Isoprenoid Engineering

Introduction

Isoprenoids, also known as terpenoids, represent one of the largest and most diverse classes of natural compounds, with over 80,000 identified structures. They are built from five-carbon units—isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)—and range from volatile fragrances and pharmaceuticals to long-chain hydrocarbons.

Isoprenoid engineering refers to the metabolic redesign of microbial or plant systems to biosynthesize isoprenoids using renewable carbon sources. This field has gained global momentum due to isoprenoids’ applications in biofuels, nutraceuticals, cosmetics, fragrances, and medicine. Using systems biology, synthetic biology, and pathway optimization, researchers are making significant strides toward sustainable and scalable production of these complex molecules.

What Products Are Produced?

• Biofuels: Isoprene, farnesene (diesel), limonene (gasoline substitute)
• Pharmaceuticals: Artemisinin (antimalarial), taxol (anticancer), carotenoids
• Nutraceuticals: β-carotene, lycopene, tocopherols (vitamin E)
• Fragrances and flavors: Linalool, menthol, geraniol
• Rubber and lubricants: Natural rubber (polyisoprene), squalene derivatives

Pathways and Production Methods

1. Native Isoprenoid Biosynthesis Pathways
• Mevalonate (MVA) Pathway (in yeast and archaea): Acetyl-CoA → IPP/DMAPP
• Methylerythritol phosphate (MEP) Pathway (in bacteria and plastids): G3P + pyruvate → IPP/DMAPP
2. Pathway Engineering
• Overexpression of rate-limiting enzymes (HMGR, DXS, IDI)
• Balancing precursor supply via acetyl-CoA, NADPH, and ATP optimization
3. Modular Isoprenoid Biosynthesis
• Combinatorial expression of terpene synthases with tailored prenyltransferases to produce specific terpenes
4. Compartmentalization and Organelle Engineering
• Targeting pathways to mitochondria, chloroplasts, or peroxisomes to enhance flux and reduce feedback inhibition
5. Dynamic Control Systems
• Use of biosensors and feedback loops to balance growth and product formation

Catalysts and Key Tools Used

• Core Enzymes:

• HMGR (HMG-CoA reductase), DXS (1-deoxy-D-xylulose synthase), IDI (isomerase)
• Terpene synthases: Limonene synthase, amorphadiene synthase, patchoulol synthase
• Prenyltransferases: GPP, FPP, GGPP synthases for C10, C15, C20 backbones

• Host Organisms:

• Saccharomyces cerevisiae, E. coli, Corynebacterium glutamicum, Yarrowia lipolytica, cyanobacteria

• Tools:

• CRISPR-Cas, synthetic operons, dynamic regulatory circuits, pathway balancing with biosensors
• Flux analysis and computational modeling

Case Study: Amyris – Farnesene for Biofuel and Cosmetics

Highlights

• Engineered S. cerevisiae using optimized MVA pathway to produce farnesene, a long-chain isoprenoid.
• Farnesene converted to farnesane, a diesel-like fuel, and used in cosmetics and lubricants.
• Partnered with TOTAL and Givaudan to commercialize farnesene-based products.

Timeline

• 2005 – Founded from UC Berkeley research on artemisinin biosynthesis
• 2010 – Scaled up farnesene production in Brazil using sugarcane feedstock
• 2015 – Launched farnesene-derived skincare and fragrance ingredients
• 2021–2023 – Expanded into clean beauty, personal care, and specialty chemicals using isoprenoid platforms

Global and Indian Startups Working in This Area

Global

• Amyris (USA) – Farnesene and other isoprenoids from yeast
• Evolva (Switzerland) – Bio-vanillin, nootkatone, and patchoulol production
• Isobionics (Netherlands) – Limonene and valencene from engineered microbes
• Conagen (USA) – High-value terpenes, including natural sweeteners and flavors

India

• String Bio (Bengaluru) – Engineering microbes for hydrocarbons including isoprene derivatives
• Seagull BioSolutions (Pune) – Working on terpenoid pathway enzymes for vaccine adjuvants and therapeutics
• IIT Madras & CSIR-IIIM – Developing pathways for aroma chemicals and plant terpenoids
• TERI – Research on isoprene production in engineered algae and microbes for biofuel applications

Market and Demand

The global isoprenoid market (including bio-based terpenes) is valued at USD 6.5 billion in 2023 and is projected to reach USD 11.4 billion by 2030, growing at a CAGR of ~8%.

Major End-Use Segments:

• Biofuels and aviation fuel additives
• Cosmetics and personal care – Anti-aging, fragrance, skincare
• Nutraceuticals – Vitamin A/E precursors, carotenoids
• Pharma – Anti-malarial, anticancer terpenoids
• Food and beverage – Natural flavors, preservatives

Key Growth Drivers

• Demand for natural, sustainable alternatives to petrochemical-based ingredients
• High-value markets in flavors, fragrances, and health
• Availability of renewable carbon feedstocks like sugar, glycerol, and CO₂
• Advances in host engineering and dynamic pathway optimization
• Strategic interest from pharma and FMCG giants in biobased actives

Challenges to Address

• Pathway complexity: Long and branched biosynthetic routes with regulatory bottlenecks
• Product toxicity and volatility: Some terpenes inhibit host growth or evaporate during fermentation
• Co-factor and precursor limitations: ATP/NADPH imbalances can limit production
• Low titers: Especially in early-stage engineered strains
• Cost-effective scale-up: Downstream recovery and purification can be energy-intensive

Progress Indicators

• 2006 – Artemisinin precursor produced via isoprenoid pathway in yeast
• 2012 – First commercial farnesene biofuel produced in Brazil
• 2016 – CRISPR tools accelerate isoprenoid flux tuning in microbes
• 2021 – Indian labs report patchoulol and geraniol from engineered E. coli
• 2024 – Isoprene biofuel platform tested in pilot scale for rubber and fuel applications

Pharmaceutical and fragrance isoprenoids in yeast are at TRL 8–9, while biofuel-oriented isoprenoids (e.g., isoprene, limonene) in photosynthetic and bacterial systems are at TRL 5–6.

Conclusion

Isoprenoid engineering is unlocking a new era of bio-based chemicals and fuels, from perfumes and medicines to sustainable aviation fuels. With modularity and diversity, isoprenoids are a flexible target for renewable manufacturing, leveraging carbon-neutral processes.

India’s biotech talent, sugar-based feedstock access, and active R&D ecosystem position it to become a leader in isoprenoid biomanufacturing—powering not only industry but also a circular bioeconomy.

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