2023-24-project-catalogue

###HIGH THROUGHPUT METAGENOME MINING FOR ENZYME DISCOVERY, LARGE-SCALE LIBRARY CREATION AND ASSAY

Project ID: 2228bd1077 (You will need this ID for your application)

Research Theme: Manufacturing The Future

UCL Lead department: Biochemical Engineering

Department Website

Lead Supervisor: Jack Jeffries

Project Summary:

As Biocatalysis plays an increasing role in industrial processes, there is a growing requirement for enzymes with wider substrate tolerances, new and higher activities. Concurrently, the requirement to find Greener and more sustainable routes to high value chemicals is becoming increasingly critical. To address this challenge, we have used Metagenomics as a source of enzymes for Green synthetic chemistry, renewable feedstock valorisation and plastic degradation.

The project will build on previous metagenomic work, constructing a semi-automated high throughput pipeline for large-scale metagenomic enzyme discovery, library creation and assay. This library will be continually expanded as new metagenomes and novel enzymes sequences are mined.

Objectives

  1. Create a bioinformatics pipeline to automate: open reading frame identification of metagenomes; DNA sequence archiving by enzyme class; and primer design for retrieval of selected targets by Polymerase Chain Reaction (PCR).
  2. Design and test high throughput PCR and cloning protocols, utilising robotic platforms, to allow for the mass retrieval of sequences identified from metagenomes.
  3. Investigate new methods for maintaining the library and assaying enzymes in parallel.
  4. Apply the newly generated library to themes, such as: plastic degradation, valorisation of biomolecules and fine chemical production.

The preferred candidate will have experience in bioinformatics, with the ability to code to the standard required to automate the metagenomics pipeline. Understanding and experience with basic molecular biology techniques, such as PCR and cloning in E. coli, is desirable but not essential. The candidate will have or be expected to gain at least an upper second-class degree or equivalent at Masters level in Biochemistry, Bioinformatics, Biochemical Engineering or related degree. The successful candidate will have the opportunity to develop a powerful new platform for enzyme discovery, identifying and assaying novel enzymes, gaining experience in metagenomics, molecular biology, biocatalysis and analytical techniques such as HPLC and Mass spectrometry