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Liu MQ, Guo Y, Wu C, Gao CX, Liu F, Hui CY. Visual arsenic detection in environmental waters: Innovating with a naked-eye biosensor for universal application. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135398. [PMID: 39096639 DOI: 10.1016/j.jhazmat.2024.135398] [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: 04/28/2024] [Revised: 07/27/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Arsenic contamination in environmental water sources poses a significant threat to human health, necessitating the development of sensitive and accessible detection methods. This study presents a multidimensional optimization of a bacterial biosensor for the susceptible and deoxyviolacein (DV)-based visual detection of arsenic. The research involved screening six different arsenic resistance (ars) operons and optimizing the genetic circuit to minimize background noise. Introducing an arsenic-specific transport channel enhanced the sensor's sensitivity to 1 nM with a quantitative range from 0.036 to 1.171 μM. The pigment-based biosensor offers a simple colorimetric approach for arsenic detection without complex instrumentation. The preferred biosensor demonstrated characteristics of anti-chelating agent interference, consistently quantified As(III) concentrations ranging from 0.036 to 1.171 μM covering the World Health Organization (WHO) drinking water limit. Innovatively, it effectively detects arsenic in seawater within a linear regression range of 0.071 to 1.125 μM. The biosensor's selectivity for arsenic was confirmed, with minimal cross-response to group 15 metals. Our naked-eye biosensor offers a novel approach for the rapid, on-site detection of arsenic in various water sources. Its simplicity, cost-effectiveness, and versatility make it a valuable tool for environmental monitoring and public health initiatives.
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Affiliation(s)
- Ming-Qi Liu
- School of Public Health, Guangdong Medical University, Dongguan 523808, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Can Wu
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chao-Xian Gao
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Fen Liu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China.
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2
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Lu C, Huang Y, Cui J, Wu J, Jiang C, Gu X, Cao Y, Yin S. Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques. ACS Synth Biol 2024; 13:2295-2312. [PMID: 39002162 DOI: 10.1021/acssynbio.4c00259] [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: 07/15/2024]
Abstract
Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.
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Affiliation(s)
- Chenjing Lu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yaying Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jian Cui
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Junhua Wu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Medical School, Nanjing University, Nanjing 210093, China
| | - Chunping Jiang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaosong Gu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine innovation center, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine innovation center, MOE Key Laboratory of High Performance Polymer Materials and Technology, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Sheng Yin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
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3
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Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem Biol 2024; 31:1447-1459. [PMID: 38925113 DOI: 10.1016/j.chembiol.2024.05.018] [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: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.
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Affiliation(s)
- Christopher Helenek
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rafał Krzysztoń
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariana Cabral
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Damiano Coraci
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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4
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Guo Y, Hu SY, Wu C, Gao CX, Hui CY. Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals. ACS OMEGA 2024; 9:33868-33881. [PMID: 39130558 PMCID: PMC11308077 DOI: 10.1021/acsomega.4c03613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
Fermentative production of natural colorants using microbial strains has emerged as a cost-effective and sustainable alternative to chemical synthesis. Visual pigments are used as signal outputs in colorimetric bacterial biosensors, a promising method for monitoring environmental pollutants. In this study, we engineered four self-sufficient indigo-forming enzymes, including HbpAv, bFMO, cFMO, and rFPMO, in a model bacterium E. coli. TrxA-bFMO was chosen for its strong ability to produce indigo under T7 lac and mer promoters' regulation. The choice of bacterial hosts, the supplementation of substrate l-tryptophan, and ventilation were crucial factors affecting indigo production. The indigo reporter validated the biosensors for Hg(II), Pb(II), As(III), and Cd(II). The biosensors reported Hg(II) as low as 14.1 nM, Pb(II) as low as 1.5 nM, and As(III) as low as 4.5 nM but increased to 25 μM for Cd(II). The detection ranges for Hg(II), Pb(II), As(III), and Cd(II) were quantified from 14.1 to 225 nM, 1.5 to 24.4 nM, 4.5 to 73.2 nM, and 25 to 200 μM, respectively. The sensitivity, responsive concentration range, and selectivity are comparable to β-galactosidase and luciferase reporter enzymes. This study suggests that engineered enzymes for indigo production have great potential for green chemical synthesis. Additionally, heterologous biosynthesis of indigo production can lead to the development of novel, low-cost, and mini-equipment bacterial biosensors with zero background noise for visual monitoring of pollutant heavy metals.
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Affiliation(s)
- Yan Guo
- National
Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen 518020, China
| | - Shun-Yu Hu
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
- Department
of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Can Wu
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
- Department
of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Chao-Xian Gao
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
| | - Chang-Ye Hui
- Department
of Pathology and Toxicology, Shenzhen Prevention
and Treatment Center for Occupational Diseases, Shenzhen 518020, China
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5
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Shao J, Qiu X, Zhang L, Li S, Xue S, Si Y, Li Y, Jiang J, Wu Y, Xiong Q, Wang Y, Chen Q, Gao T, Zhu L, Wang H, Xie M. Multi-layered computational gene networks by engineered tristate logics. Cell 2024:S0092-8674(24)00716-5. [PMID: 39089254 DOI: 10.1016/j.cell.2024.07.001] [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: 10/30/2023] [Revised: 04/19/2024] [Accepted: 07/01/2024] [Indexed: 08/03/2024]
Abstract
So far, biocomputation strictly follows traditional design principles of digital electronics, which could reach their limits when assembling gene circuits of higher complexity. Here, by creating genetic variants of tristate buffers instead of using conventional logic gates as basic signal processing units, we introduce a tristate-based logic synthesis (TriLoS) framework for resource-efficient design of multi-layered gene networks capable of performing complex Boolean calculus within single-cell populations. This sets the stage for simple, modular, and low-interference mapping of various arithmetic logics of interest and an effectively enlarged engineering space within single cells. We not only construct computational gene networks running full adder and full subtractor operations at a cellular level but also describe a treatment paradigm building on programmable cell-based therapeutics, allowing for adjustable and disease-specific drug secretion logics in vivo. This work could foster the evolution of modern biocomputers to progress toward unexplored applications in precision medicine.
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Affiliation(s)
- Jiawei Shao
- Department of Pharmacy, Center for Regenerative and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang 322000, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
| | - Xinyuan Qiu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, Hunan 410073, China; College of Computer Science and Technology, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Lihang Zhang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Research Center for Life Sciences Computing, Zhejiang Laboratory, Hangzhou, Zhejiang 311100, China
| | - Shichao Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuai Xue
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Yaqing Si
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yilin Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jian Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuhang Wu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiqi Xiong
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yukai Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qidi Chen
- Department of Pharmacy, Center for Regenerative and Aging Medicine, the Fourth Affiliated Hospital of School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang 322000, China
| | - Ting Gao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, Hunan 410073, China.
| | - Hui Wang
- Research Center for Life Sciences Computing, Zhejiang Laboratory, Hangzhou, Zhejiang 311100, China.
| | - Mingqi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China.
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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7
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Che H, Wang Z, Li Y, Nie Y, Tian X. A Stable and Sensitive Engineering Bacterial Sensor via Physical Biocontainment and Two-Stage Signal Amplification. Anal Chem 2024; 96:8807-8813. [PMID: 38714342 DOI: 10.1021/acs.analchem.4c01341] [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: 05/09/2024]
Abstract
Although engineering bacterial sensors have outstanding advantages in reflecting the actual bioavailability and continuous monitoring of pollutants, the potential escape risk of engineering microorganisms and lower detection sensitivity have always been one of the biggest challenges limiting their wider application. In this study, a core-shell hydrogel bead with functionalized silica as the core and alginate-polyacrylamide as the shell have been developed not only to realize zero escape of engineered bacteria but also to maintain cell activity in harsh environments, such as extremely acidic/alkaline pH, high salt concentration, and strong pressure. Particularly, after combining the selective preconcentration toward pollutants by functionalized core and the positive feedback signal amplification of engineering bacteria, biosensors have realized two-stage signal amplification, significantly improving the detection sensitivity and reducing the detection limit. In addition, this strategy was actually applied to the detection of As(III) and As(V) coexisting in environmental samples, and the detection sensitivity was increased by 3.23 and 4.39 times compared to sensors without signal amplification strategy, respectively, and the detection limits were as low as 0.39 and 0.86 ppb, respectively.
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Affiliation(s)
- Huachao Che
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhiyue Wang
- Civil and Environmental Engineering, University of Hawai'i, Honolulu Hawai'i 96822, United States
- Water Resources Research Center, University of Hawai'i, Honolulu, Hawai'i 96822, United States
| | - Yong Li
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yulun Nie
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xike Tian
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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Zevallos-Aliaga D, De Graeve S, Obando-Chávez P, Vaccari NA, Gao Y, Peeters T, Guerra DG. Highly Sensitive Whole-Cell Mercury Biosensors for Environmental Monitoring. BIOSENSORS 2024; 14:246. [PMID: 38785720 PMCID: PMC11117708 DOI: 10.3390/bios14050246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Whole-cell biosensors could serve as eco-friendly and cost-effective alternatives for detecting potentially toxic bioavailable heavy metals in aquatic environments. However, they often fail to meet practical requirements due to an insufficient limit of detection (LOD) and high background noise. In this study, we designed a synthetic genetic circuit specifically tailored for detecting ionic mercury, which we applied to environmental samples collected from artisanal gold mining sites in Peru. We developed two distinct versions of the biosensor, each utilizing a different reporter protein: a fluorescent biosensor (Mer-RFP) and a colorimetric biosensor (Mer-Blue). Mer-RFP enabled real-time monitoring of the culture's response to mercury samples using a plate reader, whereas Mer-Blue was analysed for colour accumulation at the endpoint using a specially designed, low-cost camera setup for harvested cell pellets. Both biosensors exhibited negligible baseline expression of their respective reporter proteins and responded specifically to HgBr2 in pure water. Mer-RFP demonstrated a linear detection range from 1 nM to 1 μM, whereas Mer-Blue showed a linear range from 2 nM to 125 nM. Our biosensors successfully detected a high concentration of ionic mercury in the reaction bucket where artisanal miners produce a mercury-gold amalgam. However, they did not detect ionic mercury in the water from active mining ponds, indicating a concentration lower than 3.2 nM Hg2+-a result consistent with chemical analysis quantitation. Furthermore, we discuss the potential of Mer-Blue as a practical and affordable monitoring tool, highlighting its stability, reliance on simple visual colorimetry, and the possibility of sensitivity expansion to organic mercury.
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Affiliation(s)
- Dahlin Zevallos-Aliaga
- Laboratorio de Moléculas Individuales, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; (D.Z.-A.); (P.O.-C.); (N.A.V.)
| | - Stijn De Graeve
- Open BioLab Brussels, Erasmushogeschool Brussel, Laarbeeklaan 121, B-1090 Jette, Belgium
| | - Pamela Obando-Chávez
- Laboratorio de Moléculas Individuales, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; (D.Z.-A.); (P.O.-C.); (N.A.V.)
| | - Nicolás A. Vaccari
- Laboratorio de Moléculas Individuales, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; (D.Z.-A.); (P.O.-C.); (N.A.V.)
| | - Yue Gao
- Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium;
| | - Tom Peeters
- Open BioLab Brussels, Erasmushogeschool Brussel, Laarbeeklaan 121, B-1090 Jette, Belgium
| | - Daniel G. Guerra
- Laboratorio de Moléculas Individuales, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; (D.Z.-A.); (P.O.-C.); (N.A.V.)
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9
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Jiang G, Gao Y, Zhou N, Wang B. CRISPR-powered RNA sensing in vivo. Trends Biotechnol 2024:S0167-7799(24)00094-5. [PMID: 38734565 DOI: 10.1016/j.tibtech.2024.04.002] [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: 01/25/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/13/2024]
Abstract
RNA sensing in vivo evaluates past or ongoing endogenous RNA disturbances, which is crucial for identifying cell types and states and diagnosing diseases. Recently, the CRISPR-driven genetic circuits have offered promising solutions to burgeoning challenges in RNA sensing. This review delves into the cutting-edge developments of CRISPR-powered RNA sensors in vivo, reclassifying these RNA sensors into four categories based on their working mechanisms, including programmable reassembly of split single-guide RNA (sgRNA), RNA-triggered RNA processing and protein cleavage, miRNA-triggered RNA interference (RNAi), and strand displacement reactions. Then, we discuss the advantages and challenges of existing methodologies in diverse application scenarios and anticipate and analyze obstacles and opportunities in forthcoming practical implementations.
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Affiliation(s)
- Guo Jiang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Yuanli Gao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Nan Zhou
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Baojun Wang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China.
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10
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Hui CY, Liu MQ, Guo Y. Synthetic bacteria designed using ars operons: a promising solution for arsenic biosensing and bioremediation. World J Microbiol Biotechnol 2024; 40:192. [PMID: 38709285 DOI: 10.1007/s11274-024-04001-2] [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: 03/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The global concern over arsenic contamination in water due to its natural occurrence and human activities has led to the development of innovative solutions for its detection and remediation. Microbial metabolism and mobilization play crucial roles in the global cycle of arsenic. Many microbial arsenic-resistance systems, especially the ars operons, prevalent in bacterial plasmids and genomes, play vital roles in arsenic resistance and are utilized as templates for designing synthetic bacteria. This review novelty focuses on the use of these tailored bacteria, engineered with ars operons, for arsenic biosensing and bioremediation. We discuss the advantages and disadvantages of using synthetic bacteria in arsenic pollution treatment. We highlight the importance of genetic circuit design, reporter development, and chassis cell optimization to improve biosensors' performance. Bacterial arsenic resistances involving several processes, such as uptake, transformation, and methylation, engineered in customized bacteria have been summarized for arsenic bioaccumulation, detoxification, and biosorption. In this review, we present recent insights on the use of synthetic bacteria designed with ars operons for developing tailored bacteria for controlling arsenic pollution, offering a promising avenue for future research and application in environmental protection.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Ming-Qi Liu
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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11
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Fan C, He N, Yuan J. Cascaded amplifying circuit enables sensitive detection of fungal pathogens. Biosens Bioelectron 2024; 250:116058. [PMID: 38281368 DOI: 10.1016/j.bios.2024.116058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/30/2024]
Abstract
The rapid and accurate detection of fungal pathogens is of utmost importance in the fields of healthcare, food safety, and environmental monitoring. In this study, we implemented a cascaded amplifying circuit in Saccharomyces cerevisiae to improve the G protein-coupled receptor (GPCR) mediated fungal detection. The GPCR signaling pathway was coupled with the galactose-regulated (GAL) system and a positive feedback loop was implemented to enhance the performance of yeast biosensor. We systematically compared four generations of biosensors for detecting the mating pheromone of Candida albicans, and the best biosensor exhibited the limit of detection (LOD) as low as 0.25 pM and the limit of quantification (LOQ) of 1 pM after 2 h incubation. Subsequently, we developed a betaxanthin-based colorimetric module for the easy visualization of signal outputs, and the resulting biosensors can give reliable naked-eye readouts. In summary, we demonstrated that cascaded amplifying circuits could substantially improve the engineered yeast biosensors with a better sensitivity and signal output magnitude, which will pave the way for their real-world applications in public health.
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Affiliation(s)
- Cong Fan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Nike He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China; Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian, 361005, China; Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China.
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12
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Mohsenin H, Wagner HJ, Rosenblatt M, Kemmer S, Drepper F, Huesgen P, Timmer J, Weber W. Design of a Biohybrid Materials Circuit with Binary Decoder Functionality. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308092. [PMID: 38118057 DOI: 10.1002/adma.202308092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited is engineered. Guided by a quantitative mathematical model and following a design-build-test-learn (DBTL) cycle, the modules are wired according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. A 2-input/4-output binary decoder for the detection of two small molecules in a material framework that can perform regulated outputs in form of distinct protease activities is designed. The here demonstrated smart material system is strongly modular and can be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.
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Affiliation(s)
- Hasti Mohsenin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Hanna J Wagner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
| | - Marcus Rosenblatt
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Svenja Kemmer
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Pitter Huesgen
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Jens Timmer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
- Saarland University, Department of Materials Science and Engineering, Campus D2 2, 66123, Saarbrücken, Germany
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13
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Sun Y, Zhang F, Ouyang Q, Luo C. The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model. iScience 2024; 27:109142. [PMID: 38384832 PMCID: PMC10879701 DOI: 10.1016/j.isci.2024.109142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Differential equation models are widely used to describe genetic regulations, predict multicomponent regulatory circuits, and provide quantitative insights. However, it is still challenging to quantitatively link the dynamic behaviors with measured parameters in synthetic circuits. Here, we propose a dynamic delay model (DDM) which includes two simple parts: the dynamic determining part and the doses-related steady-state-determining part. The dynamic determining part is usually supposed as the delay time but without a clear formula. For the first time, we give the detail formula of the dynamic determining function and provide a method for measuring all parameters of synthetic elements (include 8 activators and 5 repressors) by microfluidic system. Three synthetic circuits were built to show that the DDM can notably improve the prediction accuracy and can be used in various synthetic biology applications.
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Affiliation(s)
- Yanhong Sun
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fengyu Zhang
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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14
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [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: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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15
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Kocalar S, Miller BM, Huang A, Gleason E, Martin K, Foley K, Copeland DS, Jewett MC, Saavedra EA, Kraves S. Validation of Cell-Free Protein Synthesis Aboard the International Space Station. ACS Synth Biol 2024; 13:942-950. [PMID: 38442491 PMCID: PMC10949350 DOI: 10.1021/acssynbio.3c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand synthesis of peptide-based vaccines and biotherapeutics as well as the development of diagnostic tests for environmental contaminants and infectious agents. Unlike traditional cell-based systems, CFPS platforms do not require the maintenance of living cells and can be deployed with minimal equipment; therefore, they hold promise for applications in low-resource contexts, including spaceflight. Here, we evaluate the performance of the cell-free platform BioBits aboard the International Space Station by expressing RNA-based aptamers and fluorescent proteins that can serve as biological indicators. We validate two classes of biological sensors that detect either the small-molecule DFHBI or a specific RNA sequence. Upon detection of their respective analytes, both biological sensors produce fluorescent readouts that are visually confirmed using a hand-held fluorescence viewer and imaged for quantitative analysis. Our findings provide insights into the kinetics of cell-free transcription and translation in a microgravity environment and reveal that both biosensors perform robustly in space. Our findings lay the groundwork for portable, low-cost applications ranging from point-of-care health monitoring to on-demand detection of environmental hazards in low-resource communities both on Earth and beyond.
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Affiliation(s)
- Selin Kocalar
- Leigh
High School, 5210 Leigh
Ave, San Jose, California 95124, United States
- Massachusetts
Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Bess M. Miller
- Division
of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St, Boston, Massachusetts 02115, United States
| | - Ally Huang
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Emily Gleason
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kathryn Martin
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kevin Foley
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - D. Scott Copeland
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | | | - Sebastian Kraves
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
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16
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Yang J, Zhao X, Wang X, Xia M, Ba S, Lim BL, Hou H. Biomonitoring of heavy metals and their phytoremediation by duckweeds: Advances and prospects. ENVIRONMENTAL RESEARCH 2024; 245:118015. [PMID: 38141920 DOI: 10.1016/j.envres.2023.118015] [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: 08/30/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 12/25/2023]
Abstract
Heavy metals (HMs) contamination of water bodies severely threatens human and ecosystem health. There is growing interest in the use of duckweeds for HMs biomonitoring and phytoremediation due to their fast growth, low cultivation costs, and excellent HM uptake efficiency. In this review, we summarize the current state of knowledge on duckweeds and their suitability for HM biomonitoring and phytoremediation. Duckweeds have been used for phytotoxicity assays since the 1930s. Some toxicity tests based on duckweeds have been listed in international guidelines. Duckweeds have also been recognized for their ability to facilitate HM phytoremediation in aquatic environments. Large-scale screening of duckweed germplasm optimized for HM biomonitoring and phytoremediation is still essential. We further discuss the morphological, physiological, and molecular effects of HMs on duckweeds. However, the existing data are clearly insufficient, especially in regard to dissection of the transcriptome, metabolome, proteome responses and molecular mechanisms of duckweeds under HM stresses. We also evaluate the influence of environmental factors, exogenous substances, duckweed community composition, and HM interactions on their HM sensitivity and HM accumulation, which need to be considered in practical application scenarios. Finally, we identify challenges and propose approaches for improving the effectiveness of duckweeds for bioremediation from the aspects of selection of duckweed strain, cultivation optimization, engineered duckweeds. We foresee great promise for duckweeds as phytoremediation agents, providing environmentally safe and economically efficient means for HM removal. However, the primary limiting issue is that so few researchers have recognized the outstanding advantages of duckweeds. We hope that this review can pique the interest and attention of more researchers.
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Affiliation(s)
- Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Xiaoyu Wang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Sang Ba
- Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa, 850000, China; Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, 850000, China.
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China; HKU Shenzhen Institute of Research and Innovation, Shenzhen, China; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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17
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Du H, Liang Y, Li J, Yuan X, Tao F, Dong C, Shen Z, Sui G, Wang P. Directed Evolution of 4-Hydroxyphenylpyruvate Biosensors Based on a Dual Selection System. Int J Mol Sci 2024; 25:1533. [PMID: 38338812 PMCID: PMC10855707 DOI: 10.3390/ijms25031533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To screen for PobR mutants responsive to 4-hydroxyphenylpyruvate(HPP), we developed a dual selection system in E. coli. The positive selection of this system was used to enrich PobR mutants that identified the required ligands. The following negative selection eliminated or weakened PobR mutants that still responded to 4HB. Directed evolution of the PobR library resulted in a variant where PobRW177R was 5.1 times more reactive to 4-hydroxyphenylpyruvate than PobRWT. Overall, we developed an efficient dual selection system for directed evolution of biosensors.
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Affiliation(s)
- Hongxuan Du
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yaoyao Liang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianing Li
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Xinyao Yuan
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Fenglin Tao
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
| | - Chengjie Dong
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Zekai Shen
- School of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin 150040, China; (H.D.); (Y.L.); (J.L.); (F.T.)
- NEFU-China iGEM Team, Northeast Forestry University, Harbin 150040, China;
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Aulin College, Northeast Forestry University, Harbin 150040, China
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18
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Bello AJ, Popoola A, Okpuzor J, Ihekwaba-Ndibe AE, Olorunniji FJ. A Genetic Circuit Design for Targeted Viral RNA Degradation. Bioengineering (Basel) 2023; 11:22. [PMID: 38247899 PMCID: PMC10813695 DOI: 10.3390/bioengineering11010022] [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: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.
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Affiliation(s)
- Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Biological Sciences, Redeemer’s University, Ede 232101, Osun State, Nigeria
| | - Abdulgafar Popoola
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Medical Laboratory Science, Kwara State University, Malete, Ilorin 241102, Kwara State, Nigeria
| | - Joy Okpuzor
- Department of Cell Biology & Genetics, University of Lagos, Akoka, Lagos 101017, Lagos State, Nigeria;
| | | | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
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19
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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20
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Chiang AJ, Hasty J. Design of synthetic bacterial biosensors. Curr Opin Microbiol 2023; 76:102380. [PMID: 37703812 DOI: 10.1016/j.mib.2023.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/19/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Novel whole-cell bacterial biosensor designs require an emphasis on moving toward field deployment. Many current sensors are characterized under specified laboratory conditions, which frequently do not represent actual deployment conditions. To this end, recent developments such as toolkits for probing new host chassis that are more robust to environments of interest, have paved the way for improved designs. Strategies for rational tuning of genetic components or tools such as genetic amplifiers or designs that allow post hoc tuning are essential in optimizing existing biosensors for practical application. Furthermore, recent work has seen a rise in directed evolution techniques, which can be immensely valuable in both tuning existing sensors and developing sensors for new analytes that lack characterized sensors. Combined with advancements in bioinformatics and capabilities in rewiring two-component systems, many new sensors can be established, broadening biosensor use cases. Last, recent work in CRISPR-based dynamic regulation and memory mechanisms, as well as kill-switches for biosafety and innovative output integration concepts, represents promising steps toward designing bacterial biosensors for deployment in dynamic and heterogeneous conditions.
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Affiliation(s)
- Alyssa J Chiang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California San Diego, La Jolla, CA, USA
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21
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Zhu K, Chen D, Cai Y, Zhang T, Ma J, Bao L, Zhao F, Wu L, Chen S. Engineering the Ultrasensitive Visual Whole-Cell Biosensors by Evolved MerR and 5' UTR for Detection of Ultratrace Mercury. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16964-16973. [PMID: 37863904 DOI: 10.1021/acs.est.3c04915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The existing mercury whole-cell biosensors (WCBs, parts per billion range) are not able to meet the real-world requirements due to their lack of sensitivity for the detection of ultratrace mercury in the environment. Ultratrace mercury is a potential threat to human health via the food chain. Here, we developed an ultrasensitive mercury WCB by directed evolution of the mercury-responsive transcriptional activator (MerR) sensing module to detect ultratrace mercury. Subsequently, the mutant WCB (m4-1) responding to mercury in the parts per trillion range after 1 h of induction was obtained. Its detection limit (LOD) was 0.313 ng/L, comparable to those of some analytical instruments. Surprisingly, the m4-1 WCB also responded to methylmercury (LOD = 98 ng/L), which is far more toxic than inorganic mercury. For more convenient detection, we have increased another green fluorescent protein reporter module with an optimized 5' untranslated region (5' UTR) sequence. This yields two visual WCBs with an enhanced fluorescence output. At a concentration of 2.5 ng/L, the fluorescence signals can be directly observed by the naked eye. With the combination of mobile phone imaging and image processing software, the 2GC WCB provided simple, rapid, and reliable quantitative and qualitative analysis of real samples (LOD = 0.307 ng/L). Taken together, these results indicate that the ultrasensitive visual whole-cell biosensors for ultratrace mercury detection are successfully designed using a combination of directed evolution and synthetic biotechnology.
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Affiliation(s)
- Kaili Zhu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, P. R. China
- University of Science and Technology of China, Hefei 230026, China, P. R. China
| | - Dongdong Chen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, P. R. China
| | - Yeshen Cai
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, P. R. China
- University of Science and Technology of China, Hefei 230026, China, P. R. China
| | - TianYi Zhang
- School of Public Health, Wannan Medical College, Wuhu 241002, P. R. China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, P. R. China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, P. R. China
| | - Feng Zhao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, P. R. China
| | - Lijun Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, P. R. China
- University of Science and Technology of China, Hefei 230026, China, P. R. China
| | - Shaopeng Chen
- School of Public Health, Wannan Medical College, Wuhu 241002, P. R. China
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22
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Hoces D, Miguens Blanco J, Hernández-López RA. A synthetic biology approach to engineering circuits in immune cells. Immunol Rev 2023; 320:120-137. [PMID: 37464881 DOI: 10.1111/imr.13244] [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: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
Abstract
A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the engineering of cells with customized responses. In cancer therapeutics, engineering T cells with circuits have the potential to overcome the challenges of current approaches, for example, by allowing specific recognition and killing of cancer cells. Recent advances also facilitate engineering integrated circuits for the controlled release of therapeutic molecules at specified locations, for example, in a solid tumor. In this review, we discuss recent strategies and applications of synthetic receptor circuits aimed at enhancing immune cell functions for cancer immunotherapy. We begin by introducing the concept of circuits in networks at the molecular and cellular scales and provide an analysis of the development and implementation of several synthetic circuits in T cells that have the goal to overcome current challenges in cancer immunotherapy. These include specific targeting of cancer cells, increased T-cell proliferation, and persistence in the tumor microenvironment. By harnessing the power of synthetic biology, and the characteristics of certain circuit architectures, it is now possible to engineer a new generation of immune cells that recognize cancer cells, while minimizing off-target toxicities. We specifically discuss T-cell circuits for antigen density sensing. These circuits allow targeting of solid tumors that share antigens with normal tissues. Additionally, we explore designs for synthetic circuits that could control T-cell differentiation or T-cell fate as well as the concept of synthetic multicellular circuits that leverage cellular communication and division of labor to achieve improved therapeutic efficacy. As our understanding of cell biology expands and novel tools for genome, protein, and cell engineering are developed, we anticipate further innovative approaches to emerge in the design and engineering of circuits in immune cells.
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Affiliation(s)
- Daniel Hoces
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Jesús Miguens Blanco
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rogelio A Hernández-López
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford, California, USA
- Chan-Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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23
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Liu H, Zhang L, Wang W, Hu H, Ouyang X, Xu P, Tang H. An Intelligent Synthetic Bacterium for Chronological Toxicant Detection, Biodegradation, and Its Subsequent Suicide. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304318. [PMID: 37705081 PMCID: PMC10625131 DOI: 10.1002/advs.202304318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Indexed: 09/15/2023]
Abstract
Modules, toolboxes, and synthetic biology systems may be designed to address environmental bioremediation. However, weak and decentralized functional modules require complex control. To address this issue, an integrated system for toxicant detection and biodegradation, and subsequent suicide in chronological order without exogenous inducers is constructed. Salicylic acid, a typical pollutant in industrial wastewater, is selected as an example to demonstrate this design. Biosensors are optimized by regulating the expression of receptors and reporters to get 2-fold sensitivity and 6-fold maximum output. Several stationary phase promoters are compared, and promoter Pfic is chosen to express the degradation enzyme. Two concepts for suicide circuits are developed, with the toxin/antitoxin circuit showing potent lethality. The three modules are coupled in a stepwise manner. Detection and biodegradation, and suicide are sequentially completed with partial attenuation compared to pre-integration, except for biodegradation, being improved by the replacements of ribosome binding site. Finally, a long-term stability test reveals that the engineered strain maintained its function for ten generations. The study provides a novel concept for integrating and controlling functional modules that can accelerate the transition of synthetic biology from conceptual to practical applications.
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Affiliation(s)
- Huan Liu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Lige Zhang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Weiwei Wang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Haiyang Hu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
| | - Hongzhi Tang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiP. R. China
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24
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Song YL, He XL, Li Y, Wang M, Jiang M, Xu L, Yu X. Homogeneous detection of viral nucleic acid via selective recognition proximity ligation and signal amplification with T7 transcription and CRISPR/Cas12a system. Anal Chim Acta 2023; 1280:341881. [PMID: 37858564 DOI: 10.1016/j.aca.2023.341881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
The synthetic biology has employed the synthetic gene networks through engineering to construct various functions in biological systems. However, the use of gene circuits to create sensors for detecting low-abundance targets has been limited due to the lack of signal amplification strategies beyond direct output of detection signals. To address this issue, we introduce a novel method utilizing Selective Recognition Proximity Ligation and signal amplification with T7 Transcription and CRISPR/Cas12a system (SRPL-TraCs), which permits the incorporation of cell-free gene circuits with signal amplification and enables the construction of high-order cascade signal amplification strategy to detect biomarkers in homogeneous systems. Specifically, the SRPL-TraCs utilizes selective recognition proximity ligation with high-fidelity T4 DNA ligase and generates a unique crRNA via T7 transcription, along with target-activated Cas12a/crRNA system to achieve excellent specificity for HIV-1 DNA. With this straightforward synthetic biology-based method, the proposed SRPL-TraCs has the potential to detect numerous other interesting targets beyond the nucleic acids.
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Affiliation(s)
- Yong-Li Song
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiang-Lan He
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yong Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ming Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Xu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
| | - Xu Yu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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25
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Franco RAL, Brenner G, Zocca VFB, de Paiva GB, Lima RN, Rech EL, Amaral DT, Lins MRCR, Pedrolli DB. Signal Amplification for Cell-Free Biosensors, an Analog-to-Digital Converter. ACS Synth Biol 2023; 12:2819-2826. [PMID: 37792474 DOI: 10.1021/acssynbio.3c00227] [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: 10/06/2023]
Abstract
Toehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been successfully engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and SARS-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficiently contained leakage, boosted the expression fold change from OFF to ON, and decreased the detection limit of the switches by 3-4 orders of magnitude. Ultimately, the integrase circuit converted the analog switches' signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer.
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Affiliation(s)
- Rafael A L Franco
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Gabriel Brenner
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Vitória F B Zocca
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Gabriela B de Paiva
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Rayane N Lima
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology - Synthetic Biology, 70770-917 Brasília, Brazil
| | - Elibio L Rech
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology - Synthetic Biology, 70770-917 Brasília, Brazil
| | - Danilo T Amaral
- Federal University of ABC (UFABC), Center for Natural and Human Sciences, Campus Santo André, Avenida dos Estados 5001, 09210-580 Santo André, Brazil
| | - Milca R C R Lins
- Federal University of ABC (UFABC), Center for Natural and Human Sciences, Campus Santo André, Avenida dos Estados 5001, 09210-580 Santo André, Brazil
| | - Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
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26
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Wei K, He M, Zhang J, Zhao C, Nie C, Zhang T, Liu Y, Chen T, Jiang J, Chu X. A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo. Angew Chem Int Ed Engl 2023; 62:e202307025. [PMID: 37615278 DOI: 10.1002/anie.202307025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.
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Affiliation(s)
- Kaiji Wei
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Chuan Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tong Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yi Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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27
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Zhang C, Li Z, Liu J, Liu C, Zhang H, Lee WG, Yao C, Guo H, Xu F. Synthetic Gene Circuit-Based Assay with Multilevel Switch Enables Background-Free and Absolute Quantification of Circulating Tumor DNA. RESEARCH (WASHINGTON, D.C.) 2023; 6:0217. [PMID: 37789988 PMCID: PMC10543738 DOI: 10.34133/research.0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023]
Abstract
Circulating tumor DNA (ctDNA) detection has found widespread applications in tumor diagnostics and treatment, where the key is to obtain accurate quantification of ctDNA. However, this remains challenging due to the issue of background noise associated with existing assays. In this work, we developed a synthetic gene circuit-based assay with multilevel switch (termed CATCH) for background-free and absolute quantification of ctDNA. The multilevel switch combining a small transcription activating RNA and a toehold switch was designed to simultaneously regulate transcription and translation processes in gene circuit to eliminate background noise. Moreover, such a multilevel switch-based gene circuit was integrated with a Cas9 nickase H840A (Cas9n) recognizer and a molecular beacon reporter to form CATCH for ctDNA detection. The CATCH can be implemented in one-pot reaction at 35 °C with virtually no background noise, and achieve robust absolute quantification of ctDNA when integrated with a digital chip (i.e., digital CATCH). Finally, we validated the clinical capability of CATCH by detecting drug-resistant ctDNA mutations from the plasma of 76 non-small cell lung cancer (NSCLC) patients, showing satisfying clinical sensitivity and specificity. We envision that the simple and robust CATCH would be a powerful tool for next-generation ctDNA detection.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
- TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China
| | - Jie Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Won Gu Lee
- Department of Mechanical Engineering,
Kyung Hee University, Yongin 17104, Republic of Korea
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital,
Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
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28
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Yuan J, Zhao K, Tan X, Xue R, Zeng Y, Ratti C, Trivedi P. Perspective on the development of synthetic microbial community (SynCom) biosensors. Trends Biotechnol 2023; 41:1227-1236. [PMID: 37183053 DOI: 10.1016/j.tibtech.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Synthetic microbial community (SynCom) biosensors are a promising technology for detecting and responding to environmental cues and target molecules. SynCom biosensors use engineered microorganisms to create a more complex and diverse sensing system, enabling them to respond to stimuli with enhanced sensitivity and accuracy. Here, we give a definition of SynCom biosensors, outline their construction workflow, and discuss current biosensing technology. We also highlight the challenges and future for developing and optimizing SynCom biosensors and the potential applications in agriculture and food management, biotherapeutic development, home sensing, urban and environmental monitoring, and the One Health foundation. We believe SynCom biosensors could be used in a real-time and remote-controlled manner to sense the chaos of constantly dynamic environments.
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Affiliation(s)
- Jing Yuan
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA; Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Ran Xue
- Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
| | - Carlo Ratti
- Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA
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29
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Peng R, Ba F, Li J, Cao J, Zhang R, Liu WQ, Ren J, Liu Y, Li J, Ling S. Embedding Living Cells with a Mechanically Reinforced and Functionally Programmable Hydrogel Fiber Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305583. [PMID: 37498452 DOI: 10.1002/adma.202305583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 07/28/2023]
Abstract
Living materials represent a new frontier in functional material design, integrating synthetic biology tools to endow materials with programmable, dynamic, and life-like characteristics. However, a major challenge in creating living materials is balancing the tradeoff between structural stability, mechanical performance, and functional programmability. To address this challenge, a sheath-core living hydrogel fiber platform that synergistically integrates living bacteria with hydrogel fibers to achieve both functional diversity and structural and mechanical robustness is proposed. In the design, microfluidic spinning is used to produce hydrogel fiber, which offers advantages in both structural and functional designability due to their hierarchical porous architectures that can be tailored and their mechanical performance that can be enhanced through a variety of post-processing approaches. By introducing living bacteria, the platform is endowed with programmable functionality and life-like capabilities. This work reconstructs the genetic circuits of living bacteria to express chromoproteins and fluorescent proteins as two prototypes that enable the coloration of living fibers and sensing water pollutants by monitoring the amount of fluorescent protein expressed. Altogether, this study establishes a structure-property-function optimized living hydrogel fiber platform, providing a new tool for accelerating the practical applications of the emerging living material systems.
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Affiliation(s)
- Ruoxuan Peng
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jiayi Cao
- College of Fashion and Design, Donghua University, 1882 West Yan'an Road, Shanghai, 200051, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Jing Ren
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
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30
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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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Li J, Yang C, Zhang L, Li C, Xie S, Fu T, Zhang Z, Li L, Qi L, Lyu Y, Chen F, He L, Tan W. Phase Separation of DNA-Encoded Artificial Cells Boosts Signal Amplification for Biosensing. Angew Chem Int Ed Engl 2023; 62:e202306691. [PMID: 37455257 DOI: 10.1002/anie.202306691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Life-like hierarchical architecture shows great potential for advancing intelligent biosensing, but modular expansion of its sensitivity and functionality remains a challenge. Drawing inspiration from intracellular liquid-liquid phase separation, we discovered that a DNA-encoded artificial cell with a liquid core (LAC) can enhance peroxidase-like activity of Hemin and its DNA G-quadruplex aptamer complex (DGAH) without substrate-selectivity, unlike its gelled core (GAC) counterpart. The LAC is easily engineered as an ultrasensitive biosensing system, benefiting from DNA's high programmability and unique signal amplification capability mediated by liquid-liquid phase separation. As proof of concept, its versatility was successfully demonstrated by coupling with two molecular recognition elements to monitor tumor-related microRNA and profile cancer cell phenotypes. This scalable design philosophy offers new insights into the design of next generation of artificial cells-based biosensors.
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Affiliation(s)
- Juncai Li
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Cai Yang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Lizhuan Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Chunying Li
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Sitao Xie
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ziwen Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Longjie Li
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lubin Qi
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Lei He
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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Ge ZB, Chen MM, Xie WY, Huang K, Zhao FJ, Wang P. Natural Microbial Reactor-Based Sensing Platform for Highly Sensitive Detection of Inorganic Arsenic in Rice Grains. Anal Chem 2023; 95:11467-11474. [PMID: 37462477 DOI: 10.1021/acs.analchem.3c01857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Rice is a major dietary source of inorganic arsenic (iAs), a highly toxic arsenical that accumulates in rice and poses health risks to rice-based populations. However, the availability of detection methods for iAs in rice grains is limited. In this study, we developed a novel approach utilizing a natural bacterial biosensor, Escherichia coli AW3110 (pBB-ArarsR-mCherry), in conjunction with amylase hydrolysis for efficient extraction, enabling high-throughput and quantitative detection of iAs in rice grains. The biosensor exhibits high specificity for arsenic and distinguishes between arsenite [As(III)] and arsenate [As(V)] by modulating the concentration of PO43- in the detection system. We determined the iAs concentrations in 19 rice grain samples with varying total As concentrations and compared our method with the standard technique of microwave digestion coupled with HPLC-ICP-MS. Both methods exhibited comparable results, without no significant bias in the concentrations of As(III) and As(V). The whole-cell biosensor demonstrated excellent reproducibility and a high signal-to-noise ratio, achieving a limit of detection of 16 μg kg-1 [As(III)] and 29 μg kg-1 [As(V)]. These values are considerably lower than the maximum allowable level (100 μg kg-1) for infant rice supplements established by the European Union. Our straightforward sensing strategy presents a promising tool for detecting iAs in other food samples.
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Affiliation(s)
- Zhan-Biao Ge
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming-Ming Chen
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Wan-Ying Xie
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Zhi R, Cheng N, Li G, Deng Y. Biosensor-based high-throughput screening enabled efficient adipic acid production. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12669-z. [PMID: 37421473 DOI: 10.1007/s00253-023-12669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
Adipic acid is an industrially important chemical, but the current approach to synthesize it can be of serious pollution to the environment. Rencently, bio-based production of adipic acid has significantly advanced with the development of metabolic engineering and synthetic biology. However, genetic heterogeneity-caused decrease of product titer has largely limited the industrialization of chemicals like adipic acid. Therefore, in the attempt to overcome this challenge, we constitutively expressed the reverse adipate degradation pathway, designed and optimized an adipic acid biosensor, and established a high-throughput screening platform to screen for high-performance strains based on the optimized biosensor. Using this platform, we successfully screened a strain with an adipic acid titer of 188.08 mg·L-1. Coupling the screening platform with fermentation optimization, the titer of adipic acid reached 531.88 mg·L-1 under shake flask fermentation, which achieved an 18.78-fold improvement comparing to the initial strain. Scale-up fermentation in a 5-L fermenter utilizing the screened high-performance strain was eventually conducted, in which the adipic acid titer reached 3.62 g·L-1. Overall, strategies developed in this study proved to be a potentially efficient method in reducing the genetic heterogeneity and was expected to provide guidance in helping to build a more efficient industrial screening process. KEY POINTS: • Developed a fine-tuned adipic acid biosensor. • Established a high-throughput screening platform to screen high-performance strains. • The titer of adipic acid reached 3.62 g·L-1 in a 5-L fermenter.
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Affiliation(s)
- Rui Zhi
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Cheng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Guohui Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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Wang X, Zhou N, Wang B. Bacterial synthetic biology: tools for novel drug discovery. Expert Opin Drug Discov 2023; 18:1087-1097. [PMID: 37482696 DOI: 10.1080/17460441.2023.2239704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
INTRODUCTION Bacterial synthetic biology has provided powerful tools to revolutionize the drug discovery process. These tools can be harnessed to generate bacterial novel pharmaceutical compounds with enhanced bioactivity and selectivity or to create genetically modified microorganisms as living drugs. AREAS COVERED This review provides a current overview of the state-of-the-art in bacterial synthetic biology tools for novel drug discovery. The authors discuss the application of these tools including bioinformatic tools, CRISPR tools, engineered bacterial transcriptional regulators, and synthetic biosensors for novel drug discovery. Additionally, the authors present the recent progress on reprogramming bacteriophages as living drugs to fight against antibiotic-resistant pathogens. EXPERT OPINION The field of using bacterial synthetic biology tools for drug discovery is rapidly advancing. However, challenges remain in developing reliable and robust methods to engineer bacteria. Further advancements in synthetic biology hold promise to speed up drug discovery, facilitating the development of novel therapeutics against various diseases.
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Affiliation(s)
- Xiyan Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Nan Zhou
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, China
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Li W, Xu Y, Zhang Y, Li P, Zhu X, Feng C. Cell-Free Biosensing Genetic Circuit Coupled with Ribozyme Cleavage Reaction for Rapid and Sensitive Detection of Small Molecules. ACS Synth Biol 2023; 12:1657-1666. [PMID: 37196142 DOI: 10.1021/acssynbio.3c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Synthetic biological systems have been utilized to develop a wide range of genetic circuits and components that enhance the performance of biosensing systems. Among them, cell-free systems are emerging as important platforms for synthetic biology applications. Genetic circuits play an essential role in cell-free systems, mainly consisting of sensing modules, regulation modules, and signal output modules. Currently, fluorescent proteins and aptamers are commonly used as signal outputs. However, these signal output modes cannot simultaneously achieve faster signal output, more accurate and reliable performance, and signal amplification. Ribozyme is a highly structured and catalytic RNA molecule that can specifically recognize and cut specific substrate sequences. Here, by adopting ribozyme as the signal output, we developed a cell-free biosensing genetic circuit coupled with the ribozyme cleavage reaction, enabling rapid and sensitive detection of small molecules. More importantly, we have also successfully constructed a 3D-printed sensor array and thereby achieved high-throughput analysis of an inhibitory drug. Furthermore, our method will help expand the application range of ribozyme in the field of synthetic biology and also optimize the signal output system of cell-free biosensing, thus promoting the development of cell-free synthetic biology in biomedical research, clinical diagnosis, environmental monitoring, and food inspection.
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Affiliation(s)
- Wenxing Li
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yiming Xu
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yue Zhang
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Pengfei Li
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
- Shaoxing Institute of Shanghai University, Shaoxing 312071, 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
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Zhou X, Zhang X, Peng Y, Douka AI, You F, Yao J, Jiang X, Hu R, Yang H. Electroactive Microorganisms in Advanced Energy Technologies. Molecules 2023; 28:molecules28114372. [PMID: 37298848 DOI: 10.3390/molecules28114372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Large-scale production of green and pollution-free materials is crucial for deploying sustainable clean energy. Currently, the fabrication of traditional energy materials involves complex technological conditions and high costs, which significantly limits their broad application in the industry. Microorganisms involved in energy production have the advantages of inexpensive production and safe process and can minimize the problem of chemical reagents in environmental pollution. This paper reviews the mechanisms of electron transport, redox, metabolism, structure, and composition of electroactive microorganisms in synthesizing energy materials. It then discusses and summarizes the applications of microbial energy materials in electrocatalytic systems, sensors, and power generation devices. Lastly, the research progress and existing challenges for electroactive microorganisms in the energy and environment sectors described herein provide a theoretical basis for exploring the future application of electroactive microorganisms in energy materials.
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Affiliation(s)
- Xingchen Zhou
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Xianzheng Zhang
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Yujie Peng
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Abdoulkader Ibro Douka
- State Key Laboratory of Fine Chemicals, Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
| | - Feng You
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Junlong Yao
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Xueliang Jiang
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
| | - Ruofei Hu
- Department of Food Science and Chemical Engineering, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Huan Yang
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Wuhan Institute of Technology, No. 206 Guanggu 1st Road, Wuhan 430205, China
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He Z, Shen J, Li Q, Yang Y, Zhang D, Pan X. Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162148. [PMID: 36758696 DOI: 10.1016/j.scitotenv.2023.162148] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jiaquan Shen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qunqun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yingli Yang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China.
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Chen S, Chen X, Su H, Guo M, Liu H. Advances in Synthetic-Biology-Based Whole-Cell Biosensors: Principles, Genetic Modules, and Applications in Food Safety. Int J Mol Sci 2023; 24:ijms24097989. [PMID: 37175695 PMCID: PMC10178329 DOI: 10.3390/ijms24097989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
A whole-cell biosensor based on synthetic biology provides a promising new method for the on-site detection of food contaminants. The basic components of whole-cell biosensors include the sensing elements, such as transcription factors and riboswitches, and reporting elements, such as fluorescence, gas, etc. The sensing and reporting elements are coupled through gene expression regulation to form a simple gene circuit for the detection of target substances. Additionally, a more complex gene circuit can involve other functional elements or modules such as signal amplification, multiple detection, and delay reporting. With the help of synthetic biology, whole-cell biosensors are becoming more versatile and integrated, that is, integrating pre-detection sample processing, detection processes, and post-detection signal calculation and storage processes into cells. Due to the relative stability of the intracellular environment, whole-cell biosensors are highly resistant to interference without the need of complex sample preprocessing. Due to the reproduction of chassis cells, whole-cell biosensors replicate all elements automatically without the need for purification processing. Therefore, whole-cell biosensors are easy to operate and simple to produce. Based on the above advantages, whole-cell biosensors are more suitable for on-site detection than other rapid detection methods. Whole-cell biosensors have been applied in various forms such as test strips and kits, with the latest reported forms being wearable devices such as masks, hand rings, and clothing. This paper examines the composition, construction methods, and types of the fundamental components of synthetic biological whole-cell biosensors. We also introduce the prospect and development trend of whole-cell biosensors in commercial applications.
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Affiliation(s)
- Shijing Chen
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiaolin Chen
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongfei Su
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Mingzhang Guo
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Huilin Liu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
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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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Ghataora JS, Gebhard S, Reeksting BJ. Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis. ACS Synth Biol 2023; 12:735-749. [PMID: 36629785 PMCID: PMC10028694 DOI: 10.1021/acssynbio.2c00545] [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: 01/12/2023]
Abstract
Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.
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Affiliation(s)
- Jasdeep S Ghataora
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Susanne Gebhard
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Bianca J Reeksting
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Chen D, Xu S, Li S, Tao S, Li L, Chen S, Wu L. Directly Evolved AlkS-Based Biosensor Platform for Monitoring and High-Throughput Screening of Alkane Production. ACS Synth Biol 2023; 12:832-841. [PMID: 36779413 DOI: 10.1021/acssynbio.2c00620] [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: 02/14/2023]
Abstract
Biosynthetic alkane using acyl-ACP aldehyde reductase (AAR) and aldehyde-deformylating oxygenase (ADO) from cyanobacteria is considered a promising alternative for the production of biofuels and chemical feedstocks. However, the lack of suitable screening methods to improve the catalytic efficiency of AAR and ADO has hindered further improvements in alkane production. Herein, a novel alkane biosensor was developed based on transcriptional factor AlkS by directed evolution, which shows sensitive dynamic response curves for exogenous long-chain alkanes as well as in situ monitoring of endogenously produced alkanes. The evolved biosensor enables high-throughput screening of alkane-producing strains from the AAR and ADO mutant library, which led to a 13-fold increase in the production of long-chain alkanes, including a 22-fold increase of C15. This study is the first to improve the alkane production through biosensors, which provides a good reference for the establishment of microbial cell factories for alkane production.
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Affiliation(s)
- Dongdong Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shunlan Li
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shipin Tao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Luzhi Li
- School of Biology, Food and Environment, Hefei University, Hefei 230041, China
| | - Shaopeng Chen
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lijun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
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43
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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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44
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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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45
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Kieffer C, Genot AJ, Rondelez Y, Gines G. Molecular Computation for Molecular Classification. Adv Biol (Weinh) 2023; 7:e2200203. [PMID: 36709492 DOI: 10.1002/adbi.202200203] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 01/30/2023]
Abstract
DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal-processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low-cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high-tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, IRL 2820, University of Tokyo, Tokyo, 153-8505, Japan
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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46
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [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: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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Huan YW, Brown R, Wang B. An adenine/thymidine-rich region is integral to RepL-mediated DNA replication. Front Microbiol 2023; 14:1095671. [PMID: 36846746 PMCID: PMC9948254 DOI: 10.3389/fmicb.2023.1095671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
The lytic replication of bacteriophage P1 requires RepL expression and the lytic stage origin, oriL, which is postulated to be located within repL gene sequence. The exact sequence of P1 oriL and the mechanism(s) of RepL-mediated DNA replication, however, are not fully understood. By using repL gene expression to induce DNA replication of a gfp and a rfp reporter plasmids, we demonstrated that synonymous base substitution in an adenine/thymidine-rich region of repL gene sequence, termed AT2, significantly inhibited the RepL-mediated signal amplification. Contrastingly, mutations in an IHF and two DnaA binding sites did not affect the RepL-mediated signal amplification significantly. A truncated repL sequence with the AT2 region allowed RepL-mediated signal amplification in trans therefore verifying a significant role of the AT2 region in RepL-mediated DNA replication. A combination of repL gene expression and a non-protein-coding copy of repL gene sequence (termed nc-repL) was able to amplify the output of an arsenic biosensor. Furthermore, mutation(s) at single or multiple positions within the AT2 region produced varying levels of RepL-mediated signal amplification. Overall, our results provide novel insights into the identity and location of P1 oriL as well as demonstrating the potential of using repL constructs to amplify and modulate the output of genetic biosensors.
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Affiliation(s)
- Yang Wei Huan
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Russell Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Research Center for Biological Computation, Zhejiang Laboratory, Hangzhou, China
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48
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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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49
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Van Raad D, Huber T. eCell Technology for Cell-Free Protein Synthesis, Biosensing, and Remediation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:129-146. [PMID: 37306701 DOI: 10.1007/10_2023_225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The eCell technology is a recently introduced, specialized protein production platform with uses in a multitude of biotechnological applications. This chapter summarizes the use of eCell technology in four selected application areas. Firstly, for detecting heavy metal ions, specifically mercury, in an in vitro protein expression system. Results show improved sensitivity and lower limit of detection compared to comparable in vivo systems. Secondly, eCells are semipermeable, stable, and can be stored for extended periods of time, making them a portable and accessible technology for bioremediation of toxicants in extreme environments. Thirdly and fourthly, applications of eCell technology are shown to facilitate expression of correctly folded disulfide-rich proteins and incorporate chemically interesting derivatives of amino acids into proteins which are toxic to in vivo protein expression. Overall, eCell technology presents a cost-effective and efficient method for biosensing, bioremediation, and protein production.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
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50
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Usai F, Loi G, Scocozza F, Bellato M, Castagliuolo I, Conti M, Pasotti L. Design and biofabrication of bacterial living materials with robust and multiplexed biosensing capabilities. Mater Today Bio 2022; 18:100526. [PMID: 36632629 PMCID: PMC9826803 DOI: 10.1016/j.mtbio.2022.100526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The intertwined adoption of synthetic biology and 3D bioprinting has the potential to improve different application fields by fabricating engineered living materials (ELMs) with unnatural genetically-encoded sense & response capabilities. However, efforts are still needed to streamline the fabrication of sensing ELMs compatible with field use and improving their functional complexity. To investigate these two unmet needs, we adopted a workflow to reproducibly construct bacterial ELMs with synthetic biosensing circuits that provide red pigmentation as visible readout in response to different proof-of-concept chemical inducers. We first fabricated single-input/single-output ELMs and we demonstrated their robust performance in terms of longevity (cell viability and evolutionary stability >15 days, and long-term storage >1 month), sensing in harsh, non-sterile or nutrient-free conditions compatible with field use (soil, water, and clinical samples, including real samples from Pseudomonas aeruginosa infected patients). Then, we fabricated ELMs including multiple spatially-separated biosensor strains to engineer: level-bar materials detecting molecule concentration ranges, multi-input/multi-output devices with multiplexed sensing and information processing capabilities, and materials with cell-cell communication enabling on-demand pattern formation. Overall, we showed successful field use and multiplexed functioning of reproducibly fabricated ELMs, paving the way to a future automation of the prototyping process and boosting applications of such devices as in-situ monitoring tools or easy-to-use sensing kits.
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Affiliation(s)
- Francesca Usai
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Giada Loi
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Franca Scocozza
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Massimo Bellato
- Department of Information Engineering, University of Padua, Via Gradenigo 6b, 35131 Padua, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Michele Conti
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy,Corresponding author.
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy,Corresponding author.
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