be a source of inspiration to bioengineering applications.
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Affiliation(s)
- Georgette Femerling
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Víctor H. Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Luis Muñiz-Rascado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | | | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
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30
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McDonald ND, Love CE, Gibbons HS. The ChpR transcriptional regulator of Sinorhizobium meliloti senses 3,5,6-trichloropyridinol, a degradation product of the organophosphate pesticide chlorpyrifos. Access Microbiol 2022; 3:000297. [PMID: 35024557 PMCID: PMC8749142 DOI: 10.1099/acmi.0.000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
The global use of organophosphate insecticides (OPPs) and the growing concern of off-target side effects due to OPP exposure has prompted the need for sensitive and economical detection methods. Here we set out to engineer a previously identified OPP responsive transcription factor, ChpR, from Sinorhizobium melilotii to respond to alternative OPPs and generate a repertoire of whole-cell biosensors for OPPs. The ChpR transcription factor and cognate promoter P chpA, have been shown to activate transcription in the presence of the OPP chlorpyrifos (CPF). Utilizing a GFP reporter regulated by ChpR in a whole-cell biosensor we found that the system responds significantly better to 3,5,6-trichloro-2-pyridinol (TCP), the main degradation product of CPF, compared to CPF itself. This biosensor was able to respond to TCP at 390 nM within 4 h compared to 50 µM of CPF in 7 h. The ChpR-P chpA , and the activating ligand TCP, were able to regulate expression of a kanamycin resistance/sucrose sensitivity (kan/sacB) selection/counterselection module suitable for high throughput mutagenesis screening studies. The ability to control both GFP and the kan/sacB module demonstrates the utility of this reporter for the detection of CPF affected areas. The ChpR-P chpA system serves as an additional positive regulator switch to add to the growing repertoire of controllers available within synthetic biology.
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Affiliation(s)
- Nathan D McDonald
- United States Army Combat Capabilities Development Command - Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Courtney E Love
- United States Army Combat Capabilities Development Command - Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Henry S Gibbons
- United States Army Combat Capabilities Development Command - Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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31
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Machado LFM, Dixon N. Directed Evolution of Transcription Factor-Based Biosensors for Altered Effector Specificity. Methods Mol Biol 2022; 2461:175-193. [PMID: 35727451 DOI: 10.1007/978-1-0716-2152-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transcription factor-based biosensors are important tools in Synthetic Biology for the sensing of industrially valuable molecules and clinically important metabolites, therefore presenting applications in the bioremediation, industrial biotechnology, and biomedical fields. The directed evolution of allosteric transcription factors (aTFs) with the aim of altering effector specificity has the potential for the development of new biosensors to detect natural and nonnatural molecules, expanding the scope of available aTF-based biosensors. In this chapter, we delineate a general method for the directed evolution of aTFs. The theory of library design is discussed, along with the detailed methodology for an improved transformation of combined libraries, and the experimental search space by counterselection using fluorescence-activated cell sorting (FACS) is presented.
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32
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Permsirivisarn P, Yuenyao A, Pramanpol N, Charoenwattanasatien R, Suginta W, Chaiyen P, Pakotiprapha D. Mechanism of transcription regulation by Acinetobacter baumannii HpaR in the catabolism of p-hydroxyphenylacetate. FEBS J 2021; 289:3217-3240. [PMID: 34967505 DOI: 10.1111/febs.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022]
Abstract
HpaR is a transcription regulator in the MarR family that controls the expression of the gene cluster responsible for conversion of p-hydroxyphenylacetate to pyruvate and succinate for cellular metabolism. Here, we report the biochemical and structural characterization of Acinetobacter baumannii HpaR (AbHpaR) and its complex with cognate DNA. Our study revealed that AbHpaR binds upstream of the divergently transcribed hpaA gene and the meta-cleavage operon, as well as the hpaR gene, thereby repressing their transcription by blocking access of RNA polymerase. Structural analysis of AbHpaR-DNA complex revealed that the DNA binding specificity can be achieved via a combination of both direct and indirect DNA sequence readouts. DNA binding of AbHpaR is weakened by 3,4-dihydroxyphenylacetate (DHPA), which is the substrate of the meta-cleavage reactions; this likely leads to expression of the target genes. Based on our findings, we propose a model for how A. baumannii controls transcription of HPA-metabolizing genes, which highlights the independence of global catabolite repression and could be beneficial for metabolic engineering towards bioremediation applications.
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Affiliation(s)
- Permkun Permsirivisarn
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Anan Yuenyao
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nuttawan Pramanpol
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000, Thailand.,National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | | | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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33
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Kaczmarek JA, Prather KLJ. Effective use of biosensors for high-throughput library screening for metabolite production. J Ind Microbiol Biotechnol 2021; 48:6339276. [PMID: 34347108 PMCID: PMC8788864 DOI: 10.1093/jimb/kuab049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022]
Abstract
The development of fast and affordable microbial production from recombinant pathways is a challenging endeavor, with targeted improvements difficult to predict due to the complex nature of living systems. To address the limitations in biosynthetic pathways, much work has been done to generate large libraries of various genetic parts (promoters, RBSs, enzymes, etc.) to discover library members that bring about significantly improved levels of metabolite production. To evaluate these large libraries, high throughput approaches are necessary, such as those that rely on biosensors. There are various modes of operation to apply biosensors to library screens that are available at different scales of throughput. The effectiveness of each biosensor-based method is dependent on the pathway or strain to which it is applied, and all approaches have strengths and weaknesses to be carefully considered for any high throughput library screen. In this review, we discuss the various approaches used in biosensor screening for improved metabolite production, focusing on transcription factor-based biosensors.
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Affiliation(s)
- Jennifer A Kaczmarek
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02142, USA
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34
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Lin H, Rodríguez-Serrano AF, Hsing IM. Rational design of allosterically regulated toehold mediated strand displacement circuits for sensitive and on-site detection of small molecule metabolites. Analyst 2021; 146:7144-7151. [PMID: 34734587 DOI: 10.1039/d1an01488a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Development of small molecule biosensors enables rapid and de-centralized small molecule detection that meets the demands of routine health monitoring and rapid diagnosis. Among them, allosteric transcription factor (aTF)-based biosensors have shown potential in modular design of small molecule detection platforms due to their ligand-regulated DNA binding activity. Here, we expand the capabilities of a biosensor that leverages the aTF-based regulation of toehold-mediated strand displacement (TMSD) circuits for uric acid (UA) detection in non-invasive salivary samples by utilizing the UA-responsive aTF HucR. The impact of the low ligand affinity of the native HucR was addressed by engineering a two-pass TMSD circuit with in silico rational design. This combined strategy achieved enrichment of the output signal and overcame the negative impact of the matrix effect on the sensitivity and overall response of the biosensor when using real samples, which enabled semi-quantitative detection in the normal salivary UA levels. As well, enhancements provided by the two-pass design halved the turnaround time to less than 15 minutes. To sum up, the two-cycle DNA circuit design enabled aTF-based simple, rapid and one-step non-invasive salivary UA detection, showing its potential in metabolite detection for health monitoring.
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Affiliation(s)
- Haosi Lin
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Alan F Rodríguez-Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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35
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Jones K, Snodgrass HM, Belsare K, Dickinson BC, Lewis JC. Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis. ACS CENTRAL SCIENCE 2021; 7:1581-1590. [PMID: 34584960 PMCID: PMC8461764 DOI: 10.1021/acscentsci.1c00811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 05/04/2023]
Abstract
Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage-assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate that we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Ketaki Belsare
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- E-mail:
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
- E-mail:
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36
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Yeom SJ, Le TK, Yun CH. P450-driven plastic-degrading synthetic bacteria. Trends Biotechnol 2021; 40:166-179. [PMID: 34243985 DOI: 10.1016/j.tibtech.2021.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/27/2022]
Abstract
Plastic contamination currently threatens a wide variety of ecosystems and presents damaging repercussions and negative consequences for many wildlife species. Sustainable plastic waste management is an important approach to environmental protection and a necessity in the current life cycle of plastics in nature. Plastic biodegradation by microorganisms is a notable possible solution. This opinion article includes a proposal to use hypothetical P450 enzymes with an engineered active site as potent trigger biocatalysts to biodegrade polyethylene (PE) via in-chain hydroxylation into smaller products of linear aliphatic alcohols and alkanoic acids based on cascade enzymatic reactions. Furthermore, we propose the adoption of P450 into plastic-eating synthetic bacteria for PE biodegradation. This strategy can be applicable to other dense plastics, such as polypropylene (PP) and polystyrene (PS).
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Affiliation(s)
- Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
| | - Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea.
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37
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Sekurova ON, Sun YQ, Zehl M, Rückert C, Stich A, Busche T, Kalinowski J, Zotchev SB. Coupling of the engineered DNA "mutator" to a biosensor as a new paradigm for activation of silent biosynthetic gene clusters in Streptomyces. Nucleic Acids Res 2021; 49:8396-8405. [PMID: 34197612 PMCID: PMC8373060 DOI: 10.1093/nar/gkab583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/31/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
DNA replication fidelity in Streptomyces bacteria, prolific producers of many medically important secondary metabolites, is understudied, while in Escherichia coli it is controlled by DnaQ, the ϵ subunit of DNA polymerase III (DNA PolIII). Manipulation of dnaQ paralogues in Streptomyces lividans TK24, did not lead to increased spontaneous mutagenesis in this bacterium suggesting that S. lividans DNA PolIII uses an alternative exonuclease activity for proofreading. In Mycobacterium tuberculosis, such activity is attributed to the DnaE protein representing α subunit of DNA PolIII. Eight DnaE mutants designed based on the literature data were overexpressed in S. lividans, and recombinant strains overexpressing two of these mutants displayed markedly increased frequency of spontaneous mutagenesis (up to 1000-fold higher compared to the control). One of these ‘mutators’ was combined in S. lividans with a biosensor specific for antibiotic coelimycin, which biosynthetic gene cluster is present but not expressed in this strain. Colonies giving a positive biosensor signal appeared at a frequency of ca 10–5, and all of them were found to produce coelimycin congeners. This result confirmed that our approach can be applied for chemical- and radiation-free mutagenesis in Streptomyces leading to activation of orphan biosynthetic gene clusters and discovery of novel bioactive secondary metabolites.
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Affiliation(s)
- Olga N Sekurova
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Yi-Qian Sun
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Austria
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Anna Stich
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Sergey B Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
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38
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Abstract
One of the most prominent features of genetically encoded biosensors (GEBs) is their evolvability-the ability to invent new sensory functions using mutations. Among the GEBs, the transcription factor-based biosensors (TF-biosensors) is the focus of this review. We also discuss how this class of sensors can be highly evolvable and how we can exploit it. With an established platform for directed evolution, researchers can create, or evolve, new TF-biosensors. Directed evolution experiments have revealed the TF-biosensors' evolvability, which is based partially on their characteristic physicochemical properties.
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Affiliation(s)
- Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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Cortés-Avalos D, Martínez-Pérez N, Ortiz-Moncada MA, Juárez-González A, Baños-Vargas AA, Estrada-de Los Santos P, Pérez-Rueda E, Ibarra JA. An update of the unceasingly growing and diverse AraC/XylS family of transcriptional activators. FEMS Microbiol Rev 2021; 45:6219864. [PMID: 33837749 DOI: 10.1093/femsre/fuab020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/31/2021] [Indexed: 01/09/2023] Open
Abstract
Transcriptional factors play an important role in gene regulation in all organisms, especially in Bacteria. Here special emphasis is placed in the AraC/XylS family of transcriptional regulators. This is one of the most abundant as many predicted members have been identified and more members are added because more bacterial genomes are sequenced. Given the way more experimental evidence has mounded in the past decades, we decided to update the information about this captivating family of proteins. Using bioinformatics tools on all the data available for experimentally characterized members of this family, we found that many members that display a similar functional classification can be clustered together and in some cases they have a similar regulatory scheme. A proposal for grouping these proteins is also discussed. Additionally, an analysis of surveyed proteins in bacterial genomes is presented. Altogether, the current review presents a panoramic view into this family and we hope it helps to stimulate future research in the field.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Noemy Martínez-Pérez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Mario A Ortiz-Moncada
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Aylin Juárez-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo A Baños-Vargas
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México.,Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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40
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Qureshi NA, Bakhtiar SM, Faheem M, Shah M, Bari A, Mahmood HM, Sohaib M, Mothana RA, Ullah R, Jamal SB. Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus. Front Genet 2021; 12:564056. [PMID: 33841489 PMCID: PMC8027347 DOI: 10.3389/fgene.2021.564056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/16/2021] [Indexed: 12/21/2022] Open
Abstract
Streptococcus gallolysticus (Sg) is an opportunistic Gram-positive, non-motile bacterium, which causes infective endocarditis, an inflammation of the inner lining of the heart. As Sg has acquired resistance with the available antibiotics, therefore, there is a dire need to find new therapeutic targets and potent drugs to prevent and treat this disease. In the current study, an in silico approach is utilized to link genomic data of Sg species with its proteome to identify putative therapeutic targets. A total of 1,138 core proteins have been identified using pan genomic approach. Further, using subtractive proteomic analysis, a set of 18 proteins, essential for bacteria and non-homologous to host (human), is identified. Out of these 18 proteins, 12 cytoplasmic proteins were selected as potential drug targets. These selected proteins were subjected to molecular docking against drug-like compounds retrieved from ZINC database. Furthermore, the top docked compounds with lower binding energy were identified. In this work, we have identified novel drug and vaccine targets against Sg, of which some have already been reported and validated in other species. Owing to the experimental validation, we believe our methodology and result are significant contribution for drug/vaccine target identification against Sg-caused infective endocarditis.
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Affiliation(s)
- Nosheen Afzal Qureshi
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Syeda Marriam Bakhtiar
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hafiz M Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Sohaib
- Department of Soil Science, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ramzi A Mothana
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
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41
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Rodríguez-Serrano AF, Hsing IM. Allosteric Regulation of DNA Circuits Enables Minimal and Rapid Biosensors of Small Molecules. ACS Synth Biol 2021; 10:371-378. [PMID: 33481567 DOI: 10.1021/acssynbio.0c00545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detection of environmental pollutants is crucial to safeguard ecological and public health. Here, we report a modular biosensing approach for the detection of contaminants based on the regulation of a minimal DNA signal amplifier and transducer circuit by allosteric transcription factors and their cognate ligands. We leverage the competition between allosteric proteins and an endonuclease to modulate cascade toehold-mediated strand displacement reactions, which are triggered in the presence of specific effectors and sustained by the endonuclease. We built two optical biosensors for the detection of tetracyclines and macrolides in water using repressors TetR and MphR, respectively. We demonstrate that our minimal, fast, and single-step biosensors can successfully detect antibiotics in nanomolar levels and apply them to report the presence of spiked-in antibiotics in water samples in a matter of minutes, suggesting great potential for monitoring of water contaminants.
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Affiliation(s)
- Alan F. Rodríguez-Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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42
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Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas. mSystems 2021; 6:6/1/e00753-20. [PMID: 33436508 PMCID: PMC7901475 DOI: 10.1128/msystems.00753-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria of the Pseudomonas genus, including the major human pathogen Pseudomonas aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized. Transcription factors (TFs) are instrumental in the bacterial response to new environmental conditions. They can act as direct signal sensors and subsequently induce changes in gene expression leading to physiological adaptation. Here, by combining transcriptome sequencing (RNA-seq) and cistrome determination (DAP-seq), we studied a family of eight TFs in Pseudomonas aeruginosa. This family, encompassing TFs with XRE-like DNA-binding and cupin signal-sensing domains, includes the metabolic regulators ErfA, PsdR, and PauR and five so-far-unstudied TFs. The genome-wide delineation of their regulons identified 39 regulatory interactions with genes mostly involved in metabolism. We found that the XRE-cupin TFs are inhibitors of their neighboring genes, forming local, functional units encoding proteins with functions in condition-specific metabolic pathways. Growth phenotypes of isogenic mutants highlighted new roles for PauR and PA0535 in polyamines and arginine metabolism. The phylogenetic analysis of this family of regulators across the bacterial kingdom revealed a wide diversity of such metabolic regulatory modules and identified species with potentially higher metabolic versatility. Numerous genes encoding uncharacterized XRE-cupin TFs were found near metabolism-related genes, illustrating the need of further systematic characterization of transcriptional regulatory networks in order to better understand the mechanisms of bacterial adaptation to new environments. IMPORTANCE Bacteria of the Pseudomonas genus, including the major human pathogen Pseudomonas aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized. With the recent advances in high-throughput sequencing methods, it is now possible to fill this knowledge gap and help the understanding of how bacteria adapt and thrive in new environments. By leveraging these methods, we provide an example of a comprehensive analysis of an entire family of transcription factors and bring new insights into metabolic and regulatory adaptation in the Pseudomonas genus.
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43
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Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O’Halloran TV, Zhang Y. CueR activates transcription through a DNA distortion mechanism. Nat Chem Biol 2021; 17:57-64. [PMID: 32989300 PMCID: PMC9904984 DOI: 10.1038/s41589-020-00653-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023]
Abstract
The MerR-family transcription factors (TFs) are a large group of bacterial proteins responding to cellular metal ions and multiple antibiotics by binding within central RNA polymerase-binding regions of a promoter. While most TFs alter transcription through protein-protein interactions, MerR TFs are capable of reshaping promoter DNA. To address the question of which mechanism prevails, we determined two cryo-EM structures of transcription activation complexes (TAC) comprising Escherichia coli CueR (a prototype MerR TF), RNAP holoenzyme and promoter DNA. The structures reveal that this TF promotes productive promoter-polymerase association without canonical protein-protein contacts seen between other activator proteins and RNAP. Instead, CueR realigns the key promoter elements in the transcription activation complex by clamp-like protein-DNA interactions: these induce four distinct kinks that ultimately position the -10 element for formation of the transcription bubble. These structural and biochemical results provide strong support for the DNA distortion paradigm of allosteric transcriptional control by MerR TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Steven J. Philips
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kui Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Jing Shi
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Liqiang Shen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juncao Xu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Thomas V. O’Halloran
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.,The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Corresponding author: (T.V.O.); (Y.F.); (Y.Z.)
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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44
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Ferreira SS, Antunes MS. Re-engineering Plant Phenylpropanoid Metabolism With the Aid of Synthetic Biosensors. FRONTIERS IN PLANT SCIENCE 2021; 12:701385. [PMID: 34603348 PMCID: PMC8481569 DOI: 10.3389/fpls.2021.701385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/23/2021] [Indexed: 05/03/2023]
Abstract
Phenylpropanoids comprise a large class of specialized plant metabolites with many important applications, including pharmaceuticals, food nutrients, colorants, fragrances, and biofuels. Therefore, much effort has been devoted to manipulating their biosynthesis to produce high yields in a more controlled manner in microbial and plant systems. However, current strategies are prone to significant adverse effects due to pathway complexity, metabolic burden, and metabolite bioactivity, which still hinder the development of tailor-made phenylpropanoid biofactories. This gap could be addressed by the use of biosensors, which are molecular devices capable of sensing specific metabolites and triggering a desired response, as a way to sense the pathway's metabolic status and dynamically regulate its flux based on specific signals. Here, we provide a brief overview of current research on synthetic biology and metabolic engineering approaches to control phenylpropanoid synthesis and phenylpropanoid-related biosensors, advocating for the use of biosensors and genetic circuits as a step forward in plant synthetic biology to develop autonomously-controlled phenylpropanoid-producing plant biofactories.
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45
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Kim H, Seong W, Rha E, Lee H, Kim SK, Kwon KK, Park KH, Lee DH, Lee SG. Machine learning linked evolutionary biosensor array for highly sensitive and specific molecular identification. Biosens Bioelectron 2020; 170:112670. [DOI: 10.1016/j.bios.2020.112670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022]
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46
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Li X, Jiang X, Xu M, Fang Y, Wang Y, Sun G, Guo J. Identification of stress-responsive transcription factors with protein-bound Escherichia coli genomic DNA libraries. AMB Express 2020; 10:199. [PMID: 33140118 PMCID: PMC7606416 DOI: 10.1186/s13568-020-01133-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 11/10/2022] Open
Abstract
Bacteria promoters along with operators are crucial elements in the control of gene expression in microbes in response to environmental stress changes. A genome-wide promoter DNA regulatory library is in demand to be developed for a microbe reporter method to monitor the existence of any given environmental stress substance. In this study, we utilized Escherichia coli (E. coli) as a model system for the preparation of both cell lysates and genomic DNA fragments. Through enriching protein-bound DNA fragments to construct luciferase reporter libraries, we found that, of 280 clones collected and sequenced, 131 clones contained either the promoter-35 and -10 conservative sequences and/or an operator transcription factor binding sites (TFBS) region. To demonstrate the functionality of the identified clones, five of 131 clones containing LexA binding sequence have been demonstrated to be induced in response to mitomycin C treatment. To evaluate our libraries as a functional screening library, 80 randomly picked up clones were cultured and treated with and without MMC, where two clones were shown to have greater than twofold induction. In addition, two arsenite-responsive clones were identified from 90 clones, one having the well-known ArsR and another having the osmotically inducible lipoprotein (OsmE1). The newly discovered osmE1 has been quantitatively validated to be induced by arsenite treatment with real-time PCR in a dose response and time course manner. This enriching protein-bound DNA luciferase reporter libraries and functional screening facilitate the identification of stress-responsive transcriptional factors in microbes. We developed functional libraries containing E. coli genomic-wide protein-bound DNA as enhancers/operators to regulate downstream luciferase in response to stress.
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47
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Chen M, Grazon C, Sensharma P, Nguyen TT, Feng Y, Chern M, Baer RC, Varongchayakul N, Cook K, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection. ACS APPLIED MATERIALS & INTERFACES 2020; 12:43513-43521. [PMID: 32893612 DOI: 10.1021/acsami.0c13489] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immobilization of biosensors in or on a functional material is critical for subsequent device development and translation to wearable technology. Here, we present the development and assessment of an immobilized quantum dot-transcription factor-nucleic acid complex for progesterone detection as a first step toward such device integration. The sensor, composed of a polyhistidine-tagged transcription factor linked to a quantum dot and a fluorophore-modified cognate DNA, is embedded within a hydrogel as an immobilization matrix. The hydrogel is optically transparent, soft, and flexible as well as traps the quantum dot-transcription factor DNA assembly but allows free passage of the analyte, progesterone. Upon progesterone exposure, DNA dissociates from the quantum dot-transcription factor DNA assembly resulting in an attenuated ratiometric fluorescence output via Förster resonance energy transfer. The sensor performs in a dose-dependent manner with a limit of detection of 55 nM. Repeated analyte measurements are similarly successful. Our approach combines a systematically characterized hydrogel as an immobilization matrix and a transcription factor-DNA assembly as a recognition/transduction element, offering a promising framework for future biosensor devices.
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Affiliation(s)
- Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- CNRS, Bordeaux INP, LCPO, UMR 5629, Univ. Bordeaux, F-33600 Pessac, France
| | - Prerana Sensharma
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Thuy T Nguyen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yunpeng Feng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Margaret Chern
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - R C Baer
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Nitinun Varongchayakul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Katherine Cook
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | | | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mark W Grinstaff
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
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48
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Iwasaki RS, Batey RT. SPRINT: a Cas13a-based platform for detection of small molecules. Nucleic Acids Res 2020; 48:e101. [PMID: 32797156 PMCID: PMC7515716 DOI: 10.1093/nar/gkaa673] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/15/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in biological engineering have made detection of nucleic acids in samples more rapid, inexpensive and sensitive using CRISPR-based approaches. We expand one of these Cas13a-based methods to detect small molecules in a one-batch assay. Using SHERLOCK-based profiling of in vitrotranscription (SPRINT), in vitro transcribed RNA sequence-specifically triggers the RNase activity of Cas13a. This event activates its non-specific RNase activity, which enables cleavage of an RNA oligonucleotide labeled with a quencher/fluorophore pair and thereby de-quenches the fluorophore. This fluorogenic output can be measured to assess transcriptional output. The use of riboswitches or proteins to regulate transcription via specific effector molecules is leveraged as a coupled assay that transforms effector concentration into fluorescence intensity. In this way, we quantified eight different compounds, including cofactors, nucleotides, metabolites of amino acids, tetracycline and monatomic ions in samples. In this manner, hundreds of reactions can be easily quantified in a few hours. This increased throughput also enables detailed characterization of transcriptional regulators, synthetic compounds that inhibit transcription, or other coupled enzymatic reactions. These SPRINT reactions are easily adaptable to portable formats and could therefore be used for the detection of analytes in the field or at point-of-care situations.
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Affiliation(s)
- Roman S Iwasaki
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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49
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Chern M, Garden PM, Baer RC, Galagan JE, Dennis AM. Transcription Factor Based Small‐Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Margaret Chern
- Division of Materials Science and Engineering Boston University Boston MA USA
| | - Padric M. Garden
- Department of Biomedical Engineering Boston University Boston MA USA
| | - R C. Baer
- Department of Microbiology Boston University Boston MA USA
| | - James E. Galagan
- Department of Biomedical Engineering Boston University Boston MA USA
- Department of Microbiology Boston University Boston MA USA
- National Emerging Infectious Diseases Laboratories Boston University Boston MA USA
| | - Allison M. Dennis
- Division of Materials Science and Engineering Boston University Boston MA USA
- Department of Biomedical Engineering Boston University Boston MA USA
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50
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Chern M, Garden PM, Baer RC, Galagan JE, Dennis AM. Transcription Factor Based Small-Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay. Angew Chem Int Ed Engl 2020; 59:21597-21602. [PMID: 32945589 DOI: 10.1002/anie.202007575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 12/26/2022]
Abstract
Recently, allosteric transcription factors (TFs) were identified as a novel class of biorecognition elements for in vitro sensing, whereby an indicator of the differential binding affinity between a TF and its cognate DNA exhibits dose-dependent responsivity to an analyte. Described is a modular bead-based biosensor design that can be applied to such TF-DNA-analyte systems. DNA-functionalized beads enable efficient mixing and spatial separation, while TF-labeled semiconductor quantum dots serve as bright fluorescent indicators of the TF-DNA bound (on bead) and unbound states. The prototype sensor for derivatives of the antibiotic tetracycline exhibits nanomolar sensitivity with visual detection of bead fluorescence. Facile changes to the sensor enable sensor response tuning without necessitating changes to the biomolecular affinities. Assay components self-assemble, and readout by eye or digital camera is possible within 5 minutes of analyte addition, making sensor use facile, rapid, and instrument-free.
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Affiliation(s)
- Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, USA
| | - Padric M Garden
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Department of Microbiology, Boston University, Boston, MA, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Allison M Dennis
- Division of Materials Science and Engineering, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
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