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So KK, Le NMT, Nguyen NL, Kim DH. Improving expression and assembly of difficult-to-express heterologous proteins in Saccharomyces cerevisiae by culturing at a sub-physiological temperature. Microb Cell Fact 2023; 22:55. [PMID: 36959657 PMCID: PMC10035479 DOI: 10.1186/s12934-023-02065-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Escherichia coli heat labile toxin B subunit (LTB) is one of the most popular oral vaccine adjuvants and intestine adsorption enhancers. It is often expressed as a fusion partner with target antigens to enhance their immunogenicity as well as gut absorbability. However, high expression levels of a fusion protein are critical to the outcome of immunization experiments and the success of subsequent vaccine development efforts. In order to improve the expression and functional assembly of LTB-fusion proteins using Saccharomyces cerevisiae, we compared their expression under culture conditions at a sub-physiological temperature 20 °C with their expression under a standard 30 °C. RESULTS The assembled expression of LTB-EDIII2 (LTB fused to the envelope domain III (EDIII) of Dengue virus serotype 2), which was expressed at the level of 20 µg/L in our previous study, was higher when the expression temperature was 20 °C as opposed to 30 °C. We also tested whether the expression and functional assembly of a difficult-to-express LTB fusion protein could be increased. The assembled expression of the difficult-to-express LTB-VP1 fusion protein (LTB fused to VP1 antigen of Foot-and-Mouth Disease Virus) dramatically increased, although the total amount of expressed protein was still lower than that of LTB-EDIII2. Slight but significant increase in the expression of well-known reporter protein eGFP, which has previously been shown to be increased by cultivation at 20 °C, was also observed in our expression system. As no significant changes in corresponding transcripts levels and cell growth were observed between 20 °C and 30 °C, we infer that translation and post-translational assembly are responsible for these enhancements. CONCLUSIONS The effects of lowering the expression temperature from 30 °C to 20 °C on protein expression and folding levels in S. cerevisiae, using several proteins as models, are reported. When heterologous proteins are expressed at 20 °C, a greater amount of (specially, more assembled) functional proteins accumulated than at 30 °C. Although further studies are required to understand the molecular mechanisms, our results suggest that lowering the expression temperature is a convenient strategy for improving the expression of relatively complexly structured and difficult-to-express proteins in S. cerevisiae.
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Affiliation(s)
- Kum-Kang So
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc My Tieu Le
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc-Luong Nguyen
- Department of Biology, College of Sciences, Hue University, Hue, 530000, Vietnam.
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
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Zhao X, Yu H, Liang Q, Zhou J, Li J, Du G, Chen J. Stepwise Optimization of Inducible Expression System for the Functional Secretion of Horseradish Peroxidase in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4059-4068. [PMID: 36821527 DOI: 10.1021/acs.jafc.2c09117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Horseradish peroxidase (HRP) is a plant-derived glycoprotein that can be developed as a food additive to cross-link proteins or biopolymers. Although Saccharomyces cerevisiae has advantages in the production of food-grade HRP, the low expressional level and inefficient secretion hindered its application values. After comparing the effects of constitutive and inducible expression on cell growth, the strength of HRP expression was roughly tuned by replacing core regions of the promoter in the GAL80-knockout strain and further finely tuned by terminator screening. Additionally, the most suitable signal peptide was selected, and the pre-peptide with pro-peptides was modified to balance the transport of HRP in the endoplasmic reticulum. The extracellular HRP activity of the best strain reached 13 506 U/L at the fermenter level, 330-fold higher than the previous result of 41 U/L in S. cerevisiae. The strategy can be applied to alleviate the inhibition of cell growth caused by the expression of toxic proteins and improve their secretion.
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Affiliation(s)
- Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Haibo Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Qingfeng Liang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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3
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Wefelmeier K, Ebert BE, Blank LM, Schmitz S. Mix and Match: Promoters and Terminators for Tuning Gene Expression in the Methylotrophic Yeast Ogataea polymorpha. Front Bioeng Biotechnol 2022; 10:876316. [PMID: 35620471 PMCID: PMC9127203 DOI: 10.3389/fbioe.2022.876316] [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: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
The yeast Ogataea polymorpha is an upcoming host for bio-manufacturing due to its unique physiological properties, including its broad substrate spectrum, and particularly its ability to utilize methanol as the sole carbon and energy source. However, metabolic engineering tools for O. polymorpha are still rare. In this study we characterized the influence of 6 promoters and 15 terminators on gene expression throughout batch cultivations with glucose, glycerol, and methanol as carbon sources as well as mixes of these carbon sources. For this characterization, a short half-life Green Fluorescent Protein (GFP) variant was chosen, which allows a precise temporal resolution of gene expression. Our promoter studies revealed how different promoters do not only influence the expression strength but also the timepoint of maximal expression. For example, the expression strength of the catalase promoter (pCAT) and the methanol oxidase promoter (pMOX) are comparable on methanol, but the maximum expression level of the pCAT is reached more than 24 h earlier. By varying the terminators, a 6-fold difference in gene expression was achieved with the MOX terminator boosting gene expression on all carbon sources by around 50% compared to the second-strongest terminator. It was shown that this exceptional increase in gene expression is achieved by the MOX terminator stabilizing the mRNA, which results in an increased transcript level in the cells. We further found that different pairing of promoters and terminators or the expression of a different gene (β-galactosidase gene) did not influence the performance of the genetic parts. Consequently, it is possible to mix and match promoters and terminators as independent elements to tune gene expression in O. polymorpha.
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Affiliation(s)
- Katrin Wefelmeier
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Lars M Blank
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Simone Schmitz
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
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4
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Liu X, Cui Z, Su T, Lu X, Hou J, Qi Q. Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica. Microb Biotechnol 2022; 15:2223-2234. [PMID: 35436041 PMCID: PMC9328735 DOI: 10.1111/1751-7915.14060] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
With the rapid development of synthetic biology, the oleaginous yeast Yarrowia lipolytica has become an attractive microorganism for chemical production. To better optimize and reroute metabolic pathways, we have expanded the CRISPR‐based gene expression toolkit of Y. lipolytica. By sorting the integration sites associated with high expression, new neutral integration sites associated with high expression and high integration efficiency were identified. Diverse genetic components, including promoters and terminators, were also characterized to expand the expression range. We found that in addition to promoters, the newly characterized terminators exhibited large variations in gene expression. These genetic components and integration sites were then used to regulate genes involved in the lycopene biosynthesis pathway, and different levels of lycopene production were achieved. The CRISPR‐based gene expression toolkit developed in this study will facilitate the genetic engineering of Y. lipolytica.
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Affiliation(s)
- Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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5
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Otto M, Liu D, Siewers V. Saccharomyces cerevisiae as a Heterologous Host for Natural Products. Methods Mol Biol 2022; 2489:333-367. [PMID: 35524059 DOI: 10.1007/978-1-0716-2273-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell factories can provide a sustainable supply of natural products with applications as pharmaceuticals, food-additives or biofuels. Besides being an important model organism for eukaryotic systems, Saccharomyces cerevisiae is used as a chassis for the heterologous production of natural products. Its success as a cell factory can be attributed to the vast knowledge accumulated over decades of research, its overall ease of engineering and its robustness. Many methods and toolkits have been developed by the yeast metabolic engineering community with the aim of simplifying and accelerating the engineering process.In this chapter, a range of methodologies are highlighted, which can be used to develop novel natural product cell factories or to improve titer, rate and yields of an existing cell factory with the goal of developing an industrially relevant strain. The addressed topics are applicable for different stages of a cell factory engineering project and include the choice of a natural product platform strain, expression cassette design for heterologous or native genes, basic and advanced genetic engineering strategies, and library screening methods using biosensors. The many engineering methods available and the examples of yeast cell factories underline the importance and future potential of this host for industrial production of natural products.
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Affiliation(s)
- Maximilian Otto
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dany Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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6
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Efficient Conversion of Glycerol to Ethanol by an Engineered Saccharomyces cerevisiae Strain. Appl Environ Microbiol 2021; 87:e0026821. [PMID: 34524902 DOI: 10.1128/aem.00268-21] [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: 11/20/2022] Open
Abstract
Glycerol is an eco-friendly solvent that enhances plant biomass decomposition via glycerolysis in many pretreatment methods. Nonetheless, inefficient conversion of glycerol to ethanol by natural Saccharomyces cerevisiae limits its use in these processes. In this study, we have developed an efficient glycerol-converting yeast strain by genetically modifying the oxidation of cytosolic NAD (NADH) by an O2-dependent dynamic shuttle and abolishing both glycerol phosphorylation and biosynthesis in S. cerevisiae strain D452-2, as well as by vigorous expression of whole genes in the dihydroxyacetone (DHA) pathway (Candida utilis glycerol facilitator, Ogataea polymorpha glycerol dehydrogenase, endogenous dihydroxyacetone kinase, and triosephosphate isomerase). The engineered strain showed conversion efficiencies (CE) up to 0.49 g ethanol/g glycerol (98% of theoretical CE), with a production rate of >1 g liter-1 h-1 when glycerol was supplemented in a single fed-batch fermentation in a rich medium. Furthermore, the engineered strain converted a mixture of glycerol and glucose into bioethanol (>86 g/liter) with 92.8% CE. To the best of our knowledge, this is the highest reported titer of bioethanol produced from glycerol and glucose. Notably, we developed a glycerol-utilizing transformant from a parent strain which cannot utilize glycerol as a sole carbon source. The developed strain converted glycerol to ethanol with a productivity of 0.44 g liter-1 h-1 on minimal medium under semiaerobic conditions. Our findings will promote the utilization of glycerol in eco-friendly biorefineries and integrate bioethanol and plant oil industries. IMPORTANCE With the development of efficient lignocellulosic biorefineries, glycerol has attracted attention as an eco-friendly biomass-derived solvent that can enhance the dissociation of lignin and cell wall polysaccharides during the pretreatment process. Coconversion of glycerol with the sugars released from biomass after glycerolysis increases the resources for ethanol production and lowers the burden of component separation. However, low conversion efficiency from glycerol and sugars limits the industrial application of this process. Therefore, the generation of an efficient glycerol-fermenting yeast will promote the applicability of integrated biorefineries. Hence, metabolic flux control in yeast grown on glycerol will lead to the generation of cell factories that produce chemicals, which will boost biodiesel and bioethanol industries. Additionally, the use of glycerol-fermenting yeast will reduce global warming and generation of agricultural waste, leading to the establishment of a sustainable society.
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7
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Ito Y, Terai G, Ishigami M, Hashiba N, Nakamura Y, Bamba T, Kumokita R, Hasunuma T, Asai K, Ishii J, Kondo A. Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic Acids Res 2021; 48:13000-13012. [PMID: 33257988 PMCID: PMC7736810 DOI: 10.1093/nar/gkaa1066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, terminator sequences not only terminate transcription but also affect expression levels of the protein-encoded upstream of the terminator. The non-conventional yeast Pichia pastoris (syn. Komagataella phaffii) has frequently been used as a platform for metabolic engineering but knowledge regarding P. pastoris terminators is limited. To explore terminator sequences available to tune protein expression levels in P. pastoris, we created a 'terminator catalog' by testing 72 sequences, including terminators from S. cerevisiae or P. pastoris and synthetic terminators. Altogether, we found that the terminators have a tunable range of 17-fold. We also found that S. cerevisiae terminator sequences maintain function when transferred to P. pastoris. Successful tuning of protein expression levels was shown not only for the reporter gene used to define the catalog but also using betaxanthin production as an example application in pathway flux regulation. Moreover, we found experimental evidence that protein expression levels result from mRNA abundance and in silico evidence that levels reflect the stability of mRNA 3'-UTR secondary structure. In combination with promoter selection, the novel terminator catalog constitutes a basic toolbox for tuning protein expression levels in metabolic engineering and synthetic biology in P. pastoris.
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Affiliation(s)
- Yoichiro Ito
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan
| | - Misa Ishigami
- Technology Research Association of Highly Efficient Gene Design, Kobe 650-0047, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design, Kobe 650-0047, Japan
| | - Yasuyuki Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
| | - Ryota Kumokita
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
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8
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Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora. J Microbiol 2020; 58:1037-1045. [DOI: 10.1007/s12275-020-0213-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023]
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9
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Genetic circuit design automation for yeast. Nat Microbiol 2020; 5:1349-1360. [DOI: 10.1038/s41564-020-0757-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 11/08/2022]
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10
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Yang BX, Xie CY, Xia ZY, Wu YJ, Li B, Tang YQ. The effect of xylose reductase genes on xylitol production by industrial Saccharomyces cerevisiae in fermentation of glucose and xylose. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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Transcriptional control of gene expression in Pichia pastoris by manipulation of terminators. Appl Microbiol Biotechnol 2020; 104:7841-7851. [DOI: 10.1007/s00253-020-10785-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
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12
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de Jongh RP, van Dijk AD, Julsing MK, Schaap PJ, de Ridder D. Designing Eukaryotic Gene Expression Regulation Using Machine Learning. Trends Biotechnol 2020; 38:191-201. [DOI: 10.1016/j.tibtech.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022]
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13
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Hector RE, Mertens JA, Nichols NN. Development and characterization of vectors for tunable expression of both xylose-regulated and constitutive gene expression in Saccharomyces yeasts. N Biotechnol 2019; 53:16-23. [DOI: 10.1016/j.nbt.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
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14
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Matsuyama T. Recent developments in terminator technology in Saccharomyces cerevisiae. J Biosci Bioeng 2019; 128:655-661. [PMID: 31324384 DOI: 10.1016/j.jbiosc.2019.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Metabolically engineered microorganisms that produce useful organic compounds will be helpful for realizing a sustainable society. The budding yeast Saccharomyces cerevisiae has high utility as a metabolic engineering platform because of its high fermentation ability, non-pathogenicity, and ease of handling. When producing yeast strains that produce exogenous compounds, it is a prerequisite to control the expression of exogenous enzyme-encoding genes. Terminator region in a gene expression cassette, as well as promoter region, could be used to improve metabolically engineered yeasts by increasing or decreasing the expression of the target enzyme-encoding genes. The findings on terminators have grown rapidly in the last decade, so an overview of these findings should provide a foothold for new developments.
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15
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Wang Z, Wei L, Sheng Y, Zhang G. Yeast Synthetic Terminators: Fine Regulation of Strength through Linker Sequences. Chembiochem 2019; 20:2383-2389. [DOI: 10.1002/cbic.201900163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Zhaoxia Wang
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Linna Wei
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Yue Sheng
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Genlin Zhang
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
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16
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Synthetic biology toolkits and applications in Saccharomyces cerevisiae. Biotechnol Adv 2018; 36:1870-1881. [PMID: 30031049 DOI: 10.1016/j.biotechadv.2018.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022]
Abstract
Synthetic biologists construct biological components and systems to look into biological phenomena and drive a myriad of practical applications that aim to tackle current global challenges in energy, healthcare and the environment. While most tools have been established in bacteria, particularly Escherichia coli, recent years have seen parallel developments in the model yeast strain Saccharomyces cerevisiae, one of the most well-understood eukaryotic biological system. Here, we outline the latest advances in yeast synthetic biology tools based on a framework of abstraction hierarchies of parts, circuits and genomes. In brief, the creation and characterization of biological parts are explored at the transcriptional, translational and post-translational levels. Using characterized parts as building block units, the designing of functional circuits is elaborated with examples. In addition, the status and potential applications of synthetic genomes as a genome level platform for biological system construction are also discussed. In addition to the development of a toolkit, we describe how those tools have been applied in the areas of drug production and screening, study of disease mechanisms, pollutant sensing and bioremediation. Finally, we provide a future outlook of yeast as a workhorse of eukaryotic genetics and a chosen chassis in this field.
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17
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Markham KA, Alper HS. Synthetic Biology Expands the Industrial Potential of Yarrowia lipolytica. Trends Biotechnol 2018; 36:1085-1095. [PMID: 29880228 DOI: 10.1016/j.tibtech.2018.05.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 10/14/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica is quickly emerging as the most popular non-conventional (i.e., non-model organism) yeast in the bioproduction field. With a high propensity for flux through tricarboxylic acid (TCA) cycle intermediates and biological precursors such as acetyl-CoA and malonyl-CoA, this host is especially well suited to meet our industrial chemical production needs. Recent progress in synthetic biology tool development has greatly enhanced our ability to rewire this organism, with advances in genetic component design, CRISPR technologies, and modular cloning strategies. In this review we investigate recent developments in metabolic engineering and describe how the new tools being developed help to realize the full industrial potential of this host. Finally, we conclude with our vision of the developments that will be necessary to enhance future engineering efforts.
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Affiliation(s)
- Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA.
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18
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Morse NJ, Gopal MR, Wagner JM, Alper HS. Yeast Terminator Function Can Be Modulated and Designed on the Basis of Predictions of Nucleosome Occupancy. ACS Synth Biol 2017; 6:2086-2095. [PMID: 28771342 DOI: 10.1021/acssynbio.7b00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The design of improved synthetic parts is a major goal of synthetic biology. Mechanistically, nucleosome occupancy in the 3' terminator region of a gene has been found to correlate with transcriptional expression. Here, we seek to establish a predictive relationship between terminator function and predicted nucleosome positioning to design synthetic terminators in the yeast Saccharomyces cerevisiae. In doing so, terminators improved net protein output from these expression cassettes nearly 4-fold over their original sequence with observed increases in termination efficiency to 96%. The resulting terminators were indeed depleted of nucleosomes on the basis of mapping experiments. This approach was successfully applied to synthetic, de novo, and native terminators. The mode of action of these modifications was mainly through increased termination efficiency, rather than half-life increases, perhaps suggesting a role in improved mRNA maturation. Collectively, these results suggest that predicted nucleosome depletion can be used as a heuristic approach for improving terminator function, though the underlying mechanism remains to be shown.
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Affiliation(s)
- Nicholas J. Morse
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Madan R. Gopal
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - James M. Wagner
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta
Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
- Institute
for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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19
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Wei L, Wang Z, Zhang G, Ye B. Characterization of Terminators in Saccharomyces cerevisiae and an Exploration of Factors Affecting Their Strength. Chembiochem 2017; 18:2422-2427. [PMID: 29058813 DOI: 10.1002/cbic.201700516] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Indexed: 11/06/2022]
Abstract
Terminators in eukaryotes play an important role in regulating the transcription process by influencing mRNA stability, translational efficiency, and localization. Herein, the strengths of 100 natural terminators in Saccharomyces cerevisiae have been characterized by inserting each terminator downstream of the TYS1p-enhanced green fluorescent protein (eGFP) reporter gene and measuring the fluorescent intensity (FI) of eGFP. Within this library, there are 45 strong terminators, 31 moderate terminators, and 24 weak terminators. The strength of these terminators, relative to that of PGK1t standard terminator, ranges from 0.0613 to 1.8002, with a mean relative FI of 0.9945. Mutating the control elements of terminators further suggests that the efficiency element has an important effect on terminator strength. The use of strong terminators will result in an enhanced level of mRNA and protein production; this indicates that gene expression can be directly influenced by terminator selection. Pairing a terminator with an inducible promoter or a strong constitutive promoter has less effect on gene expression; however, pairing with a week promoter will significantly increase the level of gene expression. Through exchange of the reporter genes, it can be demonstrated that the terminator functions as a genetic component and is independent of the coding region. This work demonstrates that the terminator is an important regulatory element and can be considered in applications for the fine-tuning of gene expression and metabolic pathways.
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Affiliation(s)
- Linna Wei
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical, Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, P.R. China
| | - Zhaoxia Wang
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical, Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, P.R. China
| | - Genlin Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical, Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, P.R. China
| | - Bangce Ye
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical, Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, P.R. China
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20
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The Mitotic Exit Network Regulates Spindle Pole Body Selection During Sporulation of Saccharomyces cerevisiae. Genetics 2017; 206:919-937. [PMID: 28450458 DOI: 10.1534/genetics.116.194522] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/11/2017] [Indexed: 01/11/2023] Open
Abstract
Age-based inheritance of centrosomes in eukaryotic cells is associated with faithful chromosome distribution in asymmetric cell divisions. During Saccharomyces cerevisiae ascospore formation, such an inheritance mechanism targets the yeast centrosome equivalents, the spindle pole bodies (SPBs) at meiosis II onset. Decreased nutrient availability causes initiation of spore formation at only the younger SPBs and their associated genomes. This mechanism ensures encapsulation of nonsister genomes, which preserves genetic diversity and provides a fitness advantage at the population level. Here, by usage of an enhanced system for sporulation-induced protein depletion, we demonstrate that the core mitotic exit network (MEN) is involved in age-based SPB selection. Moreover, efficient genome inheritance requires Dbf2/20-Mob1 during a late step in spore maturation. We provide evidence that the meiotic functions of the MEN are more complex than previously thought. In contrast to mitosis, completion of the meiotic divisions does not strictly rely on the MEN whereas its activity is required at different time points during spore development. This is reminiscent of vegetative MEN functions in spindle polarity establishment, mitotic exit, and cytokinesis. In summary, our investigation contributes to the understanding of age-based SPB inheritance during sporulation of S. cerevisiae and provides general insights on network plasticity in the context of a specialized developmental program. Moreover, the improved system for a developmental-specific tool to induce protein depletion will be useful in other biological contexts.
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21
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Gao M, Cao M, Suástegui M, Walker J, Rodriguez Quiroz N, Wu Y, Tribby D, Okerlund A, Stanley L, Shanks JV, Shao Z. Innovating a Nonconventional Yeast Platform for Producing Shikimate as the Building Block of High-Value Aromatics. ACS Synth Biol 2017; 6:29-38. [PMID: 27600996 DOI: 10.1021/acssynbio.6b00132] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The shikimate pathway serves an essential role in many organisms. Not only are the three aromatic amino acids synthesized through this pathway, but many secondary metabolites also derive from it. Decades of effort have been invested into engineering Saccharomyces cerevisiae to produce shikimate and its derivatives. In addition to the ability to express cytochrome P450, S. cerevisiae is generally recognized as safe for producing compounds with nutraceutical and pharmaceutical applications. However, the intrinsically complicated regulations involved in central metabolism and the low precursor availability in S. cerevisiae has limited production levels. Here we report the development of a new platform based on Scheffersomyces stipitis, whose superior xylose utilization efficiency makes it particularly suited to produce the shikimate group of compounds. Shikimate was produced at 3.11 g/L, representing the highest level among shikimate pathway products in yeasts. Our work represents a new exploration toward expanding the current collection of microbial factories.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Mingfeng Cao
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Miguel Suástegui
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - James Walker
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Natalia Rodriguez Quiroz
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Yutong Wu
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Dana Tribby
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Adam Okerlund
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Levi Stanley
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Jacqueline V. Shanks
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
| | - Zengyi Shao
- Department of Chemical and Biological
Engineering, ‡NSF Engineering Research Center
for Biorenewable Chemicals (CBiRC), §Department of Chemistry, ∥Interdepartmental Microbiology
Program, Iowa State University, Ames, Iowa 50011, United States
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22
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Enhancement of protein production via the strong DIT1 terminator and two RNA-binding proteins in Saccharomyces cerevisiae. Sci Rep 2016; 6:36997. [PMID: 27845367 PMCID: PMC5109538 DOI: 10.1038/srep36997] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 11/10/2022] Open
Abstract
Post-transcriptional upregulation is an effective way to increase the expression of transgenes and thus maximize the yields of target chemicals from metabolically engineered organisms. Refractory elements in the 3′ untranslated region (UTR) that increase mRNA half-life might be available. In Saccharomyces cerevisiae, several terminator regions have shown activity in increasing the production of proteins by upstream coding genes; among these terminators the DIT1 terminator has the highest activity. Here, we found in Saccharomyces cerevisiae that two resident trans-acting RNA-binding proteins (Nab6p and Pap1p) enhance the activity of the DIT1 terminator through the cis element GUUCG/U within the 3′-UTR. These two RNA-binding proteins could upregulate a battery of cell-wall–related genes. Mutagenesis of the DIT1 terminator improved its activity by a maximum of 500% of that of the standard PGK1 terminator. Further understanding and improvement of this system will facilitate inexpensive and stable production of complicated organism-derived drugs worldwide.
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23
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Ito Y, Yamanishi M, Ikeuchi A, Imamura C, Matsuyama T. Combinatorial Screening for Transgenic Yeasts with High Cellulase Activities in Combination with a Tunable Expression System. PLoS One 2015; 10:e0144870. [PMID: 26692026 PMCID: PMC4687128 DOI: 10.1371/journal.pone.0144870] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/24/2015] [Indexed: 01/26/2023] Open
Abstract
Combinatorial screening used together with a broad library of gene expression cassettes is expected to produce a powerful tool for the optimization of the simultaneous expression of multiple enzymes. Recently, we proposed a highly tunable protein expression system that utilized multiple genome-integrated target genes to fine-tune enzyme expression in yeast cells. This tunable system included a library of expression cassettes each composed of three gene-expression control elements that in different combinations produced a wide range of protein expression levels. In this study, four gene expression cassettes with graded protein expression levels were applied to the expression of three cellulases: cellobiohydrolase 1, cellobiohydrolase 2, and endoglucanase 2. After combinatorial screening for transgenic yeasts simultaneously secreting these three cellulases, we obtained strains with higher cellulase expressions than a strain harboring three cellulase-expression constructs within one high-performance gene expression cassette. These results show that our method will be of broad use throughout the field of metabolic engineering.
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Affiliation(s)
- Yoichiro Ito
- Matsuyama Research Group, TOYOTA Central Research and Development Laboratories Incorporation, Nagakute, Aichi, Japan
- * E-mail: (TM); (YI)
| | - Mamoru Yamanishi
- Matsuyama Research Group, TOYOTA Central Research and Development Laboratories Incorporation, Nagakute, Aichi, Japan
| | - Akinori Ikeuchi
- Biotechnology Laboratory, TOYOTA Central Research and Development Laboratories Incorporation, Nagakute, Aichi, Japan
| | - Chie Imamura
- Biotechnology Laboratory, TOYOTA Central Research and Development Laboratories Incorporation, Nagakute, Aichi, Japan
| | - Takashi Matsuyama
- Matsuyama Research Group, TOYOTA Central Research and Development Laboratories Incorporation, Nagakute, Aichi, Japan
- * E-mail: (TM); (YI)
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24
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Leavitt JM, Alper HS. Advances and current limitations in transcript-level control of gene expression. Curr Opin Biotechnol 2015; 34:98-104. [DOI: 10.1016/j.copbio.2014.12.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022]
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25
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Affiliation(s)
| | - Hal S. Alper
- McKetta Department of Chemical Engineering and
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712;
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26
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Ito Y, Yamanishi M, Ikeuchi A, Matsuyama T. A highly tunable system for the simultaneous expression of multiple enzymes in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:12-6. [PMID: 24927017 DOI: 10.1021/sb500096y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Control of the expression levels of multiple enzymes in transgenic yeasts is essential for the effective production of complex molecules through fermentation. Here, we propose a tunable strategy for the control of expression levels based on the design of terminator regions and other gene-expression control elements in Saccharomyces cerevisiae. Our genome-integrated system, which is capable of producing high expression levels over a wide dynamic range, will broadly enable metabolic engineering and synthetic biology. We demonstrated that the activities of multiple cellulases and the production of ethanol were doubled in a transgenic yeast constructed with our system compared with those achieved with a standard expression system.
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Affiliation(s)
- Yoichiro Ito
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Mamoru Yamanishi
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Akinori Ikeuchi
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Takashi Matsuyama
- Matsuyama Research Group and ‡Biotechnology Laboratory, Toyota Central Research and Development Laboratories, Inc., 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
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27
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Jensen MK, Keasling JD. Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res 2015; 15:1-10. [PMID: 25041737 DOI: 10.1111/1567-1364.12185] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/04/2014] [Accepted: 07/10/2014] [Indexed: 11/29/2022] Open
Abstract
The last 20 years of metabolic engineering has enabled bio-based production of fuels and chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this work has been accomplished using engineered microorganisms that act as chemical factories. Although the time required to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead.
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Affiliation(s)
- Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.,Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA
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28
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Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 2014; 15:1-10. [DOI: 10.1111/1567-1364.12188] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Redden
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
| | - Nicholas Morse
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
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