1
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Hoffmann SA, Cai Y. Engineering stringent genetic biocontainment of yeast with a protein stability switch. Nat Commun 2024; 15:1060. [PMID: 38316765 PMCID: PMC10844650 DOI: 10.1038/s41467-024-44988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Synthetic biology holds immense promise to tackle key problems in resource use, environmental remediation, and human health care. However, comprehensive safety measures are lacking to employ engineered microorganisms in open-environment applications. Genetically encoded biocontainment systems may solve this issue. Here, we describe such a system based on conditional stability of essential proteins. We used a destabilizing domain degron stabilized by estradiol addition (ERdd). We ERdd-tagged 775 essential genes and screened for strains with estradiol dependent growth. Three genes, SPC110, DIS3 and RRP46, were found to be particularly suitable targets. Respective strains showed no growth defect in the presence of estradiol and strong growth inhibition in its absence. SPC110-ERdd offered the most stringent containment, with an escape frequency of <5×10-7. Removal of its C-terminal domain decreased the escape frequency further to <10-8. Being based on conditional protein stability, the presented approach is mechanistically orthogonal to previously reported genetic biocontainment systems.
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Affiliation(s)
- Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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2
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Chang T, Ding W, Yan S, Wang Y, Zhang H, Zhang Y, Ping Z, Zhang H, Huang Y, Zhang J, Wang D, Zhang W, Xu X, Shen Y, Fu X. A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid. Nat Commun 2023; 14:6487. [PMID: 37838746 PMCID: PMC10576815 DOI: 10.1038/s41467-023-42358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.
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Affiliation(s)
- Tiantian Chang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Weichao Ding
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Shirui Yan
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yun Wang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Haoling Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yu Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Zhi Ping
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Huiming Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Yijian Huang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Jiahui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, Shenzhen, 518083, China
| | - Dan Wang
- Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science, BNU-HKBU United International College, Zhuhai, 519087, China
- BNU-HKBU United International College, Zhuhai, 519087, China
| | - Wenwei Zhang
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Yue Shen
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
| | - Xian Fu
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Changzhou, 213299, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China.
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3
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Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, Boeke JD, Wheeler N, Cai Y. Safety by design: Biosafety and biosecurity in the age of synthetic genomics. iScience 2023; 26:106165. [PMID: 36895643 PMCID: PMC9988571 DOI: 10.1016/j.isci.2023.106165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Technologies to profoundly engineer biology are becoming increasingly affordable, powerful, and accessible to a widening group of actors. While offering tremendous potential to fuel biological research and the bioeconomy, this development also increases the risk of inadvertent or deliberate creation and dissemination of pathogens. Effective regulatory and technological frameworks need to be developed and deployed to manage these emerging biosafety and biosecurity risks. Here, we review digital and biological approaches of a range of technology readiness levels suited to address these challenges. Digital sequence screening technologies already are used to control access to synthetic DNA of concern. We examine the current state of the art of sequence screening, challenges and future directions, and environmental surveillance for the presence of engineered organisms. As biosafety layer on the organism level, we discuss genetic biocontainment systems that can be used to created host organisms with an intrinsic barrier against unchecked environmental proliferation.
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Affiliation(s)
- Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - James Diggans
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, 610 Commonwealth Avenue, Boston, MA 02215, USA
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tom Knight
- Ginkgo Bioworks, 27 Drydock Avenue, Boston, MA 02210, USA
| | - Emily Leproust
- Twist Bioscience, 681 Gateway Boulevard, South San Francisco, CA 9408, USA
| | - Jef D Boeke
- Institute for Systems Genetics, and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, 435 East 30th Street, New York, NY 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Nicole Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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4
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Hooker CA, Hanafy R, Hillman ET, Muñoz Briones J, Solomon KV. A Genetic Engineering Toolbox for the Lignocellulolytic Anaerobic Gut Fungus Neocallimastix frontalis. ACS Synth Biol 2023; 12:1034-1045. [PMID: 36920337 DOI: 10.1021/acssynbio.2c00502] [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: 03/16/2023]
Abstract
Anaerobic fungi are powerful platforms for biotechnology that remain unexploited due to a lack of genetic tools. These gut fungi encode the largest number of lignocellulolytic carbohydrate active enzymes (CAZymes) in the fungal kingdom, making them attractive for applications in renewable energy and sustainability. However, efforts to genetically modify anaerobic fungi have remained limited due to inefficient methods for DNA uptake and a lack of characterized genetic parts. We demonstrate that anaerobic fungi are naturally competent for DNA and leverage this to develop a nascent genetic toolbox informed by recently acquired genomes for transient transformation of anaerobic fungi. We validate multiple selectable markers (HygR and Neo), an anaerobic reporter protein (iRFP702), enolase and TEF1A promoters, TEF1A terminator, and a nuclear localization tag for protein compartmentalization. This work establishes novel methods to reliably transform the anaerobic fungus Neocallimastix frontalis, thereby paving the way for strain development and various synthetic biology applications.
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Affiliation(s)
- Casey A Hooker
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Radwa Hanafy
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Ethan T Hillman
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Javier Muñoz Briones
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kevin V Solomon
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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5
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Murakami H, Sano K, Motomura K, Kuroda A, Hirota R. Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system. J Biosci Bioeng 2023; 135:190-195. [PMID: 36653270 DOI: 10.1016/j.jbiosc.2022.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/18/2023]
Abstract
Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.
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Affiliation(s)
- Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kosuke Sano
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kei Motomura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
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6
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Zhu X, Zhaoyang Zhang, Bin Jia, Yuan Y. Current advances of biocontainment strategy in synthetic biology. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Peng B, Esquirol L, Lu Z, Shen Q, Cheah LC, Howard CB, Scott C, Trau M, Dumsday G, Vickers CE. An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae. Nat Commun 2022; 13:2895. [PMID: 35610221 PMCID: PMC9130285 DOI: 10.1038/s41467-022-30529-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Bottlenecks in metabolic pathways due to insufficient gene expression levels remain a significant problem for industrial bioproduction using microbial cell factories. Increasing gene dosage can overcome these bottlenecks, but current approaches suffer from numerous drawbacks. Here, we describe HapAmp, a method that uses haploinsufficiency as evolutionary force to drive in vivo gene amplification. HapAmp enables efficient, titratable, and stable integration of heterologous gene copies, delivering up to 47 copies onto the yeast genome. The method is exemplified in metabolic engineering to significantly improve production of the sesquiterpene nerolidol, the monoterpene limonene, and the tetraterpene lycopene. Limonene titre is improved by 20-fold in a single engineering step, delivering ∼1 g L-1 in the flask cultivation. We also show a significant increase in heterologous protein production in yeast. HapAmp is an efficient approach to unlock metabolic bottlenecks rapidly for development of microbial cell factories.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia. .,CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Lygie Esquirol
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Qianyi Shen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia.,Biocatalysis and Synthetic Biology Team, CSIRO Land and Water, Black Mountain Science and Innovation Park, Canberra, ACT, 2061, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia.
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8
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Pantoja Angles A, Valle-Pérez AU, Hauser C, Mahfouz MM. Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications. Front Bioeng Biotechnol 2022; 10:830200. [PMID: 35186907 PMCID: PMC8847691 DOI: 10.3389/fbioe.2022.830200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Many applications of synthetic biology require biological systems in engineered microbes to be delivered into diverse environments, such as for in situ bioremediation, biosensing, and applications in medicine and agriculture. To avoid harming the target system (whether that is a farm field or the human gut), such applications require microbial biocontainment systems (MBSs) that inhibit the proliferation of engineered microbes. In the past decade, diverse molecular strategies have been implemented to develop MBSs that tightly control the proliferation of engineered microbes; this has enabled medical, industrial, and agricultural applications in which biological processes can be executed in situ. The customization of MBSs also facilitate the integration of sensing modules for which different compounds can be produced and delivered upon changes in environmental conditions. These achievements have accelerated the generation of novel microbial systems capable of responding to external stimuli with limited interference from the environment. In this review, we provide an overview of the current approaches used for MBSs, with a specific focus on applications that have an immediate impact on multiple fields.
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Affiliation(s)
- Aaron Pantoja Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
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9
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Yoo JI, Navaratna TA, Kolence P, O’Malley MA. GPCR-FEX: A Fluoride-Based Selection System for Rapid GPCR Screening and Engineering. ACS Synth Biol 2022; 11:39-45. [PMID: 34979077 DOI: 10.1021/acssynbio.1c00030] [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: 11/29/2022]
Abstract
The directed evolution of proteins comprises a search of sequence space for variants that improve a target phenotype, yet identification of desirable variants is inherently limited by library size and screening ability. Selections that couple protein phenotype to cell viability accelerate identification of promising variants by depleting libraries of undesirable variants en masse. Here, we introduce GPCR-FEX, a stringent selection platform that couples G-protein coupled receptor (GPCR) signaling to expression of a fluoride ion exporter (FEX)-GFP fusion gene and concomitant cellular fluoride tolerance in yeast. The GPCR-FEX platform works to deplete inactive GPCR variants from the library prior to high-throughput fluorescence-based cell sorting for rapid, inexpensive screening of receptor libraries that sample an expanded sequence space. Using this system, FEX1 was placed under the control of either PFUS1 or PFIG1, promoters activated upon agonist binding by the native yeast GPCRs, Ste2p or Ste3p. Addition of a C-terminal degron to FEX1p enhanced the dynamic range of cell growth between agonist-treated and untreated cells. Using deep sequencing to enumerate population members, we show rapid selection of a previously engineered Ste2p receptor mutant strain over wild-type Ste2p in a model library enrichment experiment. Overall, the GPCR-FEX platform provides a mechanism to rapidly engineer GPCRs, which are important cellular sensors for synthetic biology.
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Affiliation(s)
- Justin I. Yoo
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Tejas A. Navaratna
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Patrick Kolence
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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10
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Tong YJ, Yu LD, Li N, Fu Q, Xu K, Wei J, Ye YX, Xu J, Zhu F, Pawliszyn J, Ouyang G. Ratiometric fluorescent probe for the on-site monitoring of coexisted Hg 2+ and F - in sequence. Anal Chim Acta 2021; 1183:338967. [PMID: 34627509 DOI: 10.1016/j.aca.2021.338967] [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: 05/31/2021] [Revised: 08/05/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
The monitoring of mercury and fluoride ions (Hg2+ and F-) has aroused wide concerns owing to the high toxicity of Hg2+ and the duplicitous nature of F- to human health. As far as we known, more than 100 million people in poverty-stricken areas are still at high risk of being over-exposed to Hg2+ and F- via drinking water. Simple and cost-effective luminescent methods are highly promising for on-site water monitoring in rural areas. However, the development of multipurpose luminescent probes that are accurate and sensitive remains challenging. Herein, a new strategy for rationally designing a multipurpose ratiometric probe is present. The obtained probe is consisted of two emission units with energy transfer between them, which exhibit high coordination affinities to the two coexisted toxic targets (Hg2+ and F-), respectively. Thus, two distinct routes for efficiently modulating the energy transfer in the probe are present to trigger the responses to the two targets in sequence. By detecting the shift of the emission color with a smartphone, an on-site water monitoring method is successfully established with the detection limits as low as 2.7 nM for Hg2+ and 1.9 μM for F-. The present study can expend the toolbox for water monitoring in rural regions.
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Affiliation(s)
- Yuan-Jun Tong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lu-Dan Yu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nan Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Fu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ke Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiajun Wei
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Xin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianqiao Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L3G1, Canada
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China; Chemistry College, Center of Advanced Analysis and Gene Sequencing, Zhengzhou University, Kexue Avenue 100, Zhengzhou, 450001, China; Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangdong Academy of Sciences, 100 Xianlie Middle Road, Guangzhou, 510070, China
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11
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Podolsky IA, Seppälä S, Xu H, Jin YS, O'Malley MA. A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast. Metab Eng 2021; 66:137-147. [PMID: 33887459 DOI: 10.1016/j.ymben.2021.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/23/2021] [Accepted: 04/12/2021] [Indexed: 01/08/2023]
Abstract
In the yeast Saccharomyces cerevisiae, microbial fuels and chemicals production on lignocellulosic hydrolysates is constrained by poor sugar transport. For biotechnological applications, it is desirable to source transporters with novel or enhanced function from nonconventional organisms in complement to engineering known transporters. Here, we identified and functionally screened genes from three strains of early-branching anaerobic fungi (Neocallimastigomycota) that encode sugar transporters from the recently discovered Sugars Will Eventually be Exported Transporter (SWEET) superfamily in Saccharomyces cerevisiae. A novel fungal SWEET, NcSWEET1, was identified that localized to the plasma membrane and complemented growth in a hexose transporter-deficient yeast strain. Single cross-over chimeras were constructed from a leading NcSWEET1 expression-enabling domain paired with all other candidate SWEETs to broadly scan the sequence and functional space for enhanced variants. This led to the identification of a chimera, NcSW1/PfSW2:TM5-7, that enhanced the growth rate significantly on glucose, fructose, and mannose. Additional chimeras with varied cross-over junctions identified residues in TM1 that affect substrate selectivity. Furthermore, we demonstrate that NcSWEET1 and the enhanced NcSW1/PfSW2:TM5-7 variant facilitated novel co-consumption of glucose and xylose in S. cerevisiae. NcSWEET1 utilized 40.1% of both sugars, exceeding the 17.3% utilization demonstrated by the control HXT7(F79S) strain. Our results suggest that SWEETs from anaerobic fungi are beneficial tools for enhancing glucose and xylose co-utilization and offers a promising step towards biotechnological application of SWEETs in S. cerevisiae.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Haiqing Xu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproduct Innovation (CABBI), Urbana, IL, 61801, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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