Engineering Biology for Sustainable Isoprenoid Production

About the Project

Background: Isoprenoids represent one of the largest and most diverse classes of natural products, with applications spanning nutrition, health, Pharma and industry. Industrially most isoprenoids of commercial use command annual sales markets in the region of $1 to 2 billion.

Biosynthetically all isoprenoids share two universal C5 building blocks, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), produced via two distinct pathways: (i) The mevalonate (MVA) pathway in the cytosol and (ii) The methylerythritol phosphate (MEP) pathway in plastid organelle. In ISOPRO, we focus on two high-value isoprenoids as demonstration molecules: Astaxanthin, a ketocarotenoid pigment derived from the plastid IPP/DMAPP pool and Squalene, a triterpene synthesized from the cytosolic MVA pathway.

Astaxanthin is widely used as a pigment and antioxidant across multiple sectors. In aquaculture, it is an essential feed additive that colours the flesh of salmon, shrimp, and trout, while enhancing immune function. Its inclusion accounts for ~20% of total feed costs. Beyond aquaculture, astaxanthin offers proven health benefits as a potent antioxidant.

Current challenge: Industrial production relies on chemical synthesis using petrochemical precursors and rare metal catalysts, methods with poor environmental credentials.

Squalene is a precursor of phytosterols and has diverse industrial uses, including cosmetics, cholesterol control, and antioxidant formulations [8,9]. Its most critical role is as a vaccine adjuvant, where squalene-based emulsions (e.g., MF59®) enhance immune responses to antigens. MF59 is widely used in vaccines for malaria, hepatitis, HIV, and pandemic influenza.

Current challenge: The primary source of squalene is deep-sea shark liver oil—an unsustainable practice. The COVID-19 pandemic highlighted that global demand far exceeds supply, threatening future vaccine production.

Our team has developed renewable plant-based platforms in Solanaceae species (tomato and tobacco) to produce astaxanthin and squalene at scale, demonstrating industrial feasibility. However, for ketocarotenoids, multi-omic analyses indicate that plastid metabolism is approaching its physiological limits, while for squalene, orthogonal engineering in plastids avoids conversion to phytosterols and does not significantly disrupt metabolism.

Thus, in this proposal the applicants intend to develop further genetic resources, strategies and tools that will address, (i) if orthogonal engineering can improve cellular and metabolic plasticity and (ii) provide a new strategy to advance the competitiveness of biobased production chassis. The study will use the isoprenoids, astaxanthin and squalene as demonstration molecules but the findings are generically applicable to other products requiring sustainable solutions.

Aims: Our aim is to use two valuable industrial isoprenoid molecules, to demonstrate how an engineering biology approach can be used to synthesise these isoprenoids in their atypical subcellular organelles. Astaxanthin will be produced in the cytosol and squalene in the plastid in planta. It is hypothesised that this approach will circumvent existing regulatory mechanisms and generate alternative sequestration mechanisms beyond the existing cellular adaptation presently observed.

Objectives:

1. Generate a suite of multi-gene constructs for cytosolic production of carotenoids (astaxanthin) from endogenous isopentenyl pyrophosphate (IPP) and/or farnesyl pyrophosphate pools.
2. Evaluate astaxanthin production in Nicotiana species through transient and stable transformation procedures.
3. Create a unique Nicotiana chassis capable of producing astaxanthin in the cytosol and plastid derived squalene.
4. Biochemical and molecular characterisation of these new biobased chassis for isoprenoid production.

Training: This project will provide the candidate with generic training in Biochemistry and Molecular Biology. Specifically, metabolite analysis, enzyme assays. The molecular techniques will include vector construction, modern gene editing approaches transcripts analysis and transgenesis.

Environment: The laboratory is fully equipped with advanced analytical and plant growth facilities to support the proposed research. Dedicated instrumentation includes GC-MS (×3), GC-FID, HPLC-PDA (×2), HPLC-PDA with radiodetector, UPLC-PDA, and real-time PCR systems, including digital droplet PCR (Bio-Rad QX200). Plant growth resources comprise 800 m² of glasshouses, a controlled tissue culture room for transformations, growth chambers, and 600 m² of polytunnels.

Our state-of-the-art analytical suite features complementary mass spectrometry platforms: LC-QTOF-MS/MS) for metabolomics and proteomics and LC-QQQ-MS (Agilent 6470) for precise quantitative analysis.

Protein purification is supported by multiple ultracentrifuges and a Cytiva ÄKTA Pure system with a full range of columns. Imaging capabilities include Scanning and Transmission Electron Microscopes.

The research environment is collaborative, diverse, and strongly supportive of career development. The Concordat to Support the Career Development of Researchers (www.researchdevelopmentconcordat.ac.uk) is fully implemented, and the investigators actively promote progression opportunities for all team members.

Funding Notes

Supervisor has applied for funding and is awaiting outcomes.

If the candidates have the correct qualifications and/or access to own funding or partial funding, either from their home country or own finances, your application can be considered.