151
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Production of the cyanogenic glycoside dhurrin in yeast. Metab Eng Commun 2019; 9:e00092. [PMID: 31110942 PMCID: PMC6512747 DOI: 10.1016/j.mec.2019.e00092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/27/2019] [Accepted: 04/27/2019] [Indexed: 12/26/2022] Open
Abstract
Cyanogenic glycosides are defense compounds found in a wide range of plant species, including many crops. We demonstrate that the cyanogenic glucoside dhurrin, naturally found in sorghum, can be produced at high titers in Saccharomyces cerevisiae, constituting the first report of cyanogenic glycoside production in a microbe. Genetic modifications to increase the supply of the dhurrin precursor tyrosine enabled dhurrin production in excess of 80 mg/L. The dhurrin-producing yeast strain was used as a chassis to investigate previously uncharacterized enzymes identified close to the biosynthetic gene cluster containing the dhurrin pathway enzymes. This work shows the potential of heterologous expression in yeast to facilitate investigations of plant cyanogenic glycoside pathways. First production of cyanogenic glycosides in a microbe. Strategies for optimizing production of cyanogenic glycosides. Platform for rapidly characterizing the enzymes which constitute cyanogenic glycoside biosynthetic pathways.
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152
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Cook TB, Pfleger BF. Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts. MEDCHEMCOMM 2019; 10:668-681. [PMID: 31191858 PMCID: PMC6540960 DOI: 10.1039/c9md00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
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153
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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154
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Liu D, Liu H, Qi H, Guo XJ, Jia B, Zhang JL, Yuan YJ. Constructing Yeast Chimeric Pathways To Boost Lipophilic Terpene Synthesis. ACS Synth Biol 2019; 8:724-733. [PMID: 30779549 DOI: 10.1021/acssynbio.8b00360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Synthetic chimeric biological system offers opportunities to illuminate principles of designing life, and a primary step is constructing synthetic chimeric pathways. Here, we constructed yeast chimeric pathways by transferring the genes from Saccharomyces cerevisiae pathways into another budding yeast Yarrowia lipolytica for in vivo assembly. We efficiently diversified gene option, combination, localization order, and copy number as expected. Convergence of two yeast pathways, especially mevalonic acid (MVA) pathways, remarkably enhanced synthesis of a lipophilic terpene, lycopene. In the selected champion strain with 50-fold of enhanced lycopene production, the chimeric MVA pathway gathered three S. cerevisiae genes with particular copies and locations. Amazingly, therein we discovered distinct transcriptional up-regulation of three significant pathways correlated with acetyl-CoA supply and tuning of cellular lipid amounts and composition. Modulating these pathways further improved lycopene production to 150-fold, a final 259 mg/L (approximately 80 mg/g DCW). We primarily showed the capacity of boosting the synthesis of lipophilic products with yeast chimeric pathways.
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Affiliation(s)
- Duo Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hong Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hao Qi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Xue-Jiao Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Jin-Lai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
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155
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Hong KQ, Fu XM, Dong SS, Xiao DG, Dong J. Modulating acetate ester and higher alcohol production in Saccharomyces cerevisiae through the cofactor engineering. J Ind Microbiol Biotechnol 2019; 46:1003-1011. [PMID: 30969383 DOI: 10.1007/s10295-019-02176-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
Flavor production by esters or by higher alcohols play a key role in the sensorial quality of fermented alcoholic beverages. In Saccharomyces cerevisiae cells, the syntheses of esters and higher alcohols are considerably influenced by intracellular CoA levels catalyzed by pantothenate kinase. In this work, we examined the effects of cofactor CoA and acetyl-CoA synthesis on the metabolism of esters and higher alcohols. Strains 12α-BAP2 and 12α+ATF1 where generated by deleting and overexpressing BAP2 (encoded branched-chain amino acid permease) and ATF1 (encoded alcohol acetyl transferases), respectively, in the parent 12α strains. Then, 12α-BAP2+CAB1 and 12α-BAP2+CAB3 strains were obtained by overexpressing CAB1 (encoded pantothenate kinase Cab1) and CAB3 (encoded pantothenate kinase Cab3) in the 12α-BAP2 strain, and 12α-BAP2+CAB1+ATF1 and 12α-BAP2+CAB3+ATF1 were generated by overexpressing ATF1 in the pantothenate kinase overexpression strains. The acetate ester level in 12α-BAP2 was slightly changed relative to that in the control strain 12α, whereas the acetate ester levels in 12α-BAP2+CAB1, 12α-BAP2+CAB3, 12α-BAP2+CAB1+ATF1, and 12α-BAP2+CAB3+ATF1 were distinctly increased (44-118% for ethyl acetate and 18-57% for isoamyl acetate). The levels of n-propanol, methyl-1-butanol, isopentanol, isobutanol, and phenethylol levels were changed and varied among the six engineered strains. The levels of acetate esters and higher alcohols can be modulated by changing the CoA and acetyl-CoA levels. The method proposed in this work supplies a practical means of breeding yeast strains by modulating acetate ester and higher alcohol production.
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Affiliation(s)
- Kun-Qiang Hong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xiao-Meng Fu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Sheng-Sheng Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Jian Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China.
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156
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Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv 2019; 37:730-745. [PMID: 30951810 DOI: 10.1016/j.biotechadv.2019.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Keke Wei
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 200232, China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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157
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Liu H, Fan J, Wang C, Li C, Zhou X. Enhanced β-Amyrin Synthesis in Saccharomyces cerevisiae by Coupling An Optimal Acetyl-CoA Supply Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3723-3732. [PMID: 30808164 DOI: 10.1021/acs.jafc.9b00653] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
β-Amyrin is a plant-derived triterpenoid skeleton with wide applications in food and medical industry. β-Amyrin biosynthesis in Saccharomyces cerevisiae is derived from the mevalonate pathway with cytosolic acetyl-CoA as a precursor. In this work, endogenous and several heterologous acetyl-CoA synthesis pathways were coupled to β-amyrin production and a combinational acetyl-CoA supply route was demonstrated to be optimal due to more balanced redox cofactors, much lower energy consumption, and glucose utilization as well as significantly enhanced β-amyrin production (a 200% increase compared to the original β-amyrin-producing strain). Further disruption of an acetyl-CoA competing pathway led to a 330% increase in β-amyrin production as compared to the original strain. Finally, the engineered strain harboring the optimal pathway configuration achieved a final β-amyrin production of 279.0 ± 13.0 mg/L in glucose fed-batch fermentation, which is the highest as ever reported. This work provides an efficient platform for triterpenoid biosynthesis in Saccharomyces cerevisiae.
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Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Jingjing Fan
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Chen Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300072 , China
| | - Xiaohong Zhou
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China
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158
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Adames NR, Gallegos JE, Peccoud J. Yeast genetic interaction screens in the age of CRISPR/Cas. Curr Genet 2019; 65:307-327. [PMID: 30255296 PMCID: PMC6420903 DOI: 10.1007/s00294-018-0887-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022]
Abstract
The ease of performing both forward and reverse genetics in Saccharomyces cerevisiae, along with its stable haploid state and short generation times, has made this budding yeast the consummate model eukaryote for genetics. The major advantage of using budding yeast for reverse genetics is this organism's highly efficient homology-directed repair, allowing for precise genome editing simply by introducing DNA with homology to the chromosomal target. Although plasmid- and PCR-based genome editing tools are quite efficient, they depend on rare spontaneous DNA breaks near the target sequence. Consequently, they can generate only one genomic edit at a time, and the edit must be associated with a selectable marker. However, CRISPR/Cas technology is efficient enough to permit markerless and multiplexed edits in a single step. These features have made CRISPR/Cas popular for yeast strain engineering in synthetic biology and metabolic engineering applications, but it has not been widely employed for genetic screens. In this review, we critically examine different methods to generate multi-mutant strains in systematic genetic interaction screens and discuss the potential of CRISPR/Cas to supplement or improve on these methods.
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Affiliation(s)
- Neil R Adames
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jenna E Gallegos
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jean Peccoud
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA.
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159
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Stepwise increase in the production of 13R-manoyl oxide through metabolic engineering of Saccharomyces cerevisiae. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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160
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Ji CH, Kim H, Kang HS. Synthetic Inducible Regulatory Systems Optimized for the Modulation of Secondary Metabolite Production in Streptomyces. ACS Synth Biol 2019; 8:577-586. [PMID: 30807691 DOI: 10.1021/acssynbio.9b00001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Biosynthesis of secondary metabolites is a highly complex process that often requires tight control of their production, as overproduction of metabolites could be toxic and also may cause metabolic burden to their hosts. Tight control of metabolite production could be achieved by expressing key biosynthetic genes under control of an inducible regulatory system. In this study, we employed the modular design approach to build a high performance synthetic inducible regulatory system that displays a large dynamic range and thus is well-suited for the modulation of secondary metabolite production in Streptomyces. To this end, an inducible regulatory system was divided into three separate functional modules: (1) the induction module, (2) the target expression module, and (3) the repressor expression module. Then, these three separate modules were individually optimized in a stepwise manner and assembled to a new system. First, the cumate (CMT) induction module was chosen as the best performing induction module based on the large dynamic range and moderate inducer sensitivity. Then the CMT induction module maintained its performance when combined with diverse constitutive target expression modules, in which overall dynamic ranges varied depending on maximum promoter strengths. Lastly, the repressor expression module was optimized to achieve complete elimination of leaky expression, further increasing the dynamic range of the system. We also demonstrate that any strong constitutive regulatory system could be converted into an inducible regulatory system by simple CRISPR/Cas9-aided markerless insertion of an operator sequence whenever tight control of gene expression is required. We believe that the synthetic inducible regulatory system we report here would become a useful tool in modulating secondary metabolite production in Streptomyces.
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Affiliation(s)
- Chang-Hun Ji
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hiyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hahk-Soo Kang
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
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161
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Zhao Q, Wang L, Luo Y. Recent advances in natural products exploitation in Streptomyces via synthetic biology. Eng Life Sci 2019; 19:452-462. [PMID: 32625022 DOI: 10.1002/elsc.201800137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 02/08/2019] [Accepted: 03/01/2019] [Indexed: 02/05/2023] Open
Abstract
Natural products of microbial origin have proven to be the wellspring of clinically useful compounds for human therapeutics. Streptomyces species are predominant sources of bioactive compounds, most of which serve as potential drug candidates. While the exploitation of natural products has been severely reduced over the past two decades, the growing crisis of evolution and dissemination of drug resistant pathogens have again attracted great interest in this field. The emerging synthetic biology has been heralded as a new bioengineering platform to discover novel bioactive compounds and expand bioactive natural products diversity and production. Herein, we review recent advances in the natural products exploitation of Streptomyces with the applications of synthetic biology from three major aspects, including recently developed synthetic biology tools, natural products biosynthetic pathway engineering strategies as well as chassis host modifications.
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Affiliation(s)
- Qiyuan Zhao
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
| | - Liping Wang
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
| | - Yunzi Luo
- Department of Gastroenterology Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center of Biotherapy Chengdu P. R. China
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162
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Enhanced ethanol production from industrial lignocellulose hydrolysates by a hydrolysate-cofermenting Saccharomyces cerevisiae strain. Bioprocess Biosyst Eng 2019; 42:883-896. [PMID: 30820665 DOI: 10.1007/s00449-019-02090-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a hydrolysate-cofermenting Saccharomyces cerevisiae strain was obtained through one step in vivo DNA assembly of pentose-metabolizing pathway genes, followed by consecutive adaptive evolution in pentose media containing acetic acid, and direct screening in biomass hydrolysate media. The strain was able to coferment glucose and xylose in synthetic media with the respective maximal specific rates of glucose and xylose consumption, and ethanol production of 3.47, 0.38 and 1.62 g/g DW/h, with an ethanol titre of 41.07 g/L and yield of 0.42 g/g. Industrial wheat straw hydrolysate fermentation resulted in maximal specific rates of glucose and xylose consumption, and ethanol production of 2.61, 0.54 and 1.38 g/g DW/h, respectively, with an ethanol titre of 54.11 g/L and yield of 0.44 g/g. These are among the best for wheat straw hydrolysate fermentation through separate hydrolysis and cofermentation.
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163
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Wang L, Wang H, Liu H, Zhao Q, Liu B, Wang L, Zhang J, Zhu J, Bao R, Luo Y. Improved CRISPR-Cas12a-assisted one-pot DNA editing method enables seamless DNA editing. Biotechnol Bioeng 2019; 116:1463-1474. [PMID: 30730047 DOI: 10.1002/bit.26938] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 02/05/2023]
Abstract
As the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a (previously known as Cpf1) system cleaves double-stranded DNA and produces a sticky end, it could serve as a useful tool for DNA assembly/editing. To broaden its application, a variety of engineered FnCas12a proteins are generated with expanded protospacer adjacent motif (PAM) requirements. Two variants (FnCas12a-EP15 and EP16) increased the targeting range of FnCas12a by approximately fourfold. They can efficiently recognize a broad range of PAM sequences including YN (Y = C or T), TAC and CAA. Meanwhile, based on our demonstration that FnCas12a is active from 16 to 60°C, we developed an "improved CRISPR-Cas12a-assisted one-pot DNA editing" (iCOPE) method to facilitate DNA editing by combining the crRNA transcription, digestion, and ligation in one pot. By applying iCOPE, the editing efficiency reached 72-100% for two DNA fragment assemblies, and for the 21 kb large DNA construct modification, the editing efficiency can reach 100%. Thanks to the advantages of Cas12a, iCOPE with only one digestion enzyme could replace current a variety of restriction enzymes to perform the cloning in one pot with almost no sequence constraints. Taken together, this study offers an expanded DNA targeting scope of CRISPR systems and could serve as an efficient seamless one-pot DNA editing tool.
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Affiliation(s)
- Liping Wang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Haojun Wang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Huayi Liu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Qiyuan Zhao
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Bing Liu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Lian Wang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jun Zhang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jie Zhu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yunzi Luo
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
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164
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Song L, Chen Y, Guo Q, Huang S, Guo X, Xiao D. Regulating the Golgi apparatus sorting of proteinase A to decrease its excretion in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:601-612. [PMID: 30715625 DOI: 10.1007/s10295-019-02147-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/24/2019] [Indexed: 11/30/2022]
Abstract
Beer foam stability, a key factor in evaluating overall beer quality, is influenced by proteinase A (PrA). Actin-severing protein cofilin and Golgi apparatus-localized Ca2+ ATPase Pmr1 are involved in protein sorting at the trans-Golgi network (TGN) in yeast Curwin et al. (Mol Biol Cell 23:2327-2338, 2012). To reduce PrA excretion into the beer fermentation broth, we regulated the Golgi apparatus sorting of PrA, thereby facilitating the delivery of more PrA to the vacuoles in the yeast cells. In the present study, the cofilin-coding gene COF1 and the Pmr1-coding gene PMR1 were overexpressed in the parental strain W303-1A and designated as W + COF1 and W + PMR1, respectively. The relative expression levels of COF1 in W + COF1 and PMR1 in W + PMR1 were 5.26- and 19.76-fold higher than those in the parental strain. After increases in the expression levels of cofilin and Pmr1 were confirmed, the PrA activities in the wort broth fermented with W + COF1, W + PMR1, and W303-1A were measured. Results showed that the extracellular PrA activities of W + COF1 and W + PMR1 were decreased by 9.24% and 13.83%, respectively, at the end of the main fermentation compared with that of W303-1A. Meanwhile, no apparent differences were found on the fermentation performance of recombinant and parental strains. The research uncovers an effective strategy for decreasing PrA excretion in Saccharomyces cerevisiae.
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Affiliation(s)
- Lulu Song
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Qinghuan Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Siyao Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
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165
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Wang P, Wei W, Ye W, Li X, Zhao W, Yang C, Li C, Yan X, Zhou Z. Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at high-efficiency. Cell Discov 2019; 5:5. [PMID: 30652026 PMCID: PMC6331602 DOI: 10.1038/s41421-018-0075-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/19/2018] [Accepted: 11/02/2018] [Indexed: 12/13/2022] Open
Abstract
Synthetic biology approach has been frequently applied to produce plant rare bioactive compounds in microbial cell factories by fermentation. However, to reach an ideal manufactural efficiency, it is necessary to optimize the microbial cell factories systemically by boosting sufficient carbon flux to the precursor synthesis and tuning the expression level and efficiency of key bioparts related to the synthetic pathway. We previously developed a yeast cell factory to produce ginsenoside Rh2 from glucose. However, the ginsenoside Rh2 yield was too low for commercialization due to the low supply of the ginsenoside aglycone protopanaxadiol (PPD) and poor performance of the key UDP-glycosyltransferase (UGT) (biopart UGTPg45) in the final step of the biosynthetic pathway. In the present study, we constructed a PPD-producing chassis via modular engineering of the mevalonic acid pathway and optimization of P450 expression levels. The new yeast chassis could produce 529.0 mg/L of PPD in shake flasks and 11.02 g/L in 10 L fed-batch fermentation. Based on this high PPD-producing chassis, we established a series of cell factories to produce ginsenoside Rh2, which we optimized by improving the C3–OH glycosylation efficiency. We increased the copy number of UGTPg45, and engineered its promoter to increase expression levels. In addition, we screened for more efficient and compatible UGT bioparts from other plant species and mutants originating from the direct evolution of UGTPg45. Combining all engineered strategies, we built a yeast cell factory with the greatest ginsenoside Rh2 production reported to date, 179.3 mg/L in shake flasks and 2.25 g/L in 10 L fed-batch fermentation. The results set up a successful example for improving yeast cell factories to produce plant rare natural products, especially the glycosylated ones.
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Affiliation(s)
- Pingping Wang
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Wei Wei
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Wei Ye
- 2University of Chinese Academy of Sciences, Beijing, 100049 China.,Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai, 200031 China
| | - Xiaodong Li
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenfang Zhao
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Chengshuai Yang
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaojing Li
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xing Yan
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Zhihua Zhou
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
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166
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Ma Z, Zhang H, Li L, Chen M, Wang PG. Direct Cloning of Bacterial Surface Polysaccharide Gene Cluster for One-Step Production of Glycoconjugate Vaccine. ACS Infect Dis 2019; 5:74-78. [PMID: 30445812 DOI: 10.1021/acsinfecdis.8b00187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial pathogen infections are fast-growing public health threats and worldwide problems. Glycoconjugate vaccines are among the most effective means in combating such infections. Recent advances in bacterial protein glycan coupling technology (PGCT) have revolutionized the production of glycoconjugate vaccines and drawn enormous attention from both researchers and pharmaceutical companies. Cloning of bacterial surface polysaccharide gene cluster is a prerequisite for the application of PGCT. In this study, we applied the RecET direct cloning strategy for rapid and efficient cloning of O-antigen polysaccharide gene clusters from Escherichia coli serotypes O25b, O26, and O55 in a high-fidelity manner. Then, these gene clusters were applied in PGCT to produce corresponding glycoconjugates. Subsequent immunological studies verified the abilities of glycoconjugate vaccine candidates O25-maltose-binding protein (MBP), O26-MBP, and O55-MBP to generate serotype-specific antibodies and confer protection against E. coli infections. The combination of RecET direct cloning and PGCT makes the rapid production of glycoconjugate vaccines against fast-expanding bacterial pathogens possible.
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Affiliation(s)
- Zhongrui Ma
- Department of Chemistry, Georgia State University, 100 Piedmont Avenue, Atlanta, Georgia 30303, United States
| | - Huajie Zhang
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 27 ShanDa Nan Road, Jinan, Shandong 250100, China
| | - Lei Li
- Department of Chemistry, Georgia State University, 100 Piedmont Avenue, Atlanta, Georgia 30303, United States
| | - Min Chen
- National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 27 ShanDa Nan Road, Jinan, Shandong 250100, China
| | - Peng George Wang
- Department of Chemistry, Georgia State University, 100 Piedmont Avenue, Atlanta, Georgia 30303, United States
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167
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Hao Z, Su X. Fast gene disruption in Trichoderma reesei using in vitro assembled Cas9/gRNA complex. BMC Biotechnol 2019; 19:2. [PMID: 30626373 PMCID: PMC6325762 DOI: 10.1186/s12896-018-0498-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/27/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND CRISPR/Cas9 has wide application potentials in a variety of biological species including Trichoderma reesei, a filamentous fungus workhorse for cellulase production. However, expression of Cas9 heterologously in the host cell could be time-consuming and sometimes even troublesome. RESULTS We tested two gene disruption methods in T. reesei using CRISPR/Cas9 in this study. The intracellularly expressed Cas9 led to unexpected off-target gene disruption in T. reesei QM9414, favoring inserting 9- or 12-bp at 70- and 100-bp downstream of the targeted ura5. An alternative method was, therefore, established by assembling Cas9 and gRNA in vitro, followed by transformation of the ribonucleoprotein complex with a plasmid containing the pyr4 marker gene into T. reesei TU-6. When the gRNA targeting cbh1 was used, eight among the twenty seven transformants were found to lose the ability to express CBH1, indicative of successful cbh1 disruption through genome editing. Large DNA fragments including the co-transformed plasmid, chromosomal genes, or a mixture of these nucleotides, were inserted in the disrupted cbh1 locus. CONCLUSIONS Direct transformation of Cas9/gRNA complex into the cell is a fast means to disrupt a gene in T. reesei and may find wide applications in strain improvement and functional genomics study.
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Affiliation(s)
- Zhenzhen Hao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China.
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168
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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169
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Improving lycopene production in Saccharomyces cerevisiae through optimizing pathway and chassis metabolism. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2018.09.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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170
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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171
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Zhao F, Bai P, Nan W, Li D, Zhang C, Lu C, Qi H, Lu W. A modular engineering strategy for high‐level production of protopanaxadiol from ethanol by
Saccharomyces cerevisiae. AIChE J 2018. [DOI: 10.1002/aic.16502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fanglong Zhao
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Peng Bai
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Weihua Nan
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Dashuai Li
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Chuanbo Zhang
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Chunzhe Lu
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Haishan Qi
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
| | - Wenyu Lu
- Dept. of Biological EngineeringSchool of Chemical Engineering and Technology, Tianjin University Tianjin P.R. China
- Key Laboratory of System BioengineeringTianjin University, Ministry of Education Tianjin P.R. China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin University, SynBio Res Platform Tianjin P.R. China
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172
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Qiao J, Luo Z, Cui S, Zhao H, Tang Q, Mo C, Ma X, Ding Z. Modification of isoprene synthesis to enable production of curcurbitadienol synthesis in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2018; 46:147-157. [PMID: 30535727 DOI: 10.1007/s10295-018-2116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/23/2022]
Abstract
Cucurbitane-type triterpenoids such as mogrosides and cucurbitacins that are present in the plants of Cucurbitaceae are widely used in Asian traditional medicine. Cucurbitadienol is the skeleton of cucurbitane-type triterpenoids. As an alternative production strategy, we developed baker's yeast Saccharomyces cerevisiae as a microbial host for the eventual transformation of cucurbitadienol. The synthetic pathway of cucurbitadienol was constructed in Saccharomyces cerevisiae by introducing the cucurbitadienol synthase gene from different plants, resulting in 7.80 mg cucurbitadienol from 1 L of fermentation broth. Improving supplies of isoprenoid precursors was then investigated for increasing cucurbitadienol production. Cucurbitadienol production increased to 21.47 mg/L through the overexpression of a global regulatory factor (UPC2) gene of triterpenoid synthase. In addition, knockout of the ERG7 gene increased cucurbitadienol production from 21.47 to 61.80 mg/L. Finally, fed-batch fermentation was performed, and 63.00 mg/L cucurbitadienol was produced. This work is an important step towards the total biosynthesis of valuable cucurbitane-type triterpenoids and demonstrates the potential for developing a sustainable and secure yeast biomanufacturing platform for triterpenoids.
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Affiliation(s)
- Jing Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Shengrong Cui
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Huan Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qi Tang
- National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resources and Initiative and Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Changming Mo
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Zimian Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
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173
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Liang L, Heveran C, Liu R, Gill RT, Nagarajan A, Cameron J, Hubler M, Srubar WV, Cook SM. Rational Control of Calcium Carbonate Precipitation by Engineered Escherichia coli. ACS Synth Biol 2018; 7:2497-2506. [PMID: 30384588 DOI: 10.1021/acssynbio.8b00194] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ureolytic bacteria ( e.g., Sporosarcina pasteurii) can produce calcium carbonate (CaCO3). Tailoring the size and shape of biogenic CaCO3 may increase the range of useful applications for these crystals. However, wild type Sporosarcina pasteurii is difficult to genetically engineer, limiting control of the organism and its crystal precipitates. Therefore, we designed, constructed, and compared different urease operons and expression levels for CaCO3 production in engineered Escherichia coli strains. We quantified urease expression and calcium uptake and characterized CaCO3 crystal phase and morphology for 13 engineered strains. There was a weak relationship between urease expression and crystal size, suggesting that genes surrounding the urease gene cluster affect crystal size. However, when evaluating strains with a wider range of urease expression levels, there was a negative relationship between urease activity and polycrystal size (e.g., larger crystals with lower activity). The resulting range of crystal morphologies created by the rationally designed strains demonstrates the potential for controlling biogenic CaCO3 precipitation.
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Affiliation(s)
| | | | | | | | | | - Jeffrey Cameron
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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174
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Heterologous expression-facilitated natural products' discovery in actinomycetes. J Ind Microbiol Biotechnol 2018; 46:415-431. [PMID: 30446891 DOI: 10.1007/s10295-018-2097-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/21/2018] [Indexed: 12/22/2022]
Abstract
Actinomycetes produce many of the drugs essential for human and animal health as well as crop protection. Genome sequencing projects launched over the past two decades reveal dozens of cryptic natural product biosynthetic gene clusters in each actinomycete genome that are not expressed under regular laboratory conditions. This so-called 'chemical dark matter' represents a potentially rich untapped resource for drug discovery in the genomic era. Through improved understanding of natural product biosynthetic logic coupled with the development of bioinformatic and genetic tools, we are increasingly able to access this 'dark matter' using a wide variety of strategies with downstream potential application in drug development. In this review, we discuss recent research progress in the field of cloning of natural product biosynthetic gene clusters and their heterologous expression in validating the potential of this methodology to drive next-generation drug discovery.
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175
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Gao X, Caiyin Q, Zhao F, Wu Y, Lu W. Engineering Saccharomyces cerevisiae for Enhanced Production of Protopanaxadiol with Cofermentation of Glucose and Xylose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12009-12016. [PMID: 30350965 DOI: 10.1021/acs.jafc.8b04916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Protopanaxadiol (PPD), an active triterpene compound, is the precursor of high-value ginsenosides. In this study, we report a strategy for the enhancement of PPD production in Saccharomyces cerevisiae by cofermentation of glucose and xylose. In mixed sugar fermentation, strain GW6 showed higher PPD titer and yield than that obtained from glucose cultivation. Then, engineering strategies were implemented on GW6 to enhance the PPD yields, such as adjustment of the central carbon metabolism, optimization of the mevalonate pathway, reinforcement of the xylose assimilation pathway, and regulation of cofactor balance, namely, overexpression of xPK/PTA, ERG10/ERG12/ERG13, XYL1/XYL2/TAL1, and POS5, respectively. In particular, the final obtained strain GW10, harboring overexpressed POS5, exhibited the highest PPD yield, which was 2.06 mg of PPD/g of mixed sugar. In a 5-L fermenter, PPD titer reached 152.37 mg/L. These promising results demonstrate the great advantages of mixed sugar over glucose for high-yield production of PPD.
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Affiliation(s)
- Xiao Gao
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , People's Republic of China
| | - Qinggele Caiyin
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , People's Republic of China
| | - Fanglong Zhao
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , People's Republic of China
| | - Yufen Wu
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , People's Republic of China
| | - Wenyu Lu
- School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , People's Republic of China
- Key Laboratory of System Bioengineering (Tianjin University) , Ministry of Education , Tianjin 300072 , People's Republic of China
- SynBio Research Platform , Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300072 , People's Republic of China
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176
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Liu R, Deng Z, Liu T. Streptomyces species: Ideal chassis for natural product discovery and overproduction. Metab Eng 2018; 50:74-84. [DOI: 10.1016/j.ymben.2018.05.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/26/2022]
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177
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Okano K, Honda K, Taniguchi H, Kondo A. De novo design of biosynthetic pathways for bacterial production of bulk chemicals and biofuels. FEMS Microbiol Lett 2018; 365:5087733. [DOI: 10.1093/femsle/fny215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Kenji Okano
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Kohsuke Honda
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Hironori Taniguchi
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657–8501, Japan
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178
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Lu C, Zhang C, Zhao F, Li D, Lu W. Biosynthesis of ursolic acid and oleanolic acid inSaccharomyces cerevisiae. AIChE J 2018. [DOI: 10.1002/aic.16370] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chunzhe Lu
- Dept. of Biological Engineering; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 China
| | - Chuanbo Zhang
- Dept. of Biological Engineering; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 China
| | - Fanglong Zhao
- Dept. of Biological Engineering; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 China
| | - Dashuai Li
- Dept. of Biological Engineering; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 China
| | - Wenyu Lu
- Dept. of Biological Engineering; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 China
- Key Laboratory of system bioengineering (Tianjin University), Ministry of Education; Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin 300072 China
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179
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Yan F, Burgard C, Popoff A, Zaburannyi N, Zipf G, Maier J, Bernauer HS, Wenzel SC, Müller R. Synthetic biology approaches and combinatorial biosynthesis towards heterologous lipopeptide production. Chem Sci 2018; 9:7510-7519. [PMID: 30319751 PMCID: PMC6180311 DOI: 10.1039/c8sc02046a] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products.
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products. Here we developed a new assembly strategy based on type IIS endonucleases and elaborate synthetic DNA platforms, which could be used to seamlessly assemble and engineer biosynthetic gene clusters (BGCs). By applying this versatile tool, we designed and assembled more than thirty different artificial myxochromide BGCs, each around 30 kb in size, and established heterologous expression platforms using a derivative of Myxococcus xanthus DK1622 as a host. In addition to the five native types of myxochromides (A, B, C, D and S), novel lipopeptide structures were produced by combinatorial exchange of nonribosomal peptide synthetase (NRPS) encoding genes from different myxochromide BGCs. Inspired by the evolutionary diversification of the native myxochromide megasynthetases, the ancestral A-type NRPS was engineered by inactivation, deletion, or duplication of catalytic domains and successfully converted into functional B-, C- and D-type megasynthetases. The constructional design approach applied in this study enables combinatorial engineering of complex synthetic BGCs and has great potential for the exploitation of other natural product biosynthetic pathways.
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Affiliation(s)
- Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Christian Burgard
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Alexander Popoff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Gregor Zipf
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Josef Maier
- IStLS - Information Services to Life Sciences , Härlestraße 24/1 , 78727 Oberndorf am Neckar/Boll , Germany
| | - Hubert S Bernauer
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Silke C Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
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180
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Liu Q, Yu T, Campbell K, Nielsen J, Chen Y. Modular Pathway Rewiring of Yeast for Amino Acid Production. Methods Enzymol 2018; 608:417-439. [PMID: 30173772 DOI: 10.1016/bs.mie.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amino acids find various applications in biotechnology in view of their importance in the food, feed, pharmaceutical, and personal care industries as nutrients, additives, and drugs, respectively. For the large-scale production of amino acids, microbial cell factories are widely used and the development of amino acid-producing strains has mainly focused on prokaryotes Corynebacterium glutamicum and Escherichia coli. However, the eukaryote Saccharomyces cerevisiae is becoming an even more appealing microbial host for production of amino acids and derivatives because of its superior molecular and physiological features, such as amenable to genetic engineering and high tolerance to harsh conditions. To transform S. cerevisiae into an industrial amino acid production platform, the highly coordinated and multiple layers regulation in its amino acid metabolism should be relieved and reconstituted to optimize the metabolic flux toward synthesis of target products. This chapter describes principles, strategies, and applications of modular pathway rewiring in yeast using the engineering of l-ornithine metabolism as a paradigm. Additionally, detailed protocols for in vitro module construction and CRISPR/Cas-mediated pathway assembly are provided.
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Affiliation(s)
- Quanli 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
| | - Tao Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Kate Campbell
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Yun Chen
- 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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181
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Liu T, Zhang C, Lu W. Heterologous production of levopimaric acid in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:114. [PMID: 30021574 PMCID: PMC6050663 DOI: 10.1186/s12934-018-0964-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022] Open
Abstract
Background Levopimaric acid (LA), a type of diterpene resin acid produced by plants, is a significant industrial intermediate that is mainly produced via phytoextraction. This work aimed to apply synthetic biology to produce LA in yeast strains from a simple carbon source. Results Levopimaradiene (LP), the precursor of LA, was produced via LP synthase (LPS) expression in yeast. LPS was then modified by N-terminal truncating and site-directed mutagenesis. The strain containing t79LPSMM (79 N-terminal amino acid truncating and M593I/Y700F mutation) produced 6.92 mg/L of LP, which were 23-fold higher than the strain containing LPS. Next, t79LPSMM was expressed in a new metabolically engineered chassis, and the final LP production increased 164-folds to 49.21 mg/L. Three cytochrome P450 reductases (CPRs) were co-expressed with CYP720B1 (the enzyme responsible for LA production from LP) in yeast to evaluate their LA producing abilities, and the CPR from Taxus cuspidata (TcCPR) was found to be the best (achieved 23.13 mg/L of LA production). CYP720B1 and TcCPR genes overexpression in the multi-copy site of the S.cerevisiae genome led to a 1.9-fold increase in LA production to 45.24 mg/L in a shake-flask culture. Finally, LA production was improved to 400.31 mg/L via fed-batch fermentation in a 5-L bioreactor. Conclusions This is the first report to produce LA in a yeast cell factory and the highest titer of LA is achieved. Electronic supplementary material The online version of this article (10.1186/s12934-018-0964-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ting Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of System Bioengineering, Tianjin University, Ministry of Education, Tianjin, 300072, People's Republic of China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), SynBio Res Platform, Tianjin, 300072, People's Republic of China.
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182
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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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183
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Tarasava K, Oh EJ, Eckert CA, Gill RT. CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes. Biotechnol J 2018; 13:e1700586. [DOI: 10.1002/biot.201700586] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/09/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Katia Tarasava
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
- Biosciences Center, National Renewable Energy Laboratory; Golden CO USA
| | - Ryan T. Gill
- Chemical and Biological Engineering, University of Colorado; Boulder CO USA
- Renewable and Sustainable Energy Institute, University of Colorado; Boulder CO USA
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184
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Vanegas KG, Larsen AB, Eichenberger M, Fischer D, Mortensen UH, Naesby M. Indirect and direct routes to C-glycosylated flavones in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:107. [PMID: 29986709 PMCID: PMC6036675 DOI: 10.1186/s12934-018-0952-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND C-glycosylated flavones have recently attracted increased attention due to their possible benefits in human health. These biologically active compounds are part of the human diet, and the C-linkage makes them more resistant to hydrolysis and degradation than O-glycosides. In contrast to O-glycosyltransferases, few C-glycosyltransferases (CGTs) have so far been characterized. Two different biosynthetic routes for C-glycosylated flavones have been identified in plants. Depending on the type of C-glycosyltransferase, flavones can be glycosylated either directly or indirectly via C-glycosylation of a 2-hydroxyflavanone intermediate formed by a flavanone 2-hydroxylase (F2H). RESULTS In this study, we reconstructed the pathways in the yeast Saccharomyces cerevisiae, to produce some relevant CGT substrates, either the flavanones naringenin and eriodictyol or the flavones apigenin and luteolin. We then demonstrated two-step indirect glycosylation using combinations of F2H and CGT, to convert 2-hydroxyflavanone intermediates into the 6C-glucoside flavones isovitexin and isoorientin, and the 8C-glucoside flavones vitexin and orientin. Furthermore, we established direct glycosylation of flavones using the recently identified GtUF6CGT1 from Gentiana triflora. The ratio between 6C and 8C glycosylation depended on the CGT used. The indirect route resulted in mixtures, similar to what has been reported for in vitro experiments. In this case, hydroxylation at the flavonoid 3'-position shifted the ratio towards the 8C-glucosylated orientin. The direct flavone glycosylation by GtUF6CGT1, on the other hand, resulted exclusively in 6C-glucosides. CONCLUSIONS The current study features yeast as a promising host for production of flavone C-glycosides, and it provides a set of tools and strains for identifying and studying CGTs and their mechanisms of C-glycosylation.
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Affiliation(s)
- Katherina Garcia Vanegas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs, Lyngby, Copenhagen, Denmark
| | | | | | - David Fischer
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs, Lyngby, Copenhagen, Denmark
| | - Michael Naesby
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland.
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185
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Garcia-Ruiz E, Auxillos J, Li T, Dai J, Cai Y. YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast. Methods Enzymol 2018; 608:277-306. [PMID: 30173765 DOI: 10.1016/bs.mie.2018.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For many years, researchers have devised elegant techniques to assemble genetic parts into larger constructs. Recently, increasing needs for complex DNA constructs has driven countless attempts to optimize DNA assembly methods for improved efficiency, fidelity, and modularity. These efforts have resulted in simple, robust, standardized, and fast protocols that enable the implementation of high-throughput DNA assembly projects for the fabrication of large synthetic genetic constructs. Recently our groups have developed the YeastFab assembly, a highly efficient method for the design and construction of DNA-building blocks based on the native elements from Saccharomyces cerevisiae. Furthermore, these standardized DNA parts can be readily characterized and assembled into transcriptional units and pathways. In this chapter, we describe the protocols to assemble pathways from characterized standardized yeast parts using YeastFab.
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Affiliation(s)
- Eva Garcia-Ruiz
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jamie Auxillos
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Tianyi Li
- Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Junbiao Dai
- Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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186
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Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
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Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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187
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Wu T, Li S, Zhang B, Bi C, Zhang X. Engineering Saccharomyces cerevisiae for the production of the valuable monoterpene ester geranyl acetate. Microb Cell Fact 2018; 17:85. [PMID: 29866124 PMCID: PMC5987629 DOI: 10.1186/s12934-018-0930-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/11/2018] [Indexed: 11/24/2022] Open
Abstract
Background Geranyl acetate is widely used in the fragrance and cosmetic industries, and thus has great economic value. However, plants naturally produce a mixture of hundreds of esters, and geranyl acetate is usually only present in trace amounts, which makes its economical extraction from plant sources practically impossible. As an ideal host for heterologous production of fragrance compound, the Saccharomyces cerevisiae has never been engineered to produce the esters, such as geranyl acetate. Results In this study, a heterologous geranyl acetate synthesis pathway was constructed in S. cerevisiae for the first time, and a titer of 0.63 mg/L geranyl acetate was achieved. By expressing an Erg20 mutant to divert carbon flux from FPP to GPP, the geranyl acetate production increased to 2.64 mg/L. However, the expression of heterologous GPP had limited effect. The highest production of 13.27 mg/L geranyl acetate was achieved by additional integration and expression of tHMG1, IDI1 and MAF1. Furthermore, through optimizing fermentation conditions, the geranyl acetate titer increased to 22.49 mg/L. Conclusions We constructed a monoterpene ester producing cell factory in S. cerevisiae for the first time, and demonstrated the great potential of this system for the heterologous production of a large group of economically important fragrance compounds. Electronic supplementary material The online version of this article (10.1186/s12934-018-0930-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Bolin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
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188
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Abstract
Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N2 fixation is energetically highly expensive, and an energy-generating process such as photosynthesis can meet the energy demand of N2 fixation. However, synthesis and expression of nitrogenase are exquisitely sensitive to the presence of oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N2. Here, we demonstrate a feasible way to engineer nitrogenase activity in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. In addition, we have identified the minimal nif cluster required for such activity in Synechocystis 6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels of nif genes. Importantly, the O2 tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineered Synechocystis 6803 strains that, remarkably, have more than 30% of the N2 fixation activity of Cyanothece 51142, the highest such activity established in any nondiazotrophic oxygenic photosynthetic organism. This report establishes a baseline for the ultimate goal of engineering nitrogen fixation ability in crop plants. Application of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes and the widespread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow to crop plants the ability to fix atmospheric N2in situ. One long-term approach is to transfer all nif genes from a prokaryote to plant cells and to express nitrogenase in an energy-producing organelle, chloroplast, or mitochondrion. In this context, Synechocystis 6803, the nondiazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.
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189
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Schultz C, Lian J, Zhao H. Metabolic Engineering of Saccharomyces cerevisiae Using a Trifunctional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion. Methods Enzymol 2018; 608:265-276. [PMID: 30173764 DOI: 10.1016/bs.mie.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Design and construction of an optimal microbial cell factory typically requires overexpression, knockdown, and knockout of multiple gene targets. In this chapter, we describe a combinatorial metabolic engineering strategy utilizing an orthogonal trifunctional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables multiplexed perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. To implement this system, three orthogonal Cas proteins were utilized: dLbCpf1 fused to a transcriptional activator, dSpCas9 fused to a transcriptional repressor, and SaCas9 for gene deletion. Deletion was accomplished by the introduction of a 28bp frame-shift mutation using a homology donor on the guide RNA expression vector. This approach enables the application of metabolic engineering to systematically optimize phenotypes of interest through a combination of gain-, reduction-, and loss-of-function mutations. Finally, we describe the construction of the CRISPR-AID system and its application toward engineering an example phenotype, surface display of recombinant Trichoderma reesei endoglucanase II.
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Affiliation(s)
- Carl Schultz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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190
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MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae. Metab Eng 2018; 47:294-302. [DOI: 10.1016/j.ymben.2018.03.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/20/2018] [Accepted: 03/31/2018] [Indexed: 11/20/2022]
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191
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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192
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Vieira Gomes AM, Souza Carmo T, Silva Carvalho L, Mendonça Bahia F, Parachin NS. Comparison of Yeasts as Hosts for Recombinant Protein Production. Microorganisms 2018; 6:microorganisms6020038. [PMID: 29710826 PMCID: PMC6027275 DOI: 10.3390/microorganisms6020038] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis, and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.
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Affiliation(s)
- Antonio Milton Vieira Gomes
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Talita Souza Carmo
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Lucas Silva Carvalho
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Frederico Mendonça Bahia
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
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193
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Metabolic engineering of Pichia pastoris. Metab Eng 2018; 50:2-15. [PMID: 29704654 DOI: 10.1016/j.ymben.2018.04.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/11/2022]
Abstract
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported. An outstanding early example of metabolic engineering in P. pastoris was the humanization of protein glycosylation. More recently the cell metabolism was engineered also to enhance the productivity of heterologous proteins. The last few years have seen an increased number of metabolic pathway design and engineering in P. pastoris, mainly towards the production of complex (secondary) metabolites. In this review, we discuss the potential role of P. pastoris as a platform for metabolic engineering, its strengths, and major requirements for future developments of chassis strains based on synthetic biology principles.
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194
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Li Y, Li S, Thodey K, Trenchard I, Cravens A, Smolke CD. Complete biosynthesis of noscapine and halogenated alkaloids in yeast. Proc Natl Acad Sci U S A 2018; 115:E3922-E3931. [PMID: 29610307 PMCID: PMC5924921 DOI: 10.1073/pnas.1721469115] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbial biosynthesis of plant natural products from simple building blocks is a promising approach toward scalable production and modification of high-value compounds. The pathway for biosynthesis of noscapine, a potential anticancer compound, from canadine was recently elucidated as a 10-gene cluster from opium poppy. Here we demonstrate the de novo production of noscapine in Saccharomyces cerevisiae, through the reconstruction of a biosynthetic pathway comprising over 30 enzymes from plants, bacteria, mammals, and yeast itself, including 7 plant endoplasmic reticulum (ER)-localized enzymes. Optimization directed to tuning expression of pathway enzymes, host endogenous metabolic pathways, and fermentation conditions led to an over 18,000-fold improvement from initial noscapine titers to ∼2.2 mg/L. By feeding modified tyrosine derivatives to the optimized noscapine-producing strain we further demonstrated microbial production of halogenated benzylisoquinoline alkaloids. This work highlights the potential for microbial biosynthetic platforms to support the synthesis of valuable and novel alkaloid compounds, which can advance alkaloid-based drug discovery and development.
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Affiliation(s)
- Yanran Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521
| | - Sijin Li
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | | | | | - Aaron Cravens
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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195
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Garcia-Ruiz E, HamediRad M, Zhao H. Pathway Design, Engineering, and Optimization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:77-116. [PMID: 27629378 DOI: 10.1007/10_2016_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.
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Affiliation(s)
- Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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196
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Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St. Onge RP, Tang Y, Hillenmeyer ME. HEx: A heterologous expression platform for the discovery of fungal natural products. SCIENCE ADVANCES 2018; 4:eaar5459. [PMID: 29651464 PMCID: PMC5895447 DOI: 10.1126/sciadv.aar5459] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/26/2018] [Indexed: 05/18/2023]
Abstract
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.
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Affiliation(s)
- Colin J. B. Harvey
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Curt R. Fischer
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Stanford ChEM-H (Chemistry, Engineering and Medicine for Human Health), Stanford University, Palo Alto, CA 94304, USA
| | - Hsiao-Ching Lin
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Jian Li
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Brian Naughton
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James Cherry
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Molly Miranda
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yong Fuga Li
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Angela M. Chu
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James R. Hennessy
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Gergana A. Vandova
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Diane Inglis
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Raeka S. Aiyar
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University, Palo Alto, CA 94304, USA
| | - Chaitan Khosla
- Stanford ChEM-H (Chemistry, Engineering and Medicine for Human Health), Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemistry, Stanford University, Palo Alto, CA 94304, USA
| | - Robert P. St. Onge
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Maureen E. Hillenmeyer
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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197
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Eriksen DT, Chao R, Zhao H. Applying Advanced DNA Assembly Methods to Generate Pathway Libraries. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Dawn T. Eriksen
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Ran Chao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Huimin Zhao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
- University of Illinois at Urbana-Champaign; Departments of Chemistry, Biochemistry, and Bioengineering, 600 South Mathews Avenue; Urbana IL 61801 USA
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198
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A semi-synthetic regulon enables rapid growth of yeast on xylose. Nat Commun 2018; 9:1233. [PMID: 29581426 PMCID: PMC5964326 DOI: 10.1038/s41467-018-03645-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/01/2018] [Indexed: 01/27/2023] Open
Abstract
Nutrient assimilation is the first step that allows biological systems to proliferate and produce value-added products. Yet, implementation of heterologous catabolic pathways has so far relied on constitutive gene expression without consideration for global regulatory systems that may enhance nutrient assimilation and cell growth. In contrast, natural systems prefer nutrient-responsive gene regulation (called regulons) that control multiple cellular functions necessary for cell survival and growth. Here, in Saccharomyces cerevisiae, by partially- and fully uncoupling galactose (GAL)-responsive regulation and metabolism, we demonstrate the significant growth benefits conferred by the GAL regulon. Next, by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy. This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth. Efficient assimilation of nutrients is essential for the production of value-added products in microbial fermentation. Here the authors design a semi-synthetic xylose regulon to improve growth characteristics of Saccharomyces cerevisiae on this non-native sugar.
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199
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HamediRad M, Lian J, Li H, Zhao H. RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization. Biotechnol Bioeng 2018; 115:1552-1560. [DOI: 10.1002/bit.26570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/28/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Mohammad HamediRad
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
| | - Jiazhang Lian
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
- College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
| | - Hejun Li
- Department of Agricultural and Biological EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Huimin Zhao
- Department of Chemical and Biomolecular EngineeringCarl R. Woese Institute for Genomic BiologyUrbanaIllinois
- Departments of Chemistry Biochemistry and BioengineeringUniversity of Illinois at UrbanaUrbanaIllinois
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200
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Abstract
Serine integrases catalyze precise rearrangement of DNA through site-specific recombination of small sequences of DNA called attachment (att) sites. Unlike other site-specific recombinases, the recombination reaction driven by serine integrases is highly directional and can only be reversed in the presence of an accessory protein called a recombination directionality factor (RDF). The ability to control reaction directionality has led to the development of serine integrases as tools for controlled rearrangement and modification of DNA in synthetic biology, gene therapy, and biotechnology. This review discusses recent advances in serine integrase technologies focusing on their applications in genome engineering, DNA assembly, and logic and data storage devices.
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Affiliation(s)
- Christine A. Merrick
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
| | - Jia Zhao
- Novo
Nordisk (China) Pharmaceuticals Co., Ltd., Lei Shing Hong Center, Guangshunnan Avenue, Beijing 100102, China
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
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