Review Article
Open Access
Rational Design of Plant Chemical Factories: CRISPR-Based Metabolic Engineering in Medicinal and Aromatic Plants
1
Agricultural Biotechnology Research Institute of Iran, AREEO, Isfahan 84156-83111, Iran
2
Zanjan Agricultural and Natural Resources Research and Education Center, AREEO, Zanjan, Iran
Corresponding Author:
Saeid Kadkhodaei,
[email protected]
Volume 1, Issue 1
2025
Received: 14 December 2025
Accepted: 14 February 2026
Published: 12 March 2026
Article Information
Abstract
Medicinal and aromatic plants (MAPs) serve as biochemical factories producing valuable secondary metabolites, yet their potential is limited by low yields, tissue-specific accumulation, and co-production of toxic compounds. Traditional improvement methods have achieved only incremental gains, highlighting the need for precision metabolic engineering. CRISPR/Cas genome editing has revolutionized this field by enabling targeted modifications from gene knockouts to single-nucleotide changes. This review examines core strategies in applying genome editing to engineer MAP metabolic pathways, including gene disruption, transcriptional modulation, and multiplex editing to redirect flux, eliminate competing pathways, and remove toxic branches. Case studies demonstrate successes in alkaloid engineering—such as clean chemotypes with pure hyoscyamine in Atropa belladonna (>50% yield increase) and detoxified Symphytum officinale—and terpenoid enhancement with three-fold glycyrrhizin increase in licorice through combined blocking and overexpression. These examples showcase CRISPR's surgical precision for improving pharmaceutical purity, safety, and production efficiency. We discuss integration with multi-omics for systems-level optimization and explore emerging frontiers including base editing, prime editing, and CRISPR-directed evolution for enzyme optimization. As these technologies mature, genome editing will transform MAPs into customizable cellular factories delivering sustainable, high-value bioproducts.
Graphical Abstract
Keywords
CRISPR/Cas9
metabolic engineering
medicinal plants
alkaloid biosynthesis
terpenoid biosynthesis
gene knockout
pathway optimization
secondary metabolism
Data Availability Statement
Not applicable.
Funding
This work was supported without any funding.
Conflicts of Interest
The authors declare no conflicts of interest.
AI Use Statement
The authors declare that no generative AI was used in the preparation of this manuscript.
Ethical Approval and Consent to Participate
Not applicable.
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APA Style
Kadkhodaei, S., Shahabadi, H. Z., & Hosseini-Monfared, H. (2026). Rational Design of Plant Chemical Factories: CRISPR-Based Metabolic Engineering in Medicinal and Aromatic Plants. Plant Innovation Journal, 1(1), 18–26. https://doi.org/10.62762/PIJ.2025.283212
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TY - JOUR AU - Kadkhodaei, Saeid AU - Shahabadi, Hassan Zadabbas AU - Hosseini-Monfared, Hossein PY - 2026 DA - 2026/03/12 TI - Rational Design of Plant Chemical Factories: CRISPR-Based Metabolic Engineering in Medicinal and Aromatic Plants JO - Plant Innovation Journal T2 - Plant Innovation Journal JF - Plant Innovation Journal VL - 1 IS - 1 SP - 18 EP - 26 DO - 10.62762/PIJ.2025.283212 UR - https://www.icck.org/article/abs/PIJ.2025.283212 KW - CRISPR/Cas9 KW - metabolic engineering KW - medicinal plants KW - alkaloid biosynthesis KW - terpenoid biosynthesis KW - gene knockout KW - pathway optimization KW - secondary metabolism AB - Medicinal and aromatic plants (MAPs) serve as biochemical factories producing valuable secondary metabolites, yet their potential is limited by low yields, tissue-specific accumulation, and co-production of toxic compounds. Traditional improvement methods have achieved only incremental gains, highlighting the need for precision metabolic engineering. CRISPR/Cas genome editing has revolutionized this field by enabling targeted modifications from gene knockouts to single-nucleotide changes. This review examines core strategies in applying genome editing to engineer MAP metabolic pathways, including gene disruption, transcriptional modulation, and multiplex editing to redirect flux, eliminate competing pathways, and remove toxic branches. Case studies demonstrate successes in alkaloid engineering—such as clean chemotypes with pure hyoscyamine in Atropa belladonna (>50% yield increase) and detoxified Symphytum officinale—and terpenoid enhancement with three-fold glycyrrhizin increase in licorice through combined blocking and overexpression. These examples showcase CRISPR's surgical precision for improving pharmaceutical purity, safety, and production efficiency. We discuss integration with multi-omics for systems-level optimization and explore emerging frontiers including base editing, prime editing, and CRISPR-directed evolution for enzyme optimization. As these technologies mature, genome editing will transform MAPs into customizable cellular factories delivering sustainable, high-value bioproducts. SN - pending PB - Institute of Central Computation and Knowledge LA - English ER -
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@article{Kadkhodaei2026Rational,
author = {Saeid Kadkhodaei and Hassan Zadabbas Shahabadi and Hossein Hosseini-Monfared},
title = {Rational Design of Plant Chemical Factories: CRISPR-Based Metabolic Engineering in Medicinal and Aromatic Plants},
journal = {Plant Innovation Journal},
year = {2026},
volume = {1},
number = {1},
pages = {18-26},
doi = {10.62762/PIJ.2025.283212},
url = {https://www.icck.org/article/abs/PIJ.2025.283212},
abstract = {Medicinal and aromatic plants (MAPs) serve as biochemical factories producing valuable secondary metabolites, yet their potential is limited by low yields, tissue-specific accumulation, and co-production of toxic compounds. Traditional improvement methods have achieved only incremental gains, highlighting the need for precision metabolic engineering. CRISPR/Cas genome editing has revolutionized this field by enabling targeted modifications from gene knockouts to single-nucleotide changes. This review examines core strategies in applying genome editing to engineer MAP metabolic pathways, including gene disruption, transcriptional modulation, and multiplex editing to redirect flux, eliminate competing pathways, and remove toxic branches. Case studies demonstrate successes in alkaloid engineering—such as clean chemotypes with pure hyoscyamine in Atropa belladonna (>50\% yield increase) and detoxified Symphytum officinale—and terpenoid enhancement with three-fold glycyrrhizin increase in licorice through combined blocking and overexpression. These examples showcase CRISPR's surgical precision for improving pharmaceutical purity, safety, and production efficiency. We discuss integration with multi-omics for systems-level optimization and explore emerging frontiers including base editing, prime editing, and CRISPR-directed evolution for enzyme optimization. As these technologies mature, genome editing will transform MAPs into customizable cellular factories delivering sustainable, high-value bioproducts.},
keywords = {CRISPR/Cas9, metabolic engineering, medicinal plants, alkaloid biosynthesis, terpenoid biosynthesis, gene knockout, pathway optimization, secondary metabolism},
issn = {pending},
publisher = {Institute of Central Computation and Knowledge}
}
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