Sustainable Biosynthesis: Repurposing oxidative enzymes from plant microbiomes


   School of Biological Sciences

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  Dr Binuraj Menon, Dr G Scarlett, Dr William King  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Applications are invited for a three-year PhD fully funded via one of our doctoral training partnership (DTP) - South coast Biosciences DTP (SoCoBioDTP) to commence in October 2024. 

The PhD will be based at the Centre for Enzyme Innovation (CEI) in the School of Biological Sciences, the University of Portsmouth and will be supervised by Dr Binuraj Menon, Dr Garry Scarlet  and Dr William King (University of Southampton)

Candidates applying for this project will be eligible to compete for UKRI-funded studentships of SoCoBio DTP, which include tuition fees at the UK rate plus a tax-free maintenance stipend to support living costs, and an annual Research Training Support Grant (RTSG). We also welcome international applicants and will fund full overseas fees. We also accept applications from international students with independently sourced bursaries and scholarships to cover the difference between home and overseas fee rates.

The work on this project could involve:

● PhD research work at the renowned Centre for Enzyme Innovation (CEI), a new state-of-the-art laboratory facilities for the enzyme based research with expert teams from across the world; joined specifically to address the plastic pollution via enzyme-enabled solutions.

● To study novel enzymes from plants and plant associated microbiome via Bio-physical, Bio-catalytic and Structural Biology based techniques. 

● To investigate and study the microbial interaction with plant natural product biosynthesis, as well as exploiting these enzymes for manufacturing value added chemicals and polymers.

● Directed evolution, high-throughput screening, Chemical synthesis, molecular docking and AI based computational studies to identify and evolve new generation of enzymes. 

Project description

The development of enzymatic routes to biosynthesise or derivatise molecular scaffolds with amide or carboxylic acid functional groups is a major challenge for pharmaceutical and agrochemical sectors.

The current enzymatic routes mainly utilize aminolysis of esters (by lipases) and/or amidation of carboxylic acid (by CAR enzymes). However, none of these methods can be used to directly convert inexpensive amino acids to their respective amide or acid derivatives. Enzymatic systems that can perform these reactions efficiently with wider range of substrates under mild conditions and in absence of expensive cofactor recycling, has a great potential to make a bigger impact in the biocatalytic field for the synthesis of many value-added chemicals. Though monooxygenase-based unique oxidative decarboxylation of amino acids to form amides/acids is reported in plants and associated microbiomes, until now these pathways are not explored for their synthetic applications.

Recently, by exploiting Auxin (-a plant hormone) biosynthesis pathway in plants and plant associated microbiome, our research group has developed methods to produce various synthetic auxins, highlighting importance of these methods. In this PhD project, the main objective is to exploit similar oxidative enzymatic systems and to repurpose them for biosynthesising various bioactive molecules. We have identified and initially characterised several potential flavin dependent amino acid monooxygenases from plant and associated microbiome for this and they will be studied using various biophysical and biochemical techniques, along with the active site and protein engineering strategies to improve their substrate scope. Finally, we will use these methods for the direct synthesis of specialised chemicals and their intermediates, such as various carboxylic acid amide (CAA) fungicides and different plant hormones. As these molecules when produced in vivo within microbial cells could modulate plant microbial interactions, their bioactivity will be tested under natural conditions.

This project represents an exciting opportunity for the candidate to work in many cross-disciplinary areas, and to get trained and develop many skills in Chemical Biology and Enzymology, which is suited for industrial jobs. This project will also give the candidate an experience in bioinformatics, biophysics and structural biology. The ideal candidate will have some background experience in both wet lab biology and/or organic synthesis. This project is suited for students having a Biology, Biochemistry, Chemistry or Biotechnology background. We will provide full training for the selected candidate to work independently and to excel in their research work.

General admissions criteria

You'll need a good first degree from an UK or internationally recognised university (BSc/MSci 2:1 and/or Masters (MSc or MRes) at Merit/Distinction level (>60%)) in an appropriate subject and/or evidence of significant relevant professional experience equivalent to Masters level. English language proficiency at a minimum of IELTS band 6.5 with no component score below 6.0.

We welcome applications from candidates with sustained experience beyond their undergraduate degree level that is specifically relevant to biosciences research. This includes students with degrees in science or engineering-disciplines outside of biology.

Specific candidate requirements

You will need a first or upper second-class honours degree or a good Master’s degree in related area (such as Biochemistry/Biochemical or Biological Sciences), and be able to demonstrate good problem-solving abilities and experience with laboratory skills in Molecular Biology and/or Biochemical analysis/techniques. A good knowledge about current developments in Biocatalysis, Organic synthesis, Enzymes and Biotechnology would be a significant advantage. Also, those who have research experience in internationally recognised laboratories/institutes with a peer-reviewed publication will be looked upon favourably (e.g., arising from Master’s, Bachelor’s, or other previous collaborative research work).

How to Apply

We’d encourage you to contact Dr Binuraj Menon ([Email Address Removed]) to discuss your interest before you apply, quoting the project code BIOL11

Make sure to submit a personal statement, proof of your degrees and grades, details of two referees, proof of your English language proficiency and an up-to-date CV. SoCoBioDTP’sHow to Apply’ page offers further guidance on the PhD application process. 


Biological Sciences (4) Chemistry (6)

Funding Notes

DTP offers UKRI-funded studentships which include tuition fees at the UK rate plus a tax-free maintenance stipend to support living costs, and an annual Research Training Support Grant (RTSG).
Also accept applications from international students with independently sourced bursaries to cover the difference between home and overseas fee rates.
The travel costs to the UK, student VISA application fees and associated costs (for example immigration healthcare surcharge) are not covered for international students awarded a studentship.
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