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Zhou Y, Li T, He X, Wang X, Wang F, Li X. Efficient Biosynthesis of (+)-α-Pinene and de Novo Synthesis of (+)- cis-Verbenol in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39140858 DOI: 10.1021/acs.jafc.4c05387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Bark beetles, major pests that bore into forest stems, cause significant economic damage to forests globally. (+)-α-Pinene is the precursor to (+)-cis-verbenol, a crucial component of the aggregation pheromones produced by bark beetles. This paper describes the de novo synthesis of (+)-cis-verbenol in Escherichia coli. Initially, the truncation position of (+)-α-pinene synthase (PtPS30 from Pinus taeda) and monoterpene precursor (geranyl diphosphate/neryl diphosphate) synthases were evaluated. Neryl diphosphate synthase from Solanum lycopersicum (SlNPPS1) and truncated (+)-α-pinene synthase (PtPS30-39) were selected as promising candidates. Subsequently, the titer of (+)-α-pinene was significantly increased 8.9-fold by using the fusion tag CM29, which enhanced the solubility of PtPS30-39. In addition, by optimizing expression elements (ribosomal binding sites, linkers, and up elements) and overexpressing CM29*PtPS30-39, a yield of 134.12 mg/L (+)-α-pinene was achieved. Finally, the first de novo synthesis of enantiopure (+)-cis-verbenol was achieved by introducing a cytochrome P450 mutant from Pseudomonas putida (P450camF89W,Y98F,L246A), resulting in a yield of 11.13 mg/L. This study lays the groundwork for developing verbenol-based trapping technology for controlling bark beetles.
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Affiliation(s)
- Yujunjie Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Tao Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xilong He
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
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2
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Khalkho JP, Beck A, Priyanka, Panda B, Chandra R. Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids. Arch Microbiol 2024; 206:340. [PMID: 38960981 DOI: 10.1007/s00203-024-04067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.
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Affiliation(s)
- Jaya Prabha Khalkho
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Abhishek Beck
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Priyanka
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Banishree Panda
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Ramesh Chandra
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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3
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Ye C, Li M, Gao J, Zuo Y, Xiao F, Jiang X, Cheng J, Huang L, Xu Z, Lian J. Metabolic engineering of Pichia pastoris for overproduction of cis-trans nepetalactol. Metab Eng 2024; 84:83-94. [PMID: 38897449 DOI: 10.1016/j.ymben.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Monoterpene indole alkaloids (MIAs) are a group of plant-derived natural products with high-value medicinal properties. However, their availability for clinical application is limited due to challenges in plant extraction. Microbial production has emerged as a promising strategy to meet the clinical demands for MIAs. The biosynthetic pathway of cis-trans nepetalactol, which serves as the universal iridoid scaffold for all MIAs, has been successfully identified and reconstituted. However, bottlenecks and challenges remain to construct a high-yielding platform strain for cis-trans nepetalactol production, which is vital for subsequent MIAs biosynthesis. In the present study, we focused on engineering of Pichia pastoris cell factories to enhance the production of geraniol, 8-hydroxygeraniol, and cis-trans nepetalactol. By targeting the biosynthetic pathway from acetyl-CoA to geraniol in both peroxisomes and cytoplasm, we achieved comparable geraniol titers in both compartments. Through protein engineering, we found that either G8H or CPR truncation increased the production of 8-hydroxygeraniol, with a 47.8-fold and 14.0-fold increase in the peroxisomal and cytosolic pathway strain, respectively. Furthermore, through a combination of dynamical control of ERG20, precursor and cofactor supply engineering, diploid engineering, and dual subcellular compartmentalization engineering, we achieved the highest ever reported production of cis-trans nepetalactol, with a titer of 4429.4 mg/L using fed-batch fermentation in a 5-L bioreactor. We anticipate our systematic metabolic engineering strategies to facilitate the development of P. pastoris cell factories for sustainable production of MIAs and other plant natural products.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Feng Xiao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Xiaojing Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jintao Cheng
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China.
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4
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Yang Y, Zou Y, Chen X, Sun H, Hua X, Johnston L, Zeng X, Qiao S, Ye C. Metabolic engineering of Escherichia coli for the production of 5-aminolevulinic acid based on combined metabolic pathway modification and reporter-guided mutant selection (RGMS). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:82. [PMID: 38886801 PMCID: PMC11184883 DOI: 10.1186/s13068-024-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields such as medicine, nutrition and agriculture. Metabolic engineering is an efficient strategy to improve microbial production of 5-ALA. RESULTS In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement. A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via both C4 and C5 pathways was applied herein. The expression of a modified hemARS gene and rational metabolic engineering by gene knockouts significantly improved ALA production from 765.9 to 2056.1 mg/L. Next, we tried to improve ALA production by RGMS-directed evolution of eamA gene. After RGMS, the ALA yield of strain A2-ASK reached 2471.3 mg/L in flask. Then, we aimed to improve the oxidation resistance of cells by overexpressing sodB and katE genes and ALA yield reached 2703.8 mg/L. A final attempt is to replace original promoter of hemB gene in genome with a weaker one to decrease its expression. After 24 h cultivation, a high ALA yield of 19.02 g/L was achieved by 108-ASK in a 5 L fermenter. CONCLUSIONS These results suggested that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification and optimization of gene expression.
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Affiliation(s)
- Yuting Yang
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Yuhong Zou
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Haidong Sun
- National Feed Engineering Technology Research Centre, Beijing, 100193, China
| | - Xia Hua
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Lee Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, 56267, USA
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Changchuan Ye
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.
- Department of Animal Science, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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5
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Holtz M, Acevedo-Rocha CG, Jensen MK. Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals. Curr Opin Biotechnol 2024; 87:103110. [PMID: 38503222 DOI: 10.1016/j.copbio.2024.103110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.
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Affiliation(s)
- Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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6
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Smit SJ, Ayten S, Radzikowska BA, Hamilton JP, Langer S, Unsworth WP, Larson TR, Buell CR, Lichman BR. The genomic and enzymatic basis for iridoid biosynthesis in cat thyme (Teucrium marum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1589-1602. [PMID: 38489316 DOI: 10.1111/tpj.16698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
Iridoids are non-canonical monoterpenoids produced by both insects and plants. An example is the cat-attracting and insect-repelling volatile iridoid nepetalactone, produced by Nepeta sp. (catmint) and aphids. Recently, both nepetalactone biosynthetic pathways were elucidated, showing a remarkable convergent evolution. The iridoid, dolichodial, produced by Teucrium marum (cat thyme) and multiple insect species, has highly similar properties to nepetalactone but its biosynthetic origin remains unknown. We set out to determine the genomic, enzymatic, and evolutionary basis of iridoid biosynthesis in T. marum. First, we generated a de novo chromosome-scale genome assembly for T. marum using Oxford Nanopore Technologies long reads and proximity-by-ligation Hi-C reads. The 610.3 Mb assembly spans 15 pseudomolecules with a 32.9 Mb N50 scaffold size. This enabled identification of iridoid biosynthetic genes, whose roles were verified via activity assays. Phylogenomic analysis revealed that the evolutionary history of T. marum iridoid synthase, the iridoid scaffold-forming enzyme, is not orthologous to typical iridoid synthases but is derived from its conserved paralog. We discovered an enzymatic route from nepetalactol to diverse iridoids through the coupled activity of an iridoid oxidase cytochrome P450 and acetyltransferases, via an inferred acylated intermediate. This work provides a genomic resource for specialized metabolite research in mints and demonstration of the role of acetylation in T. marum iridoid diversity. This work will enable future biocatalytic or biosynthetic production of potent insect repellents, as well as comparative studies into iridoid biosynthesis in insects.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Sefa Ayten
- Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, Georgia, 30602, USA
| | - Barbara A Radzikowska
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - John P Hamilton
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
- Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, 30602, USA
| | - Swen Langer
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Tony R Larson
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - C Robin Buell
- Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, Georgia, 30602, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
- Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, 30602, USA
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
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7
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He J, Liu X, Li C. Engineering Electron Transfer Pathway of Cytochrome P450s. Molecules 2024; 29:2480. [PMID: 38893355 PMCID: PMC11173547 DOI: 10.3390/molecules29112480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Cytochrome P450s (P450s), a superfamily of heme-containing enzymes, existed in animals, plants, and microorganisms. P450s can catalyze various regional and stereoselective oxidation reactions, which are widely used in natural product biosynthesis, drug metabolism, and biotechnology. In a typical catalytic cycle, P450s use redox proteins or domains to mediate electron transfer from NAD(P)H to heme iron. Therefore, the main factors determining the catalytic efficiency of P450s include not only the P450s themselves but also their redox-partners and electron transfer pathways. In this review, the electron transfer pathway engineering strategies of the P450s catalytic system are reviewed from four aspects: cofactor regeneration, selection of redox-partners, P450s and redox-partner engineering, and electrochemically or photochemically driven electron transfer.
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Affiliation(s)
- Jingting He
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi 832003, China;
| | - Xin Liu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Chun Li
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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8
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Liu Y, Zhao X, Gan F, Chen X, Deng K, Crowe SA, Hudson GA, Belcher MS, Schmidt M, Astolfi MCT, Kosina SM, Pang B, Shao M, Yin J, Sirirungruang S, Iavarone AT, Reed J, Martin LBB, El-Demerdash A, Kikuchi S, Misra RC, Liang X, Cronce MJ, Chen X, Zhan C, Kakumanu R, Baidoo EEK, Chen Y, Petzold CJ, Northen TR, Osbourn A, Scheller H, Keasling JD. Complete biosynthesis of QS-21 in engineered yeast. Nature 2024; 629:937-944. [PMID: 38720067 PMCID: PMC11111400 DOI: 10.1038/s41586-024-07345-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/22/2024] [Indexed: 05/23/2024]
Abstract
QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans1,2. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis3,4. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host's native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families-a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases-from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure-activity relationship, and will thus enable the rational design of potent vaccine adjuvants.
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Affiliation(s)
- Yuzhong Liu
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Xixi Zhao
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Fei Gan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Xiaoyue Chen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Samantha A Crowe
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Graham A Hudson
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Michael S Belcher
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Maria C T Astolfi
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bo Pang
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Minglong Shao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jing Yin
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sasilada Sirirungruang
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Anthony T Iavarone
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Amr El-Demerdash
- John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
| | | | | | - Xiaomeng Liang
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael J Cronce
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Xiulai Chen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chunjun Zhan
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Henrik Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
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9
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Dias SL, Chuang L, Liu S, Seligmann B, Brendel FL, Chavez BG, Hoffie RE, Hoffie I, Kumlehn J, Bültemeier A, Wolf J, Herde M, Witte CP, D'Auria JC, Franke J. Biosynthesis of the allelopathic alkaloid gramine in barley by a cryptic oxidative rearrangement. Science 2024; 383:1448-1454. [PMID: 38547266 DOI: 10.1126/science.adk6112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024]
Abstract
The defensive alkaloid gramine not only protects barley and other grasses from insects but also negatively affects their palatability to ruminants. The key gene for gramine formation has remained elusive, hampering breeding initiatives. In this work, we report that a gene encoding cytochrome P450 monooxygenase CYP76M57, which we name AMI synthase (AMIS), enables the production of gramine in Nicotiana benthamiana, Arabidopsis thaliana, and Saccharomyces cerevisiae. We reconstituted gramine production in the gramine-free barley (Hordeum vulgare) variety Golden Promise and eliminated it from cultivar Tafeno by Cas-mediated gene editing. In vitro experiments unraveled that an unexpected cryptic oxidative rearrangement underlies this noncanonical conversion of an amino acid to a chain-shortened biogenic amine. The discovery of the genetic basis of gramine formation now permits tailor-made optimization of gramine-linked traits in barley by plant breeding.
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Affiliation(s)
- Sara Leite Dias
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Ling Chuang
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Shenyu Liu
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Benedikt Seligmann
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Fabian L Brendel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Benjamin G Chavez
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Robert E Hoffie
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Iris Hoffie
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Jochen Kumlehn
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Arne Bültemeier
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Johanna Wolf
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Seeland OT Gatersleben, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
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10
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Petersen SD, Levassor L, Pedersen CM, Madsen J, Hansen LG, Zhang J, Haidar AK, Frandsen RJN, Keasling JD, Weber T, Sonnenschein N, K. Jensen M. teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. PLoS Comput Biol 2024; 20:e1011929. [PMID: 38457467 PMCID: PMC10954146 DOI: 10.1371/journal.pcbi.1011929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/20/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024] Open
Abstract
Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.
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Affiliation(s)
- Søren D. Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lucas Levassor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christine M. Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jan Madsen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lea G. Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ahmad K. Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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11
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Raghavan I, Juman R, Wang ZQ. The non-mevalonate pathway requires a delicate balance of intermediates to maximize terpene production. Appl Microbiol Biotechnol 2024; 108:245. [PMID: 38421431 PMCID: PMC10904526 DOI: 10.1007/s00253-024-13077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Terpenes are valuable industrial chemicals whose demands are increasingly being met by bioengineering microbes such as E. coli. Although the bioengineering efforts commonly involve installing the mevalonate (MVA) pathway in E. coli for terpene production, the less studied methylerythritol phosphate (MEP) pathway is a more attractive target due to its higher energy efficiency and theoretical yield, despite its tight regulation. In this study, we integrated an additional copy of the entire MEP pathway into the E. coli genome for stable, marker-free terpene production. The genomically integrated strain produced more monoterpene geraniol than a plasmid-based system. The pathway genes' transcription was modulated using different promoters to produce geraniol as the reporter of the pathway flux. Pathway genes, including dxs, idi, and ispDF, expressed from a medium-strength promoter, led to the highest geraniol production. Quantifying the MEP pathway intermediates revealed that the highest geraniol producers had high levels of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), but moderate levels of the pathway intermediates upstream of these two building blocks. A principal component analysis demonstrated that 1-deoxy-D-xylulose 5-phosphate (DXP), the product of the first enzyme of the pathway, was critical for determining the geraniol titer, whereas MEP, the product of DXP reductoisomerase (Dxr or IspC), was the least essential. This work shows that an intricate balance of the MEP pathway intermediates determines the terpene yield in engineered E. coli. The genetically stable and intermediate-balanced strains created in this study will serve as a chassis for producing various terpenes. KEY POINTS: • Genome-integrated MEP pathway afforded higher strain stability • Genome-integrated MEP pathway produced more terpene than the plasmid-based system • High monoterpene production requires a fine balance of MEP pathway intermediates.
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Affiliation(s)
- Indu Raghavan
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Rosheena Juman
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo, the State University of New York, 653 Cooke Hall, Buffalo, New York, NY14260, USA.
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12
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Dror MJ, Misa J, Yee DA, Chu AM, Yu RK, Chan BB, Aoyama LS, Chaparala AP, O'Connor SE, Tang Y. Engineered biosynthesis of plant heteroyohimbine and corynantheine alkaloids in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2024; 51:kuad047. [PMID: 38140980 PMCID: PMC10995622 DOI: 10.1093/jimb/kuad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are a class of natural products comprised of thousands of structurally unique bioactive compounds with significant therapeutic values. Due to difficulties associated with isolation from native plant species and organic synthesis of these structurally complex molecules, microbial production of MIAs using engineered hosts are highly desired. In this work, we report the engineering of fully integrated Saccharomyces cerevisiae strains that allow de novo access to strictosidine, the universal precursor to thousands of MIAs at 30-40 mg/L. The optimization efforts were based on a previously reported yeast strain that is engineered to produce high titers of the monoterpene precursor geraniol through compartmentalization of mevalonate pathway in the mitochondria. Our approaches here included the use of CRISPR-dCas9 interference to identify mitochondria diphosphate transporters that negatively impact the titer of the monoterpene, followed by genetic inactivation; the overexpression of transcriptional regulators that increase cellular respiration and mitochondria biogenesis. Strain construction included the strategic integration of genes encoding both MIA biosynthetic and accessory enzymes into the genome under a variety of constitutive and inducible promoters. Following successful de novo production of strictosidine, complex alkaloids belonging to heteroyohimbine and corynantheine families were reconstituted in the host with introduction of additional downstream enzymes. We demonstrate that the serpentine/alstonine pair can be produced at ∼5 mg/L titer, while corynantheidine, the precursor to mitragynine can be produced at ∼1 mg/L titer. Feeding of halogenated tryptamine led to the biosynthesis of analogs of alkaloids in both families. Collectively, our yeast strain represents an excellent starting point to further engineer biosynthetic bottlenecks in this pathway and to access additional MIAs and analogs through microbial fermentation. ONE SENTENCE SUMMARY An Saccharomyces cerevisiae-based microbial platform was developed for the biosynthesis of monoterpene indole alkaloids, including the universal precursor strictosidine and further modified heteroyohimbine and corynantheidine alkaloids.
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Affiliation(s)
- Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angela M Chu
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Rachel K Yu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bradley B Chan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lauren S Aoyama
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anjali P Chaparala
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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13
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Bureau JA, Oliva ME, Dong Y, Ignea C. Engineering yeast for the production of plant terpenoids using synthetic biology approaches. Nat Prod Rep 2023; 40:1822-1848. [PMID: 37523210 DOI: 10.1039/d3np00005b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.
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Affiliation(s)
| | | | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
| | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
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14
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Agrawal A, Yang Z, Blenner M. Engineering Yarrowia lipolytica for the biosynthesis of geraniol. Metab Eng Commun 2023; 17:e00228. [PMID: 38029016 PMCID: PMC10652127 DOI: 10.1016/j.mec.2023.e00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Geraniol is a monoterpene with wide applications in the food, cosmetics, and pharmaceutical industries. Microbial production has largely used model organisms lacking favorable properties for monoterpene production. In this work, we produced geraniol in metabolically engineered Yarrowia lipolytica. First, two plant-derived geraniol synthases (GES) from Catharanthus roseus (Cr) and Valeriana officinalis (Vo) were tested based on previous reports of activity. Both wild type and truncated mutants of GES (without signal peptide targeting chloroplast) were examined by co-expressing with MVA pathway enzymes tHMG1 and IDI1. Truncated CrGES (tCrGES) produced the most geraniol and thus was used for further experimentation. The initial strain was obtained by overexpression of the truncated HMG1, IDI and tCrGES. The acetyl-CoA precursor pool was enhanced by overexpressing mevalonate pathway genes such as ERG10, HMGS or MVK, PMK. The final strain overexpressing 3 copies of tCrGES and single copies of ERG10, HMGS, tHMG1, IDI produced approximately 1 g/L in shake-flask fermentation. This is the first demonstration of geraniol production in Yarrowia lipolytica and the highest de novo titer reported to date in yeast.
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Affiliation(s)
- Ayushi Agrawal
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
| | - Zhiliang Yang
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, 590 Avenue 1743, University of Delaware, Newark, DE, 19713, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, 206 S. Palmetto Blvd., Clemson, SC, 29634, USA
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15
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Zhang Y, Yuan M, Wu X, Zhang Q, Wang Y, Zheng L, Chiu T, Zhang H, Lan L, Wang F, Liao Y, Gong X, Yan S, Wang Y, Shen Y, Fu X. The construction and optimization of engineered yeast chassis for efficient biosynthesis of 8-hydroxygeraniol. MLIFE 2023; 2:438-449. [PMID: 38818263 PMCID: PMC10989129 DOI: 10.1002/mlf2.12099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 06/01/2024]
Abstract
Microbial production of monoterpenoid indole alkaloids (MIAs) provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values. However, efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase (G8H). In this study, we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets. Through genome mining, we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo. We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments. Finally, the combination of the engineered chassis, optimized biosynthesis pathway, and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain. Overall, this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.
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Affiliation(s)
- Yu Zhang
- BGI ResearchShenzhenChina
- BGI ResearchHangzhouChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
| | | | | | | | | | | | | | | | | | | | | | - Xuemei Gong
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
| | - Shirui Yan
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Yun Wang
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Yue Shen
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Xian Fu
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
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16
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López-López D, Razo-Hernández RS, Millán-Pacheco C, Leyva-Peralta MA, Peña-Morán OA, Sánchez-Carranza JN, Rodríguez-López V. Ligand-Based Drug Design of Genipin Derivatives with Cytotoxic Activity against HeLa Cell Line: A Structural and Theoretical Study. Pharmaceuticals (Basel) 2023; 16:1647. [PMID: 38139774 PMCID: PMC10748106 DOI: 10.3390/ph16121647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Cervical cancer is a malignant neoplastic disease, mainly associated to HPV infection, with high mortality rates. Among natural products, iridoids have shown different biological activities, including cytotoxic and antitumor effects, in different cancer cell types. Geniposide and its aglycone Genipin have been assessed against different types of cancer. In this work, both iridoids were evaluated against HeLa and three different cervical cancer cell lines. Furthermore, we performed a SAR analysis incorporating 13 iridoids with a high structural similarity to Geniposide and Genipin, also tested in the HeLa cell line and at the same treatment time. Derived from this analysis, we found that the dipole moment (magnitude and direction) is key for their cytotoxic activity in the HeLa cell line. Then, we proceeded to the ligand-based design of new Genipin derivatives through a QSAR model (R2 = 87.95 and Q2 = 62.33) that incorporates different quantum mechanic molecular descriptor types (ρ, ΔPSA, ∆Polarizability2, and logS). Derived from the ligand-based design, we observed that the presence of an aldehyde or a hydroxymethyl in C4, hydroxyls in C1, C6, and C8, and the lack of the double bond in C7-C8 increased the predicted biological activity of the iridoids. Finally, ten simple iridoids (D9, D107, D35, D36, D55, D56, D58, D60, D61, and D62) are proposed as potential cytotoxic agents against the HeLa cell line based on their predicted IC50 value and electrostatic features.
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Affiliation(s)
- Diana López-López
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.L.-L.); (C.M.-P.); (J.N.S.-C.)
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Quimioinformática y Diseño de Fármacos, Centro de Investigación en Dinámica Celular, Instituto de investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - César Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.L.-L.); (C.M.-P.); (J.N.S.-C.)
| | - Mario Alberto Leyva-Peralta
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, H. Caborca, Sonora 83621, Mexico;
| | - Omar Aristeo Peña-Morán
- Departamento de Ciencias Farmacéuticas, División de Ciencias de la Salud, Universidad Autónoma del Estado de Quintana Roo, Chetumal 77019, Mexico;
| | | | - Verónica Rodríguez-López
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico; (D.L.-L.); (C.M.-P.); (J.N.S.-C.)
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17
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Wu Y, Liu C, Koganitsky A, Gong FL, Li S. Discovering Dynamic Plant Enzyme Complexes in Yeast for Kratom Alkaloid Pathway Identification. Angew Chem Int Ed Engl 2023; 62:e202307995. [PMID: 37549372 PMCID: PMC10530425 DOI: 10.1002/anie.202307995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Discovering natural product biosynthetic pathways of medicinal plants is challenging and laborious. Capturing the coregulation patterns of pathway enzymes, particularly transcriptomic regulation, has proven an effective method to accelerate pathway identification. In this study, we developed a yeast-based screening method to capture the protein-protein interactions (PPI) between plant enzymes, which is another useful pattern to complement the prevalent approach. Combining this method with plant multiomics analysis, we discovered four enzyme complexes and their organized pathways from kratom, an alkaloid-producing plant. The four pathway branches involved six enzymes, including a strictosidine synthase, a strictosidine β-D-glucosidase (MsSGD), and four medium-chain dehydrogenase/reductases (MsMDRs). PPI screening selected six MsMDRs interacting with MsSGD from 20 candidates predicted by multiomics analysis. Four of the six MsMDRs were then characterized as functional, indicating the high selectivity of the PPI screening method. This study highlights the opportunity of leveraging post-translational regulation features to discover novel plant natural product biosynthetic pathways.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Chang Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Anna Koganitsky
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
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18
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Salim V, Jarecki SA, Vick M, Miller R. Advances in Metabolic Engineering of Plant Monoterpene Indole Alkaloids. BIOLOGY 2023; 12:1056. [PMID: 37626942 PMCID: PMC10452178 DOI: 10.3390/biology12081056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Monoterpene indole alkaloids (MIAs) encompass a diverse family of over 3000 plant natural products with a wide range of medical applications. Further utilizations of these compounds, however, are hampered due to low levels of abundance in their natural sources, causing difficult isolation and complex multi-steps in uneconomical chemical syntheses. Metabolic engineering of MIA biosynthesis in heterologous hosts is attractive, particularly for increasing the yield of natural products of interest and expanding their chemical diversity. Here, we review recent advances and strategies which have been adopted to engineer microbial and plant systems for the purpose of generating MIAs and discuss the current issues and future developments of manufacturing MIAs by synthetic biology approaches.
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Affiliation(s)
- Vonny Salim
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Sara-Alexis Jarecki
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Marshall Vick
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Ryan Miller
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA;
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19
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Jiang H, Wang X. Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances. Biotechnol Adv 2023; 65:108151. [PMID: 37037288 DOI: 10.1016/j.biotechadv.2023.108151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023]
Abstract
Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.
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Affiliation(s)
- Hui Jiang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China
| | - Xi Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China; College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, PR China.
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20
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Naseri G. A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast. Nat Commun 2023; 14:1916. [PMID: 37024483 PMCID: PMC10079933 DOI: 10.1038/s41467-023-37627-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Secondary natural products (NPs) are a rich source for drug discovery. However, the low abundance of NPs makes their extraction from nature inefficient, while chemical synthesis is challenging and unsustainable. Saccharomyces cerevisiae and Pichia pastoris are excellent manufacturing systems for the production of NPs. This Perspective discusses a comprehensive platform for sustainable production of NPs in the two yeasts through system-associated optimization at four levels: genetics, temporal controllers, productivity screening, and scalability. Additionally, it is pointed out critical metabolic building blocks in NP bioengineering can be identified through connecting multilevel data of the optimized system using deep learning.
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Affiliation(s)
- Gita Naseri
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117, Berlin, Germany.
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115, Berlin, Germany.
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21
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Yu J, Lv D, Zhang L. De novo Biosynthesis of a Vinblastine Precursor in Pichia pastoris. Synth Syst Biotechnol 2023; 8:300-301. [PMID: 37096075 PMCID: PMC10121913 DOI: 10.1016/j.synbio.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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22
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Milne N, Sáez-Sáez J, Nielsen AM, Dyekjaer JD, Rago D, Kristensen M, Wulff T, Borodina I. Engineering Saccharomyces cerevisiae for the de novo Production of Halogenated Tryptophan and Tryptamine Derivatives. ChemistryOpen 2023; 12:e202200266. [PMID: 36929157 PMCID: PMC10068768 DOI: 10.1002/open.202200266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The indole scaffold is a recurring structure in multiple bioactive heterocycles and natural products. Substituted indoles like the amino acid tryptophan serve as a precursor for a wide range of natural products with pharmaceutical or agrochemical applications. Inspired by the versatility of these compounds, medicinal chemists have for decades exploited indole as a core structure in the drug discovery process. With the aim of tuning the properties of lead drug candidates, regioselective halogenation of the indole scaffold is a common strategy. However, chemical halogenation is generally expensive, has a poor atom economy, lacks regioselectivity, and generates hazardous waste streams. As an alternative, in this work we engineer the industrial workhorse Saccharomyces cerevisiae for the de novo production of halogenated tryptophan and tryptamine derivatives. Functional expression of bacterial tryptophan halogenases together with a partner flavin reductase and a tryptophan decarboxylase resulted in the production of halogenated tryptophan and tryptamine with chlorine or bromine. Furthermore, by combining tryptophan halogenases, production of di-halogenated molecules was also achieved. Overall, this works paves the road for the production of new-to-nature halogenated natural products in yeast.
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Affiliation(s)
- Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Annette Munch Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Jane Dannow Dyekjaer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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23
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Raorane ML, Manz C, Hildebrandt S, Mielke M, Thieme M, Keller J, Bunzel M, Nick P. Cell type matters: competence for alkaloid metabolism differs in two seed-derived cell strains of Catharanthus roseus. PROTOPLASMA 2023; 260:349-369. [PMID: 35697946 PMCID: PMC9931846 DOI: 10.1007/s00709-022-01781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Since the discovery of the anticancer drugs vinblastine and vincristine, Catharanthus roseus has been intensively studied for biosynthesis of several terpene indole alkaloids (TIAs). Due to their low abundance in plant tissues at a simultaneously high demand, modes of production alternative to conventional extraction are mandatory. Plant cell fermentation might become one of these alternatives, yet decades of research have shown limited success to certain product classes, leading to the question: how to preserve the intrinsic ability to produce TIAs (metabolic competence) in cell culture? We used the strategy to use the developmental potency of mature embryos to generate such strains. Two cell strains (C1and C4) from seed embryos of Catharanthus roseus were found to differ not only morphologically, but also in their metabolic competence. This differential competence became manifest not only under phytohormone elicitation, but also upon feeding with alkaloid pathway precursors. The more active strain C4 formed larger cell aggregates and was endowed with longer mitochondria. These cellular features were accompanied by higher alkaloid accumulation in response to methyl jasmonate (MeJA) elicitation. The levels of catharanthine could be increased significantly, while the concurrent vindoline branch of the pathway was blocked, such that no bisindole alkaloids were detectable. By feeding vindoline to MeJA-elicited C4 cells, vincristine became detectable; however, only to marginal amounts. In conclusion, these results show that cultured cells are not "de-differentiated", but can differ in metabolic competence. In addition to elicitation and precursor feeding, the cellular properties of the "biomatter" are highly relevant for the success of plant cell fermentation.
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Affiliation(s)
- Manish L Raorane
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.
- Institute of Pharmacy, Martin-Luther-University, Hoher Weg 8, 06120, Halle-WittenbergHalle (Saale), Germany.
| | - Christina Manz
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Sarah Hildebrandt
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Marion Mielke
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Marc Thieme
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Judith Keller
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Mirko Bunzel
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
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24
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Lemos Cruz P, Carqueijeiro I, Koudounas K, Bomzan DP, Stander EA, Abdallah C, Kulagina N, Oudin A, Lanoue A, Giglioli-Guivarc'h N, Nagegowda DA, Papon N, Besseau S, Clastre M, Courdavault V. Identification of a second 16-hydroxytabersonine-O-methyltransferase suggests an evolutionary relationship between alkaloid and flavonoid metabolisms in Catharanthus roseus. PROTOPLASMA 2023; 260:607-624. [PMID: 35947213 DOI: 10.1007/s00709-022-01801-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The medicinal plant Catharanthus roseus biosynthesizes many important drugs for human health, including the anticancer monoterpene indole alkaloids (MIAs) vinblastine and vincristine. Over the past decades, the continuous increase in pharmaceutical demand has prompted several research groups to characterize MIA biosynthetic pathways for considering future metabolic engineering processes of supply. In line with previous work suggesting that diversification can potentially occur at various steps along the vindoline branch, we were here interested in investigating the involvement of distinct isoforms of tabersonine-16-O-methyltransferase (16OMT) which plays a pivotal role in the MIA biosynthetic pathway. By combining homology searches based on the previously characterized 16OMT1, phylogenetic analyses, functional assays in yeast, and biochemical and in planta characterizations, we identified a second isoform of 16OMT, referred to as 16OMT2. 16OMT2 appears to be a multifunctional enzyme working on both MIA and flavonoid substrates, suggesting that a constrained evolution of the enzyme for accommodating the MIA substrate has probably occurred to favor the apparition of 16OMT2 from an ancestral specific flavonoid-O-methyltransferase. Since 16OMT1 and 16OMT2 displays a high sequence identity and similar kinetic parameters for 16-hydroxytabersonine, we postulate that 16OMT1 may result from a later 16OMT2 gene duplication accompanied by a continuous neofunctionalization leading to an almost complete loss of flavonoid O-methyltransferase activity. Overall, these results participate in increasing our knowledge on the evolutionary processes that have likely led to enzyme co-optation for MIA synthesis.
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Affiliation(s)
- Pamela Lemos Cruz
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Ines Carqueijeiro
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Emily Amor Stander
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Cécile Abdallah
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Natalja Kulagina
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Audrey Oudin
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR, ICAT, F-49000, Angers, France
| | - Sébastien Besseau
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
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25
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Ozber N, Yu L, Hagel JM, Facchini PJ. Strong Feedback Inhibition of Key Enzymes in the Morphine Biosynthetic Pathway from Opium Poppy Detectable in Engineered Yeast. ACS Chem Biol 2023; 18:419-430. [PMID: 36735832 DOI: 10.1021/acschembio.2c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Systematic screening of morphine pathway intermediates in engineered yeast revealed key biosynthetic enzymes displaying potent feedback inhibition: 3'-hydroxy-N-methylcoclaurine 4'-methyltransferase (4'OMT), which yields (S)-reticuline, and the coupled salutaridinol-7-O-acetyltransferase (SalAT) and thebaine synthase (THS2) enzyme system that produces thebaine. The addition of deuterated reticuline-d1 to a yeast strain able to convert (S)-norcoclaurine to (S)-reticuline showed reduced product accumulation in response to the feeding of all four successive pathway intermediates. Similarly, the addition of deuterated thebaine-d3 to a yeast strain able to convert salutaridine to thebaine showed reduced product accumulation from exogenous salutaridine or salutaridinol. In vitro analysis showed that reticuline is a noncompetitive inhibitor of 4'OMT, whereas thebaine exerts mixed inhibition on SalAT/THS2. In a yeast strain capable of de novo morphine biosynthesis, the addition of reticuline and thebaine resulted in the accumulation of several pathway intermediates. In contrast, morphine had no effect, suggesting that circumventing the interaction of reticuline and thebaine with 4'OMT and SalAT/THS2, respectively, could substantially increase opiate alkaloid titers in engineered yeast.
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Affiliation(s)
- Natali Ozber
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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26
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MYC2: A Master Switch for Plant Physiological Processes and Specialized Metabolite Synthesis. Int J Mol Sci 2023; 24:ijms24043511. [PMID: 36834921 PMCID: PMC9963318 DOI: 10.3390/ijms24043511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The jasmonic acid (JA) signaling pathway plays important roles in plant defenses, development, and the synthesis of specialized metabolites synthesis. Transcription factor MYC2 is a major regulator of the JA signaling pathway and is involved in the regulation of plant physiological processes and specialized metabolite synthesis. Based on our understanding of the mechanism underlying the regulation of specialized metabolite synthesis in plants by the transcription factor MYC2, the use of synthetic biology approaches to design MYC2-driven chassis cells for the synthesis of specialized metabolites with high medicinal value, such as paclitaxel, vincristine, and artemisinin, seems to be a promising strategy. In this review, the regulatory role of MYC2 in JA signal transduction of plants to biotic and abiotic stresses, plant growth, development and specialized metabolite synthesis is described in detail, which will provide valuable reference for the use of MYC2 molecular switches to regulate plant specialized metabolite biosynthesis.
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27
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Jiang CX, Yu JX, Fei X, Pan XJ, Zhu NN, Lin CL, Zhou D, Zhu HR, Qi Y, Wu ZG. Gene coexpression networks allow the discovery of two strictosidine synthases underlying monoterpene indole alkaloid biosynthesis in Uncaria rhynchophylla. Int J Biol Macromol 2023; 226:1360-1373. [PMID: 36442554 DOI: 10.1016/j.ijbiomac.2022.11.249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Plant-derived monoterpene indole alkaloids (MIAs) from Uncaria rhynchophylla (UR) have huge medicinal properties in treating Alzheimer's disease, Parkinson's disease, and depression. Although many bioactive UR-MIA products have been isolated as drugs, their biosynthetic pathway remains largely unexplored. In this study, untargeted metabolome identified 79 MIA features in UR tissues (leaf, branch stem, hook stem, and stem), of which 30 MIAs were differentially accumulated among different tissues. Short time series expression analysis captured 58 pathway genes and 12 hub regulators responsible for UR-MIA biosynthesis and regulation, which were strong links with main UR-MIA features. Coexpression networks further pointed to two strictosidine synthases (UrSTR1/5) that were coregulated with multiple MIA-related genes and highly correlated with UR-MIA features (r > 0.7, P < 0.005). Both UrSTR1/5 catalyzed the formation of strictosidine with tryptamine and secologanin as substrates, highlighting the importance of key residues (UrSTR1: Glu309, Tyr155; UrSTR5: Glu295, Tyr141). Further, overexpression of UrSTR1/5 in UR hairy roots constitutively increased the biosynthesis of bioactive UR-MIAs (rhynchophylline, isorhynchophylline, corynoxeine, etc), whereas RNAi of UrSTR1/5 significantly decreased UR-MIA biosynthesis. Collectively, our work not only provides candidates for reconstituting the biosynthesis of bioactive UR-MIAs in heterologous hosts but also highlights a powerful strategy for mining natural product biosynthesis in medicinal plants.
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Affiliation(s)
- Cheng-Xi Jiang
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Jia-Xing Yu
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Xuan Fei
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiao-Jun Pan
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Ning-Ning Zhu
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Chong-Liang Lin
- The 1(st) Affiliated Hospital of WMU, The 1(st) School of Medicine, Wenzhou Medical University, Wenzhou 325025, China
| | - Dan Zhou
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Hao-Ru Zhu
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Yu Qi
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhi-Gang Wu
- Key Laboratory of Traditional Chinese Medicine Research, School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China.
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28
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Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
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Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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29
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Abstract
Covering: 2015 to 2022Fungal terpenoids are of large structural diversity and often exhibit interesting biological activities. Recent work has focused on two main aspects: (1) the discovery and understanding of unknown biosynthetic genes and pathways, and (2) the usage of already known biosynthetic genes in the construction of high yielding production strains. Both aspects will be covered in this review article that aims to summarise the most important work of the past few years.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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30
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Wu Y, Liu C, Gong FL, Li S. Discovering dynamic plant enzyme complexes in yeast for novel alkaloid pathway identification from a medicinal plant kratom. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524293. [PMID: 36711573 PMCID: PMC9882157 DOI: 10.1101/2023.01.16.524293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Discovering natural product biosynthetic pathways from medicinal plants is challenging and laborious, largely due to the complexity of the transcriptomics-driven pathway prediction process. Here we developed a novel approach that captures the protein-level connections between enzymes for pathway discovery with improved accuracy. We proved that heterologous protein-protein interaction screening in yeast enabled the efficient discovery of both dynamic plant enzyme complexes and the pathways they organize. This approach discovered complexes and pathways in the monoterpene indole alkaloid metabolism of a medicinal plant, kratom with high success rate. Screening using a strictosidine β-D-glucosidase (MsSGD1) against 19 medium-chain dehydrogenase/reductases (MsMDRs) identified five MsSGD1-MsMDR complexes. Three out of the five interacting MsMDRs were then proven functional, while the remaining 14 non-interacting candidates did not show obvious activities. The work discovered three branched pathways by combining transcriptomics, metabolomics, and heterologous PPI screening and demonstrated a new plant pathway discovery strategy.
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Affiliation(s)
| | | | - Franklin L. Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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31
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Chen SL, Liu TS, Zhang WG, Xu JZ. Cofactor Engineering for Efficient Production of α-Farnesene by Rational Modification of NADPH and ATP Regeneration Pathway in Pichia pastoris. Int J Mol Sci 2023; 24:ijms24021767. [PMID: 36675279 PMCID: PMC9860691 DOI: 10.3390/ijms24021767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 01/18/2023] Open
Abstract
α-Farnesene, an acyclic volatile sesquiterpene, plays important roles in aircraft fuel, food flavoring, agriculture, pharmaceutical and chemical industries. Here, by re-creating the NADPH and ATP biosynthetic pathways in Pichia pastoris, we increased the production of α-farnesene. First, the native oxiPPP was recreated by overexpressing its essential enzymes or by inactivating glucose-6-phosphate isomerase (PGI). This revealed that the combined over-expression of ZWF1 and SOL3 increases α-farnesene production by improving NADPH supply, whereas inactivating PGI did not do so because it caused a reduction in cell growth. The next step was to introduce heterologous cPOS5 at various expression levels into P. pastoris. It was discovered that a low intensity expression of cPOS5 aided in the production of α-farnesene. Finally, ATP was increased by the overexpression of APRT and inactivation of GPD1. The resultant strain P. pastoris X33-38 produced 3.09 ± 0.37 g/L of α-farnesene in shake flask fermentation, which was 41.7% higher than that of the parent strain. These findings open a new avenue for the development of an industrial-strength α-farnesene producer by rationally modifying the NADPH and ATP regeneration pathways in P. pastoris.
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32
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Lim PK, Julca I, Mutwil M. Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data. Comput Struct Biotechnol J 2023; 21:1639-1650. [PMID: 36874159 PMCID: PMC9976193 DOI: 10.1016/j.csbj.2023.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The immense structural diversity of products and intermediates of plant specialized metabolism (specialized metabolites) makes them rich sources of therapeutic medicine, nutrients, and other useful materials. With the rapid accumulation of reactome data that can be accessible on biological and chemical databases, along with recent advances in machine learning, this review sets out to outline how supervised machine learning can be used to design new compounds and pathways by exploiting the wealth of said data. We will first examine the various sources from which reactome data can be obtained, followed by explaining the different machine learning encoding methods for reactome data. We then discuss current supervised machine learning developments that can be employed in various aspects to help redesign plant specialized metabolism.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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33
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Sun S, Shen X, Li Y, Li Y, Wang S, Li R, Zhang H, Shen G, Guo B, Wei J, Xu J, St-Pierre B, Chen S, Sun C. Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism. NATURE PLANTS 2023; 9:179-190. [PMID: 36522449 DOI: 10.1038/s41477-022-01291-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) are among the most diverse specialized metabolites in plants and are of great pharmaceutical importance. We leveraged single-cell transcriptomics to explore the spatial organization of MIA metabolism in Catharanthus roseus leaves, and the transcripts of 20 MIA genes were first localized, updating the model of MIA biosynthesis. The MIA pathway was partitioned into three cell types, consistent with the results from RNA in situ hybridization experiments. Several candidate transporters were predicted to be essential players shuttling MIA intermediates between inter- and intracellular compartments, supplying potential targets to increase the overall yields of desirable MIAs in native plants or heterologous hosts through metabolic engineering and synthetic biology. This work provides not only a universal roadmap for elucidating the spatiotemporal distribution of biological processes at single-cell resolution, but also abundant cellular and genetic resources for further investigation of the higher-order organization of MIA biosynthesis, transport and storage.
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Affiliation(s)
- Sijie Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaofeng Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rucan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huibo Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guoan Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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34
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Mukherjee M, Wang ZQ. A well-characterized polycistronic-like gene expression system in yeast. Biotechnol Bioeng 2023; 120:260-271. [PMID: 36168285 DOI: 10.1002/bit.28247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/14/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
Efficient expression of multiple genes is critical to yeast metabolic engineering for the bioproduction of bulk and fine chemicals. A yeast polycistronic expression system is of particular interest because one promoter can drive the expression of multiple genes. 2A viral peptides enable the cotranslation of multiple proteins from a single mRNA by ribosomal skipping. However, the wide adaptation of 2A viral peptides for polycistronic-like gene expression in yeast awaits in-depth characterizations. Additionally, a one-step assembly of such a polycistronic-like system is highly desirable. To this end, we have developed a modular cloning (MoClo) compatible 2A peptide-based polycistronic-like system capable of expressing multiple genes from a single promoter in yeast. Characterizing the bi-, tri-, and quad-cistronic expression of fluorescent proteins showed high cleavage efficiencies of three 2A peptides: E2A from equine rhinitis B virus, P2A from porcine teschovirus-1, and O2A from Operophtera brumata cypovirus-18. Applying the polycistronic-like system to produce geraniol, a valuable industrial compound, resulted in comparable or higher titers than using conventional monocistronic constructs. In summary, this highly-characterized polycistronic-like gene expression system is another tool to facilitate multigene expression for metabolic engineering in yeast.
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Affiliation(s)
- Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA
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35
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Gao D, Liu T, Gao J, Xu J, Gou Y, Pan Y, Li D, Ye C, Pan R, Huang L, Xu Z, Lian J. De Novo Biosynthesis of Vindoline and Catharanthine in Saccharomyces cerevisiae. BIODESIGN RESEARCH 2022; 2022:0002. [PMID: 37905202 PMCID: PMC10593122 DOI: 10.34133/bdr.0002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/02/2023] Open
Abstract
Vinblastine has been used clinically as one of the most potent therapeutics for the treatment of several types of cancer. However, the traditional plant extraction method suffers from unreliable supply, low abundance, and extremely high cost. Here, we use synthetic biology approach to engineer Saccharomyces cerevisiae for de novo biosynthesis of vindoline and catharanthine, which can be coupled chemically or biologically to vinblastine. On the basis of a platform strain with sufficient supply of precursors and cofactors for biosynthesis, we reconstituted, debottlenecked, and optimized the biosynthetic pathways for the production of vindoline and catharanthine. The vindoline biosynthetic pathway represents one of the most complicated pathways ever reconstituted in microbial cell factories. Using shake flask fermentation, our engineered yeast strains were able to produce catharanthine and vindoline at a titer of 527.1 and 305.1 μg·liter-1, respectively, without accumulating detectable amount of pathway intermediates. This study establishes a representative example for the production of valuable plant natural products in yeast.
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Affiliation(s)
- Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Junhao Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yingjia Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Dongfang Li
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou 310027, China
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Grzech D, Hong B, Caputi L, Sonawane PD, O’Connor SE. Engineering the Biosynthesis of Late-Stage Vinblastine Precursors Precondylocarpine Acetate, Catharanthine, Tabersonine in Nicotiana benthamiana. ACS Synth Biol 2022; 12:27-34. [PMID: 36516122 PMCID: PMC9872167 DOI: 10.1021/acssynbio.2c00434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Vinblastine is a chemotherapy agent produced by the plant Catharanthus roseus in small quantities. Currently, vinblastine is sourced by isolation or semisynthesis. Nicotiana benthamiana is a plant heterologous host that can be used for reconstitution of biosynthetic pathways as an alternative natural product sourcing strategy. Recently, the biosynthesis of the late-stage vinblastine precursors precondylocarpine acetate, catharanthine, and tabersonine have been fully elucidated. However, the large number of enzymes involved in the pathway and the unstable nature of intermediates make the reconstitution of late-stage vinblastine precursor biosynthesis challenging. We used the N. benthamiana chassis and a state-of-art modular vector assembly to optimize the six biosynthetic steps leading to production of precondylocarpine acetate from the central intermediate strictosidine (∼2.7 mg per 1 g frozen tissue). After selecting the optimal regulatory element combination, we constructed four transcriptional unit assemblies and tested their efficiency. Finally, we successfully reconstituted the biosynthetic steps leading to production of catharanthine and tabersonine.
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Affiliation(s)
- Dagny Grzech
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, 07745 Jena, Germany
| | - Benke Hong
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, 07745 Jena, Germany
| | - Lorenzo Caputi
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, 07745 Jena, Germany
| | - Prashant D. Sonawane
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, 07745 Jena, Germany
| | - Sarah E. O’Connor
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, 07745 Jena, Germany,
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37
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Improved protein glycosylation enabled heterologous biosynthesis of monoterpenoid indole alkaloids and their unnatural derivatives in yeast. Metab Eng Commun 2022; 16:e00215. [PMID: 36569379 PMCID: PMC9772838 DOI: 10.1016/j.mec.2022.e00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
With over 3000 reported structures, monoterpenoid indole alkaloids (MIAs) constitute one of the largest alkaloid groups in nature, including the clinically important anticancer drug vinblastine and its semi-synthetic derivatives from Catharanthus roseus (Madagascar's periwinkle). With the elucidation of the complete 28-step biosynthesis for anhydrovinblastine, it is possible to investigate the heterologous production of vinblastine and other medicinal MIAs. In this study, we successfully expressed the flavoenzyme O-acetylstemmadenine oxidase in Saccharomyces cerevisiae (baker's yeast) by signal peptide modification, which is a vinblastine biosynthetic gene that has not been functionally expressed in this system. We also reported the simultaneous integration of ∼18 kb MIA biosynthetic gene cassettes as single copies into four genomic loci of baker's yeast by CRISPR-Cas9, which enabled the biosynthesis of vinblastine precursors catharanthine and tabersonine from the feedstocks secologanin and tryptamine. We further demonstrated the biosynthesis of fluorinated and hydroxylated catharanthine and tabersonine derivatives using our yeasts, which showed that the MIA biosynthesis accommodates unnatural substrates, and the system can be further explored to produce other complex MIAs.
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38
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Perrin J, Besseau S, Papon N, Courdavault V. Boosting lignan-precursor synthesis in yeast cell factories through co-factor supply optimization. Front Bioeng Biotechnol 2022; 10:1079801. [DOI: 10.3389/fbioe.2022.1079801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
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39
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Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen HJ, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks RP, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (BETHESDA, MD.) 2022; 12:jkac268. [PMID: 36200869 PMCID: PMC9713385 DOI: 10.1093/g3journal/jkac268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2023]
Abstract
Vinca minor, also known as the lesser periwinkle, is a well-known species from the Apocynaceae, native to central and southern Europe. This plant synthesizes monoterpene indole alkaloids, which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 monoterpene indole alkaloids it produces, V. minor mainly accumulates vincamine, which is commercially used as a nootropic. Using a combination of Oxford Nanopore Technologies long read- and Illumina short-read sequencing, a 679,098 Mb V. minor genome was assembled into 296 scaffolds with an N50 scaffold length of 6 Mb, and encoding 29,624 genes. These genes were functionally annotated and used in a comparative genomic analysis to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. Furthermore, homology-based monoterpene indole alkaloid gene predictions together with a metabolic analysis across 4 different V. minor tissue types guided the identification of candidate monoterpene indole alkaloid genes. These candidates were finally used to identify monoterpene indole alkaloid gene clusters, which combined with synteny analysis allowed for the discovery of a functionally validated vincadifformine-16-hydroxylase, reinforcing the potential of this dataset for monoterpene indole alkaloids gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown monoterpene indole alkaloid biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale monoterpene indole alkaloid production.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
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40
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Singh G, Sharma S, Rawat S, Sharma RK. Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1009-1028. [PMID: 36038144 DOI: 10.1071/fp21294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.
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Affiliation(s)
- Gopal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India; and Present address: Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Shikha Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
| | - Sandeep Rawat
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Present address: G. B. Pant National Institute of Himalayan Environment and Sustainable Development, Sikkim Regional Centre, Pangthang, Gangtok 737101, Sikkim, India
| | - Ram Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; and Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, Uttar Pradesh, India
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Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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42
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Li F, Bordeleau S, Kim KH, Turcotte J, Davis B, Liu L, Bayen S, De Luca V, Dastmalchi M. A lesion-mimic mutant of Catharanthus roseus accumulates the opioid agonist, akuammicine. PHYTOCHEMISTRY 2022; 203:113422. [PMID: 36055422 DOI: 10.1016/j.phytochem.2022.113422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Catharanthus roseus is a medicinal plant that produces an abundance of monoterpenoid indole alkaloids (MIAs), notably including the anticancer compounds vinblastine and vincristine. While the canonical pathway leading to these drugs has been resolved, the regulatory and catalytic mechanisms controlling many lateral branches of MIA biosynthesis remain largely unknown. Here, we describe an ethyl methanesulfonate (EMS) C. roseus mutant (M2-117523) that accumulates high levels of MIAs. The mutant exhibited stunted growth, partially chlorotic leaves, with deficiencies in chlorophyll biosynthesis, and a lesion-mimic phenotype. The lesions were sporadic and spontaneous, appearing after the first true bifoliate and continuing throughout development. The lesions are also the site of high concentrations of akuammicine, a minor constituent of wild type C. roseus leaves. In addition to akuammicine, the lesions were enriched in 25 other MIAs, resulting, in part, from a higher metabolic flux through the pathway. The unique metabolic shift was associated with significant upregulation of biosynthetic and regulatory genes involved in the MIA pathway, including the transcription factors WRKY1, CrMYC2, and ORCA2, and the biosynthetic genes STR, GO, and Redox1. Following the lesion-mimic mutant (LMM) phenotype, the accumulation of akuammicine is jasmonate (JA)-inducible, suggesting a role in plant defence response. Akuammicine is medicinally significant, as a weak opioid agonist, with a preference for the κ-opioid receptor, and a potential anti-diabetic. Further study of akuammicine biosynthesis and regulation can guide plant and heterologous engineering for medicinal uses.
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Affiliation(s)
- Fanfan Li
- Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Stephen Bordeleau
- Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Kyung Hee Kim
- Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Jonathan Turcotte
- Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Benjamin Davis
- Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Lan Liu
- Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Stéphane Bayen
- Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Vincenzo De Luca
- Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Mehran Dastmalchi
- Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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43
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Srinivasan P, Smolke CD. Fields to fermentors: Brewing botanical chemotherapeutic precursors using genetically engineered yeast. MED 2022; 3:727-729. [DOI: 10.1016/j.medj.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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44
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Ye C, Yang Y, Chen X, Yang L, Hua X, Yang M, Zeng X, Qiao S. Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification. J Biol Eng 2022; 16:26. [PMID: 36229878 PMCID: PMC9563957 DOI: 10.1186/s13036-022-00307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields. In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement based on known regulatory and metabolic information and CRISPR/Cas9 mediated gene knockout. RESULTS A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via the C5 pathway was applied herein. The rational metabolic engineering by gene knockouts significantly improved ALA production from 662.3 to 1601.7 mg/L. In addition, we managed to synergistically produce ALA via the C4 pathway in recombinant strain. The expression of a modified hemA gene, encoding an ALA synthase from Rhodobacter sphaeroides, improved ALA production from 1601.7 to 2099.7 mg/L. After 24 h cultivation, a yield of 0.210 g ALA per g glucose was achieved by constructed E. coli D5:FYABD-RSA. CONCLUSION Our study revealed that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification and optimization of gene expression.
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Affiliation(s)
- Changchuan Ye
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.,Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Yuting Yang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.,Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Lijie Yang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.,Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xia Hua
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Mengjie Yang
- National Feed Engineering Technology Research Centre, Beijing, 100193, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.,Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China. .,Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China.
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Functional characterization of secologanin synthase-like homologous genes suggests their involvement in the biosynthesis of diverse metabolites in the secoiridoid biosynthetic pathway of Camptotheca acuminata Decne. Int J Biol Macromol 2022; 222:2594-2602. [DOI: 10.1016/j.ijbiomac.2022.10.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/19/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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Vasilev N. Medicinal Plants: Guests and Hosts in the Heterologous Expression of High-Value Products. PLANTA MEDICA 2022; 88:1175-1189. [PMID: 34521134 DOI: 10.1055/a-1576-4148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Medicinal plants play an important dual role in the context of the heterologous expression of high-value pharmaceutical products. On the one hand, the classical biochemical and modern omics approaches allowed for the discovery of various genes encoding biosynthetic pathways in medicinal plants. Recombinant DNA technology enabled introducing these genes and regulatory elements into host organisms and enhancing the heterologous production of the corresponding secondary metabolites. On the other hand, the transient expression of foreign DNA in plants facilitated the production of numerous proteins of pharmaceutical importance. This review summarizes several success stories of the engineering of plant metabolic pathways in heterologous hosts. Likewise, a few examples of recombinant protein expression in plants for therapeutic purposes are also highlighted. Therefore, the importance of medicinal plants has grown immensely as sources for valuable products of low and high molecular weight. The next step ahead for bioengineering is to achieve more success stories of industrial-scale production of secondary plant metabolites in microbial systems and to fully exploit plant cell factories' commercial potential for recombinant proteins.
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Affiliation(s)
- Nikolay Vasilev
- TU Dortmund University, Biochemical and Chemical Engineering, Technical Biochemistry, Dortmund, Germany
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Reconstitution of monoterpene indole alkaloid biosynthesis in genome engineered Nicotiana benthamiana. Commun Biol 2022; 5:949. [PMID: 36088516 PMCID: PMC9464250 DOI: 10.1038/s42003-022-03904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 12/17/2022] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse class of plant natural products that include a number of medicinally important compounds. We set out to reconstitute the pathway for strictosidine, a key intermediate of all MIAs, from central metabolism in Nicotiana benthamiana. A disadvantage of this host is that its rich background metabolism results in the derivatization of some heterologously produced molecules. Here we use transcriptomic analysis to identify glycosyltransferases that are upregulated in response to biosynthetic intermediates and produce plant lines with targeted mutations in the genes encoding them. Expression of the early MIA pathway in these lines produces a more favorable product profile. Strictosidine biosynthesis was successfully reconstituted, with the best yields obtained by the co-expression of 14 enzymes, of which a major latex protein-like enzyme (MLPL) from Nepeta (catmint) is critical for improving flux through the iridoid pathway. The removal of endogenous glycosyltransferases does not impact the yields of strictosidine, highlighting that the metabolic flux of the pathway enzymes to a stable biosynthetic intermediate minimizes the need to engineer the endogenous metabolism of the host. The production of strictosidine in planta expands the range of MIA products amenable to biological synthesis. The biosynthesis of strictosidine, a key intermediate of monoterpene indole alkaloids, was successfully reconstructed in Nicotiana benthamiana, demonstrating the potential of Nicotiana benthamiana as a bioproduction chassis for small molecules.
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48
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Expanding the terpene biosynthetic code with non-canonical 16 carbon atom building blocks. Nat Commun 2022; 13:5188. [PMID: 36057727 PMCID: PMC9440906 DOI: 10.1038/s41467-022-32921-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
Humankind relies on specialized metabolites for medicines, flavors, fragrances, and numerous other valuable biomaterials. However, the chemical space occupied by specialized metabolites, and, thus, their application potential, is limited because their biosynthesis is based on only a handful of building blocks. Engineering organisms to synthesize alternative building blocks will bypass this limitation and enable the sustainable production of molecules with non-canonical chemical structures, expanding the possible applications. Herein, we focus on isoprenoids and combine synthetic biology with protein engineering to construct yeast cells that synthesize 10 non-canonical isoprenoid building blocks with 16 carbon atoms. We identify suitable terpene synthases to convert these building blocks into C16 scaffolds and a cytochrome P450 to decorate the terpene scaffolds and produce different oxygenated compounds. Thus, we reconstruct the modular structure of terpene biosynthesis on 16-carbon backbones, synthesizing 28 different non-canonical terpenes, some of which have interesting odorant properties.
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Levac D, Flores PC, De Luca V. Molecular and biochemical characterization of Catharanthus roseus perivine-N β-methyltransferase. PHYTOCHEMISTRY 2022; 201:113266. [PMID: 35671807 DOI: 10.1016/j.phytochem.2022.113266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
The biosynthesis of monoterpenoid indole alkaloids in Catharanthus roseus has been most extensively studied, leading to the detailed characterization of the pathway for the formation of their well-known anticancer alkaloids. The present study describes the identification, molecular cloning, and functional expression of C. roseus perivine-Nβ-methyltransferase (PeNMT) that converts perivine to Nβ-methylperivine (vobasine). PeNMT is member of a recently discovered γ-tocopherol-like N-methyltransferase (γ-TLMT) gene family that displays high substrate specificity and that appears to have evolved in the Vinceae tribe of Apocynaceae family where most N-methylated MIAs have been identified in the phytochemical literature.
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Affiliation(s)
- Dylan Levac
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada.
| | - Paulo Cázares Flores
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada.
| | - Vincenzo De Luca
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada.
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Williams D, Brzezinski W, Gordon H, De Luca V. Site directed mutagenesis of Catharanthus roseus (+)-vincadifformine 19-hydroxylase (CYP71BY3) results in two distinct enzymatic functions. PHYTOCHEMISTRY 2022; 201:113265. [PMID: 35660549 DOI: 10.1016/j.phytochem.2022.113265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
The most abundant monoterpenoid indole alkaloids (MIAs) in Catharanthus roseus roots include lochnericine and (+)-echitovenine. The formation of (+)-echitovenine involves a 3-step pathway including (+)-vincadifformine-19-hydroxylase (V19H) that differentiates it from a parallel pathway involved in the formation of lochnericine, hörhammericine and its O-acetylated derivative. Homology based modeling and docking experiments in the present study show that (+) and (-) vincadifformine can occupy the V19H active site and is proven experimentally by showing that (-)-vincadifformine is a competitive inhibitor of V19H. Comparative modeling of V19H with tabersonine 3-oxidase (T3O) and tabersonine 19-hydroxylase (T19H) that accept (-)-aspidosperma MIAs identified four conserved amino acid residues in T3O and T19H that were different in the V19H binding site and were used to generate a series of single-, double-, or four-point mutations in V19H. While all mutants retained their ability to convert (+)-vincadifformine to (+)-minovincinine only the four-point mutant gained T3O activity enabling it to convert (-)-tabersonine to tabersonine 2,3-epoxide. The gain of T3O-like activity following mutagenesis without the loss of V19H activity supports the hypothesis that V19H shares a common ancestor to T3O which is involved in vindoline biosynthesis in C. roseus leaves.
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Affiliation(s)
- Danielle Williams
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Weronika Brzezinski
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Heather Gordon
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Vincenzo De Luca
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
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