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Nora LC, Cassiano MHA, Santana ÍP, Guazzaroni ME, Silva-Rocha R, da Silva RR. Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data. Front Microbiol 2023; 13:1069443. [PMID: 36687612 PMCID: PMC9853887 DOI: 10.3389/fmicb.2022.1069443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
The demand for robust microbial cell factories that produce valuable biomaterials while resisting stresses imposed by current bioprocesses is rapidly growing. Rhodosporidium toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. To explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 and 42°C) and two ethanol concentrations (2 and 4%), while the other used the inexpensive and abundant sugarcane juice as substrate. Differential expression and functional analysis were implemented using transcriptomic data to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in studying gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.
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Affiliation(s)
- Luísa Czamanski Nora
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil,*Correspondence: Luísa Czamanski Nora,
| | | | - Ítalo Paulino Santana
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ricardo Roberto da Silva
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil,Ricardo Roberto da Silva,
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2
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Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci 2022; 13:6715-6731. [PMID: 35756504 PMCID: PMC9172442 DOI: 10.1039/d1sc06921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University Boston MA 02215 USA .,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629 F-33600 Pessac France .,University Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 F-33400 Talence France
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University Boston MA 02215 USA
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology, Boston UniversityBostonMA 02118USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | | | | | - Allison M. Dennis
- Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| | - James E. Galagan
- Department of Microbiology, Boston UniversityBostonMA 02118USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston UniversityBostonMA 02215USA,Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
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3
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Engineering of Synthetic Transcriptional Switches in Yeast. Life (Basel) 2022; 12:life12040557. [PMID: 35455048 PMCID: PMC9030632 DOI: 10.3390/life12040557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 02/04/2023] Open
Abstract
Transcriptional switches can be utilized for many purposes in synthetic biology, including the assembly of complex genetic circuits to achieve sophisticated cellular systems and the construction of biosensors for real-time monitoring of intracellular metabolite concentrations. Although to date such switches have mainly been developed in prokaryotes, those for eukaryotes are increasingly being reported as both rational and random engineering technologies mature. In this review, we describe yeast transcriptional switches with different modes of action and how to alter their properties. We also discuss directed evolution technologies for the rapid and robust construction of yeast transcriptional switches.
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4
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Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun 2022; 13:270. [PMID: 35022416 PMCID: PMC8755756 DOI: 10.1038/s41467-021-27852-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Branched-chain amino acid (BCAA) metabolism fulfills numerous physiological roles and can be harnessed to produce valuable chemicals. However, the lack of eukaryotic biosensors specific for BCAA-derived products has limited the ability to develop high-throughput screens for strain engineering and metabolic studies. Here, we harness the transcriptional regulator Leu3p from Saccharomyces cerevisiae to develop a genetically encoded biosensor for BCAA metabolism. In one configuration, we use the biosensor to monitor yeast production of isobutanol, an alcohol derived from valine degradation. Small modifications allow us to redeploy Leu3p in another biosensor configuration that monitors production of the leucine-derived alcohol, isopentanol. These biosensor configurations are effective at isolating high-producing strains and identifying enzymes with enhanced activity from screens for branched-chain higher alcohol (BCHA) biosynthesis in mitochondria as well as cytosol. Furthermore, this biosensor has the potential to assist in metabolic studies involving BCAA pathways, and offers a blueprint to develop biosensors for other products derived from BCAA metabolism. There are a lack of eukaryotic biosensors specific for branched-chain amino acid (BCAA)-derived products. Here the authors report a genetically encoded biosensor for BCAA metabolism based on the Leu3p transcriptional regulator; they use this to monitor yeast production of isobutanol and isopentanol.
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5
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Torres‐Bacete J, Luís García J, Nogales J. A portable library of phosphate-depletion based synthetic promoters for customable and automata control of gene expression in bacteria. Microb Biotechnol 2021; 14:2643-2658. [PMID: 33783967 PMCID: PMC8601176 DOI: 10.1111/1751-7915.13808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/14/2021] [Indexed: 12/14/2022] Open
Abstract
Industrial biotechnology gene expression systems relay on constitutive promoters compromising cellular growth from the start of the bioprocess, or on inducible devices, which require manual addition of cognate inducers. To overcome this shortcoming, we engineered an automata regulatory system based on cell-stress mechanisms. Specifically, we engineered a synthetic and highly portable phosphate-depletion library of promoters inspired by bacterial PHO starvation system (Pliar promoters). Furthermore, we fully characterized 10 synthetic promoters within the background of two well-known bacterial workhorses such as E. coli W and P. putida KT2440. The promoters displayed an interesting host-dependent performance and a wide strength spectrum ranging from 0.4- to 1.3-fold when compared to the wild-type phosphatase alkaline promoter (PphoA). By comparing with available gene expression systems, we proved the suitability of this new library for the automata and effective decoupling of growth from production in P. putida. Growth phase-dependent expression of these promoters could therefore be activated by fine tuning the initial concentration of phosphate in the medium. Finally, the Pliar library was implemented in the SEVA platform in a ready-to-use mode allowing its broad use by the scientific community.
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Affiliation(s)
- Jesús Torres‐Bacete
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)Madrid28049Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
| | - José Luís García
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas (CIB)Centro Nacional de Biotecnología (CSIC)MadridSpain
| | - Juan Nogales
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)Madrid28049Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
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6
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Baumann L, Bruder S, Kabisch J, Boles E, Oreb M. High-Throughput Screening of an Octanoic Acid Producer Strain Library Enables Detection of New Targets for Increasing Titers in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:1077-1086. [PMID: 33979526 DOI: 10.1021/acssynbio.0c00600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Octanoic acid is an industrially relevant compound with applications in antimicrobials or as a precursor for biofuels. Microbial biosynthesis through yeast is a promising alternative to current unsustainable production methods. To increase octanoic acid titers in Saccharomyces cerevisiae, we use a previously developed biosensor that is based on the octanoic acid responsive pPDR12 promotor coupled to GFP. We establish a biosensor strain amenable for high-throughput screening of an octanoic acid producer strain library. Through development, optimization, and execution of a high-throughput screening approach, we were able to detect two new genetic targets, KCS1 and FSH2, which increased octanoic acid titers through combined overexpression by about 55% compared to the parental strain. Neither target has yet been reported to be involved in fatty acid biosynthesis. The presented methodology can be employed to screen any genetic library and thereby more genes involved in improving octanoic acid production can be detected in the future.
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Affiliation(s)
- Leonie Baumann
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Stefan Bruder
- Department of Biology, Computer-aided Synthetic Biology, Technical University Darmstadt, Schnittspahnstr. 1, 64287 Darmstadt, Germany
| | - Johannes Kabisch
- Department of Biology, Computer-aided Synthetic Biology, Technical University Darmstadt, Schnittspahnstr. 1, 64287 Darmstadt, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
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7
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Regulatory control circuits for stabilizing long-term anabolic product formation in yeast. Metab Eng 2020; 61:369-380. [DOI: 10.1016/j.ymben.2020.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
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8
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Boada Y, Vignoni A, Picó J, Carbonell P. Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of Cell Factories. iScience 2020; 23:101305. [PMID: 32629420 PMCID: PMC7334618 DOI: 10.1016/j.isci.2020.101305] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/05/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Transcription factor-based biosensors naturally occur in metabolic pathways to maintain cell growth and to provide a robust response to environmental fluctuations. Extended metabolic biosensors, i.e., the cascading of a bio-conversion pathway and a transcription factor (TF) responsive to the downstream effector metabolite, provide sensing capabilities beyond natural effectors for implementing context-aware synthetic genetic circuits and bio-observers. However, the engineering of such multi-step circuits is challenged by stability and robustness issues. In order to streamline the design of TF-based biosensors in metabolic pathways, here we investigate the response of a genetic circuit combining a TF-based extended metabolic biosensor with an antithetic integral circuit, a feedback controller that achieves robustness against environmental fluctuations. The dynamic response of an extended biosensor-based regulated flavonoid pathway is analyzed in order to address the issues of biosensor tuning of the regulated pathway under industrial biomanufacturing operating constraints.
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Affiliation(s)
- Yadira Boada
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain; Centro Universitario EDEM, Escuela de Empresarios, Muelle de la Aduana s/n, La Marina de València, 46024 Valencia, Spain
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Jesús Picó
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain
| | - Pablo Carbonell
- Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de València, Camí de Vera S/N, 46022 Valencia, Spain.
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9
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Zhang L, Guo W, Lu Y. Advances in Cell‐Free Biosensors: Principle, Mechanism, and Applications. Biotechnol J 2020; 15:e2000187. [DOI: 10.1002/biot.202000187] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Liyuan Zhang
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Wei Guo
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
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10
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Qiu C, Chen X, Rexida R, Shen Y, Qi Q, Bao X, Hou J. Engineering transcription factor-based biosensors for repressive regulation through transcriptional deactivation design in Saccharomyces cerevisiae. Microb Cell Fact 2020; 19:146. [PMID: 32690010 PMCID: PMC7372789 DOI: 10.1186/s12934-020-01405-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/13/2020] [Indexed: 12/27/2022] Open
Abstract
Background With the development of engineering the microbial cell factories, biosensors have been used widely for regulation of cellular metabolism and high-throughput screening. However, most of the biosensors constructed in Saccharomyces cerevisiae are designed for transcriptional activation. Very few studies have dedicated to the development of genetic circuit for repressive regulation, which is also indispensable for the dynamic control of metabolism. Results In this study, through transcriptional deactivation design, we developed transcription-factor-based biosensors to allow repressive regulation in response to ligand. Using a malonyl-CoA sensing system as an example, the biosensor was constructed and systematically engineered to optimize the dynamic range by comparing transcriptional activity of the activators, evaluating the positions and numbers of the operators in the promoter and comparing the effects of different promoters. A biosensor with 82% repression ratio was obtained. Based on this design principle, another two biosensors, which sense acyl-CoA or xylose and downregulate gene expression, were also successfully constructed. Conclusions Our work systematically optimized the biosensors for repressive regulation in yeast for the first time. It provided useful framework to construct similar biosensors. Combining the widely reported biosensors for transcriptional activation with the biosensors developed here, it is now possible to construct biosensors with opposing transcriptional activities in yeast. ![]()
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Affiliation(s)
- Chenxi Qiu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China
| | - Xiaoxu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, People's Republic of China
| | - Reheman Rexida
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China.,State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qi Lu University of Technology, Jinan, 250353, People's Republic of China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, People's Republic of China.
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11
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Lv Y, Gu Y, Xu J, Zhou J, Xu P. Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield. Metab Eng 2020; 61:79-88. [PMID: 32445959 PMCID: PMC7510839 DOI: 10.1016/j.ymben.2020.05.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 11/23/2022]
Abstract
Metabolic addiction, an organism that is metabolically addicted with a compound to maintain its growth fitness, is an underexplored area in metabolic engineering. Microbes with heavily engineered pathways or genetic circuits tend to experience metabolic burden leading to degenerated or abortive production phenotype during long-term cultivation or scale-up. A promising solution to combat metabolic instability is to tie up the end-product with an intermediary metabolite that is essential to the growth of the producing host. Here we present a simple strategy to improve both metabolic stability and pathway yield by coupling chemical addiction with negative autoregulatory genetic circuits. Naringenin and lipids compete for the same precursor malonyl-CoA with inversed pathway yield in oleaginous yeast. Negative autoregulation of the lipogenic pathways, enabled by CRISPRi and fatty acid-inducible promoters, repartitions malonyl-CoA to favor flavonoid synthesis and increased naringenin production by 74.8%. With flavonoid-sensing transcriptional activator FdeR and yeast hybrid promoters to control leucine synthesis and cell grwoth fitness, this amino acid feedforward metabolic circuit confers a flavonoid addiction phenotype that selectively enrich the naringenin-producing pupulation in the leucine auxotrophic yeast. The engineered yeast persisted 90.9% of naringenin titer up to 324 generations. Cells without flavonoid addiction regained growth fitness but lost 94.5% of the naringenin titer after cell passage beyond 300 generations. Metabolic addiction and negative autoregulation may be generalized as basic tools to eliminate metabolic heterogeneity, improve strain stability and pathway yield in long-term and large-scale bioproduction.
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Affiliation(s)
- Yongkun Lv
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA; School of Chemical Engineering, Zhengzhou University, Zhengzhou, Henan, 450001, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yang Gu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, Henan, 450001, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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12
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Martin-Yken H. Yeast-Based Biosensors: Current Applications and New Developments. BIOSENSORS 2020; 10:E51. [PMID: 32413968 PMCID: PMC7277604 DOI: 10.3390/bios10050051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/23/2022]
Abstract
Biosensors are regarded as a powerful tool to detect and monitor environmental contaminants, toxins, and, more generally, organic or chemical markers of potential threats to human health. They are basically composed of a sensor part made up of either live cells or biological active molecules coupled to a transducer/reporter technological element. Whole-cells biosensors may be based on animal tissues, bacteria, or eukaryotic microorganisms such as yeasts and microalgae. Although very resistant to adverse environmental conditions, yeasts can sense and respond to a wide variety of stimuli. As eukaryotes, they also constitute excellent cellular models to detect chemicals and organic contaminants that are harmful to animals. For these reasons, combined with their ease of culture and genetic modification, yeasts have been commonly used as biological elements of biosensors since the 1970s. This review aims first at giving a survey on the different types of yeast-based biosensors developed for the environmental and medical domains. We then present the technological developments currently undertaken by academic and corporate scientists to further drive yeasts biosensors into a new era where the biological element is optimized in a tailor-made fashion by in silico design and where the output signals can be recorded or followed on a smartphone.
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Affiliation(s)
- Helene Martin-Yken
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR 792 Toulouse Biotechnology Institute (TBI), 31400 Toulouse, France; ; Tel.: +689-89-52-31-88
- Institut de Recherche pour le Développement (IRD), Faa’a, 98702 Tahiti, French Polynesia
- Unite Mixte de Recherche n°241 Ecosystemes Insulaires et Oceaniens, Université de la Polynésie Française, Faa’a, 98702 Tahiti, French Polynesia
- Laboratoire de Recherche sur les Biotoxines Marines, Institut Louis Malardé, Papeete, 98713 Tahiti, French Polynesia
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13
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Genetic Biosensor Design for Natural Product Biosynthesis in Microorganisms. Trends Biotechnol 2020; 38:797-810. [PMID: 32359951 DOI: 10.1016/j.tibtech.2020.03.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/28/2022]
Abstract
Low yield and low titer of natural products are common issues in natural product biosynthesis through microbial cell factories. One effective way to resolve such bottlenecks is to design genetic biosensors to monitor and regulate the biosynthesis of target natural products. In this review, we evaluate the most recent advances in the design of genetic biosensors for natural product biosynthesis in microorganisms. In particular, we examine strategies for selection of genetic parts and construction principles for the design and evaluation of genetic biosensors. We also review the latest applications of transcription factor- and riboswitch-based genetic biosensors in natural product biosynthesis. Lastly, we discuss challenges and solutions in designing genetic biosensors for the biosynthesis of natural products in microorganisms.
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14
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Ambri F, D’Ambrosio V, Di Blasi R, Maury J, Jacobsen SAB, McCloskey D, Jensen MK, Keasling JD. High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast. ACS Synth Biol 2020; 9:218-226. [PMID: 31935067 DOI: 10.1021/acssynbio.9b00333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-molecule binding allosteric transcription factors (aTFs) derived from bacteria enable real-time monitoring of metabolite abundances, high-throughput screening of genetic designs, and dynamic control of metabolism. Yet, engineering of reporter promoter designs of prokaryotic aTF biosensors in eukaryotic cells is complex. Here we investigate the impact of aTF binding site positions at single-nucleotide resolution in >300 reporter promoter designs in Saccharomyces cerevisiae. From this we identify biosensor output landscapes with transient and distinct aTF binding site position effects for aTF repressors and activators, respectively. Next, we present positions for tunable reporter promoter outputs enabling metabolite-responsive designs for a total of four repressor-type and three activator-type aTF biosensors with dynamic output ranges up to 8- and 26-fold, respectively. This study highlights aTF binding site positions in reporter promoters as key for successful biosensor engineering and that repressor-type aTF biosensors allows for more flexibility in terms of choice of binding site positioning compared to activator-type aTF biosensors.
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Affiliation(s)
- Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Vasil D’Ambrosio
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Roberto Di Blasi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jerome Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | | | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jay. D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
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15
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Li JW, Zhang XY, Wu H, Bai YP. Transcription Factor Engineering for High-Throughput Strain Evolution and Organic Acid Bioproduction: A Review. Front Bioeng Biotechnol 2020; 8:98. [PMID: 32140463 PMCID: PMC7042172 DOI: 10.3389/fbioe.2020.00098] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/03/2020] [Indexed: 01/15/2023] Open
Abstract
Metabolic regulation of gene expression for the microbial production of fine chemicals, such as organic acids, is an important research topic in post-genomic metabolic engineering. In particular, the ability of transcription factors (TFs) to respond precisely in time and space to various small molecules, signals and stimuli from the internal and external environment is essential for metabolic pathway engineering and strain development. As a key component, TFs are used to construct many biosensors in vivo using synthetic biology methods, which can be used to monitor the concentration of intracellular metabolites in organic acid production that would otherwise remain “invisible” within the intracellular environment. TF-based biosensors also provide a high-throughput screening method for rapid strain evolution. Furthermore, TFs are important global regulators that control the expression levels of key enzymes in organic acid biosynthesis pathways, therefore determining the outcome of metabolic networks. Here we review recent advances in TF identification, engineering, and applications for metabolic engineering, with an emphasis on metabolite monitoring and high-throughput strain evolution for the organic acid bioproduction.
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Affiliation(s)
- Jia-Wei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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16
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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17
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Thompson MG, Costello Z, Hummel NFC, Cruz-Morales P, Blake-Hedges JM, Krishna RN, Skyrud W, Pearson AN, Incha MR, Shih PM, Garcia-Martin H, Keasling JD. Robust Characterization of Two Distinct Glutarate Sensing Transcription Factors of Pseudomonas putida l-Lysine Metabolism. ACS Synth Biol 2019; 8:2385-2396. [PMID: 31518500 DOI: 10.1021/acssynbio.9b00255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A significant bottleneck in synthetic biology involves screening large genetically encoded libraries for desirable phenotypes such as chemical production. However, transcription factor-based biosensors can be leveraged to screen thousands of genetic designs for optimal chemical production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of csiR homologues were analyzed, and their DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added, confirming that it acts as a genetic repressor. Both transcription factors and cognate promoters were then cloned into broad host range vectors to create two glutarate biosensors. Their respective sensing performance features were characterized, and more sensitive derivatives of the GcdR biosensor were created by manipulating the expression of the transcription factor. Sensor vectors were then reintroduced into P. putida and evaluated for their ability to respond to glutarate and various lysine metabolites. Additionally, we developed a novel mathematical approach to describe the usable range of detection for genetically encoded biosensors, which may be broadly useful in future efforts to better characterize biosensor performance.
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Affiliation(s)
- Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Niklas F. C. Hummel
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Department of Plant Biology, University of California, Davis, Davis, California 95616, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Centro de Biotecnologia FEMSA, Instituto Tecnologico y de Estudios Superiores de Monterrey, 64849 Monterrey, Mexico
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rohith N. Krishna
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Will Skyrud
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew R. Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Patrick M. Shih
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Department of Plant Biology, University of California, Davis, Davis, California 95616, United States
| | - Hector Garcia-Martin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Program in Bioengineering, University of California, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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18
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Dabirian Y, Li X, Chen Y, David F, Nielsen J, Siewers V. Expanding the Dynamic Range of a Transcription Factor-Based Biosensor in Saccharomyces cerevisiae. ACS Synth Biol 2019; 8:1968-1975. [PMID: 31373795 DOI: 10.1021/acssynbio.9b00144] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolite biosensors are useful tools for high-throughput screening approaches and pathway regulation approaches. An important feature of biosensors is the dynamic range. To expand the maximum dynamic range of a transcription factor-based biosensor in Saccharomyces cerevisiae, using the fapO/FapR system from Bacillus subtilis as an example case, five native promoters, including constitutive and glucose-regulated ones, were modified. By evaluating different binding site (BS) positions in the core promoters, we identified locations that resulted in a high maximum dynamic range with low expression under repressed conditions. We further identified BS positions in the upstream element region of the TEF1 promoter that did not influence the native promoter strength but resulted in repression in the presence of a chimeric repressor consisting of FapR and the yeast repressor Mig1. These modified promoters with broad dynamic ranges will provide useful information for the engineering of future biosensors and their use in complex genetic circuits.
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Affiliation(s)
- Yasaman Dabirian
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
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19
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Wan X, Marsafari M, Xu P. Engineering metabolite-responsive transcriptional factors to sense small molecules in eukaryotes: current state and perspectives. Microb Cell Fact 2019; 18:61. [PMID: 30914048 PMCID: PMC6434827 DOI: 10.1186/s12934-019-1111-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/20/2019] [Indexed: 11/18/2022] Open
Abstract
Nature has evolved exquisite sensing mechanisms to detect cellular and environmental signals surrounding living organisms. These biosensors have been widely used to sense small molecules, detect environmental cues and diagnose disease markers. Metabolic engineers and synthetic biologists have been able to exploit metabolites-responsive transcriptional factors (MRTFs) as basic tools to rewire cell metabolism, reprogram cellular activity as well as boost cell’s productivity. This is commonly achieved by integrating sensor-actuator systems with biocatalytic functions and dynamically allocating cellular resources to drive carbon flux toward the target pathway. Up to date, most of identified MRTFs are derived from bacteria. As an endeavor to advance intelligent biomanufacturing in yeast cell factory, we will summarize the opportunities and challenges to transfer the bacteria-derived MRTFs to expand the small-molecule sensing capability in eukaryotic cells. We will discuss the design principles underlying MRTF-based biosensors in eukaryotic cells, including the choice of reliable reporters and the characterization tools to minimize background noise, strategies to tune the sensor dynamic range, sensitivity and specificity, as well as the criteria to engineer activator and repressor-based biosensors. Due to the physical separation of transcription and protein expression in eukaryotes, we argue that nuclear import/export mechanism of MRTFs across the nuclear membrane plays a critical role in regulating the MRTF sensor dynamics. Precisely-controlled MRTF response will allow us to repurpose the vast majority of transcriptional factors as molecular switches to achieve temporal or spatial gene expression in eukaryotes. Uncovering this knowledge will inform us fundamental design principles to deliver robust cell factories and enable the design of reprogrammable and predictable biological systems for intelligent biomanufacturing, smart therapeutics or precision medicine in the foreseeable future.
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Affiliation(s)
- Xia Wan
- Department of Chemical Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.,Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, Hubei, China
| | - Monireh Marsafari
- Department of Chemical Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.,Department of Agronomy and Plant Breeding, University of Guilan, Rasht, Islamic Republic of Iran
| | - Peng Xu
- Department of Chemical Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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20
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Pasternak G, Hanczyc MM. Novel method for detecting and quantifying phenol with transient response of glycolytic oscillations of synchronised yeast cells. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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21
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Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R. Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production. Front Bioeng Biotechnol 2018; 6:117. [PMID: 30338257 PMCID: PMC6178918 DOI: 10.3389/fbioe.2018.00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/02/2018] [Indexed: 01/16/2023] Open
Abstract
Since the advent of systems and synthetic biology, many studies have sought to harness microbes as cell factories through genetic and metabolic engineering approaches. Yeast and filamentous fungi have been successfully harnessed to produce fine and high value-added chemical products. In this review, we present some of the most promising advances from recent years in the use of fungi for this purpose, focusing on the manipulation of fungal strains using systems and synthetic biology tools to improve metabolic flow and the flow of secondary metabolites by pathway redesign. We also review the roles of bioinformatics analysis and predictions in synthetic circuits, highlighting in silico systemic approaches to improve the efficiency of synthetic modules.
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Affiliation(s)
- Leonardo Martins-Santana
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Luisa C Nora
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Ananda Sanches-Medeiros
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Gabriel L Lovate
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Murilo H A Cassiano
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Cell and Molecular Biology Department, Ribeirão Preto Medical School, São Paulo University (FMRP-USP), Ribeirão Preto, Brazil
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22
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Carpenter AC, Paulsen IT, Williams TC. Blueprints for Biosensors: Design, Limitations, and Applications. Genes (Basel) 2018; 9:E375. [PMID: 30050028 PMCID: PMC6115959 DOI: 10.3390/genes9080375] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/23/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range of industrial, medical, ecological, and scientific applications. Approaches to biosensor design are as diverse as their applications, with major biosensor classes including nucleic acids, proteins, and transcription factors. Each of these biosensor types has advantages and limitations based on the intended application, and the parameters that are required for optimal performance. Specifically, the choice of biosensor design must consider factors such as the ligand specificity, sensitivity, dynamic range, functional range, mode of output, time of activation, ease of use, and ease of engineering. This review discusses the rationale for designing the major classes of biosensor in the context of their limitations and assesses their suitability to different areas of biotechnological application.
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Affiliation(s)
- Alexander C Carpenter
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.
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23
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Snoek T, Romero-Suarez D, Zhang J, Ambri F, Skjoedt ML, Sudarsan S, Jensen MK, Keasling JD. An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast. ACS Synth Biol 2018; 7:995-1003. [PMID: 29613773 DOI: 10.1021/acssynbio.7b00439] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Microbes offer enormous potential for production of industrially relevant chemicals and therapeutics, yet the rapid identification of high-producing microbes from large genetic libraries is a major bottleneck in modern cell factory development. Here, we develop and apply a synthetic selection system in Saccharomyces cerevisiae that couples the concentration of muconic acid, a plastic precursor, to cell fitness by using the prokaryotic transcriptional regulator BenM driving an antibiotic resistance gene. We show that the sensor-selector does not affect production nor fitness, and find that tuning pH of the cultivation medium limits the rise of nonproducing cheaters. We apply the sensor-selector to selectively enrich for best-producing variants out of a large library of muconic acid production strains, and identify an isolate that produces more than 2 g/L muconic acid in a bioreactor. We expect that this sensor-selector can aid the development of other synthetic selection systems based on allosteric transcription factors.
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Affiliation(s)
- Tim Snoek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mette L. Skjoedt
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Suresh Sudarsan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
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