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Zeng R, Zhou F, Wang Y, Liao Z, Qian S, Luo Q, Zheng J. Polydopamine modified colloidal gold nanotag-based lateral flow immunoassay platform for highly sensitive detection of pathogenic bacteria and fast evaluation of antibacterial agents. Talanta 2024; 278:126525. [PMID: 38991406 DOI: 10.1016/j.talanta.2024.126525] [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: 04/13/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
Bacterial infection is a great threat to human health. Lateral flow immunoassays (LFIAs) with the merits of low cost, quick screening, and on-site detection are competitive technologies for bacteria detection, but their detection limits depend on the optical performance of the adopted nanotags. Herein, we presented a LFIA platform for bacteria detection using polydopamine (PDA) functionalized Au nanoparticles (denoted as Au@PDA) as the nanotag. The introduction of PDA could provide enhanced light absorption of Au, as well as numerous functional groups for conjugation. Small recognition molecules i.e. vancomycin (Van) and p-mercaptophenylboronic acid (PMBA) were covalently anchored to Au@PDA, and selected as the specific probes towards Gram-positive (G+) and Gram-negative (G-) bacteria, respectively. Taken Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) as the representative targets of G+ and G- bacteria, two LFA strips were successfully constructed based on the immuno-sandwich principle. They could quantitatively detect S. aureus and E. coli both down to 102 cfu/mL, a very competitive detection limit in comparison with other colorimetric or luminescent probes-based LFIAs. Furthermore, the proposed two strips were applied for the quantitative, accurate, and rapid detection of S. aureus and E. coli in food and human urine samples with good analytical results obtained. In addition, they were integrated as a screening platform for quick evaluation of diverse antibacterial agents within 3 h, which is remarkably shortened compared with that of the two traditional methods i.e. bacterial culture and plate-counting.
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Affiliation(s)
- Ruoxi Zeng
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China; Ningbo Cixi Institute of Biomedical Engineering, Ningbo, 315302, PR China
| | - Fangfang Zhou
- Department of Nephrology, Ningbo No. 2 Hospital, Ningbo, 315010, PR China
| | - Yuhui Wang
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China; Ningbo Cixi Institute of Biomedical Engineering, Ningbo, 315302, PR China.
| | - Zixuan Liao
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China; Ningbo Cixi Institute of Biomedical Engineering, Ningbo, 315302, PR China
| | - Sihua Qian
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China; Ningbo Cixi Institute of Biomedical Engineering, Ningbo, 315302, PR China
| | - Qun Luo
- Department of Nephrology, Ningbo No. 2 Hospital, Ningbo, 315010, PR China.
| | - Jianping Zheng
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China; Ningbo Cixi Institute of Biomedical Engineering, Ningbo, 315302, PR China.
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Kalvapalle PB, Sridhar S, Silberg JJ, Stadler LB. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory. Appl Environ Microbiol 2024; 90:e0236323. [PMID: 38551351 PMCID: PMC11022584 DOI: 10.1128/aem.02363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 04/18/2024] Open
Abstract
Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater, due to optical inaccessibility. Biosensors that could record transient exposure to analytes within a large time window for later retrieval represent a promising approach to solve the accessibility problem. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12-L-homoserine lactone) over 8 days (~70 generations) following analyte exposure. These biosensors sense the analyte and trigger the expression of a recombinase enzyme which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using quantitative PCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterized Pseudomonas isolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration and in situ investigation of microbial signaling, cross-feeding, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.IMPORTANCEMicrobes mediate ecological processes over timescales that can far exceed the half-lives of transient metabolites and signals that drive their collective behaviors. We investigated strategies for engineering microbes to stably record their transient exposure to a chemical over many generations through DNA rearrangements. We identify genetic architectures that improve memory biosensor performance and characterize these in wastewater isolates. Memory biosensors are expected to be useful for monitoring cell-cell signals in biofilms, detecting transient exposure to chemical pollutants, and observing microbial cross-feeding through short-lived metabolites within cryptic methane, nitrogen, and sulfur cycling processes. They will also enable in situ studies of microbial responses to ephemeral environmental changes, or other ecological processes that are currently challenging to monitor non-destructively using real-time biosensors and analytical instruments.
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Affiliation(s)
| | - Swetha Sridhar
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
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Li Y, Zhao Y, Du Y, Ren X, Ding H, Wang Z. Recent advances in the development and applications of luminescent bacteria-based biosensors. LUMINESCENCE 2024; 39:e4721. [PMID: 38501275 DOI: 10.1002/bio.4721] [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: 01/02/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
Luminescent bacteria-based biosensors are widely used for fast and sensitive monitoring of food safety, water quality, and other environmental pollutions. Recent advancements in biomedical engineering technology have led to improved portability, integration, and intelligence of these biotoxicity assays. Moreover, genetic engineering has played a significant role in the development of recombinant luminescent bacterial biosensors, enhancing both detection accuracy and sensitivity. This review provides an overview of recent advances in the development and applications of novel luminescent bacteria-based biosensors, and future perspectives and challenges in the cutting-edge research, market translation, and practical applications of luminescent bacterial biosensing are discussed.
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Affiliation(s)
- Yingying Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Yuankun Zhao
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
| | - Yiyang Du
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
| | - Xuechun Ren
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of Technology, Beijing, China
| | - He Ding
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of Technology, Beijing, China
| | - Zhimin Wang
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
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Hui CY, Ma BC, Hu SY, Wu C. Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:123016. [PMID: 38008253 DOI: 10.1016/j.envpol.2023.123016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/30/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Shun-Yu Hu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Can Wu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China; Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
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Tang X, Chen T, Ma Y, Mao C, Hu S, Zhang R, Yan Y, Pan Q, Feng C, Zhu X. Enzyme Reaction-Assisted Programmable Transcriptional Switches for Bioactive Molecule Detection. Anal Chem 2024; 96:331-338. [PMID: 38127443 DOI: 10.1021/acs.analchem.3c04198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Bioactive molecules are highly worthwhile to recognize and explore the latent pathogenic mechanism. Conventional methods for bioactive molecule detection, including mass spectrometry and fluorescent probe imaging, are limited due to the complex processing and signal interference. Here, we designed enzyme-reaction-assisted programmable transcriptional switches for the detection of bioactive molecules. The approach is based on the use of programmable enzyme site-specific cleavage-assisted DNA triplex-based conformational switches that, upon responding to bioactive molecules, can trigger the transcription of fluorescent light-up aptamers. Thanks to the programmable nature of the sensing platform, the method can be adapted to different bioactive molecules, and we demonstrated the enzyme-small molecule catalytic reaction combination of myeloperoxidase (MPO)-hydrogen peroxide (H2O2) as a model that transcriptional switches was capable of detecting H2O2 and possessed the specificity and anti-interference ability in vitro. Furthermore, we successfully applied the switches into cells to observe the detection feasibility in vivo, and dynamically monitored changes of H2O2 in cellular oxidative stress levels. Therefore, we attempt to amalgamate the advantages of enzyme reaction with the pluripotency of programmable transcriptional switches, which can take both fields a step further, which may promote the research of biostimuli and the construction of DNA molecular devices.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Yonggeng Ma
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Changqing Mao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Runchi Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yilin Yan
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
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Zhang X, Zhu Y, Elçin E, He L, Li B, Jiang M, Yang X, Yan XP, Zhao X, Wang Z, Wang F, Shaheen SM, Rinklebe J, Wells M. Whole-cell bioreporter application for rapid evaluation of hazardous metal bioavailability and toxicity in bioprocess. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132556. [PMID: 37757563 DOI: 10.1016/j.jhazmat.2023.132556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Assessing heavy metal bioavailability and toxicity during bioprocess is critical for advancing green biotechnology. The capability of whole-cell bioreporters to measure heavy metal bioavailability has been increasingly recognized. The advantages of this technology being applied to bioprocess monitoring are less studied. Here we investigate the potential of a cadmium- and lead-sensitive bioreporter to be used for heavy metals as a class, which holds great interest for bioprocess applications. We evaluated the bioavailability of eight individual heavy metals with bioreporter zntA, as well as the bioavailability and toxicity of mixed metals. The bioavailability and toxicity of heavy metals in bioprocess samples were also evaluated. We have demonstrated for the first time that the zntA bioreporter can effectively detect the bioavailability of zinc, nickel, and cobalt with limit of detection lower than 0.01, 0.08 and 0.5 mg·L-1, respectively. The detection limits meet the requirements of the WHO, the U.S. Environmental Protection Agency, and the China drinking water quality standards, which makes this approach reasonable for monitoring heavy metal bioavailability in bioprocess. LIVE/DEAD toxicity experiments have been conducted for the detection of mixed metal solution toxicity to zntA bioreporter which shows an EC50 (as EC50, concentration for 50% of maximal effect) value of mixed metal solution is 3.84 mg·L-1. Samples from wastewater treatment plants, sludge treatment plants and kitchen waste fermentation processes were analyzed to extend upon the laboratory results. The results of this study confirm the potential for practical applications of bioreporter technology in bioprocess monitoring. In turn, development for such practical applications is key to achieve the necessary level of commercialization to further make the routine use of bioreporters in bioprocess monitoring feasible.
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Affiliation(s)
- Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yi Zhu
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Evrim Elçin
- Department of Agricultural Biotechnology, Division of Enzyme and Microbial Biotechnology, Faculty of Agriculture, Aydın Adnan Menderes University, Aydın 09970, Turkey
| | - Lizhi He
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, Zhejiang A & F University, Lin'an 311300, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mengyuan Jiang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xing Yang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, School of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Xiu-Ping Yan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xu Zhao
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Sabry M Shaheen
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water, andWaste-Management, Laboratory of Soil, and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; King Abdulaziz University, Faculty of Meteorology, Environment, and Arid Land Agriculture, Department of Arid Land Agriculture, 21589 Jeddah, Saudi Arabia; University of Kafrelsheikh, Faculty of Agriculture, Department of Soil and Water Sciences, 33516, Kafr El-Sheikh, Egypt
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water, andWaste-Management, Laboratory of Soil, and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Mona Wells
- The Meadows Center for Water and the Environment, Texas State University, San Marcos, TX 78666, USA; Natural Sciences, Ronin Institute, Montclair, New Jersey 07043, USA
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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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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Herath HMLPB, de Silva WRM, Dassanayake RS, Gunawardene YINS, Jayasingha JRP, Gayashan MK, Afonso LOB, de Silva KMN. Validation and calibration of a novel GEM biosensor for specific detection of Cd 2+, Zn 2+, and Pb 2. BMC Biotechnol 2023; 23:52. [PMID: 38066557 PMCID: PMC10709830 DOI: 10.1186/s12896-023-00820-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In this study, we designed a novel genetic circuit sensitive to Cd2+, Zn2+ and Pb2+ by mimicking the CadA/CadR operon system mediated heavy metal homeostasis mechanism of Pseudomonas aeruginosa. The regular DNA motifs on natural operon were reconfigured and coupled with the enhanced Green Fluorescent Protein (eGFP) reporter to develop a novel basic NOT type logic gate CadA/CadR-eGFP to respond metal ions mentioned above. A Genetically Engineered Microbial (GEM)-based biosensor (E.coli-BL21:pJET1.2-CadA/CadR-eGFP) was developed by cloning the chemically synthesised CadA/CadR-eGFP gene circuit into pJET1.2-plasmid and transforming into Escherichia coli (E. coli)-BL21 bacterial cells. RESULTS The GEM-based biosensor cells indicated the reporter gene expression in the presence of Cd2+, Zn2+ and Pb2+ either singly or in combination. Further, the same biosensor cells calibrated for fluorescent intensity against heavy metal concentration generated linear graphs for Cd2+, Zn2+ and Pb2+ with the R2 values of 0.9809, 0.9761 and 0.9758, respectively as compared to non-specific metals, Fe3+ (0.0373), AsO43- (0.3825) and Ni2+ (0.8498) making our biosensor suitable for the detection of low concentration of the former metal ions in the range of 1-6 ppb. Furthermore, the GEM based biosensor cells were growing naturally within the concentration range of heavy metals, at 37 °C and optimum pH = 7.0 in the medium, resembling the characteristics of wildtype E.coli. CONCLUSION Finally, the novel GEM based biosensor cells developed in this study can be applied for detection of targeted heavy metals in low concentration ranges (1-6 ppb) at normal bacterial physiological conditions.
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Affiliation(s)
- H M L P B Herath
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - W R M de Silva
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - R S Dassanayake
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - Y I N S Gunawardene
- Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - J R P Jayasingha
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - M K Gayashan
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka
| | - L O B Afonso
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia.
| | - K M N de Silva
- Centre for Advanced Materials and Devices (CAMD), Department of Chemistry, Faculty of Science, University of Colombo, Colombo, 00300, Sri Lanka.
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10
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Mir TUG, Wani AK, Akhtar N, Katoch V, Shukla S, Kadam US, Hong JC. Advancing biological investigations using portable sensors for detection of sensitive samples. Heliyon 2023; 9:e22679. [PMID: 38089995 PMCID: PMC10711145 DOI: 10.1016/j.heliyon.2023.e22679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/29/2023] [Accepted: 11/16/2023] [Indexed: 01/14/2024] Open
Abstract
Portable biosensors are emerged as powerful diagnostic tools for analyzing intricately complex biological samples. These biosensors offer sensitive detection capabilities by utilizing biomolecules such as proteins, nucleic acids, microbes or microbial products, antibodies, and enzymes. Their speed, accuracy, stability, specificity, and low cost make them indispensable in forensic investigations and criminal cases. Notably, portable biosensors have been developed to rapidly detect toxins, poisons, body fluids, and explosives; they have proven invaluable in forensic examinations of suspected samples, generating efficient results that enable effective and fair trials. One of the key advantages of portable biosensors is their ability to provide sensitive and non-destructive detection of forensic samples without requiring extensive sample preparation, thereby reducing the possibility of false results. This comprehensive review provides an overview of the current advancements in portable biosensors for the detection of sensitive materials, highlighting their significance in advancing investigations and enhancing sensitive sample detection capabilities.
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Affiliation(s)
- Tahir ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- State Forensic Science Laboratory, Srinagar, Jammu and Kashmir, 190001, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Vaidehi Katoch
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Ulhas Sopanrao Kadam
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Jong Chan Hong
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
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11
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Duval JFL, Maffei L, Delatour E, Zaffino M, Pagnout C. Kinetics of metal detection by luminescence-based whole-cell biosensors: connecting biosensor response to metal bioavailability, speciation and cell metabolism. Phys Chem Chem Phys 2023; 25:30276-30295. [PMID: 37930226 DOI: 10.1039/d3cp04653b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Luminescent whole-cell metal biosensors are genetically engineered cells used for the detection of metals in e.g. aqueous solutions. Herein, we detail the quantitative connections between time-response of luminescent bacterial metal sensors and the bioavailability of free and complexed metal species. To that end, we formulate the biophysicochemical dynamics of metal partitioning at a biosensor/solution interface and integrate the required metabolism contribution to cell response. The formalism explains the ways in which cell signal depends on: coupled Eigen kinetics of metal complexation and diffusion of metal species to/from the interface; kinetics of metal excretion, Michaelis-Menten bioaccumulation and ensuing metal depletion from bulk solution; and kinetics of bioluminescence production following intracellular metal sequestration by regulatory metalloproteins. In turn, an expression is derived for the time-dependent cell signal as a function of interrelated (bioavai)lability of metal species and (thermo)dynamic descriptors of extra/intracellular metal complexation. Quantitative criteria are elaborated to identify scenarios where equilibrium modeling of metal speciation is incorrect, bulk metal depletion is operative, metal biouptake kinetics is governed by metal diffusion, or labile metal complexes fully contribute to cell response. Remarkably, in agreement with experiments, the theory predicts time-shifts of bioluminescence peaks with increasing concentration of biosensor and/or metal ligand in solution. We show that these shifts originate from the crosstalk between activation kinetics of cell photoactivity and speciation-dependent kinetics of bulk metal depletion. Overall, the work paves the way for the elaboration of new strategies to exploit the bioluminescence response of metal lux-biosensors at a dynamic level and evaluate metal bioavailability properties in environmental or biological aqueous samples.
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Affiliation(s)
| | - Lorenzo Maffei
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Eva Delatour
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Marie Zaffino
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
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12
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Zhu J, Wang B, Zhang Y, Wei T, Gao T. Living electrochemical biosensing: Engineered electroactive bacteria for biosensor development and the emerging trends. Biosens Bioelectron 2023; 237:115480. [PMID: 37379794 DOI: 10.1016/j.bios.2023.115480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bioelectrical interfaces made of living electroactive bacteria (EAB) provide a unique opportunity to bridge biotic and abiotic systems, enabling the reprogramming of electrochemical biosensing. To develop these biosensors, principles from synthetic biology and electrode materials are being combined to engineer EAB as dynamic and responsive transducers with emerging, programmable functionalities. This review discusses the bioengineering of EAB to design active sensing parts and electrically connective interfaces on electrodes, which can be applied to construct smart electrochemical biosensors. In detail, by revisiting the electron transfer mechanism of electroactive microorganisms, engineering strategies of EAB cells for biotargets recognition, sensing circuit construction, and electrical signal routing, engineered EAB have demonstrated impressive capabilities in designing active sensing elements and developing electrically conductive interfaces on electrodes. Thus, integration of engineered EAB into electrochemical biosensors presents a promising avenue for advancing bioelectronics research. These hybridized systems equipped with engineered EAB can promote the field of electrochemical biosensing, with applications in environmental monitoring, health monitoring, green manufacturing, and other analytical fields. Finally, this review considers the prospects and challenges of the development of EAB-based electrochemical biosensors, identifying potential future applications.
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Affiliation(s)
- Jin Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Baoguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Yixin Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tianxiang Wei
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China.
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13
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Zoheir AE, Sobol MS, Meisch L, Ordoñez-Rueda D, Kaster AK, Niemeyer CM, Rabe KS. A three-colour stress biosensor reveals multimodal response in single cells and spatiotemporal dynamics of biofilms. NPJ Biofilms Microbiomes 2023; 9:57. [PMID: 37604827 PMCID: PMC10442448 DOI: 10.1038/s41522-023-00424-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
The plethora of stress factors that can damage microbial cells has evolved sophisticated stress response mechanisms. While existing bioreporters can monitor individual responses, sensors for detecting multimodal stress responses in living microorganisms are still lacking. Orthogonally detectable red, green, and blue fluorescent proteins combined in a single plasmid, dubbed RGB-S reporter, enable simultaneous, independent, and real-time analysis of the transcriptional response of Escherichia coli using three promoters which report physiological stress (PosmY for RpoS), genotoxicity (PsulA for SOS), and cytotoxicity (PgrpE for RpoH). The bioreporter is compatible with standard analysis and Fluorescent Activated Cell Sorting (FACS) combined with subsequent transcriptome analysis. Various stressors, including the biotechnologically relevant 2-propanol, activate one, two, or all three stress responses, which can significantly impact non-stress-related metabolic pathways. Implemented in microfluidic cultivation with confocal fluorescence microscopy imaging, the RGB-S reporter enabled spatiotemporal analysis of live biofilms revealing stratified subpopulations of bacteria with heterogeneous stress responses.
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Affiliation(s)
- Ahmed E Zoheir
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Department of Genetics and Cytology, National Research Centre (NRC), Cairo, Egypt
| | - Morgan S Sobol
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Laura Meisch
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility, Heidelberg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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14
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Lee H, Xie T, Yu X, Schaffter SW, Schulman R. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552680. [PMID: 37645783 PMCID: PMC10461910 DOI: 10.1101/2023.08.10.552680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors or digital protein biosensors with detection ranges that can be tuned over two orders of magnitude. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors suitable for diverse research and diagnostic applications.
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Affiliation(s)
- Heonjoon Lee
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218
| | - Tian Xie
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Xinjie Yu
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | | | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
- Computer Science, Johns Hopkins University, Baltimore, MD 21218
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15
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Ejenavi O, Teng T, Huang W, Wang X, Zhang W, Zhang D. Online detection of alkanes by a biological-phase microextraction and biosensing (BPME-BS) device. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131316. [PMID: 37003003 DOI: 10.1016/j.jhazmat.2023.131316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Oil spill incidents occur frequently and threaten ecosystems and human health. Solid-phase microextraction allows direct alkane extraction from environmental matrices to improve the limit of detection but is unable to measure alkanes on site. A biological-phase microextraction and biosensing (BPME-BS) device was developed by immobilising an alkane chemotactic Acinetobacter bioreporter ADPWH_alk in agarose gel to achieve online alkane quantification with the aid of a photomultiplier. The BPME-BS device had a high enrichment factor (average 7.07) and a satisfactory limit of detection (0.075 mg/L) for alkanes. The quantification range was 0.1-100 mg/L, comparable to a gas chromatography flame ionisation detector and better than a bioreporter without immobilisation. ADPWH_alk cells in the BPME-BS device maintained good sensitivity under a wide range of environmental conditions, including pH (4.0-9.0), temperature (20-40 °C), and salinity (0.0-3.0%), and its response remained stable within 30 days at 4 °C. In a 7-day continual measurement, the BPME-BS device successfully visualised the dynamic concentration of alkanes, and a 7-day field test successfully captured an oil spill event, helping in source apportionment and on-scene law enforcement. Our work proved that the BPME-BS device is a powerful tool for online alkane measurement, showing substantial potential for fast detection and rapid response to oil spills on site and in situ.
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Affiliation(s)
- Odafe Ejenavi
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, UK
| | - Tingting Teng
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Wenxin Huang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Wenjing Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China.
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16
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Chen Y, Guo Y, Liu Y, Xiang Y, Liu G, Zhang Q, Yin Y, Cai Y, Jiang G. Advances in bacterial whole-cell biosensors for the detection of bioavailable mercury: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161709. [PMID: 36682565 DOI: 10.1016/j.scitotenv.2023.161709] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Mercury (Hg) and its organic compounds, especially monomethylmercury (MeHg), cause major damage to the ecosystem and human health. In surface water or sediments, microorganisms play a crucial role in the methylation and demethylation of Hg. Given that Hg transformation processes are intracellular reactions, accurate assessment of the bioavailability of Hg(II)/MeHg in the environment, particularly for microorganisms, is of major importance. Compared with traditional analytical methods, bacterial whole-cell biosensors (BWCBs) provide a more accurate, convenient, and cost-effective strategy to assess the environmental risks of Hg(II)/MeHg. This Review summarizes recent progress in the application of BWCBs in the detection of bioavailable Hg(II)/MeHg, providing insight on current challenges and strategies. The principle and components of BWCBs for Hg(II)/MeHg bioavailability analysis are introduced. Furthermore, the impact of water chemical factors on the bioavailability of Hg is discussed as are future perspectives of BWCBs in bioavailable Hg analysis and optimization of BWCBs.
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Affiliation(s)
- Yueqian Chen
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Yingying Guo
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanwei Liu
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuping Xiang
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Guangliang Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Qinghua Zhang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yongguang Yin
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yong Cai
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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17
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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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18
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Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development. Signal Transduct Target Ther 2023; 8:112. [PMID: 36906608 PMCID: PMC10007681 DOI: 10.1038/s41392-023-01375-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023] Open
Abstract
The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.
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19
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Zhang X, Zhu Y, Li B, Tefsen B, Wang Z, Wells M. We need to plan streamlined environmental impact assessment for the future X-Press Pearl disasters. MARINE POLLUTION BULLETIN 2023; 188:114705. [PMID: 36791553 DOI: 10.1016/j.marpolbul.2023.114705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The X-Press Pearl disaster illustrates the urgent needs for streamlined environmental impact assessment to inform decision making. The environmental contamination caused by the disaster is complex, and the biological impact of different environmental stressors, and at different biological scales, needs to be determined. Traditional methods for analyzing complex environmental stressors are often inefficient and do not reflect the biological impact of pollution. The combination of chemical stressors and biological impacts is the key to environmental impact assessment based on integrated monitoring. Whole-cell bioreporters are tools for rapid, efficient and quantitative detection of the bioavailability, stressor effects, and toxicity of pollutants, i.e., spanning a wide range of applications. Here we propose the view that using whole-cell bioreporter technology to streamline short-term environmental impact assessment for maritime disasters such as the X-Press Pearl is more fit-for-purpose/practical than other approaches in use.
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Affiliation(s)
- Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yi Zhu
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Boris Tefsen
- Department of Molecular Microbiology, Utrecht University, Padualaan 8, CH Utrecht 3584, Netherlands; Natural Sciences, Ronin Institute, Montclair, NJ 07043, USA
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mona Wells
- Natural Sciences, Ronin Institute, Montclair, NJ 07043, USA; The Meadows Center for Water and the Environment, Texas State University, San Marcos, TX 78666, USA.
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20
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Gillam EMJ, Kramlinger VM. Opportunities for Accelerating Drug Discovery and Development by Using Engineered Drug-Metabolizing Enzymes. Drug Metab Dispos 2023; 51:392-402. [PMID: 36460479 DOI: 10.1124/dmd.121.000743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
The study of drug metabolism is fundamental to drug discovery and development (DDD) since by mediating the clearance of most drugs, metabolic enzymes influence their bioavailability and duration of action. Biotransformation can also produce pharmacologically active or toxic products, which complicates the evaluation of the therapeutic benefit versus liability of potential drugs but also provides opportunities to explore the chemical space around a lead. The structures and relative abundance of metabolites are determined by the substrate and reaction specificity of biotransformation enzymes and their catalytic efficiency. Preclinical drug biotransformation studies are done to quantify in vitro intrinsic clearance to estimate likely in vivo pharmacokinetic parameters, to predict an appropriate dose, and to anticipate interindividual variability in response, including from drug-drug interactions. Such studies need to be done rapidly and cheaply, but native enzymes, especially in microsomes or hepatocytes, do not always produce the full complement of metabolites seen in extrahepatic tissues or preclinical test species. Furthermore, yields of metabolites are usually limiting. Engineered recombinant enzymes can make DDD more comprehensive and systematic. Additionally, as renewable, sustainable, and scalable resources, they can also be used for elegant chemoenzymatic, synthetic approaches to optimize or synthesize candidates as well as metabolites. Here, we will explore how these new tools can be used to enhance the speed and efficiency of DDD pipelines and provide a perspective on what will be possible in the future. The focus will be on cytochrome P450 enzymes to illustrate paradigms that can be extended in due course to other drug-metabolizing enzymes. SIGNIFICANCE STATEMENT: Protein engineering can generate enhanced versions of drug-metabolizing enzymes that are more stable, better suited to industrial conditions, and have altered catalytic activities, including catalyzing non-natural reactions on structurally complex lead candidates. When applied to drugs in development, libraries of engineered cytochrome P450 enzymes can accelerate the identification of active or toxic metabolites, help elucidate structure activity relationships, and, when combined with other synthetic approaches, provide access to novel structures by regio- and stereoselective functionalization of lead compounds.
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Affiliation(s)
- Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia (E.M.J.G.) and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (V.M.K.)
| | - Valerie M Kramlinger
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia (E.M.J.G.) and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (V.M.K.)
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21
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Du Y, Zhang X, Zhang H, Zhu R, Zhao Z, Han J, Zhang D, Zhang X, Zhang X, Pan X, You J, Rao Z. Direct evolution of riboflavin kinase significantly enhance flavin mononucleotide synthesis by design and optimization of flavin mononucleotide riboswitch. BIORESOURCE TECHNOLOGY 2023; 381:128774. [PMID: 36822556 DOI: 10.1016/j.biortech.2023.128774] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 05/08/2023]
Abstract
Flavin mononucleotide (FMN) is the active form of riboflavin. It has a wide range of application scenarios in the pharmaceutical and food additives. However, there are limitations in selecting generic high-throughput screening platforms that improve the properties of enzymes. First, the biosensor in response to FMN concentration was constructed using the FMN riboswitch and confirmed the function of this sensor. Next, the FMN binding site of the sensor was saturated with a mutation that increased its fluorescence range by approximately 127%. Then, the biosensor and the base editing system based on T7RNAP were combined to construct a platform for rapid mutation and screening of riboflavin kinase gene ribC mutants. The mutants screened using this platform increased the yield of FMN by 8-fold. These results indicate that the high-throughput screening platform can rapidly and effectively improve the activity of target enzymes, and provide a new route for screening industrial enzymes.
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Affiliation(s)
- Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyi Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hengwei Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Rongshuai Zhu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jin Han
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Di Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoling Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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22
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A Novel Whole-Cell Biosensor for Bioavailable Antimonite in Water and Sediments. Appl Environ Microbiol 2023; 89:e0181722. [PMID: 36602327 PMCID: PMC9888276 DOI: 10.1128/aem.01817-22] [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: 01/06/2023] Open
Abstract
Antimony (Sb) is an emerging contaminant, and its on-site speciation analysis is central to the accurate evaluation of its bioavailability and toxicity. The whole-cell biosensors (WCBs) for Sb(III) are promising but challenging due to the lack of Sb(III)-specific recognition components. Here, we constructed a novel Sb(III)-specific WCB using an Sb(III) transcriptional regulator (antR) and its cognate promoter (Pant). To prevent the promoter leakage of Pant, an additional regulatory gene, antR, was inserted downstream of the Sb(III)-inducible promoter, improving the sensitivity of the WCB by an order of magnitude and reaching the detection limit at 0.009 μM, which is lower than the WHO drinking water standard of Sb. Moreover, the WCB with double antR showed a high specificity toward Sb(III) compared with interfering ions at 3 orders of magnitude higher concentrations. This WCB was capable of measuring Sb(III) bioavailability in natural waters and sediments on-site, and its results were not statistically different from the chemical analysis. The insights gained from this work demonstrate that the addition of regulatory genes prevents promoter leakage and improves the sensitivity of WCBs in field applications. IMPORTANCE Antimony (Sb) is a redox-sensitive pollutant ubiquitous in the environment. Sb(III) is dominant in the subsurface and is readily oxidized to less toxic Sb(V) upon exposure to air, and therefore, on-site Sb speciation analysis is essential to evaluate its bioavailability and toxicity. Dissolved Sb concentration and speciation can be determined accurately using on-site chemical sensors, but chemical sensors have difficulty determining the bioavailable Sb(III) that is taken up by the cells. Here, we constructed an Sb(III)-specific whole-cell biosensor (WCB) using double Sb(III) transcriptional regulators (antR) downstream of its cognate promoter Pant. With an additional antR, the sensitivity of the WCB was improved by approximately 10 times, and the promoter leakage commonly found in WCBs was inhibited. Integrated with a tea-bag design, the WCB is able to measure Sb(III) bioavailability in natural water and sediments on-site. This study demonstrates the importance of inserting one more regulatory gene to improve sensitivity.
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Ngashangva L, Chattopadhyay S. Biosensors for point-of-care testing and personalized monitoring of gastrointestinal microbiota. Front Microbiol 2023; 14:1114707. [PMID: 37213495 PMCID: PMC10196119 DOI: 10.3389/fmicb.2023.1114707] [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: 12/02/2022] [Accepted: 04/19/2023] [Indexed: 05/23/2023] Open
Abstract
The gastrointestinal (GI) microbiota is essential in maintaining human health. Alteration of the GI microbiota or gut microbiota (GM) from homeostasis (i.e., dysbiosis) is associated with several communicable and non-communicable diseases. Thus, it is crucial to constantly monitor the GM composition and host-microbe interactions in the GI tract since they could provide vital health information and indicate possible predispositions to various diseases. Pathogens in the GI tract must be detected early to prevent dysbiosis and related diseases. Similarly, the consumed beneficial microbial strains (i.e., probiotics) also require real-time monitoring to quantify the actual number of their colony-forming units within the GI tract. Unfortunately, due to the inherent limitations associated with the conventional methods, routine monitoring of one's GM health is not attainable till date. In this context, miniaturized diagnostic devices such as biosensors could provide alternative and rapid detection methods by offering robust, affordable, portable, convenient, and reliable technology. Though biosensors for GM are still at a relatively preliminary stage, they can potentially transform clinical diagnosis in the near future. In this mini-review, we have discussed the significance and recent advancements of biosensors in monitoring GM. Finally, the progresses on future biosensing techniques such as lab-on-chip, smart materials, ingestible capsules, wearable devices, and fusion of machine learning/artificial intelligence (ML/AI) have also been highlighted.
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Affiliation(s)
- Lightson Ngashangva
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
- *Correspondence: Lightson Ngashangva,
| | - Santanu Chattopadhyay
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
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24
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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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25
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Hui CY, Hu SY, Li LM, Yun JP, Zhang YF, Yi J, Zhang NX, Guo Y. Metabolic engineering of the carotenoid biosynthetic pathway toward a specific and sensitive inorganic mercury biosensor. RSC Adv 2022; 12:36142-36148. [PMID: 36545109 PMCID: PMC9756418 DOI: 10.1039/d2ra06764a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The toxicity of mercury (Hg) mainly depends on its form. Whole-cell biosensors respond selectively to toxic Hg(ii), efficiently transformed by environmental microbes into methylmercury, a highly toxic form that builds up in aquatic animals. Metabolically engineered Escherichia coli (E. coli) have successfully produced rainbow colorants. By de novo reconstruction of the carotenoid synthetic pathway, the Hg(ii)-responsive production of lycopene and β-carotene enabled programmed E. coli to potentially become an optical biosensor for the qualitative and quantitative detection of ecotoxic Hg(ii). The red color of the lycopene-based biosensor cell pellet was visible upon exposure to 49 nM Hg(ii) and above. The orange β-carotene-based biosensor responded to a simple colorimetric assay as low as 12 nM Hg(ii). A linear response was observed at Hg(ii) concentrations ranging from 12 to 195 nM. Importantly, high specificity and good anti-interference capability suggested that metabolic engineering of the carotenoid biosynthesis was an alternative to developing a visual platform for the rapid analysis of the concentration and toxicity of Hg(ii) in environmentally polluted water.
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Shun-yu Hu
- Department of Toxicology, School of Public Health, Southern Medical UniversityGuangzhou 510515China
| | - Li-mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Jian-pei Yun
- Physical & Chemical Testing Laboratory, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Yan-fang Zhang
- Physical & Chemical Testing Laboratory, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Nai-xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
| | - Yan Guo
- Department of Toxicology, School of Public Health, Southern Medical UniversityGuangzhou 510515China,National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational DiseasesShenzhen 518020China
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26
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Wang HS, Wang XY, Ding HT, Hu XY, Li J, Cheng C, Zheng F. Oral Metal-Organic Gel Protected Whole-Cell Biosensor for in Situ Monitoring Nitrosamines in the Gastrointestinal Tract. NANO LETTERS 2022; 22:8688-8694. [PMID: 36264028 DOI: 10.1021/acs.nanolett.2c03418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nitrite, a type of food additive, has been proved convertible to genotoxic nitrosamines in the gastrointestinal tract by intestinal flora. There is no appropriate method for in situ detection of nitrosamines. Herein, plasmid-introduced Saccharomyces cerevisiae, which can respond to nitrosamine-induced DNA damage and activate pMAG1-based DNA damage repair (DDR), was designed as whole-cell biosensors (WCBs) for monitoring the in situ generated nitrosamines by a reporter gene expressing enhanced green fluorescent protein (EGFP). In order to protect the validity of WCBs (pMAG1 yeast) from the gastric acid environment, a type of metal-organic gel (MOG), coordinated by Fe3+ and 2,2'-thiodiacetic acid (TDA), was prepared to embed the WCBs. The MOG(Fe-TDA) is gastric acid resistant and can deliver the pMAG1 yeast to the gut without compromising the performance of pMAG1 yeast to detect in situ generated nitrosamines. The genotoxicity of nitrosamines converted from nitrite was successfully detected in the gastrointestinal tract of mice.
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Affiliation(s)
- Huai-Song Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China
| | - Xing-Yu Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Hao-Tian Ding
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Xin-Yuan Hu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Jie Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Chen Cheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Feng Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China
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Synthetic metabolic transducers in Saccharomyces cerevisiae as sensors for aromatic permeant acids and bioreporters of hydrocarbon metabolism. Biosens Bioelectron 2022; 220:114897. [DOI: 10.1016/j.bios.2022.114897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/18/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
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28
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Hui CY, Guo Y, Zhu DL, Li LM, Yi J, Zhang NX. Metabolic engineering of the violacein biosynthetic pathway toward a low-cost, minimal-equipment lead biosensor. Biosens Bioelectron 2022; 214:114531. [PMID: 35810697 DOI: 10.1016/j.bios.2022.114531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 02/07/2023]
Abstract
Metabolic engineered bacteria have been successfully employed to produce various natural colorants, which are expected to be used as the visually recognizable signals to develop mini-equipment biological devices for monitoring toxic heavy metals. The violacein biosynthetic pathway has been reconstructed in Escherichia coli (E. coli). Here the successful production of four violacein derivatives was achieved by integrating metabolic engineering and synthetic biology. Lead binding to the metalloregulator enables whole-cell colorimetric biosensors capable of assessing bioavailable lead. Deoxyviolacein-derived signal showed the most satisfied biosensing properties among prodeoxyviolacein (green), proviolacein (blue), deoxyviolacein (purple), and violacein (navy). The limit of detection (LOD) of pigment-based biosensors was 2.93 nM Pb(II), which is lower than that of graphite furnace atomic absorption spectrometry. Importantly, a good linear dose-response model in a wide dose range (2.93-6000 nM) was obtained in a non-cytotoxic deoxyviolacein-based biosensor, which was significantly better than cytotoxic violacein-based biosensor (2.93-750 nM). Among ten metal ions, only Cd(II) and Hg(II) exerted a slight influence on the response of the deoxyviolacein-based biosensor toward Pb(II). The deoxyviolacein-based biosensor was validated in detecting bioaccessible Pb(II) in environmental samples. Factors such as low cost and minimal-equipment requirement make this biosensor a suitable biological device for monitoring toxic lead in the environment.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - De-Long Zhu
- School of Public Health , Guangdong Medical University, Dongguan, 523808, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
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29
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Delatour E, Pagnout C, Zaffino ML, Duval JFL. Comparative Analysis of Cell Metabolic Activity Sensing by Escherichia coli rrnB P1-lux and Cd Responsive-Lux Biosensors: Time-Resolved Experiments and Mechanistic Modelling. BIOSENSORS 2022; 12:763. [PMID: 36140148 PMCID: PMC9496673 DOI: 10.3390/bios12090763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Whole-cell bacterial sensors are used in medical/environmental applications to detect chemicals, and to assess medium toxicity or stress. Non-specific constitutive biosensors generally serve the latter purpose, whereas chemical detection is performed with biosensors involving a specific chemical-inducible promoter. Herein, we show that functioning principles of specific and non-specific whole-cell biosensors are not exclusive as both can probe modulations of cell metabolic activity under stressing conditions. The demonstration is based on (i) time-resolved measurements of bioluminescence produced by constitutive rrnB P1-luxCDABE Escherichia coli biosensor in media differing with respect to carbon source, (ii) theoretical reconstruction of the measured signals using a here-reported theory for bioluminescence generated by constitutive cells, (iii) comparison between time-dependent cell photoactivity (reflecting metabolic activity) retrieved by theory with that we reported recently for cadmium-inducible PzntA-luxCDABE E. coli in media of similar compositions. Whereas signals of constitutive and non-constitutive biosensors differ in terms of shape, amplitude and peak number depending on nutritional medium conditions, analysis highlights the features shared by their respective cell photoactivity patterns mediated by the interplay between stringent response and catabolite repressions. The work advocates for the benefits of a theoretical interpretation for the time-dependent response of biosensors to unravel metabolic and physicochemical contributions to the bioluminescence signal.
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Affiliation(s)
- Eva Delatour
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Christophe Pagnout
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Marie L. Zaffino
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Jérôme F. L. Duval
- Université de Lorraine, CNRS, LIEC, UMR7360, F-54501 Vandoeuvre-lès-Nancy, France
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30
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Zhang Y, Zhao C, Bi H, Zhang X, Xue B, Li C, Wang S, Yang X, Qiu Z, Wang J, Shen Z. A cell-free paper-based biosensor dependent on allosteric transcription factors (aTFs) for on-site detection of harmful metals Hg 2+ and Pb 2+ in water. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129499. [PMID: 35816794 DOI: 10.1016/j.jhazmat.2022.129499] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Water quality monitoring requires a reliable and practical on-site detection method for heavy metal ions. Combining an in vitro transcription (IVT) technology with allosteric transcription factors (aTFs), we developed a cell-free paper-based biosensor for on-site detection of Hg2+ and Pb2+ in water. Suitable aTFs screened using surface plasmon resonance (SPR) were employed for building biosensors. ATFs could disassociate from DNA due to their specific affinity to metal ions, and fluorescent RNA was transcribed as a signal. The developed biosensor could quantitatively detect Hg2+ in a linear dynamic range of 0.5-500 nM and Pb2+ in a 1-250 nM range in a 1 h period. The LOD of the biosensor was 0.5 nM for Hg2+ and 0.1 nM for Pb2+. The recoveries ranged from 91.09% to 123.24% for actual water samples detection. Furthermore, freeze-drying was used to create a paper-based biosensor that could detect Hg2+ and Pb2+ simultaneously on-site. This research presents a useful technique for various heavy metal ion detections.
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Affiliation(s)
- Yongkang Zhang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chen Zhao
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Huaixiu Bi
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xi Zhang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Bin Xue
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Chenyu Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China
| | - Shang Wang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Xiaobo Yang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Zhigang Qiu
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China
| | - Jingfeng Wang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin 300050, China.
| | - Zhiqiang Shen
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
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31
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Chen D, Nie M, Tang W, Zhang Y, Wang J, Lan Y, Chen Y, Du W. Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip. MLIFE 2022; 1:341-349. [PMID: 38818224 PMCID: PMC10989842 DOI: 10.1002/mlf2.12039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/01/2022] [Accepted: 08/12/2022] [Indexed: 06/01/2024]
Abstract
Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wei Tang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of the Chinese Academy of SciencesBeijingChina
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32
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A novel biosensor based on antibody controlled isothermal strand displacement amplification (ACISDA) system. Biosens Bioelectron 2022; 209:114185. [DOI: 10.1016/j.bios.2022.114185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
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33
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Salzano D, Fiore D, di Bernardo M. Ratiometric control of cell phenotypes in monostrain microbial consortia. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220335. [PMID: 35858050 PMCID: PMC9277296 DOI: 10.1098/rsif.2022.0335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We address the problem of regulating and keeping at a desired balance the relative numbers between cells exhibiting a different phenotype within a monostrain microbial consortium. We propose a strategy based on the use of external control inputs, assuming each cell in the community is endowed with a reversible, bistable memory mechanism. Specifically, we provide a general analytical framework to guide the design of external feedback control strategies aimed at balancing the ratio between cells whose memory is stabilized at either one of two equilibria associated with different cell phenotypes. We demonstrate the stability and robustness properties of the control laws proposed and validate them in silico, implementing the memory element via a genetic toggle-switch. The proposed control framework may be used to allow long-term coexistence of different populations, with both industrial and biotechnological applications. As a representative example, we consider the realistic agent-based implementation of our control strategy to enable cooperative bioproduction of a dimer in a monostrain microbial consortium.
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Affiliation(s)
- Davide Salzano
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Davide Fiore
- Department of Mathematics and Applications 'R. Caccioppoli', University of Naples Federico II, Via Cintia, Monte S. Angelo, 80126 Naples, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy.,Scuola Superiore Meridionale, Largo S. Marcellino 10, 80138 Naples, Italy
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34
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Li B, Zhang X, Tefsen B, Wells M. From speciation to toxicity: Using a "Two-in-One" whole-cell bioreporter approach to assess harmful effects of Cd and Pb. WATER RESEARCH 2022; 217:118384. [PMID: 35427828 DOI: 10.1016/j.watres.2022.118384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Due to the sheer number of contaminated sites, bioavailability-based measurement and modeling of toxicity is used to triage response; despite advances, both remain relatively cumbersome. Cadmium (Cd) and lead (Pb) are two of the most toxic and globally prevalent pollutants, disproportionately impacting disadvantaged communities. Here we demonstrate the use of high throughput lights-on bioreporter technology to measure both speciation and toxicity. The organism's response is fit-for-purpose to parameterize the Biotic Ligand Model used in risk assessment of aquatic ecotoxicity and setting environmental Water Quality Criteria. Toxicity endpoints for analogous Cd and Pb models reported in literature average 71st and 44th rank-percentile sensitivity of Genus Mean Acute Values for acute toxicity (i.e., insensitive) in comparison to the bioreporter, the unique dual-mode measurement ability of which can predict toxicity endpoints from below the 5th percentile up to the 50th rank-percentile. These results are extensible to other reporters, paving the way to cost-efficient environmental risk assessment of aquatic ecotoxicity for a wide range of priority toxic pollutants.
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Affiliation(s)
- Boling Li
- Department of Environmental Science, University of Liverpool, Brownlow Hill, Liverpool L69 7ZX, UK; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Boris Tefsen
- Ronin Institute, 127 Haddon Place, Montclair, NJ 07043, United States.
| | - Mona Wells
- Ronin Institute, 127 Haddon Place, Montclair, NJ 07043, United States.
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35
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Soudier P, Rodriguez Pinzon D, Reif-Trauttmansdorff T, Hijazi H, Cherrière M, Goncalves Pereira C, Blaise D, Pispisa M, Saint-Julien A, Hamlet W, Nguevo M, Gomes E, Belkhelfa S, Niarakis A, Kushwaha M, Grigoras I. Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima. Synth Syst Biotechnol 2022; 7:791-801. [PMID: 35415278 PMCID: PMC8976095 DOI: 10.1016/j.synbio.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods’ limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.
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36
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Chen SY, Zhang Y, Li R, Wang B, Ye BC. De Novo Design of the ArsR Regulated P ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination. Anal Chem 2022; 94:7210-7218. [PMID: 35537205 PMCID: PMC9134189 DOI: 10.1021/acs.analchem.2c00055] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whole-cell biosensors for arsenic contamination are typically designed based on natural bacterial sensing systems, which are often limited by their poor performance for precisely tuning the genetic response to environmental stimuli. Promoter design remains one of the most important approaches to address such issues. Here, we use the arsenic-responsive ArsR-Pars regulation system from Escherichia coli MG1655 as the sensing element and coupled gfp or lacZ as the reporter gene to construct the genetic circuit for characterizing the refactored promoters. We first analyzed the ArsR binding site and a library of RNA polymerase binding sites to mine potential promoter sequences. A set of tightly regulated Pars promoters by ArsR was designed by placing the ArsR binding sites into the promoter's core region, and a novel promoter with maximal repression efficiency and optimal fold change was obtained. The fluorescence sensor PlacV-ParsOC2 constructed with the optimized ParsOC2 promoter showed a fold change of up to 63.80-fold (with green fluorescence visible to the naked eye) at 9.38 ppb arsenic, and the limit of detection was as low as 0.24 ppb. Further, the optimized colorimetric sensor PlacV-ParsOC2-lacZ with a linear response between 0 and 5 ppb was used to perform colorimetric reactions in 24-well plates combined with a smartphone application for the quantification of the arsenic level in groundwater. This study offers a new approach to improve the performance of bacterial sensing promoters and will facilitate the on-site application of arsenic whole-cell biosensors.
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Affiliation(s)
- Sheng-Yan Chen
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Yan Zhang
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Renjie Li
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Baojun Wang
- College
of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific
and Technological Innovation Center, Zhejiang
University, Hangzhou 311200, China,Research
Center of Biological Computation, Zhejiang
Laboratory, Hangzhou 311100, China,Centre
for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom,
| | - Bang-Ce Ye
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China,Institute
of Engineering Biology and Health, Collaborative Innovation Center
of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical
Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China,Lab of Biosystem
and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China,. Tel/Fax: 0086-21-64252094
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37
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Jeon Y, Lee Y, Jang G, Kim BG, Yoon Y. Design of Pb(II)-Specific E. coli-Based Biosensors by Engineering Regulatory Proteins and Host Cells. Front Microbiol 2022; 13:881050. [PMID: 35668759 PMCID: PMC9164158 DOI: 10.3389/fmicb.2022.881050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial cell-based biosensors have been widely developed for detecting environmental toxic materials. The znt-operon in Escherichia coli is a Zn(II)-responsive genetic system and is employed in Zn(II), Cd(II), and Hg(II)-sensing biosensors. In this study, point mutations were introduced in the regulatory protein ZntR to modulate its target selectivity, and metal ion-exporting genes, such as copA and zntA, in host cells were deleted to increase cellular metal ion levels and enhance specificity. Thus, the overall responses of the E. coli cell-based biosensors toward metal(loid) ions were increased, and their selectivity, which was originally for Cd(II) and Hg(II), was shifted to Pb(II). The gene encoding ZntA, known as the Zn(II)-translocating P-type ATPase, showed an impact on the ability of E. coli to export Pb(II), whereas copA deletion showed no significant impact. Noteworthily, the newly generated biosensors employing ZntR Cys115Ile showed the capacity to detect under 5 nM Pb(II) in solution, without response to other tested metal ions within 0–100 nM. To understand the marked effect of single point mutations on ZntR, computational modeling was employed. Although it did not provide clear answers, changes in the sequences of the metal-binding loops of ZntR modulated its transcriptional strength and target selectivity. In summary, the approaches proposed in this study can be valuable to generate new target-sensing biosensors with superior selectivity and specificity, which can in turn broaden the applicability of cell-based biosensors to monitor Pb(II) in environmental systems.
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Affiliation(s)
- Yangwon Jeon
- Department of Environmental Health Science, Konkuk University, Seoul, South Korea
| | - Yejin Lee
- Department of Environmental Health Science, Konkuk University, Seoul, South Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Bong-Gyu Kim
- Division of Environmental and Forest Science, Gyeongsang National University, Jinju, South Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul, South Korea
- *Correspondence: Youngdae Yoon
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38
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Exploiting Catabolite Repression and Stringent Response to Control Delay and Multimodality of Bioluminescence Signal by Metal Whole-Cell Biosensors: Interplay between Metal Bioavailability and Nutritional Medium Conditions. BIOSENSORS 2022; 12:bios12050327. [PMID: 35624628 PMCID: PMC9139025 DOI: 10.3390/bios12050327] [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: 04/23/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/02/2022]
Abstract
The time-dependent response of metal-detecting whole-cell luminescent bacterial sensors is impacted by metal speciation/bioavailability in solution. The comprehensive understanding of such connections requires the consideration of the bacterial energy metabolism at stake and the effects of supplied food on cells’ capability to convert bioaccumulated metals into light. Accordingly, we investigated the time response (48 h assay) of PzntA-luxCDABE Escherichia coli Cd biosensors in media differing with respect to sources of amino acids (tryptone or Lysogeny Broth) and carbon (glucose, xylose and mixtures thereof). We show that the resulting coupling between the stringent cell response and glucose/xylose-mediated catabolite repressions lead to well-defined multimodalities and shapes of the bioluminescence signal over time. Based on a recent theory for the time–response of metal-sensing luminescent bacteria, successful theoretical reconstructions of the bioluminescence signals are reported under all Cd concentrations (0–20 nM) and nutritive conditions examined. This analysis leads to the evaluation of time-dependent cell photoactivity and qualitative information on metal speciation/bioavailability in solution. Biosensor performance and the position, shape, number, and magnitude of detected peaks are discussed in relation to the metabolic pathways operative during the successive light emission modes identified here over time. Altogether, the results clarify the contributions of metal/nutrient bio-availabilities and food quality to cell response typology.
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39
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De novo design of a transcription factor for a progesterone biosensor. Biosens Bioelectron 2022; 203:113897. [DOI: 10.1016/j.bios.2021.113897] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
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40
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Synthetic biology-powered microbial co-culture strategy and application of bacterial cellulose-based composite materials. Carbohydr Polym 2022; 283:119171. [DOI: 10.1016/j.carbpol.2022.119171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022]
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41
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ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:325-342. [PMID: 34985754 DOI: 10.1007/978-1-0716-1998-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ROSALIND (RNA Output Sensors Activated by Ligand Induction) is an in vitro biosensing system that detects small molecules using regulated transcription reactions. It consists of three key components: (1) RNA polymerases, (2) allosteric protein transcription factors, and (3) synthetic DNA transcription templates that together regulate the synthesis of a fluorescence-activating RNA aptamer. The system can detect a wide range of chemicals including antibiotics, small molecules, and metal ions. We have demonstrated that ROSALIND can be lyophilized and transported at ambient conditions for water testing on-site. Here, we describe how to set up a ROSALIND reaction for detecting various chemical contaminants in water using a model transcription factor as well as how to build a new ROSALIND sensor.
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42
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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. [DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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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43
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Jiang B, Shen Y, Lu X, Du Y, Jin N, Li G, Zhang D, Xing Y. Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:460-473. [PMID: 35166274 DOI: 10.1039/d1em00405k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yaoxin Shen
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Xin Lu
- Petrochina North China Gas Marketing Company, Beijing, 100029, PR China
| | - Yufan Du
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Naifu Jin
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, PR China
- State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, 100083, PR China
- National Environmental and Energy Science and Technology International Cooperation Base, University of Science & Technology Beijing, Beijing, 100083, PR China
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44
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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: 4] [Impact Index Per Article: 2.0] [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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45
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Zhang X, Li B, Schillereff DN, Chiverrell RC, Tefsen B, Wells M. Whole-cell biosensors for determination of bioavailable pollutants in soils and sediments: Theory and practice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152178. [PMID: 34883180 DOI: 10.1016/j.scitotenv.2021.152178] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
The bioavailability of pollutants is a key factor affecting environmental risk. Whole-cell bioreporters are a demonstratedly effective tool for the investigation of pollutant bioavailability in water and soil/sediment. Unlike aqueous samples, transmittance of bioreporter optical signal is reduced in direct-contact assays with soil/sediment, which affects the accuracy of bioreporter-detected pollutant bioavailability. No studies have measured the magnitude and variability of soil/sediment effects on signal in direct-contact assays or how associated uncertainties influence results. In this study, we investigate the optical effects of soil/sediment particles in suspensions on bioreporter signal transmittance and quantify how variable these optical effects are from sample-to-sample. We find that neglecting bioreporter signal diminution by soil/sediment, as many studies do, can lead to order-of-magnitude errors in results, underestimating risk. Correction based on methods in ad hoc use (e.g. comparison to signal from non-inducible reporter or use of reference soil/sediment) are also problematic for some types of experiment, and could lead to errors in excess of 30%. Our findings have a sound basis in theory, and we provide recommendations concerning the most suitable type of approach to use for different experimental settings. Generally, if best accuracy is not needed to quantify bioavailability, for samples that have been ground, sieved, and are of reasonably uniform color, it may be possible to use a single or average correction factor, particularly for experiments performed at a single slurry concentration. For investigations studying bioavailability under varying solid-phase:water ratios (e.g., sorption/desorption), detailed compensation measurements are needed for independent variables, including each specific soil/sediment sample, slurry concentration, and in some cases bioreporter signal intensity. Our measurements and calculations indicate that best results are obtained when working in the region of ballistic photon transmittance. Findings herein will be useful in areas that require information on bioavailability, such as ecotoxicology and environmental risk assessment.
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Affiliation(s)
- Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Boling Li
- School of Environmental Science, University of Liverpool, Brownlow Hill, Liverpool L69 7ZX, United Kingdom; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, PR China
| | | | - Richard C Chiverrell
- School of Environmental Science, University of Liverpool, Brownlow Hill, Liverpool L69 7ZX, United Kingdom
| | - Boris Tefsen
- Natural Sciences, Ronin Institute, Montclair, NJ 07043, United States
| | - Mona Wells
- Natural Sciences, Ronin Institute, Montclair, NJ 07043, United States.
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46
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Elad T, Shemer B, Simanowitz S, Kabessa Y, Mizrachi Y, Gold A, Shpigel E, Agranat AJ, Belkin S. Enhancing DNT Detection by a Bacterial Bioreporter: Directed Evolution of the Transcriptional Activator YhaJ. Front Bioeng Biotechnol 2022; 10:821835. [PMID: 35237579 PMCID: PMC8882911 DOI: 10.3389/fbioe.2022.821835] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022] Open
Abstract
Detection of buried landmines is a dangerous and complicated task that consumes large financial resources and poses significant risks to the personnel involved. A potential alternative to conventional detection methodologies is the use of microbial bioreporters, capable of emitting an optical signal upon exposure to explosives, thus revealing to a remote detector the location of buried explosive devices. We have previously reported the design, construction, and optimization of an Escherichia coli-based bioreporter for the detection of 2,4,6-trinitrotoluene (TNT) and its accompanying impurity 2,4-dinitrotoluene (DNT). Here we describe the further enhancement of this bioreporter by the directed evolution of YhaJ, the transcriptional activator of the yqjF gene promoter, the sensing element of the bioreporter's molecular circuit. This process resulted in a 37-fold reduction of the detection threshold, as well as significant enhancements to signal intensity and response time, rendering this sensor strain more suitable for detecting the minute concentrations of DNT in the soil above buried landmines. The capability of this enhanced bioreporter to detect DNT buried in sand is demonstrated.
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Affiliation(s)
- Tal Elad
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Shemer
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shilat Simanowitz
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yossef Kabessa
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Mizrachi
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Azriel Gold
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Etai Shpigel
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aharon J. Agranat
- Department of Applied Physics and the Brojde Center for Innovative Engineering and Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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47
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Tavares D, van der Meer JR. Subcellular Localization Defects Characterize Ribose-Binding Mutant Proteins with New Ligand Properties in Escherichia coli. Appl Environ Microbiol 2022; 88:e0211721. [PMID: 34757821 PMCID: PMC8788693 DOI: 10.1128/aem.02117-21] [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: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Periplasmic binding proteins have been previously proclaimed as a general scaffold to design sensor proteins with new recognition specificities for nonnatural compounds. Such proteins can be integrated in bacterial bioreporter chassis with hybrid chemoreceptors to produce a concentration-dependent signal after ligand binding to the sensor cell. However, computationally designed new ligand-binding properties ignore the more general properties of periplasmic binding proteins, such as their periplasmic translocation, dynamic transition of open and closed forms, and interactions with membrane receptors. In order to better understand the roles of such general properties in periplasmic signaling behavior, we studied the subcellular localization of ribose-binding protein (RbsB) in Escherichia coli in comparison to a recently evolved set of mutants designed to bind 1,3-cyclohexanediol. As proxies for localization, we calibrated and deployed C-terminal end mCherry fluorescent protein fusions. Whereas RbsB-mCherry coherently localized to the periplasmic space and accumulated in (periplasmic) polar regions depending on chemoreceptor availability, mutant RbsB-mCherry expression resulted in high fluorescence cell-to-cell variability. This resulted in higher proportions of cells devoid of clear polar foci and of cells with multiple fluorescent foci elsewhere, suggesting poorer translocation, periplasmic autoaggregation, and mislocalization. Analysis of RbsB mutants and mutant libraries at different stages of directed evolution suggested overall improvement to more RbsB-wild-type-like characteristics, which was corroborated by structure predictions. Our results show that defects in periplasmic localization of mutant RbsB proteins partly explain their poor sensing performance. Future efforts should be directed to predicting or selecting secondary mutations outside computationally designed binding pockets, taking folding, translocation, and receptor interactions into account. IMPORTANCE Biosensor engineering relies on transcription factors or signaling proteins to provide the actual sensory functions for the target chemicals. Since for many compounds there are no natural sensory proteins, there is a general interest in methods that could unlock routes to obtaining new ligand-binding properties. Bacterial periplasmic binding proteins (PBPs) form an interesting family of proteins to explore for this purpose, because there is a large natural variety suggesting evolutionary trajectories to bind new ligands. PBPs are conserved and amenable to accurate computational binding pocket predictions. However, studying ribose-binding protein in Escherichia coli, we discovered that designed variants have defects in their proper localization in the cell, which can impair appropriate sensor signaling. This indicates that functional sensing capacity of PBPs cannot be obtained solely through computational design of the ligand-binding pocket but must take other properties of the protein into account, which are currently very difficult to predict.
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Affiliation(s)
- Diogo Tavares
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan R. van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Moratti CF, Scott C, Coleman NV. Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review. Front Bioeng Biotechnol 2022; 9:804234. [PMID: 35083206 PMCID: PMC8784404 DOI: 10.3389/fbioe.2021.804234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.
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Affiliation(s)
- Claudia F. Moratti
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
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Cregut M, Hua A, Jouanneau S, Assaf A, Cordella CBY, Thouand G, Durand MJ. Screening of metallic pollution in complex environmental samples through a transcriptomic fingerprint method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1037-1050. [PMID: 34341931 DOI: 10.1007/s11356-021-15545-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Characterizing waste ecotoxicity is laborious because of both the undefined nature of environmental samples and the diversity of contaminants that can be present. With regard to these limitations, traditional approaches do not provide information about the nature of the pollution encountered. To improve such assessments, a fluorescent library of 1870 transcriptomic reporters from Escherichia coli K12 MG1655 was used to report the ecotoxic status of environmental samples. The reliability of the approach was evaluated with 6 metallic pollutants (As, Cu, Cd, Hg, Pb, Zn) used alone and in mixture in pure and complex matrices. A total of 18 synthetic samples were used to characterize the specificity of the resulting metallic contamination fingerprints. Metallic contamination impacted 4.5 to 10.2% of the whole transcriptomic fingerprint of E. coli. The analysis revealed that a subset of 175 transcriptomic reporters is sufficient to characterize metallic contamination, regardless of the nature of the sample. A statistical model distinguished patterns due to metallic contamination and provided information about the level of toxicity with 93 to 98% confidence. The use of the transcriptomic assessment was validated for 17 complex matrices with various toxicities and metal contaminants, such as activated sludge, wastewater effluent, soil, wood and river water. The presence of metals and their associated toxicity, which seems linked to their bioavailabilities, were thereby determined. This method constitutes a possible tool to screen unknown complex samples for their metallic status and identify those for which a deeper characterization must be achieved by the use of traditional biosensors and analytical methods.
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Affiliation(s)
- Mickael Cregut
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France.
- University of Nantes, CAPACITES, 26 Bd Vincent Gâche, F-44200, Nantes, France.
| | - Anna Hua
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Sulivan Jouanneau
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Ali Assaf
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Christophe B Y Cordella
- University of Paris-Saclay, UMR AgroParisTech/INRA 914 Physiologie de la Nutrition et du Comportement Alimentaire, Rue Claude Bernard, 75, ,005, Paris, France
| | - Gérald Thouand
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Marie-José Durand
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
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