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Bayer T, Hänel L, Husarcikova J, Kunzendorf A, Bornscheuer UT. In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors. ACS OMEGA 2023; 8:23227-23239. [PMID: 37426270 PMCID: PMC10324065 DOI: 10.1021/acsomega.3c01741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Genetically encoded biosensor systems operating in living cells are versatile, cheap, and transferable tools for the detection and quantification of a broad range of small molecules. This review presents state-of-the-art biosensor designs and assemblies, featuring transcription factor-, riboswitch-, and enzyme-coupled devices, highly engineered fluorescent probes, and emerging two-component systems. Importantly, (bioinformatic-assisted) strategies to resolve contextual issues, which cause biosensors to miss performance criteria in vivo, are highlighted. The optimized biosensing circuits can be used to monitor chemicals of low molecular mass (<200 g mol-1) and physicochemical properties that challenge conventional chromatographical methods with high sensitivity. Examples herein include but are not limited to formaldehyde, formate, and pyruvate as immediate products from (synthetic) pathways for the fixation of carbon dioxide (CO2), industrially important derivatives like small- and medium-chain fatty acids and biofuels, as well as environmental toxins such as heavy metals or reactive oxygen and nitrogen species. Lastly, this review showcases biosensors capable of assessing the biosynthesis of platform chemicals from renewable resources, the enzymatic degradation of plastic waste, or the bioadsorption of highly toxic chemicals from the environment. These applications offer new biosensor-based manufacturing, recycling, and remediation strategies to tackle current and future environmental and socioeconomic challenges including the wastage of fossil fuels, the emission of greenhouse gases like CO2, and the pollution imposed on ecosystems and human health.
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Rutter JW, Dekker L, Fedorec AJH, Gonzales DT, Wen KY, Tanner LES, Donovan E, Ozdemir T, Thomas GM, Barnes CP. Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system. Biotechnol Bioeng 2021; 118:4278-4289. [PMID: 34289076 DOI: 10.1002/bit.27897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022]
Abstract
Whole-cell biosensors hold potential in a variety of industrial, medical, and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system (TCS). Here we report on the construction of a range of novel biosensors that are sensitive to acetoacetate, a molecule that plays a number of roles in human health and biology. These biosensors are based on the AtoSC TCS. An ordinary differential equation model to describe the action of the AtoSC TCS was developed and sensitivity analysis of this model used to help inform biosensor design. The final collection of biosensors constructed displayed a range of switching behaviours at physiologically relevant acetoacetate concentrations and can operate in several Escherichia coli host strains. It is envisaged that these biosensor strains will offer an alternative to currently available commercial strip tests and, in future, may be adopted for more complex in vivo or industrial monitoring applications.
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Affiliation(s)
- Jack W Rutter
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Linda Dekker
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London, UK
| | - David T Gonzales
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Ke Yan Wen
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Lewis E S Tanner
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Emma Donovan
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Tanel Ozdemir
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Geraint M Thomas
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.,Department of Genetics, Evolution and Environment, University College London, London, UK
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Krell T, Gavira JA, Velando F, Fernández M, Roca A, Monteagudo-Cascales E, Matilla MA. Histamine: A Bacterial Signal Molecule. Int J Mol Sci 2021; 22:6312. [PMID: 34204625 PMCID: PMC8231116 DOI: 10.3390/ijms22126312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria have evolved sophisticated signaling mechanisms to coordinate interactions with organisms of other domains, such as plants, animals and human hosts. Several important signal molecules have been identified that are synthesized by members of different domains and that play important roles in inter-domain communication. In this article, we review recent data supporting that histamine is a signal molecule that may play an important role in inter-domain and inter-species communication. Histamine is a key signal molecule in humans, with multiple functions, such as being a neurotransmitter or modulator of immune responses. More recent studies have shown that bacteria have evolved different mechanisms to sense histamine or histamine metabolites. Histamine sensing in the human pathogen Pseudomonas aeruginosa was found to trigger chemoattraction to histamine and to regulate the expression of many virulence-related genes. Further studies have shown that many bacteria are able to synthesize and secrete histamine. The release of histamine by bacteria in the human gut was found to modulate the host immune responses and, at higher doses, to result in host pathologies. The elucidation of the role of histamine as an inter-domain signaling molecule is an emerging field of research and future investigation is required to assess its potential general nature.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - José A. Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Avenida de las Palmeras 4, 18100 Armilla, Spain;
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - Matilde Fernández
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071 Granada, Spain; (M.F.); (A.R.)
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071 Granada, Spain; (M.F.); (A.R.)
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain; (F.V.); (E.M.-C.)
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Choi TR, Jeon JM, Bhatia SK, Gurav R, Han YH, Park YL, Park JY, Song HS, Park HY, Yoon JJ, Seo SO, Yang YH. Production of Low Molecular Weight P(3HB-co-3HV) by Butyrateacetoacetate CoA-transferase (cftAB) in Escherichia coli. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0366-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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King MM, Kayastha BB, Franklin MJ, Patrauchan MA. Calcium Regulation of Bacterial Virulence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:827-855. [PMID: 31646536 DOI: 10.1007/978-3-030-12457-1_33] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium (Ca2+) is a universal signaling ion, whose major informational role shaped the evolution of signaling pathways, enabling cellular communications and responsiveness to both the intracellular and extracellular environments. Elaborate Ca2+ regulatory networks have been well characterized in eukaryotic cells, where Ca2+ regulates a number of essential cellular processes, ranging from cell division, transport and motility, to apoptosis and pathogenesis. However, in bacteria, the knowledge on Ca2+ signaling is still fragmentary. This is complicated by the large variability of environments that bacteria inhabit with diverse levels of Ca2+. Yet another complication arises when bacterial pathogens invade a host and become exposed to different levels of Ca2+ that (1) are tightly regulated by the host, (2) control host defenses including immune responses to bacterial infections, and (3) become impaired during diseases. The invading pathogens evolved to recognize and respond to the host Ca2+, triggering the molecular mechanisms of adhesion, biofilm formation, host cellular damage, and host-defense resistance, processes enabling the development of persistent infections. In this review, we discuss: (1) Ca2+ as a determinant of a host environment for invading bacterial pathogens, (2) the role of Ca2+ in regulating main events of host colonization and bacterial virulence, and (3) the molecular mechanisms of Ca2+ signaling in bacterial pathogens.
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Affiliation(s)
- Michelle M King
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Michael J Franklin
- Department of Microbiology and Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Pramanik N, Mukherjee K, Nandy A, Mukherjee S, Kundu PP. Comparative analysis of different properties of polyhydroxyalkanoates isolated from two different bacterial strains:Alkaliphilus oremlandiiOhILAs and recombinantEscherichia coliXL1B. J Appl Polym Sci 2014. [DOI: 10.1002/app.41080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nilkamal Pramanik
- Advanced Polymer Laboratory, Department of Polymer Science and Technology; University of Calcutta; Calcutta 700009 India
| | - Khushi Mukherjee
- Advanced Polymer Laboratory, Department of Polymer Science and Technology; University of Calcutta; Calcutta 700009 India
| | - Arpita Nandy
- Advanced Polymer Laboratory, Department of Polymer Science and Technology; University of Calcutta; Calcutta 700009 India
| | - Shritama Mukherjee
- Advanced Polymer Laboratory, Department of Polymer Science and Technology; University of Calcutta; Calcutta 700009 India
| | - Patit Paban Kundu
- Advanced Polymer Laboratory, Department of Polymer Science and Technology; University of Calcutta; Calcutta 700009 India
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