1
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Williams TC, Kroukamp H, Xu X, Wightman EL, Llorente B, Borneman AR, Carpenter AC, Van Wyk N, Meier F, Collier TR, Espinosa MI, Daniel EL, Walker RS, Cai Y, Nevalainen HK, Curach NC, Deveson IW, Mercer TR, Johnson DL, Mitchell LA, Bader JS, Stracquadanio G, Boeke JD, Goold HD, Pretorius IS, Paulsen IT. Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. CELL GENOMICS 2023; 3:100379. [PMID: 38020977 PMCID: PMC10667330 DOI: 10.1016/j.xgen.2023.100379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 12/01/2023]
Abstract
Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.
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Affiliation(s)
- Thomas C. Williams
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Heinrich Kroukamp
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Xin Xu
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Elizabeth L.I. Wightman
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Briardo Llorente
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
- The Australian Genome Foundry, Sydney, NSW, Australia
| | - Anthony R. Borneman
- The Australian Wine Research Institute, Adelaide, SA 5064, Australia
- School of Agriculture, Food & Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alexander C. Carpenter
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Niel Van Wyk
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Geisenheim, Germany
| | - Felix Meier
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Thomas R.V. Collier
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Monica I. Espinosa
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Elizabeth L. Daniel
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Roy S.K. Walker
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Helena K.M. Nevalainen
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Natalie C. Curach
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Bioplatforms Australia, Research Park Drive, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Ira W. Deveson
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Timothy R. Mercer
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Daniel L. Johnson
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- The Australian Wine Research Institute, Adelaide, SA 5064, Australia
| | - Leslie A. Mitchell
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Giovanni Stracquadanio
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Hugh D. Goold
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Isak S. Pretorius
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- The Australian Genome Foundry, Sydney, NSW, Australia
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2
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Zhang FL, Zhang L, Zeng DW, Liao S, Fan Y, Champreda V, Runguphan W, Zhao XQ. Engineering yeast cell factories to produce biodegradable plastics and their monomers: Current status and prospects. Biotechnol Adv 2023; 68:108222. [PMID: 37516259 DOI: 10.1016/j.biotechadv.2023.108222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Traditional plastic products have caused serious environmental pollution due to difficulty to be degraded in the natural environment. In the recent years, biodegradable plastics are receiving increasing attention due to advantages in natural degradability and environmental friendliness. Biodegradable plastics have potential to be used in food, agriculture, industry, medicine and other fields. However, the high production cost of such plastics is the bottleneck that limits their commercialization and application. Yeasts, including budding yeast and non-conventional yeasts, are widely studied to produce biodegradable plastics and their organic acid monomers. Compared to bacteria, yeast strains are more tolerable to multiple stress conditions including low pH and high temperature, and also have other advantages such as generally regarded as safe, and no phage infection. In addition, synthetic biology and metabolic engineering of yeast have enabled its rapid and efficient engineering for bioproduction using various renewable feedstocks, especially lignocellulosic biomass. This review focuses on the recent progress in biosynthesis technology and strategies of monomeric organic acids for biodegradable polymers, including polylactic acid (PLA), polyhydroxyalkanoate (PHA), polybutylene succinate (PBS), and polybutylene adipate terephthalate (PBAT) using yeast cell factories. Improving the performance of yeast as a cell factory and strategies to improve yeast acid stress tolerance are also discussed. In addition, the critical challenges and future prospects for the production of biodegradable plastic monomer using yeast are also discussed.
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Affiliation(s)
- Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Yachao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Patwari P, Pruckner F, Fabris M. Biosensors in microalgae: A roadmap for new opportunities in synthetic biology and biotechnology. Biotechnol Adv 2023; 68:108221. [PMID: 37495181 DOI: 10.1016/j.biotechadv.2023.108221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/22/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023]
Abstract
Biosensors are powerful tools to investigate, phenotype, improve and prototype microbial strains, both in fundamental research and in industrial contexts. Genetic and biotechnological developments now allow the implementation of synthetic biology approaches to novel different classes of microbial hosts, for example photosynthetic microalgae, which offer unique opportunities. To date, biosensors have not yet been implemented in phototrophic eukaryotic microorganisms, leaving great potential for novel biological and technological advancements untapped. Here, starting from selected biosensor technologies that have successfully been implemented in heterotrophic organisms, we project and define a roadmap on how these could be applied to microalgae research. We highlight novel opportunities for the development of new biosensors, identify critical challenges, and finally provide a perspective on the impact of their eventual implementation to tackle research questions and bioengineering strategies. From studying metabolism at the single-cell level to genome-wide screen approaches, and assisted laboratory evolution experiments, biosensors will greatly impact the pace of progress in understanding and engineering microalgal metabolism. We envision how this could further advance the possibilities for unraveling their ecological role, evolutionary history and accelerate their domestication, to further drive them as resource-efficient production hosts.
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Affiliation(s)
- Payal Patwari
- SDU Biotechnology, Faculty of Engineering, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Florian Pruckner
- SDU Biotechnology, Faculty of Engineering, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Michele Fabris
- SDU Biotechnology, Faculty of Engineering, University of Southern Denmark, Odense M DK-5230, Denmark.
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4
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Dixon TA, Walker RSK, Pretorius IS. Visioning synthetic futures for yeast research within the context of current global techno-political trends. Yeast 2023; 40:443-456. [PMID: 37653687 DOI: 10.1002/yea.3897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.
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Affiliation(s)
- Thomas A Dixon
- School of Social Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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Cai Y, Zhu K, Shen L, Ma J, Bao L, Chen D, Wei L, Wei N, Liu B, Wu Y, Chen S. Evolved Biosensor with High Sensitivity and Specificity for Measuring Cadmium in Actual Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10062-10071. [PMID: 35762704 DOI: 10.1021/acs.est.2c00627] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial biosensors have great potential in contaminant detection for sensitivity, specificity, cost-effectiveness, and easy operation. However, the existing cadmium-responsive bacterial biosensors cannot meet the real-world detection requirements due to lack of sensitivity, specificity, and anti-interference capability. This study aimed to develop a bacterial biosensor for detecting the total and extractable cadmium in actual environmental samples. We constructed the cadmium-responsive biosensor with the regulatory element (cadmium resistance transcriptional regulatory, CadR) and the reporting element (GFP) and improved its performance by directed evolution. The mutant libraries of biosensors were generated by error-prone PCR and screened by continuous five-round fluorescence-activated cell sorting (FACS), and a bacteria variant epCadR5 with higher performance was finally isolated. Biosensor fluorescence intensity was measured by a microplate reader, and results showed that the evolved cadmium-responsive bacterial biosensor was of high sensitivity and specificity in detecting trace cadmium, with a detection limit of 0.45 μg/L, which is 6.8 times more specific to cadmium than that of the wild-type. Furthermore, microscopic qualitative analysis results showed that the bacteria could produce fluorescence response in a cadmium-contaminated soil matrix, and quantitative analysis results showed that the values of cadmium from epCadR5 bacteria were close to that from inductively coupled plasma-mass spectrometry. These results suggest that the biosensor may have a broad application prospect in the detection of cadmium-contaminated soil and water.
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Affiliation(s)
- Yeshen Cai
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Kaili Zhu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Dongdong Chen
- Institute of Environmental Physics and Technology, Anhui University, Hefei 230039, China
| | - Liangchen Wei
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Nan Wei
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Binmei Liu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yuejin Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Shaopeng Chen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- School of Public Health, Wannan Medical College, Wuhu 241002, China
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6
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Kong Y, Zhao Y, Yu Y, Su W, Liu Z, Fei Y, Ma J, Mi L. Single cell sorting of young yeast based on label-free fluorescence lifetime imaging microscopy. JOURNAL OF BIOPHOTONICS 2022; 15:e202100344. [PMID: 34978383 DOI: 10.1002/jbio.202100344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Saccharomyces cerevisiae is an attractive organism used in the fermentation industry and is an important model organism for virus research. The ability to sort yeast cells is important for diverse applications. Replicative aging of Saccharomyces Cerevisiae is accompanied by metabolic changes that are related to an essential coenzyme, reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H). Here, a single cell sorting method based on fluorescence lifetime imaging microscopy (FLIM) and laser-induced forward transfer (LIFT) was implemented for the first time. The aging level of yeast was determined based on the FLIM by NAD(P)H, which was a label-free and noninvasive method for studying individual cells. Then, young and active yeast cells were sorted by the LIFT system at the single cell level. During the entire experiment, a sterile and humid environment was maintained to ensure the activity of cells. The high viability of sorted cells was achieved by the LIFT combining with FLIM.
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Affiliation(s)
- Yawei Kong
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
| | - Yinping Zhao
- Institute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
| | - Yao Yu
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, Shanghai, China
| | - Wenhua Su
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
| | - Zhijia Liu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
- Institute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), School of Information Science and Technology, Fudan University, Shanghai, China
- Institute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
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7
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Miyake R, Ling H, Foo JL, Fugono N, Chang MW. Transporter-Driven Engineering of a Genetic Biosensor for the Detection and Production of Short-Branched Chain Fatty Acids in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:838732. [PMID: 35372305 PMCID: PMC8975619 DOI: 10.3389/fbioe.2022.838732] [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: 12/18/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Biosensors can be used for real-time monitoring of metabolites and high-throughput screening of producer strains. Use of biosensors has facilitated strain engineering to efficiently produce value-added compounds. Following our recent work on the production of short branched-chain fatty acids (SBCFAs) in engineered Saccharomyces cerevisiae, here we harnessed a weak organic acid transporter Pdr12p, engineered a whole-cell biosensor to detect exogenous and intracellular SBCFAs and optimized the biosensor’s performance by varying PDR12 expression. We firstly constructed the biosensor and evaluated its response to a range of short-chain carboxylic acids. Next, we optimized its sensitivity and operational range by deletion and overexpression of PDR12. We found that the biosensor responded to exogenous SBCFAs including isovaleric acid, isobutyric acid and 2-methylbutanoic acid. PDR12 deletion enhanced the biosensor’s sensitivity to isovaleric acid at a low concentration and PDR12 overexpression shifted the operational range towards a higher concentration. Lastly, the deletion of PDR12 improved the biosensor’s sensitivity to the SBCFAs produced in our previously engineered SBCFA-overproducing strain. To our knowledge, our work represents the first study on employing an ATP-binding-cassette transporter to engineer a transcription-factor-based genetic biosensor for sensing SBCFAs in S. cerevisiae. Our findings provide useful insights into SBCFA detection by a genetic biosensor that will facilitate the screening of SBCFA-overproducing strains.
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Affiliation(s)
- Ryoma Miyake
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Science & Innovation Center, Mitsubishi Chemical Corporation, Yokohama, Japan
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nobutake Fugono
- Science & Innovation Center, Mitsubishi Chemical Corporation, Yokohama, Japan
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- *Correspondence: Matthew Wook Chang,
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8
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Pretorius IS. Visualising the next frontiers in wine yeast research. FEMS Yeast Res 2022; 22:6530195. [PMID: 35175339 PMCID: PMC8916113 DOI: 10.1093/femsyr/foac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
A range of game-changing biodigital and biodesign technologies are coming of age all around us, transforming our world in complex ways that are hard to predict. Not a day goes by without news of how data-centric engineering, algorithm-driven modelling, and biocyber technologies—including the convergence of artificial intelligence, machine learning, automated robotics, quantum computing, and genome editing—will change our world. If we are to be better at expecting the unexpected in the world of wine, we need to gain deeper insights into the potential and limitations of these technological developments and advances along with their promise and perils. This article anticipates how these fast-expanding bioinformational and biodesign toolkits might lead to the creation of synthetic organisms and model systems, and ultimately new understandings of biological complexities could be achieved. A total of four future frontiers in wine yeast research are discussed in this article: the construction of fully synthetic yeast genomes, including minimal genomes; supernumerary pan-genome neochromosomes; synthetic metagenomes; and synthetic yeast communities. These four concepts are at varying stages of development with plenty of technological pitfalls to overcome before such model chromosomes, genomes, strains, and yeast communities could illuminate some of the ill-understood aspects of yeast resilience, fermentation performance, flavour biosynthesis, and ecological interactions in vineyard and winery settings. From a winemaker's perspective, some of these ideas might be considered as far-fetched and, as such, tempting to ignore. However, synthetic biologists know that by exploring these futuristic concepts in the laboratory could well forge new research frontiers to deepen our understanding of the complexities of consistently producing fine wines with different fermentation processes from distinctive viticultural terroirs. As the saying goes in the disruptive technology industry, it take years to create an overnight success. The purpose of this article is neither to glorify any of these concepts as a panacea to all ills nor to crucify them as a danger to winemaking traditions. Rather, this article suggests that these proposed research endeavours deserve due consideration because they are likely to cast new light on the genetic blind spots of wine yeasts, and how they interact as communities in vineyards and wineries. Future-focussed research is, of course, designed to be subject to revision as new data and technologies become available. Successful dislodging of old paradigms with transformative innovations will require open-mindedness and pragmatism, not dogmatism—and this can make for a catch-22 situation in an archetypal traditional industry, such as the wine industry, with its rich territorial and socio-cultural connotations.
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Affiliation(s)
- I S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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9
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Dixon TA, Williams TC, Pretorius IS. Bioinformational trends in grape and wine biotechnology. Trends Biotechnol 2021; 40:124-135. [PMID: 34108075 DOI: 10.1016/j.tibtech.2021.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
The creative destruction caused by the coronavirus pandemic is yielding immense opportunity for collaborative innovation networks. The confluence of biosciences, information sciences, and the engineering of biology, is unveiling promising bioinformational futures for a vibrant and sustainable bioeconomy. Bioinformational engineering, underpinned by DNA reading, writing, and editing technologies, has become a beacon of opportunity in a world paralysed by uncertainty. This article draws on lessons from the current pandemic and previous agricultural blights, and explores bioinformational research directions aimed at future-proofing the grape and wine industry against biological shocks from global blights and climate change.
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Affiliation(s)
- Thomas A Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, NSW 2109, Australia
| | - Isak S Pretorius
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, NSW 2109, Australia; Chancellery, Macquarie University, Sydney, NSW 2109, Australia.
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10
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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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11
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Dacquay LC, McMillen DR. Improving the design of an oxidative stress sensing biosensor in yeast. FEMS Yeast Res 2021; 21:6232160. [PMID: 33864457 PMCID: PMC8088429 DOI: 10.1093/femsyr/foab025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/15/2021] [Indexed: 12/23/2022] Open
Abstract
Transcription factor (TF)-based biosensors have proven useful for increasing biomanufacturing yields, large-scale functional screening, and in environmental monitoring. Most yeast TF-based biosensors are built from natural promoters, resulting in large DNA parts retaining considerable homology to the host genome, which can complicate biological engineering efforts. There is a need to explore smaller, synthetic biosensors to expand the options for regulating gene expression in yeast. Here, we present a systematic approach to improving the design of an existing oxidative stress sensing biosensor in Saccharomyces cerevisiae based on the Yap1 transcription factor. Starting from a synthetic core promoter, we optimized the activity of a Yap1-dependent promoter through rational modification of a minimalist Yap1 upstream activating sequence. Our novel promoter achieves dynamic ranges of activation surpassing those of the previously engineered Yap1-dependent promoter, while reducing it to only 171 base pairs. We demonstrate that coupling the promoter to a positive-feedback-regulated TF further improves the biosensor by increasing its dynamic range of activation and reducing its limit of detection. We have illustrated the robustness and transferability of the biosensor by reproducing its activity in an unconventional probiotic yeast strain, Saccharomyces boulardii. Our findings can provide guidance in the general process of TF-based biosensor design.
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Affiliation(s)
- Louis C Dacquay
- Dept of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga ON L5L 1C6, Canada
| | - David R McMillen
- Dept of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga ON L5L 1C6, Canada.,Departments of Chemistry and Physics, University of Toronto, 80 St. George St., Toronto ON M5S 3H6, Canada
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12
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Belda I, Williams TC, de Celis M, Paulsen IT, Pretorius IS. Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell. Nat Commun 2021; 12:1599. [PMID: 33707418 PMCID: PMC7952416 DOI: 10.1038/s41467-021-21877-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
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Affiliation(s)
- Ignacio Belda
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Thomas C. Williams
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Miguel de Celis
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Ian T. Paulsen
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Isak S. Pretorius
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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13
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Dixon TA, Williams TC, Pretorius IS. Sensing the future of bio-informational engineering. Nat Commun 2021; 12:388. [PMID: 33452260 PMCID: PMC7810845 DOI: 10.1038/s41467-020-20764-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
The practices of synthetic biology are being integrated into 'multiscale' designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of 'bio-informational' engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.
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Affiliation(s)
- Thomas A Dixon
- Department of Modern History, Politics and International Relations, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Thomas C Williams
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
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14
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Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae. Nat Commun 2020; 11:5564. [PMID: 33149159 PMCID: PMC7643182 DOI: 10.1038/s41467-020-19390-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/05/2020] [Indexed: 01/22/2023] Open
Abstract
Utilising one-carbon substrates such as carbon dioxide, methane, and methanol is vital to address the current climate crisis. Methylotrophic metabolism enables growth and energy generation from methanol, providing an alternative to sugar fermentation. Saccharomyces cerevisiae is an important industrial microorganism for which growth on one-carbon substrates would be relevant. However, its ability to metabolize methanol has been poorly characterised. Here, using adaptive laboratory evolution and 13C-tracer analysis, we discover that S. cerevisiae has a native capacity for methylotrophy. A systems biology approach reveals that global rearrangements in central carbon metabolism fluxes, gene expression changes, and a truncation of the uncharacterized transcriptional regulator Ygr067cp supports improved methylotrophy in laboratory evolved S. cerevisiae. This research paves the way for further biotechnological development and fundamental understanding of methylotrophy in the preeminent eukaryotic model organism and industrial workhorse, S. cerevisiae. Methylotrophic metabolism enables growth on methanol, an alternative to sugar fermentation. Here the authors use adaptive laboratory evolution to uncover native methylotrophy capacity in Saccharomyces cerevisiae.
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15
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Jha RK, Strauss CEM. Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase. ACS Synth Biol 2020; 9:1234-1239. [PMID: 32369698 DOI: 10.1021/acssynbio.0c00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single "bad" mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON1) were rapidly screened via an engineered positive-feedback circuit: a p-nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON1, which catalyzed paraoxon breakdown and PNP production. Rare active mutant colonies, picked by simple visual fluorescence of a PON1-green fluorescent protein (GFP) fusion, were characterized. In a single screening round, high (library-scale) throughput enabled the discovery of enhanced paraoxon degradation activity in PON1, including structurally unexpected mutations.
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Affiliation(s)
- Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, MS M888, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
| | - Charlie E. M. Strauss
- Bioscience Division, Los Alamos National Laboratory, MS M888, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
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16
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Zhu Y, Zhou C, Wang Y, Li C. Transporter Engineering for Microbial Manufacturing. Biotechnol J 2020; 15:e1900494. [PMID: 32298528 DOI: 10.1002/biot.201900494] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Indexed: 01/08/2023]
Abstract
Microbes play an important role in biotransformation and biosynthesis of biofuels, natural products, and polymers. Therefore, microbial manufacturing has been widely used in medicine, industry, and agriculture. However, common strategies including enzyme engineering, pathway optimization, and host engineering are generally inadequate to obtain an efficient microbial production system. Transporter engineering provides an alternative strategy to promote the transmembrane transfer of substrates, intermediates, and final products in microbial cells and thus enhances production by alleviating feedback inhibition and cytotoxicity caused by final products. According to the current studies in transport engineering, native transporters usually have low expression and poor transportation ability, resulting in inefficient transport processes and microbial production. In this review, current approaches for transporter mining, characterization, and verification are comprehensively summarized. Practical approaches to enhance the transport system in engineered cells, such as balancing transporter overexpression and cell growth, and evolution of native transporters are discussed. Furthermore, the applications of transporter engineering in microbial manufacturing, including enhancement of substrate utilization, concentration of metabolic flux to the target pathway, and acceleration of efflux and recovery of products, demonstrate its outstanding advantages and promising prospects.
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Affiliation(s)
- Ying Zhu
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chen Zhou
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Ying Wang
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Chun Li
- Department of Biochemical Engineering, Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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17
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van Wyk N, Kroukamp H, Espinosa MI, von Wallbrunn C, Wendland J, Pretorius IS. Blending wine yeast phenotypes with the aid of CRISPR DNA editing technologies. Int J Food Microbiol 2020; 324:108615. [PMID: 32371236 DOI: 10.1016/j.ijfoodmicro.2020.108615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/02/2020] [Accepted: 03/24/2020] [Indexed: 01/12/2023]
Abstract
In recent years, CRISPR/Cas9-based genetic editing has become a mainstay in many laboratories including manipulations done with yeast. We utilized this technique to generate a self-cloned wine yeast strain that overexpresses two genes of oenological relevance i.e. the glycerol-3-phosphate dehydrogenase 1 (GPD1) and the alcohol acetyltransferase 1 (ATF1) directly implicated in glycerol and acetate ester production respectively. Riesling wine made from the resulting strain showed increased glycerol and acetate ester levels compared to the parental strain. In addition, significantly less acetic acid levels were measured in wine made with yeast containing both genetic alterations compared to wine made with the strain that only overexpresses GPD1. Thus, this strain provides an alternative strategy for alleviating the accumulation of acetic acid once glycerol production is favoured during alcoholic fermentation with the addition of dramatically increasing acetate esters production.
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Affiliation(s)
- Niël van Wyk
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia; Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Geisenheim, Germany.
| | - Heinrich Kroukamp
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Monica I Espinosa
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia; CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Christian von Wallbrunn
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Geisenheim, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Geisenheim, Germany
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
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18
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Xu X, Williams TC, Divne C, Pretorius IS, Paulsen IT. Evolutionary engineering in Saccharomyces cerevisiae reveals a TRK1-dependent potassium influx mechanism for propionic acid tolerance. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:97. [PMID: 31044010 PMCID: PMC6477708 DOI: 10.1186/s13068-019-1427-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Propionic acid (PA), a key platform chemical produced as a by-product during petroleum refining, has been widely used as a food preservative and an important chemical intermediate in many industries. Microbial PA production through engineering yeast as a cell factory is a potentially sustainable alternative to replace petroleum refining. However, PA inhibits yeast growth at concentrations well below the titers typically required for a commercial bioprocess. RESULTS Adaptive laboratory evolution (ALE) with PA concentrations ranging from 15 to 45 mM enabled the isolation of yeast strains with more than threefold improved tolerance to PA. Through whole genome sequencing and CRISPR-Cas9-mediated reverse engineering, unique mutations in TRK1, which encodes a high-affinity potassium transporter, were revealed as the cause of increased propionic acid tolerance. Potassium supplementation growth assays showed that mutated TRK1 alleles and extracellular potassium supplementation not only conferred tolerance to PA stress but also to multiple organic acids. CONCLUSION Our study has demonstrated the use of ALE as a powerful tool to improve yeast tolerance to PA. Potassium transport and maintenance is not only critical in yeast tolerance to PA but also boosts tolerance to multiple organic acids. These results demonstrate high-affinity potassium transport as a new principle for improving organic acid tolerance in strain engineering.
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Affiliation(s)
- Xin Xu
- 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
| | - Christina Divne
- KTH School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Isak S. Pretorius
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
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19
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Baumann L, Rajkumar AS, Morrissey JP, Boles E, Oreb M. A Yeast-Based Biosensor for Screening of Short- and Medium-Chain Fatty Acid Production. ACS Synth Biol 2018; 7:2640-2646. [PMID: 30338986 DOI: 10.1021/acssynbio.8b00309] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Short- and medium-chain fatty acids (SMCFA) are important platform chemicals currently produced from nonsustainable resources. The engineering of microbial cells to produce SMCFA, however, lacks high-throughput methods to screen for best performing cells. Here, we present the development of a whole-cell biosensor for easy and rapid detection of SMCFA. The biosensor is based on a multicopy yeast plasmid containing the SMCFA-responsive PDR12 promoter coupled to GFP as the reporter gene. The sensor detected hexanoic, heptanoic and octanoic acid over a linear range up to 2, 1.5, and 0.75 mM, respectively, but did not show a linear response to decanoic and dodecanoic acid. We validated the functionality of the biosensor with culture supernatants of a previously engineered Saccharomyces cerevisiae octanoic acid producer strain and derivatives thereof. The biosensor signal correlated strongly with the octanoic acid concentrations as determined by gas chromatography. Thus, this biosensor enables the high-throughput screening of SMCFA producers and has the potential to drastically speed up the engineering of diverse SMCFA producing cell factories.
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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
| | - Arun S. Rajkumar
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - John P. Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - 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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20
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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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Goold HD, Wright P, Hailstones D. Emerging Opportunities for Synthetic Biology in Agriculture. Genes (Basel) 2018; 9:E341. [PMID: 29986428 PMCID: PMC6071285 DOI: 10.3390/genes9070341] [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: 06/01/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022] Open
Abstract
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.
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Affiliation(s)
- Hugh Douglas Goold
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Philip Wright
- New South Wales Department of Primary Industries, Locked Bag 21, 161 Kite St, Orange, NSW 2800, Australia.
| | - Deborah Hailstones
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
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Vickers CE, Williams TC, Peng B, Cherry J. Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Jagtap UB, Jadhav JP, Bapat VA, Pretorius IS. Synthetic biology stretching the realms of possibility in wine yeast research. Int J Food Microbiol 2017; 252:24-34. [DOI: 10.1016/j.ijfoodmicro.2017.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 01/02/2023]
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