1
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Cole J, Schulman R. Limiting the Broadcast Range of a Secreting Cell during Intercellular Signaling Using Protease-Mediated Degradation. ACS Synth Biol 2024; 13:2019-2028. [PMID: 38885472 DOI: 10.1021/acssynbio.4c00042] [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: 06/20/2024]
Abstract
Synthetic biology is revolutionizing our approaches to biocomputing, diagnostics, and environmental monitoring through the use of designed genetic circuits that perform a function within a single cell. More complex functions can be performed by multiple cells that coordinate as they perform different subtasks. Cell-cell communication using molecular signals is particularly suited for aiding in this communication, but the number of molecules that can be used in different communication channels is limited. Here we investigate how proteases can limit the broadcast range of communicating cells. We find that adding barrierpepsin to Saccharomyces cerevisiae cells in two-dimensional multicellular networks that use α-factor signaling prevents cells beyond a specific radius from responding to α-factor signals. Such limiting of the broadcast range of cells could allow multiple cells to use the same signaling molecules to direct different communication processes and functions, provided that they are far enough from one another. These results suggest a means by which complex synthetic cellular networks using only a few signals for communication could be created by structuring a community of cells to create distinct broadcast environments.
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Affiliation(s)
- Joshua Cole
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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2
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Gautam P, Sinha SK. The Blueprint of Logical Decisions in a NF-κB Signaling System. ACS OMEGA 2024; 9:22625-22634. [PMID: 38826544 PMCID: PMC11137707 DOI: 10.1021/acsomega.4c00049] [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: 01/02/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/04/2024]
Abstract
Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between phenotype diversity and the architecture of regulatory circuits is crucial since it determines the state of a biological cell. Here, we theoretically analyze how the circuit blueprints of NF-κB in cellular environments are formed and their role in determining the cells' metabolic state. The NF-κB is a collective name for a developmental conserved family of five different transcription factors that can form homodimers or heterodimers and often promote DNA looping to reprogram the inflammatory gene response. The NF-κB controls many biological functions, including cellular differentiation, proliferation, migration, and survival. Our model shows that nuclear localization of NF-κB differentially promotes logic operations such as AND, NAND, NOR, and OR in its regulatory network. Through the quantitative thermodynamic model of transcriptional regulation and systematic variation of promoter-enhancer interaction modes, we can account for the origin of various logic gates as formed in the NF-κB system. We further show that the interconversion or switching of logic gates yielded under systematic variations of the stimuli activity and DNA looping parameters. Such computation occurs in regulatory and signaling pathways in individual cells at a molecular scale, which one can exploit to design a biomolecular computer.
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Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Sudipta Kumar Sinha
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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3
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Kashiwagi FM, Wendler Miranda B, Maltempi de Souza E, Müller-Santos M. The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose. Synth Biol (Oxf) 2024; 9:ysae001. [PMID: 38249314 PMCID: PMC10799723 DOI: 10.1093/synbio/ysae001] [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: 07/10/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The FdeR regulator has been reported as a transcriptional activator dependent on the interaction with naringenin. Previously, FdeR and its cognate promoter were used to construct naringenin-sensitive sensors, though no correlation was associated between the FdeR level of expression and outputs. Therefore, to understand this correlation, we constructed a circuit with FdeR expression adjusted by the arabinose concentration through an AraC-PBAD system and the FdeR-regulated promoter controlling the expression of GFP. We observed a significant reduction in the activity of the target promoter by increasing FdeR expression, indicating that although FdeR has been primarily classified as a transcriptional activator, it also represses transcription. Leveraging the bifunctional feature of FdeR, acting as both transcriptional activator and repressor, we demonstrated that this genetic circuit, when previously switched on by naringenin, can be switched off by inducing an increased FdeR expression level. This engineered system functioned as a NIMPLY gate, effectively decreasing GFP expression by 50% when arabinose was added without removing naringenin from the medium. Exploiting FdeR versatility, this study demonstrates an innovative application of this transcriptional factor for developing novel NIMPLY gates activated by a molecule with low toxicity and nutraceutical properties that may be important for several applications. Graphical Abstract.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
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4
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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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5
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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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6
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Hui CY, Ma BC, Wang YQ, Yang XQ, Cai JM. Designed bacteria based on natural pbr operons for detecting and detoxifying environmental lead: A mini-review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115662. [PMID: 37939554 DOI: 10.1016/j.ecoenv.2023.115662] [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: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023]
Abstract
Lead (Pb), a naturally occurring element, is redistributed in the environment mainly due to anthropogenic activities. Pb pollution is a crucial public health problem worldwide due to its adverse effects. Environmental bacteria have evolved various protective mechanisms against high levels of Pb. The pbr operon, first identified in Cupriavidus metallidurans CH34, encodes a unique Pb(II) resistance mechanism involving transport, efflux, sequestration, biomineralization, and precipitation. Similar pbr operons are gradually found in diverse bacterial strains. This review focuses on the pbr-encoded Pb(II) resistance system. It summarizes various whole-cell biosensors harboring artificially designed pbr operons for Pb(II) biomonitoring with fluorescent, luminescent, and colorimetric signal output. Optimization of genetic circuits, employment of pigment-based reporters, and screening of host cells are promising in improving the sensitivity, selectivity, and response range of whole-cell biosensors. Engineered bacteria displaying Pb(II) binding and sequestration proteins, including PbrR and its derivatives, PbrR2 and PbrD, for adsorption are involved. Although synthetic bacteria show great potential in determining and removing Pb at the nanomolar level for environmental protection and food safety, some challenges must be addressed to meet demanding application requirements.
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Affiliation(s)
- Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China.
| | - Bing-Chan Ma
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China; School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yong-Qiang Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Xue-Qin Yang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Jin-Min Cai
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
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7
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Zhu DL, Guo Y, Ma BC, Lin YQ, Wang HJ, Gao CX, Liu MQ, Zhang NX, Luo H, Hui CY. Pb(II)-inducible proviolacein biosynthesis enables a dual-color biosensor toward environmental lead. Front Microbiol 2023; 14:1218933. [PMID: 37577420 PMCID: PMC10413148 DOI: 10.3389/fmicb.2023.1218933] [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: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
With the rapid development of synthetic biology, various whole-cell biosensors have been designed as valuable biological devices for the selective and sensitive detection of toxic heavy metals in environmental water. However, most proposed biosensors are based on fluorescent and bioluminescent signals invisible to the naked eye. The development of visible pigment-based biosensors can address this issue. The pbr operon from Klebsiella pneumoniae is selectively induced by bioavailable Pb(II). In the present study, the proviolacein biosynthetic gene cluster was transcriptionally fused to the pbr Pb(II) responsive element and introduced into Escherichia coli. The resultant biosensor responded to Pb(II) in a time- and dose-dependent manner. After a 5-h incubation with Pb(II), the brown pigment was produced, which could be extracted into n-butanol. Extra hydrogen peroxide treatment during n-butanol extract resulted in the generation of a stable green pigment. An increased brown signal was observed upon exposure to lead concentrations above 2.93 nM, and a linear regression was fitted from 2.93 to 3,000 nM. Extra oxidation significantly decreased the difference between parallel groups. The green signal responded to as low as 0.183 nM Pb(II), and a non-linear regression was fitted in a wide concentration range from 0.183 to 3,000 nM. The specific response toward Pb(II) was not interfered with by various metals except for Cd(II) and Hg(II). The PV-based biosensor was validated in monitoring bioaccessible Pb(II) spiked into environmental water. The complex matrices did not influence the regression relationship between spiked Pb(II) and the dual-color signals. Direct reading with the naked eye and colorimetric quantification enable the PV-based biosensor to be a dual-color and low-cost bioindicator for pollutant heavy metal.
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Affiliation(s)
- De-long Zhu
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Bing-chan Ma
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong-qin Lin
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hai-jun Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Chao-xian Gao
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Ming-qi Liu
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Nai-xing Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hao Luo
- School of Public Health, Guangdong Medical University, Dongguan, China
| | - Chang-ye Hui
- School of Public Health, Guangdong Medical University, Dongguan, China
- Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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8
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Ferreira SS, Anderson CE, Antunes MS. A logical way to reprogram plants. Biochem Biophys Res Commun 2023; 654:80-86. [PMID: 36898227 DOI: 10.1016/j.bbrc.2023.02.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Living cells constantly monitor their external and internal environments for changing conditions, stresses or developmental cues. Networks of genetically encoded components sense and process these signals following pre-defined rules in such a way that specific combinations of the presence or absence of certain signals activate suitable responses. Many biological signal integration mechanisms approximate Boolean logic operations, whereby presence or absence of signals are computed as variables with values described as either true or false, respectively. Boolean logic gates are commonly used in algebra and in computer sciences, and have long been recognized as useful information processing devices in electronic circuits. In these circuits, logic gates integrate multiple input values and produce an output signal according to pre-defined Boolean logic operations. Recent implementation of these logic operations using genetic components to process information in living cells has allowed genetic circuits to enable novel traits with decision-making capabilities. Although several literature reports describe the design and use of these logic gates to introduce new functions in bacterial, yeast and mammalian cells, similar approaches in plants remain scarce, likely due to challenges posed by the complexity of plants and the lack of some technological advances, e.g., species-independent genetic transformation. In this mini review, we have surveyed recent reports describing synthetic genetic Boolean logic operators in plants and the different gate architectures used. We also briefly discuss the potential of deploying these genetic devices in plants to bring to fruition a new generation of resilient crops and improved biomanufacturing platforms.
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Affiliation(s)
- Savio S Ferreira
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA; BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
| | - Charles E Anderson
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA; BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
| | - Mauricio S Antunes
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA; BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
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9
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Sharon JA, Dasrath C, Fujiwara A, Snyder A, Blank M, O'Brien S, Aufdembrink LM, Engelhart AE, Adamala KP. Trumpet is an operating system for simple and robust cell-free biocomputing. Nat Commun 2023; 14:2257. [PMID: 37080970 PMCID: PMC10119096 DOI: 10.1038/s41467-023-37752-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
Biological computation is becoming a viable and fast-growing alternative to traditional electronic computing. Here we present a biocomputing technology called Trumpet: Transcriptional RNA Universal Multi-Purpose GatE PlaTform. Trumpet combines the simplicity and robustness of the simplest in vitro biocomputing methods, adding signal amplification and programmability, while avoiding common shortcomings of live cell-based biocomputing solutions. We have demonstrated the use of Trumpet to build all universal Boolean logic gates. We have also built a web-based platform for designing Trumpet gates and created a primitive processor by networking several gates as a proof-of-principle for future development. The Trumpet offers a change of paradigm in biocomputing, providing an efficient and easily programmable biological logic gate operating system.
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Affiliation(s)
- Judee A Sharon
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Chelsea Dasrath
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Aiden Fujiwara
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Alessandro Snyder
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Mace Blank
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Sam O'Brien
- Department of Computer Science, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Lauren M Aufdembrink
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Aaron E Engelhart
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cellular Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, MN, USA.
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10
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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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11
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Dong X, Qi S, Khan IM, Sun Y, Zhang Y, Wang Z. Advances in riboswitch-based biosensor as food samples detection tool. Compr Rev Food Sci Food Saf 2023; 22:451-472. [PMID: 36511082 DOI: 10.1111/1541-4337.13077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022]
Abstract
Food safety has always been a hot issue of social concern, and biosensing has been widely used in the field of food safety detection. Compared with traditional aptamer-based biosensors, aptamer-based riboswitch biosensing represents higher precision and programmability. A riboswitch is an elegant example of controlling gene expression, where the target is coupled to the aptamer domain, resulting in a conformational change in the downstream expression domain and determining the signal output. Riboswitch-based biosensing can be extensively applied to the portable real-time detection of food samples. The numerous key features of riboswitch-based biosensing emphasize their sustainability, renewable, and testing, which promises to transform engineering applications in the field of food safety. This review covers recent developments in riboswitch-based biosensors. The brief history, definition, and modular design (regulatory mode, reporter, and expression platform) of riboswitch-based biosensors are explained for better insight into the design and construction. We summarize recent advances in various riboswitch-based biosensors involving theophylline, malachite green, tetracycline, neomycin, fluoride, thrombin, naringenin, ciprofloxacin, and paromomycin, aiming to provide general guidance for the design of riboswitch-based biosensors. Finally, the challenges and prospects are also summarized as a way forward stratagem and signs of progress.
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Affiliation(s)
- Xiaoze Dong
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Shuo Qi
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yuhan Sun
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Collaborative innovation center of food safety and quality control in Jiangsu Province, Food, Jiangnan University, Wuxi, China
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12
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CRISPR/Cas9 in the era of nanomedicine and synthetic biology. Drug Discov Today 2023; 28:103375. [PMID: 36174966 DOI: 10.1016/j.drudis.2022.103375] [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: 06/19/2022] [Revised: 08/15/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
The CRISPR/Cas system was first discovered as a defense mechanism in bacteria and is now used as a tool for precise gene-editing applications. Rapidly evolving, it is increasingly applied in therapeutics. However, concerns about safety, specificity, and delivery still limit its potential. In this context, we introduce the concept of nanogenetics and speculate how the rational engineering of the CRISPR/Cas machinery could advance the biomedical field. In nanogenetics, the advantages of traditional approaches of synthetic biology could be expanded by nanotechnology approaches, enabling the design of a new generation of intrinsically safe and specific genome-editing platforms.
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13
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Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol 2023; 11:1178680. [PMID: 37122866 PMCID: PMC10133563 DOI: 10.3389/fbioe.2023.1178680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.
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Hui CY, Guo Y, Zhu DL, Li LM, Yi J, Zhang NX. Metabolic engineering of the violacein biosynthetic pathway toward a low-cost, minimal-equipment lead biosensor. Biosens Bioelectron 2022; 214:114531. [PMID: 35810697 DOI: 10.1016/j.bios.2022.114531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 02/07/2023]
Abstract
Metabolic engineered bacteria have been successfully employed to produce various natural colorants, which are expected to be used as the visually recognizable signals to develop mini-equipment biological devices for monitoring toxic heavy metals. The violacein biosynthetic pathway has been reconstructed in Escherichia coli (E. coli). Here the successful production of four violacein derivatives was achieved by integrating metabolic engineering and synthetic biology. Lead binding to the metalloregulator enables whole-cell colorimetric biosensors capable of assessing bioavailable lead. Deoxyviolacein-derived signal showed the most satisfied biosensing properties among prodeoxyviolacein (green), proviolacein (blue), deoxyviolacein (purple), and violacein (navy). The limit of detection (LOD) of pigment-based biosensors was 2.93 nM Pb(II), which is lower than that of graphite furnace atomic absorption spectrometry. Importantly, a good linear dose-response model in a wide dose range (2.93-6000 nM) was obtained in a non-cytotoxic deoxyviolacein-based biosensor, which was significantly better than cytotoxic violacein-based biosensor (2.93-750 nM). Among ten metal ions, only Cd(II) and Hg(II) exerted a slight influence on the response of the deoxyviolacein-based biosensor toward Pb(II). The deoxyviolacein-based biosensor was validated in detecting bioaccessible Pb(II) in environmental samples. Factors such as low cost and minimal-equipment requirement make this biosensor a suitable biological device for monitoring toxic lead in the environment.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - De-Long Zhu
- School of Public Health , Guangdong Medical University, Dongguan, 523808, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
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15
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A Recombinase-Based Genetic Circuit for Heavy Metal Monitoring. BIOSENSORS 2022; 12:bios12020122. [PMID: 35200383 PMCID: PMC8870050 DOI: 10.3390/bios12020122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Rapid progress in the genetic circuit design enabled whole-cell biosensors (WCBs) to become prominent in detecting an extensive range of analytes with promise in many fields, from medical diagnostics to environmental toxicity assessment. However, several drawbacks, such as high background signal or low precision, limit WCBs to transfer from proof-of-concept studies to real-world applications, particularly for heavy metal toxicity monitoring. For an alternative WCB module design, we utilized Bxb1 recombinase that provides tight control as a switch to increase dose-response behavior concerning leakiness. The modularity of Bxb1 recombinase recognition elements allowed us to combine an engineered semi-specific heat shock response (HSR) promoter, sensitive to stress conditions including toxic ions such as cadmium, with cadmium resistance regulatory elements; a cadmium-responsive transcription factor and its cognitive promoter. We optimized the conditions for the recombinase-based cadmium biosensor to obtain increased fold change and shorter response time. This system can be expanded for various heavy metals to make an all-in-one type of WCB, even using semi-specific parts of a sensing system.
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17
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Hui CY, Guo Y, Liu L, Yi J. Recent advances in bacterial biosensing and bioremediation of cadmium pollution: a mini-review. World J Microbiol Biotechnol 2021; 38:9. [PMID: 34850291 DOI: 10.1007/s11274-021-03198-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
Cadmium (Cd) pollution has become a global environmental issue because Cd gets easily accumulated and translocated in the food chain, threatening human health. Considering the detrimental effects and non-biodegradability of environmental Cd, this is an urgent issue that needs to be addressed through the development of robust, cost-effective, and eco-friendly green routes for monitoring and remediating toxic levels of Cd. This article attempts to review various bacterial approaches toward biosensing and bioremediation of Cd in the environment. This review focuses on the recent development of bacterial cell-based biosensors for the detection of bioavailable Cd and the bioremediation of toxic Cd by natural or genetically-engineered bacteria. The present limitations and future perspectives of these available bacterial approaches are outlined. New trends for integrating synthetic biology and metabolic engineering into the design of bacterial biosensors and bioadsorbers are additionally highlighted.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Pennsylvania, USA
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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18
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Wan X, Saltepe B, Yu L, Wang B. Programming living sensors for environment, health and biomanufacturing. Microb Biotechnol 2021; 14:2334-2342. [PMID: 33960658 PMCID: PMC8601174 DOI: 10.1111/1751-7915.13820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 01/10/2023] Open
Abstract
Synthetic biology offers new tools and capabilities of engineering cells with desired functions for example as new biosensing platforms leveraging engineered microbes. In the last two decades, bacterial cells have been programmed to sense and respond to various input cues for versatile purposes including environmental monitoring, disease diagnosis and adaptive biomanufacturing. Despite demonstrated proof-of-concept success in the laboratory, the real-world applications of microbial sensors have been restricted due to certain technical and societal limitations. Yet, most limitations can be addressed by new technological developments in synthetic biology such as circuit design, biocontainment and machine learning. Here, we summarize the latest advances in synthetic biology and discuss how they could accelerate the development, enhance the performance and address the present limitations of microbial sensors to facilitate their use in the field. We view that programmable living sensors are promising sensing platforms to achieve sustainable, affordable and easy-to-use on-site detection in diverse settings.
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Affiliation(s)
- Xinyi Wan
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Behide Saltepe
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
| | - Luyang Yu
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | - Baojun Wang
- Centre for Synthetic and Systems BiologySchool of Biological SciencesUniversity of EdinburghEdinburghEH9 3FFUK
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
- The Provincial International Science and Technology Cooperation Base for Engineering BiologyInternational CampusZhejiang UniversityHaining314400China
- College of Life SciencesZhejiang UniversityHangzhou310058China
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19
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Kashiwagi FM, Wendler Miranda B, de Oliveira Pedrosa F, de Souza EM, Müller-Santos M. Control of Gene Expression With Quercetin-Responsive Modular Circuits. Front Bioeng Biotechnol 2021; 9:730967. [PMID: 34604189 PMCID: PMC8481877 DOI: 10.3389/fbioe.2021.730967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.
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Affiliation(s)
- Fernanda Miyuki Kashiwagi
- Postgraduate Program in Science (Biochemistry), Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Brenno Wendler Miranda
- Biological Sciences Undergraduate Course, Department of Biochemistry and Molecular Biology, Nitrogen Fixation Laboratory, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Fabio de Oliveira Pedrosa
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Emanuel Maltempi de Souza
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Marcelo Müller-Santos
- Nitrogen Fixation Laboratory, Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, Brazil
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20
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Zeng N, Wu Y, Chen W, Huang Q, Cai P. Whole-Cell Microbial Bioreporter for Soil Contaminants Detection. Front Bioeng Biotechnol 2021; 9:622994. [PMID: 33708764 PMCID: PMC7940511 DOI: 10.3389/fbioe.2021.622994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Anthropogenic activities have released various contaminants into soil that pose a serious threat to the ecosystem and human well-being. Compared to conventional analytical methodologies, microbial cell-based bioreporters are offering a flexible, rapid, and cost-effective strategy to assess the environmental risks. This review aims to summarize the recent progress in the application of bioreporters in soil contamination detection and provide insight into the challenges and current strategies. The biosensing principles and genetic circuit engineering are introduced. Developments of bioreporters to detect and quantify heavy metal and organic contaminants in soil are reviewed. Moreover, future opportunities of whole-cell bioreporters for soil contamination monitoring are discussed.
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Affiliation(s)
- Ni Zeng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yichao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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21
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Recent advances in synthetic biology-enabled and natural whole-cell optical biosensing of heavy metals. Anal Bioanal Chem 2020; 413:73-82. [PMID: 32959111 DOI: 10.1007/s00216-020-02953-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
A large number of scientific works have been published on whole-cell heavy metal biosensing based on optical transduction. The advances in the application of biotechnological tools not only have continuously improved the sensitivity, selectivity, and detection range for biosensors but also have simultaneously unveiled new challenges and restrictions for further improvements. This review highlights selected aspects of whole-cell biosensing of heavy metals using optical transducers. We have focused on the progress in genetic modulation in regulatory and reporter modules of recombinant plasmids that has enabled improvement of biosensor performance. Simultaneously, an attempt has been made to present newer platforms such as microfluidics that have generated promising results and might give a new turn to the optical biosensing field.
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22
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Huang Y, Yang S, Chen W, Li F, Xia A, Ni L, Yang G, Jin F. A Synthetic Genetic Circuit Enables Precise Quantification of Direct Repeat Deletion in Bacteria. ACS Synth Biol 2020; 9:1041-1050. [PMID: 32298577 DOI: 10.1021/acssynbio.9b00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quantification of the rate of direct repeat deletion (DRD) is an important aspect in the research of DNA rearrangement. The widely used tetracycline selection method usually introduces antibiotic pressure to the tested organism, which may interfere with the DRD process. Also the length of repeat arm (LRA) is limited by the length of the TetR coding sequence. On the basis of the fluorescent microscopy and high-throughput imaging processing, here we developed a two-module genetic circuit, termed TFDEC (which stands for three-color fluorescence-based deletion event counter), to quantify the DRD rate under neutral conditions. DRD events were determined from the state of a three-state fluorescent logic gate constructed through coupling of an OR gate and an AND gate. TFDEC was applied in Pseudomonas aeruginosa, and we found that the DRD rate was RecA-dependent for long repeat arms (>500 bp) and RecA-independent for short repeat arms (<500 bp), which was consistent with the case in Escherichia coli. In addition, the increase of DRD rate followed an S-shaped curve with the increase of LRA, while treating cells with ciprofloxacin did not change the LRA-dependence of DRD. We also detected a significant increased DRD rate for long repeat arms in the uvrD (8-fold) and radA (4-fold) mutants. Our results show that the TFDEC method could be used as a complement tool for quantification of the DRD rate in the future.
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Affiliation(s)
- Yajia Huang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Shuai Yang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Wenhui Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Feixuan Li
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Aiguo Xia
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Lei Ni
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Guang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Fan Jin
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, P. R. China
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23
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Pinto F, Thornton EL, Wang B. An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nat Commun 2020; 11:1529. [PMID: 32251274 PMCID: PMC7090010 DOI: 10.1038/s41467-020-15272-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
Inteins are protein segments capable of joining adjacent residues via a peptide bond. In this process known as protein splicing, the intein itself is not present in the final sequence, thus achieving scarless peptide ligation. Here, we assess the splicing activity of 34 inteins (both uncharacterized and known) using a rapid split fluorescent reporter characterization platform, and establish a library of 15 mutually orthogonal split inteins for in vivo applications, 10 of which can be simultaneously used in vitro. We show that orthogonal split inteins can be coupled to multiple split transcription factors to implement complex logic circuits in living organisms, and that they can also be used for the in vitro seamless assembly of large repetitive proteins with biotechnological relevance. Our work demonstrates the versatility and vast potential of an expanded library of orthogonal split inteins for their use in the fields of synthetic biology and protein engineering.
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Affiliation(s)
- Filipe Pinto
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Ella Lucille Thornton
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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Liu K, Yang J, Ding S, Gao Y. Daisy Chain Topology Based Mammalian Synthetic Circuits for RNA-Only Delivery. ACS Synth Biol 2020; 9:269-282. [PMID: 31895544 DOI: 10.1021/acssynbio.9b00313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Owing to superior safety, the RNA-only delivery synthetic circuit is more suitable for cell-based medicine. Modules which possess matching inputs and outputs could be strung by daisy-chaining to compose RNA-only delivery synthetic gene circuits. In this study, we engineered well-characterized biological parts to construct composable modules, each of which could receive signals from the upstream module and transmit the processed signal to the next module using standard interfaces. Capsid-cNOT7, through which logic gates could be changed by merely changing the type of it, was used as the core element for logical process. Daisy chain topology was used to build RNA-only delivery mammalian synthetic circuits which possess validated functions such as fan out, protein sensing, drug sensing, light sensing, 2-input logic gate, 3-input logic gate, and volatile memory, providing a new method to simplify the design of RNA-only delivery synthetic circuits.
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Affiliation(s)
- Kaiyu Liu
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yi Gao
- Second Department of Hepatobiliary Surgery, Zhujiang Hospital, State Key Laboratory of Organ Failure Research, Co-Innovation Center for Organ Failure Research, Southern Medical University, Guangzhou, China
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25
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Hicks M, Bachmann TT, Wang B. Synthetic Biology Enables Programmable Cell-Based Biosensors. Chemphyschem 2020; 21:132-144. [PMID: 31585026 PMCID: PMC7004036 DOI: 10.1002/cphc.201900739] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/03/2019] [Indexed: 01/10/2023]
Abstract
Cell-based biosensors offer cheap, portable and simple methods of detecting molecules of interest but have yet to be truly adopted commercially. Issues with their performance and specificity initially slowed the development of cell-based biosensors. With the development of rational approaches to tune response curves, the performance of biosensors has rapidly improved and there are now many biosensors capable of sensing with the required performance. This has stimulated an increased interest in biosensors and their commercial potential. However the reliability, long term stability and biosecurity of these sensors are still barriers to commercial application and public acceptance. Research into overcoming these issues remains active. Here we present the state-of-the-art tools offered by synthetic biology to allow construction of cell-based biosensors with customisable performance to meet the real world requirements in terms of sensitivity and dynamic range and discuss the research progress to overcome the challenges in terms of the sensor stability and biosecurity fears.
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Affiliation(s)
- Maggie Hicks
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
| | - Till T. Bachmann
- Infection MedicineEdinburgh Medical School: Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Baojun Wang
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
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26
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Lopreside A, Wan X, Michelini E, Roda A, Wang B. Comprehensive Profiling of Diverse Genetic Reporters with Application to Whole-Cell and Cell-Free Biosensors. Anal Chem 2019; 91:15284-15292. [PMID: 31690077 PMCID: PMC6899433 DOI: 10.1021/acs.analchem.9b04444] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Whole-cell
and cell-free transcription-translation biosensors have
recently become favorable alternatives to conventional detection methods,
as they are cost-effective, environmental friendly, and easy to use.
Importantly, the biological responses from the biosensors need to
be converted into a physicochemical signal for easy detection, and
a variety of genetic reporters have been employed for this purpose.
Reporter gene selection is vital to a sensor performance and application
success. However, it was largely based on trial and error with very
few systematic side-by-side investigations reported. To address this
bottleneck, here we compared eight reporters from three reporter categories,
i.e., fluorescent (gfpmut3, deGFP, mCherry, mScarlet-I), colorimetric
(lacZ), and bioluminescent (luxCDABE from Aliivibrio fischeri and Photorhabdus
luminescens, NanoLuc) reporters, under the
control of two representative biosensors for mercury- and quorum-sensing
molecules. Both whole-cell and cell-free formats were investigated
to assess key sensing features including limit of detection (LOD),
input and output dynamic ranges, response time, and output visibility.
For both whole-cell biosensors, the lowest detectable concentration
of analytes and the fastest responses were achieved with NanoLuc.
Notably, we developed, to date, the most sensitive whole-cell mercury
biosensor using NanoLuc as reporter, with an LOD ≤ 50.0 fM
HgCl2 30 min postinduction. For cell-free biosensors, overall, NanoLuc and deGFP led to shorter response
time and lower LOD than the others. This comprehensive profile of
diverse reporters in a single setting provides a new important benchmark
for reporter selection, aiding the rapid development of whole-cell
and cell-free biosensors for various applications in the environment
and health.
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Affiliation(s)
- Antonia Lopreside
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
| | | | - Elisa Michelini
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
| | - Aldo Roda
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
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Chen S, Xu Z, Yang W, Lin X, Li J, Li J, Yang H. Logic-Gate-Actuated DNA-Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction. Angew Chem Int Ed Engl 2019; 58:18186-18190. [PMID: 31595614 DOI: 10.1002/anie.201908971] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/18/2019] [Indexed: 02/01/2023]
Abstract
Programming cells to sense multiple inputs and activate cellular signal transduction cascades is of great interest. Although this goal has been achieved through the engineering of genetic circuits using synthetic biology tools, a nongenetic and generic approach remains highly demanded. Herein, we present an aptamer-controlled logic receptor assembly for modulating cellular signal transduction. Aptamers were engineered as "robotic arms" to capture target receptors (c-Met and CD71) and a DNA logic assembly functioned as a computer processor to handle multiple inputs. As a result, the DNA assembly brings c-Met and CD71 into close proximity, thus interfering with the ligand-receptor interactions of c-Met and inhibiting its functions. Using this principle, a set of logic gates was created that respond to DNA strands or light irradiation, modulating the c-Met/HGF signal pathways. This simple modular design provides a robust chemical tool for modulating cellular signal transduction.
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Affiliation(s)
- Shan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Xiahui Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, P. R. China
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28
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Chen S, Xu Z, Yang W, Lin X, Li J, Li J, Yang H. Logic‐Gate‐Actuated DNA‐Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908971] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- Institute of Molecular MedicineRenji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Xiahui Lin
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- College of Biological Science and EngineeringFuzhou University Fuzhou 350108 P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
- Institute of Molecular MedicineRenji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and BiologyFujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou University Fuzhou 350108 P. R. China
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29
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Nair A, Chauhan P, Saha B, Kubatzky KF. Conceptual Evolution of Cell Signaling. Int J Mol Sci 2019; 20:E3292. [PMID: 31277491 PMCID: PMC6651758 DOI: 10.3390/ijms20133292] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022] Open
Abstract
During the last 100 years, cell signaling has evolved into a common mechanism for most physiological processes across systems. Although the majority of cell signaling principles were initially derived from hormonal studies, its exponential growth has been supported by interdisciplinary inputs, e.g., from physics, chemistry, mathematics, statistics, and computational fields. As a result, cell signaling has grown out of scope for any general review. Here, we review how the messages are transferred from the first messenger (the ligand) to the receptor, and then decoded with the help of cascades of second messengers (kinases, phosphatases, GTPases, ions, and small molecules such as cAMP, cGMP, diacylglycerol, etc.). The message is thus relayed from the membrane to the nucleus where gene expression ns, subsequent translations, and protein targeting to the cell membrane and other organelles are triggered. Although there are limited numbers of intracellular messengers, the specificity of the response profiles to the ligands is generated by the involvement of a combination of selected intracellular signaling intermediates. Other crucial parameters in cell signaling are its directionality and distribution of signaling strengths in different pathways that may crosstalk to adjust the amplitude and quality of the final effector output. Finally, we have reflected upon its possible developments during the coming years.
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Affiliation(s)
- Arathi Nair
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Prashant Chauhan
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India.
| | - Katharina F Kubatzky
- Zentrum für Infektiologie, Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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30
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Kent R, Dixon N. Systematic Evaluation of Genetic and Environmental Factors Affecting Performance of Translational Riboswitches. ACS Synth Biol 2019; 8:884-901. [PMID: 30897329 PMCID: PMC6492952 DOI: 10.1021/acssynbio.9b00017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Indexed: 12/11/2022]
Abstract
Since their discovery, riboswitches have been attractive tools for the user-controlled regulation of gene expression in bacterial systems. Riboswitches facilitate small molecule mediated fine-tuning of protein expression, making these tools of great use to the synthetic biology community. However, the use of riboswitches is often restricted due to context dependent performance and limited dynamic range. Here, we report the drastic improvement of a previously developed orthogonal riboswitch achieved through in vivo functional selection and optimization of flanking coding and noncoding sequences. The behavior of the derived riboswitches was mapped under a wide array of growth and induction conditions, using a structured Design of Experiments approach. This approach successfully improved the maximal protein expression levels 8.2-fold relative to the original riboswitches, and the dynamic range was improved to afford riboswitch dependent control of 80-fold. The optimized orthogonal riboswitch was then integrated downstream of four endogenous stress promoters, responsive to phosphate starvation, hyperosmotic stress, redox stress, and carbon starvation. These responsive stress promoter-riboswitch devices were demonstrated to allow for tuning of protein expression up to ∼650-fold in response to both environmental and cellular stress responses and riboswitch dependent attenuation. We envisage that these riboswitch stress responsive devices will be useful tools for the construction of advanced genetic circuits, bioprocessing, and protein expression.
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Affiliation(s)
- R. Kent
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - N. Dixon
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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31
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Wan X, Volpetti F, Petrova E, French C, Maerkl SJ, Wang B. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat Chem Biol 2019; 15:540-548. [PMID: 30911179 DOI: 10.1038/s41589-019-0244-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022]
Abstract
Cell-based biosensors have great potential to detect various toxic and pathogenic contaminants in aqueous environments. However, frequently they cannot meet practical requirements due to insufficient sensing performance. To address this issue, we investigated a modular, cascaded signal amplifying methodology. We first tuned intracellular sensory receptor densities to increase sensitivity, and then engineered multi-layered transcriptional amplifiers to sequentially boost output expression level. We demonstrated these strategies by engineering ultrasensitive bacterial sensors for arsenic and mercury, and improved detection limit and output up to 5,000-fold and 750-fold, respectively. Coupled by leakage regulation approaches, we developed an encapsulated microbial sensor cell array for low-cost, portable and precise field monitoring, where the analyte can be readily quantified via displaying an easy-to-interpret volume bar-like pattern. The ultrasensitive signal amplifying methodology along with the background regulation and the sensing platform will be widely applicable to many other cell-based sensors, paving the way for their real-world applications.
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Affiliation(s)
- Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Francesca Volpetti
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Chris French
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK.
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32
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Andrews LB, Nielsen AAK, Voigt CA. Cellular checkpoint control using programmable sequential logic. Science 2018; 361:361/6408/eaap8987. [PMID: 30237327 DOI: 10.1126/science.aap8987] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 08/03/2018] [Indexed: 12/15/2022]
Abstract
Biological processes that require orderly progression, such as growth and differentiation, proceed via regulatory checkpoints where the cell waits for signals before continuing to the next state. Implementing such control would allow genetic engineers to divide complex tasks into stages. We present genetic circuits that encode sequential logic to instruct Escherichia coli to proceed through a linear or cyclical sequence of states. These are built with 11 set-reset latches, designed with repressor-based NOR gates, which can connect to each other and sensors. The performance of circuits with up to three latches and four sensors, including a gated D latch, closely match predictions made by using nonlinear dynamics. Checkpoint control is demonstrated by switching cells between multiple circuit states in response to external signals over days.
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Affiliation(s)
- Lauren B Andrews
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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33
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Xiang Y, Dalchau N, Wang B. Scaling up genetic circuit design for cellular computing: advances and prospects. NATURAL COMPUTING 2018; 17:833-853. [PMID: 30524216 PMCID: PMC6244767 DOI: 10.1007/s11047-018-9715-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.
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Affiliation(s)
- Yiyu Xiang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | | | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
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34
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Smock RG, Meijers R. Roles of glycosaminoglycans as regulators of ligand/receptor complexes. Open Biol 2018; 8:rsob.180026. [PMID: 30282658 PMCID: PMC6223220 DOI: 10.1098/rsob.180026] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/04/2018] [Indexed: 02/06/2023] Open
Abstract
Glycosaminoglycans (GAGs) play a widespread role in embryonic development, as deletion of enzymes that contribute to GAG synthesis lead to deficiencies in cell migration and tissue modelling. Despite the biochemical and structural characterization of individual protein/GAG interactions, there is no concept available that links the molecular mechanisms of GAG/protein engagements to tissue development. Here, we focus on the role of GAG polymers in mediating interactions between cell surface receptors and their ligands. We categorize several switches that lead to ligand activation, inhibition, selection and addition, based on recent structural studies of select receptor/ligand complexes. Based on these principles, we propose that individual GAG polymers may affect several receptor pathways in parallel, orchestrating a cellular response to an environmental cue. We believe that it is worthwhile to study the role of GAGs as molecular switches, as this may lead to novel drug candidates to target processes such as angiogenesis, neuroregeneration and tumour metastasis.
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Affiliation(s)
- Robert G Smock
- European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
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35
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Li S, Sun T, Xu C, Chen L, Zhang W. Development and optimization of genetic toolboxes for a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. Metab Eng 2018; 48:163-174. [PMID: 29883802 DOI: 10.1016/j.ymben.2018.06.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973) has been considered a good chassis candidate for "microbial cell factory" as it can perform oxygenic photosynthesis and its doubling time can be as short as 1.9 h. However, the limited genetic tools currently restrict its further research and application efforts using synthetic biology approaches. In this study, a series of genetic tools were systematically developed and optimized for Synechococcus 2973. First, the introduction of Tfp pilus assembly protein encoding gene pilN into Synechococcus 2973 successfully recovered its natural transformability, which greatly simplified the DNA transformation process. Second, a series of promoters with different strengths were evaluated and the super-strong promoters including Pcpc560 from Synechocystis sp. PCC 6803, native PpsbA2 and PpsbA3 of Synechococcus 2973 were found with the highest activity of β-galactosidase among those evaluated by miller values. Some promoters related to photosystems (i.e., PpsbA2, PpsbA3, P6803psbA2 and Pcpc560) were also demonstrated to be induced by high intensity of light. Third, three lactose induction systems were evaluated, among which Plac combined with lacIq showed the best application prospect with great induction capacity, low leakage and middle induced expression. Fourth, the translational on riboswitch theoE* , the transcriptional off riboswitches theo/yitJ and xpt(C74U)/metE and an artificial inducing system combining theoE* with T7 RNA polymerase were successfully developed and characterized in Synechococcus 2973. Finally, by using T7 induction system to control the expression of both small RNA and chaperone Hfq, a small RNA regulatory tool was developed and optimized to be a strictly inducible off system for gene regulation in Synechococcus 2973. The work here presented valuable genetic toolboxes necessary for metabolic engineering and synthetic biology research in Synechococcus 2973, which will facilitate the future application of the fast growing cyanobacterial chassis.
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Affiliation(s)
- Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Chunxiao Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, PR China
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36
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Danchin A, Sekowska A, Noria S. Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Agnieszka Sekowska
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Stanislas Noria
- Fondation Fourmentin-Guilbert; 2 avenue du Pavé Neuf Noisy le Grand 93160 France
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37
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Liu Q, Schumacher J, Wan X, Lou C, Wang B. Orthogonality and Burdens of Heterologous AND Gate Gene Circuits in E. coli. ACS Synth Biol 2018; 7:553-564. [PMID: 29240998 PMCID: PMC5820654 DOI: 10.1021/acssynbio.7b00328] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Synthetic
biology approaches commonly introduce heterologous gene
networks into a host to predictably program cells, with the expectation
of the synthetic network being orthogonal to the host background.
However, introduced circuits may interfere with the host’s
physiology, either indirectly by posing a metabolic burden and/or
through unintended direct interactions between parts of the circuit
with those of the host, affecting functionality. Here we used RNA-Seq
transcriptome analysis to quantify the interactions between a representative
heterologous AND gate circuit and the host Escherichia coli under various conditions including circuit designs and plasmid copy
numbers. We show that the circuit plasmid copy number outweighs circuit
composition for their effect on host gene expression with medium-copy
number plasmid showing more prominent interference than its low-copy
number counterpart. In contrast, the circuits have a stronger influence
on the host growth with a metabolic load increasing with the copy
number of the circuits. Notably, we show that variation of copy number,
an increase from low to medium copy, caused different types of change
observed in the behavior of components in the AND gate circuit leading
to the unbalance of the two gate-inputs and thus counterintuitive
output attenuation. The study demonstrates the circuit plasmid copy
number is a key factor that can dramatically affect the orthogonality,
burden and functionality of the heterologous circuits in the host
chassis. The results provide important guidance for future efforts
to design orthogonal and robust gene circuits with minimal unwanted
interaction and burden to their host.
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Affiliation(s)
- Qijun Liu
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, U.K
- Centre
for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR, U.K
- Department
of Chemistry and Biology, National University of Defense Technology, Changsha, 410073, China
| | - Jörg Schumacher
- Department
of Life Sciences, Imperial College London, London, SW7 2AZ, U.K
| | - Xinyi Wan
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, U.K
- Centre
for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR, U.K
| | - Chunbo Lou
- CAS
Key Laboratory of Microbial Physiological and Metabolic Engineering,
Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baojun Wang
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, U.K
- Centre
for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR, U.K
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38
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Mahajan T, Rai K. A novel optogenetically tunable frequency modulating oscillator. PLoS One 2018; 13:e0183242. [PMID: 29389936 PMCID: PMC5794059 DOI: 10.1371/journal.pone.0183242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Synthetic biology has enabled the creation of biological reconfigurable circuits, which perform multiple functions monopolizing a single biological machine; Such a system can switch between different behaviours in response to environmental cues. Previous work has demonstrated switchable dynamical behaviour employing reconfigurable logic gate genetic networks. Here we describe a computational framework for reconfigurable circuits in E.coli using combinations of logic gates, and also propose the biological implementation. The proposed system is an oscillator that can exhibit tunability of frequency and amplitude of oscillations. Further, the frequency of operation can be changed optogenetically. Insilico analysis revealed that two-component light systems, in response to light within a frequency range, can be used for modulating the frequency of the oscillator or stopping the oscillations altogether. Computational modelling reveals that mixing two colonies of E.coli oscillating at different frequencies generates spatial beat patterns. Further, we show that these oscillations more robustly respond to input perturbations compared to the base oscillator, to which the proposed oscillator is a modification. Compared to the base oscillator, the proposed system shows faster synchronization in a colony of cells for a larger region of the parameter space. Additionally, the proposed oscillator also exhibits lesser synchronization error in the transient period after input perturbations. This provides a strong basis for the construction of synthetic reconfigurable circuits in bacteria and other organisms, which can be scaled up to perform functions in the field of time dependent drug delivery with tunable dosages, and sets the stage for further development of circuits with synchronized population level behaviour.
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Affiliation(s)
- Tarun Mahajan
- Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- * E-mail:
| | - Kshitij Rai
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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39
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Saltepe B, Kehribar EŞ, Su Yirmibeşoğlu SS, Şafak Şeker UÖ. Cellular Biosensors with Engineered Genetic Circuits. ACS Sens 2018; 3:13-26. [PMID: 29168381 DOI: 10.1021/acssensors.7b00728] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing interest in building novel biological devices with designed cellular functionalities has triggered the search of innovative tools for biocomputation. Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits. Whole cell biosensors are widely used biological devices that employ several biocomputation tools to program cells for desired functions. Up to the present date, a wide range of whole-cell biosensors have been designed and implemented for disease theranostics, biomedical applications, and environmental monitoring. In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines. Additionally, we stated the novel applications of biological devices with computing functionalities for diagnosis and therapy of various diseases such as infections, cancer, or metabolic diseases, as well as the detection of environmental pollutants such as heavy metals or organic toxic compounds. Current whole-cell biosensors are innovative alternatives to classical biosensors; however, there is still a need to advance decision making capabilities by developing novel biocomputing devices.
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Affiliation(s)
- Behide Saltepe
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | | | - Urartu Özgür Şafak Şeker
- UNAM-Institute
of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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40
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Abstract
In electronic systems, dynamic random access memory (DRAM) is one of the core modules in the modern silicon computer. As for a bio‐computer, one would need a mechanism for storage of bio‐information named ‘data’, which, in binary logic, has two levels, logical high and logical low, or in the normalised form, ‘1’ and ‘0’. This study proposes a possible genetic DRAM based on the modified electronic configuration, which uses the biological reaction to fulfil an equivalent RC circuit constituting a memory cell. The authors implement fundamental functions of the genetic DRAM by incorporating a genetic toggle switch for data hold. The results of simulation verify that the basic function can be used on a bio‐storage module for the future bio‐computer.
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Affiliation(s)
- Yu-Jia Hu
- Department of Electrical Engineering, National Chung Hsing University, 402 Taichung, Taiwan
| | - Chun-Liang Lin
- Department of Electrical Engineering, National Chung Hsing University, 402 Taichung, Taiwan.
| | - Wei-Xian Li
- Department of Electrical Engineering, National Chung Hsing University, 402 Taichung, Taiwan
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41
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Brown R, Lengeling A, Wang B. Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0094-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Kuwahara H, Umarov R, Almasri I, Gao X. ACRE: Absolute concentration robustness exploration in module-based combinatorial networks. Synth Biol (Oxf) 2017; 2:ysx001. [PMID: 32995502 PMCID: PMC7513739 DOI: 10.1093/synbio/ysx001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/03/2016] [Accepted: 01/03/2017] [Indexed: 11/26/2022] Open
Abstract
To engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.
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Affiliation(s)
- Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Ramzan Umarov
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Islam Almasri
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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43
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Dubiak-Szepietowska M, Karczmarczyk A, Winckler T, Feller KH. A cell-based biosensor for nanomaterials cytotoxicity assessment in three dimensional cell culture. Toxicology 2016; 370:60-69. [PMID: 27693313 DOI: 10.1016/j.tox.2016.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Abstract
Nanoparticles (NPs) are widely used in consumer and medicinal products. The high prevalence of nanoparticles in the environment raises concerns regarding their effects on human health, but there is limited knowledge about how NPs interact with cells or tissues. Because the European Union has called for a substantial reduction of animal experiments for scientific purposes (Directive 2010/63), increased efforts are required to develop in vitro models to evaluate potentially hazardous agents. Here, we describe a new cell-based biosensor for the evaluation of NPs cytotoxicity. The new biosensor is based on transgenic human hepatoblastoma cells (HepG2) that express a secreted form of alkaline phosphatase (SEAP) as a reporter protein whose expression is induced upon activation of a stress response pathway controlled by the transcription regulator nuclear factor-κB (NF-κB). The NF-κB_HepG2 sensor cells were cultured in a Matrigel-based three dimensional environment to simulate the in vivo situation. The new biosensor cells offer the advantage of generating fast and reproducible readout at lower concentrations and shorter incubation time than conventional viability assays, avoid possible interaction between nanomaterials and assay compounds, therefore, minimize generation of false positive or negative results and indicate mechanism of toxicity through NF-κB signaling.
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Affiliation(s)
- Monika Dubiak-Szepietowska
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany.
| | - Aleksandra Karczmarczyk
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany
| | - Thomas Winckler
- Institute of Pharmacy, Friedrich Schiller University Jena, Semmelweissstrasse 10, 07743 Jena, Germany
| | - Karl-Heinz Feller
- Department of Medical Engineering and Biotechnology, Ernst-Abbe-University of Applied Sciences Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany
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44
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Tools and Principles for Microbial Gene Circuit Engineering. J Mol Biol 2016; 428:862-88. [DOI: 10.1016/j.jmb.2015.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/26/2022]
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45
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Implementation of a genetic logic circuit: bio-register. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:43-8. [PMID: 26702308 DOI: 10.1007/s11693-015-9186-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
We introduce an idea of synthesizing a class of genetic registers based on the existing sequential biological circuits, which are composed of fundamental biological gates. In the renowned literature, biological gates and genetic oscillator have been unveiled and experimentally realized in recent years. These biological circuits have formed a basis for realizing a primitive biocomputer. In the traditional computer architecture, there is an intermediate load-store section, i.e. a register, which serves as a part of the digital processor. With which, the processor can load data from a larger memory into it and proceed to conduct necessary arithmetic or logic operations. Then, manipulated data are stored back to the memory by instruction via the register. We propose here a class of bio-registers for the biocomputer. Four types of register structures are presented. In silicon experiments illustrate results of the proposed design.
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46
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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47
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Wang B, Buck M. Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules. Chem Commun (Camb) 2015; 50:11642-4. [PMID: 25062273 PMCID: PMC4185417 DOI: 10.1039/c4cc05264a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Versatile modular molecular logic gates are engineered in Escherichia coli bacteria that can sense and integrate multiple chemical molecules in customised digital logic manner.
We designed and constructed versatile modular genetic logic gates in bacterial cells. These function as digital logic 1-input Buffer gate, 2-input and 3-input AND gates with one inverted input and integrate multiple chemical input signals in customised logic manners. Such rapidly engineered devices serve to achieve increased sensing signal selectivity.
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Affiliation(s)
- Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK.
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48
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Bradley RW, Wang B. Designer cell signal processing circuits for biotechnology. N Biotechnol 2015; 32:635-43. [PMID: 25579192 PMCID: PMC4571992 DOI: 10.1016/j.nbt.2014.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/02/2014] [Accepted: 12/31/2014] [Indexed: 01/13/2023]
Abstract
Microorganisms are able to respond effectively to diverse signals from their environment and internal metabolism owing to their inherent sophisticated information processing capacity. A central aim of synthetic biology is to control and reprogramme the signal processing pathways within living cells so as to realise repurposed, beneficial applications ranging from disease diagnosis and environmental sensing to chemical bioproduction. To date most examples of synthetic biological signal processing have been built based on digital information flow, though analogue computing is being developed to cope with more complex operations and larger sets of variables. Great progress has been made in expanding the categories of characterised biological components that can be used for cellular signal manipulation, thereby allowing synthetic biologists to more rationally programme increasingly complex behaviours into living cells. Here we present a current overview of the components and strategies that exist for designer cell signal processing and decision making, discuss how these have been implemented in prototype systems for therapeutic, environmental, and industrial biotechnological applications, and examine emerging challenges in this promising field.
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Affiliation(s)
- Robert W Bradley
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK.
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49
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French CE, Horsfall L, Barnard DK, Duedu K, Fletcher E, Joshi N, Kane SD, Lakhundi SS, Liu CK, Oltmanns J, Radford D, Salinas A, White J, Elfick A. Beyond Genetic Engineering: Technical Capabilities in the Application Fields of Biocatalysis and Biosensors. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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50
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Advances and computational tools towards predictable design in biological engineering. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:369681. [PMID: 25161694 PMCID: PMC4137594 DOI: 10.1155/2014/369681] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/09/2014] [Indexed: 11/21/2022]
Abstract
The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated.
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