The laboratory has a long-standing interest in the biosynthesis, regulation, and manipulation of isoprenoids, particularly the natural pigments known as carotenoids. These compounds include nutritional and industrial carotenoids such as astaxanthin, zeaxanthin, beta-carotene, lycopene, phytoene and apocarotenoids. 

Figure 1. The Biosynthesis of carotenoids in chloroplasts and chromoplasts (10.1111/pbi.13073).

These molecules have key roles in the prevention of human disease states and can only be acquired in a dietary manner. In addition, carotenoids or their derivatives are also involved in plant and microbial developmental processes and commercially they are utilised across multiple industrial sectors, being deployed as colorants, health supplements and bioactives used in the pharma industry. The functional importance of carotenoids and other isoprenoids means that their modulation in biological systems can contribute to addressing our present and future societal and economic global challenges. These challenges include, food and nutritional security, sustainable production/manufacturing and combating the effects of climate change. Scheme 1 highlights our ongoing research focus aimed at harnessing biological systems to address these pertinent global challenges.

1. Sustainable production of high-value chemicals.

Traditional breeding, metabolic engineering approaches, Synthetic Biology and New Plant Breeding Techniques (NPBTs), such as gene editing are being deployed to generate plant and microbial cell factories. The goal of the approach is to replace or reduce our dependence of fossil fuel derived processes, by creating biobased solutions. Our typical plant-based systems include tomato, potato and tobacco, while the microbial chasses of choice include Escherichia coli, diverse Bacillus (10.1016/j.bbalip.2010.12.009) and Mycobacterium species and the non-conventional yeast Xanthophyllomyces dendrorhous (formally Phaffia rhodozyma). Examples developed in the laboratory include the production of ketocarotenoids (astaxanthin) in plants which has been demonstrated by feasibility studies in both aquaculture and poultry (10.1111/pbi.13073, 10.1073/pnas.170834911 & 10.1111/pbi.14196), other examples are the vaccine adjuvants such as squalene and the cosmetic ingredient phytoene.

Figure 2. Tomato lines engineered to produce high ketocarotenoids.

2. Food and nutritional security.

Metabolic engineering and Synthetic Biology approaches have been used to decipher carotenoid/isoprenoid formation and its regulation in ripe fruit. Modulating key enzymatic steps and regulators has then been deployed to create a suite of nutrient dense tomato varieties, with altered lycopene, b-carotene, and zeaxanthin (10.1038/76523, 10.1073/pnas.241374598, 10.1105/tpc.113.116210). In addition to carotenoids simultaneous production of multiple antioxidants has been achieved (10.1105/tpc.110.073866 ). Metabolomics has ben used to characterise diversity panels in crop species such as tomato (10.1038/srep03859), Capsicum (10.1093/jxb/erz086) and Root Tuber and Banana germplasm in collaboration with the CGIAR centers CIAT-Alliance, CIP and IITA (10.1007/s11306-017-1279-7, 10.1016/j.phytochem.2022.113409, 10.1016/j.foodchem.2023.137481) . From fixed donor lines the work performed has contributed to the release of varieties into the marketplace (e.g., www.burpee.com/tomato-vivacious-hybrid-prod600099). More recently the laboratory has been involved in the characterisation of mutants were the signalling and biochemical components responsible for nutrient uptake and the establishment of beneficial microbials have been modulated (www.ensa.ac.uk).  

Scheme 2. RTB CGIAR reporting the contribution of metabolomics at RHUL to the breeding of crops.

3. Technology, tools, and resource development.

Metabolite analysis underpins our activities. Our platforms include, untargeted metabolomics using LC-MS/MS (10.1093/plphys/kiad269), metabolite profiling using GC-MS/LC-MS 10.1007/s11306-013-0553-6, 10.1099/mic.0.000325 and targeted analysis (10.1046/j.1365-313x.2000.00896.x). Lipidomics (10.1016/j.phytochem.2022.113409) and LC-triple Quad MS (10.1111/pbi.13073) for phytohormones. Our proteomic analysis includes quantitative and qualitative analysis (10.1002/pmic.201200480) and protein purification from native and heterologous sources. In vitro/cell-free assays in planta and following expression in E.coli have been developed for key enzymes in carotenoid/isoprenoid biosynthesis, particularly herbicide targets. The laboratory has dedicated pipelines for multiplexed transcript determinations (e.g., digital droplet PCR). In house tools for the integration of omic datasets and visualisation of data are available. Sub-organelle (subplastid) fractionation is established and being used to perform spatial metabolomics and proteomics (10.1016/bs.mie.2022.03.001). Of particular interest is the characterisation of the plastoglobuli (10.1101/2023.01.05.522848) These methodologies have also been used to evaluate New Plant Breeding Techniques (NPBTs), (10.1016/j.jplph.2021.153378,   10.1007/s11248-023-00347-9).

Figure 3. Metabolomic workflows deployed in the laboratory.

Group infrastructure. The group has dedicated analytical apparatus; GC-MS (x3), GC-FID, HPLC-PDA (x2), HPLC-PDA-radiodetector, UPLC-PDA, real-time PCR machines and digital PCR. Plant growth facilities include glasshouses, controlled tissue culture room for transformations, chambers and polytunnels. State-of-the-art analytical suite has been established with complementary MS platforms; 2x LC-accurate mass Q-TOF-MS/MS (Agilent IM-6560, Agilent iFunnel 6550), serving both metabolomic and proteomic applications and LC-QQQ-MS (Agilent 6470) for accurate quantitative analysis. For protein preparation the multiple Ultra- centrifuges (Optima XE, Beckman Coulter) and protein purification (BioRAD) with a range of complementary columns. The laboratory has dedicated Qiagen PCR and RT-PCR equipment include digital (droplet) PCR (BioRAD OX200).

Opportunities. For prospective MSc, PhD, Post-doctoral positions, fellowships (e.g., EU-MCSF) in any of the themes described please contact p.fraser@rhul.ac.uk.