Project Outline

Most of the bioactive molecules used in agriculture and medicine are made by microorganisms. For instance, Abamectin derives from actinomycete bacteria and is one of the most widely used insecticides in crop protection, with a global market of $938 million every year. Similarly, penicillin and cephalosporin antibiotics come from fungi and represent together 47% ($19.8 billion) of the global antibiotic market. This project will focus on natural product discovery from microorganism to address the rise of antimicrobial resistance and the need for greener alternatives to currently used pesticides.

Objectives

Work in the Alberti lab focuses on the discovery of natural products, such as antimicrobials and anticancer molecules, made by microorganisms, i.e. higher fungi and actinomycete bacteria.^1,2

The main objectives of the PhD project will be:

• To perform bioinformatics analysis on cryptic biosynthetic gene clusters that are likely to produce novel bioactive compounds.
• To reconstitute the enzymatic pathway of interest in an industrially relevant heterologous host, such as Saccharomyces cerevisiae or Aspergillus oryzae.
• To rewire the metabolism of the heterologous host to improve production of the biopharmaceutical of interest.

Methods

This multidisciplinary PhD project will allow the student to develop knowledge in the fields of molecular and synthetic biology, microbial genomics and analytical chemistry.

Genomic and transcriptomic data will be generated for the microorganism of interest and subjected to bioinformatic analyses, in order to pinpoint genes and gene clusters putatively involved in the pathway under study. Gene cloning techniques, such as Golden Gate assembly, Gibson assembly and yeast-based homologous recombination, will be used to clone the genes of interest and assemble them into suitable expression vectors for the chosen heterologous host. Heterologous expression of the genes of interest will allow us to recreate and elucidate the enzymatic pathway in an industrially relevant microorganism, e.g. S. cerevisiae or A. oryzae. Metabolic analyses will be performed in order to characterise the reaction products and define the catalytic function of the enzymes. Genetic engineering will be performed (e.g. through CRISPR/Cas9) with the aim to improve the production of the biopharmaceutical of interest.

Relevant papers

https://www.alberti-lab.com/

1. Tamizi, A-A, Mat-Amin, N, Weaver, JA, Olumakaiye, RT, Akbar, MA, Jin, S, Bunawan, H,* Alberti, F* (2022) Genome Sequencing and Analysis of Trichoderma (Hypocreaceae) Isolates Exhibiting Antagonistic Activity against the Papaya Dieback Pathogen, Erwinia mallotivora. Journal of Fungi 8, 246. https://doi.org/10.3390/jof8030246.
2. Alberti, F,* Leng, D, Wilkening, I, Tosin, M, Song, L, Corre, C. * (2019) Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery. Chemical Science 10 (2): 453-463. doi: 10.1039/C8SC03814G.

Techniques

• Genomic and transcriptomic analyses
• Bioinformatic analyses of microbial genomes and gene clusters
• PCR, gene cloning, CRISPR/Cas9 and other molecular biology techniques
• Generation of engineered microbial strains
• Liquid chromatography-mass spectrometry (LC-MS)
• Nuclear magnetic resonance (NMR) spectroscopy