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Zuo Y, Zhao M, Gou Y, Huang L, Xu Z, Lian J. Transportation engineering for enhanced production of plant natural products in microbial cell factories. Synth Syst Biotechnol 2024; 9:742-751. [PMID: 38974023 PMCID: PMC11224930 DOI: 10.1016/j.synbio.2024.05.014] [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: 04/09/2024] [Revised: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Plant natural products (PNPs) exhibit a wide range of biological activities and have essential applications in various fields such as medicine, agriculture, and flavors. Given their natural limitations, the production of high-value PNPs using microbial cell factories has become an effective alternative in recent years. However, host metabolic burden caused by its massive accumulation has become one of the main challenges for efficient PNP production. Therefore, it is necessary to strengthen the transmembrane transport process of PNPs. This review introduces the discovery and mining of PNP transporters to directly mediate PNP transmembrane transportation both intracellularly and extracellularly. In addition to transporter engineering, this review also summarizes several auxiliary strategies (such as small molecules, environmental changes, and vesicles assisted transport) for strengthening PNP transportation. Finally, this review is concluded with the applications and future perspectives of transportation engineering in the construction and optimization of PNP microbial cell factories.
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Affiliation(s)
- 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
| | - Minghui Zhao
- 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
| | - Yuanwei Gou
- 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
| | - 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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2
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Jung S, Maeda HA. Debottlenecking the L-DOPA 4,5-dioxygenase step with enhanced tyrosine supply boosts betalain production in Nicotiana benthamiana. PLANT PHYSIOLOGY 2024; 195:2456-2471. [PMID: 38498597 DOI: 10.1093/plphys/kiae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Synthetic biology provides emerging tools to produce valuable compounds in plant hosts as sustainable chemical production platforms. However, little is known about how supply and utilization of precursors is coordinated at the interface of plant primary and specialized metabolism, limiting our ability to efficiently produce high levels of target specialized metabolites in plants. L-Tyrosine is an aromatic amino acid precursor of diverse plant natural products including betalain pigments, which are used as the major natural food red colorants and more recently a visual marker for plant transformation. Here, we studied the impact of enhanced L-tyrosine supply on the production of betalain pigments by expressing arogenate dehydrogenase (TyrA) from table beet (Beta vulgaris, BvTyrAα), which has relaxed feedback inhibition by L-tyrosine. Unexpectedly, betalain levels were reduced when BvTyrAα was coexpressed with the betalain pathway genes in Nicotiana benthamiana leaves; L-tyrosine and 3,4-dihydroxy-L-phenylalanine (L-DOPA) levels were drastically elevated but not efficiently converted to betalains. An additional expression of L-DOPA 4,5-dioxygenase (DODA), but not CYP76AD1 or cyclo-DOPA 5-O-glucosyltransferase, together with BvTyrAα and the betalain pathway, drastically enhanced betalain production, indicating that DODA is a major rate-limiting step of betalain biosynthesis in this system. Learning from this initial test and further debottlenecking the DODA step maximized betalain yield to an equivalent or higher level than that in table beet. Our data suggest that balancing between enhanced supply ("push") and effective utilization ("pull") of precursor by alleviating a bottleneck step is critical in successful plant synthetic biology to produce high levels of target compounds.
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Affiliation(s)
- Soyoung Jung
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Kou C, Liu J, Yin X, He D, Liu J, Hua X, Ma R, Sun W, Xue Z, Ma P. Efficient heterologous biosynthesis of verazine, a metabolic precursor of the anti-cancer drug cyclopamine, in Nicotiana benthamiana. PLANT COMMUNICATIONS 2024; 5:100831. [PMID: 38308438 PMCID: PMC11211220 DOI: 10.1016/j.xplc.2024.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Chengxi Kou
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Jingling Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Di He
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China
| | - Rui Ma
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China; Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin 150040, China.
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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4
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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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Diaz-Bárcena A, Fernandez-Pacios L, Giraldo P. Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L. Biomolecules 2023; 14:2. [PMID: 38275743 PMCID: PMC10813097 DOI: 10.3390/biom14010002] [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: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cofactors in the apo state and in three complexes with substrate (S)-reticuline in DRS and intermediate 1,2-dehydroreticuline in DRS and in DRR. Since no experimental structure exists for REPI, we used its AlphaFold model as a scaffold to build up these four systems, which were submitted to all-atom molecular dynamics (MD) simulations. A comparison of MD results for the four systems revealed key dynamic changes associated with cofactor and ligand binding and provided a dynamic picture of the evolution of their structures and interactions. We also explored the possible dynamic occurrence of tunnels and electrostatic highways potentially involved in alternative mechanisms for channeling the intermediate from DRS to DRR.
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Affiliation(s)
- Alba Diaz-Bárcena
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (L.F.-P.); (P.G.)
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6
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Chainani Y, Bonnanzio G, Tyo KE, Broadbelt LJ. Coupling chemistry and biology for the synthesis of advanced bioproducts. Curr Opin Biotechnol 2023; 84:102992. [PMID: 37688985 DOI: 10.1016/j.copbio.2023.102992] [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: 06/15/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 09/11/2023]
Abstract
Chemical and biological syntheses can both lead to a myriad of compounds. Biology enables us to harness the metabolism of microbial cell factories to produce key target molecules from renewable biomass-derived substrates. Although bio-based feedstocks are sustainably sourced and more benign than the rapidly depleting fossil fuels that chemical processes have historically relied on, limiting pathways solely to biological reactions may not equate to a greener process overall. In fact, bioreactors rely on substantial quantities of water and can be inefficient since organisms typically operate around ambient conditions and are sensitive to perturbations in their environment. Hybridizing biosynthetic pathways with green chemistry can instead be a more potent strategy to reduce our net manufacturing footprint. Emerging chemistries have demonstrated considerable success in performing complex transformations on biological feedstocks without significant solvent use. Many of these transformations would be too slow to perform enzymatically or infeasible altogether. Here, we put forth the concept that by carefully considering the merits and drawbacks of synthetic biology and chemistry as well as one's own use case, there exist many opportunities for coupling the two. Merging these syntheses can unlock a wider suite of functional group transformations, thereby enabling future manufacturing processes to sustainably access a larger space of valuable, platform chemicals.
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Affiliation(s)
- Yash Chainani
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Geoffrey Bonnanzio
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Keith Ej Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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Sokolova N, Peng B, Haslinger K. Design and engineering of artificial biosynthetic pathways-where do we stand and where do we go? FEBS Lett 2023; 597:2897-2907. [PMID: 37777818 DOI: 10.1002/1873-3468.14745] [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: 07/03/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini-review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.
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Affiliation(s)
- Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Bo Peng
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
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8
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Zhao W, Liu M, Liu K, Liu H, Liu X, Liu J. An Enzymatic Strategy for the Selective Methylation of High-Value-Added Tetrahydroprotoberberine Alkaloids. Int J Mol Sci 2023; 24:15214. [PMID: 37894895 PMCID: PMC10607743 DOI: 10.3390/ijms242015214] [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: 09/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Tetrahydroprotoberberines (THPBs) are plant-specific alkaloids with significant medicinal value. They are present in trace amounts in plants and are difficult to chemically synthesize due to stereoselectivity and an unfavorable environment. In this study, a selective methylation strategy was developed for the biocatalysis of seven high-value-added THPB compounds using 4'-O-methyltransferase (Cj4'OMT), norcoclaurine 6-O-methyltransferase (Cj6OMT), and (S)-scoulerine 9-O-methyltransferase (SiSOMT and PsSOMT) in engineered E. coli. The methyltransferases Cj4'OMT, Cj6OMT, PsSOMT, and SiSOMT were expressed heterologously in E. coli. Compound 1 (10-methoxy-2,3,9-tetrahydroxyberbine) was synthesized using the recombinant E. coli strain Cj4'OMT and the substrate 2,3,9,10-tetrahydroxyberbine. Compound 2 (9-methoxy-2,3,10-tetrahydroxyberbine) was produced in the recombinant Escherichia coli (E. coli) strain PsSOMT, and compounds 2 and 3 (discretamine) were produced in the recombinant E. coli strain SiSOMT. Compounds 4 (9,10-methoxy-2,3-tetrahydroxyberbine) and 5 (corypalmine) were obtained by co-culturing the recombinant strains Cj4'OMT and SiSOMT with substrate. Compounds 6 (scoulerine) and 7 (isoscoulerine) were produced by co-culturing the substrate with the recombinant strains Cj4'OMT and Cj6OMT. To increase the yield of novel compound 2, the flask culture conditions of the engineered SiSOMT strain were optimized, resulting in the production of 165.74 mg/L of this compound. This study thus presents an enzymatic approach to the synthesis of high-value-added THPBs with minimum environmental wastage.
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Affiliation(s)
- Wanli Zhao
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Manyu Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Kemeng Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Hanqing Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Xiufeng Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Jihua Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (W.Z.)
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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10
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Qiao S, Bai F, Cai P, Zhou YJ, Yao L. An improved CRISPRi system in Pichia pastoris. Synth Syst Biotechnol 2023; 8:479-485. [PMID: 37692202 PMCID: PMC10485788 DOI: 10.1016/j.synbio.2023.06.008] [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: 02/21/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 09/12/2023] Open
Abstract
CRISPR interference (CRISPRi) has been developed and widely used for gene repression in various hosts. Here we report an improved CRISPRi system in Pichia pastoris by fusing dCas9 with endogenous transcriptional repressor domains. The CRISPRi system shows strong repression of eGFP, with the highest efficiency of 85%. Repression of native genes is demonstrated by targeting AOX1 promoter. AOX1 is efficiently repressed and the mutant strains show much slower growth in methanol medium. Effects of gRNA expression and processing on CRISPRi efficiency is also investigated. It is found that gRNA processing by HH/HDV ribozymes or Csy4 endoribonuclease generating clean gRNA is critical to achieve strong repression, and Csy4 cleavage shows higher repression efficiency. However, gRNA expression using native tRNA transcription and processing systems results in relatively weaker repression of eGFP. By expression of two gRNAs targeting promoters of eGFP and AOX1 in an array together with Cys4 recognition sites, both genes can be repressed simultaneously. Cys4-mediated gRNA array processing is further applied to repress fatty acyl-CoA synthetase genes (FAA1 and FAA2). Both genes are efficiently repressed, demonstrating that Cys4 endoribonuclease has the ability to cleave gRNAs array and can be can be used for multiplexed gene repression in P. pastoris.
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Affiliation(s)
- Shujing Qiao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Bai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Peng Cai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
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11
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Mao J, Mohedano MT, Fu J, Li X, Liu Q, Nielsen J, Siewers V, Chen Y. Fine-tuning of p-coumaric acid synthesis to increase (2S)-naringenin production in yeast. Metab Eng 2023; 79:192-202. [PMID: 37611820 DOI: 10.1016/j.ymben.2023.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
(2S)-Naringenin is a key precursor for biosynthesis of various high-value flavonoids and possesses a variety of nutritional and pharmaceutical properties on human health. Systematic optimization approaches have been employed to improve (2S)-naringenin production in different microbial hosts. However, very few studies have focused on the spatiotemporal distribution of (2S)-naringenin and the related pathway intermediate p-coumaric acid, which is an important factor for efficient production. Here, we first optimized the (2S)-naringenin biosynthetic pathway by alleviating the bottleneck downstream of p-coumaric acid and increasing malonyl-CoA supply, which improved (2S)-naringenin production but significant accumulation of p-coumaric acid still existed extracellularly. We thus established a dual dynamic control system through combining a malonyl-CoA biosensor regulator and an RNAi strategy, to autonomously control the synthesis of p-coumaric acid with the supply of malonyl-CoA. Furthermore, screening potential transporters led to identification of Pdr12 for improved (2S)-naringenin production and reduced accumulation of p-coumaric acid. Finally, a titer of 2.05 g/L (2S)-naringenin with negligible accumulation of p-coumaric acid was achieved in a fed batch fermentation. Our work highlights the importance of systematic control of pathway intermediates for efficient microbial production of plant natural products.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Marta Tous Mohedano
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jing Fu
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Xiaowei Li
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Quanli Liu
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, DK2200, Copenhagen N, Denmark
| | - Verena Siewers
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.
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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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