NPRONET - Natural products discovery and bioengineering network

Funded Business Interaction Vouchers

Development of understanding of the genetic elements for biosurfactant production by a basidiomycete yeast – Mark Caddick – The University of Liverpool

Project partners – Doug Cossar – Croda Europe Ltd

Abstract

Biosurfactants have the potential to transform the specialty chemicals industry. They provide typically higher performance characteristics at lower temperatures than conventional materials. In addition they often demonstrate synergistic behaviour and added benefits such as narrow spectrum antibiosis. However, other than a very limited number of cases, the yield of such products is too low to be other than niche market products. To bring biosurfactants to a broader market requires a significant increase in yield. This is optimally achieved by developing an understanding of the genes involved in biosynthesis of the biosurfactant along with insight into their control and regulation. This project will determine the genome sequence of a strain known to produce a particular biosurfactant with known economic potential. In comparison with related strains and using standard gene function annotation methods, the probable gene cluster encoding this phenotype will be identified. A transcriptomic approach will be applied to determine the relationship of gene transcription and product accumulation. This will validate the identity of the gene cluster and provide further insight into the key components of the biosynthetic apparatus. This work will provide a platform to conduct a programme of directed mutagenesis leading to creation of strains with enhanced yield. Further expansion is envisaged to probe the structure to activity relationship of the molecule and thereafter precisely engineer performance variants for specific applications.

Discovery of potential pyrrolizidine natural products by genomic scanning of actinomycetes from NCIMB culture collection – Hai Deng – University of Aberdeen

Project partners – Carol Philips – NCIMB Ltd

Abstract

The discovery of natural products, an important source of human medicines, is critical for the development of new therapeutics against health threats, including cancer and multidrug-resistant pathogens. Yet, in recent years, industrial efforts for natural product discovery has been hampered due to a variety of reasons, including the repeated discovery of previously known compounds. Many have suggested that the solution lies in genomics and focusing research efforts on strains that encode genes for the biosynthesis of uncharacterized natural products can dereplicate, streamline, and accelerate the discovery process. This project is designed to maximise the chance of harnessing a group of previously underexploited bacterial pyrrolizidine alkaloids (PAs). Pyrrolizidines constitute an important nucleus in many pharmaceutically important agents. Naturally occurring PAs are mainly discovered from plants and fungi. Only a few PAs have been discovered from bacteria to date. Bacterial PAs display promising antibacterial and antitumour activities and have attracted considerable interest from academic research groups and the pharmaceutical industry. This group of metabolites, however, have been underexploited for many years. Recently, we elucidated the biosynthetic pathway of bacterial PAs, legonmycins, for the first time and characterized the monooxygenase enzyme LgnC (encoded by lgnC). Building on this track record, we used bioinformatics analysis on available genomic data and found that genes for the synthesis of PA-like metabolites may be ubiquitously present in bacterial genomes. We have developed a methodology needed for gene-based discovery of PA biosynthetic loci. This method relies on the fact that the PA biosynthetic pathways contain the key LgnC-like monooxygenases. Thus amplification of an internal fragment of lgnC with degenerate primers is sufficient to identify strains or plasmid clones that encode PA biosynthetic pathways. Our preliminary results are encouraging. NPRONET funding will enable us to employ this targeted gene-based screening method by mining a collection of actinomycete strains in NCIMB Ltd for PA discovery. The success of this short project will allow us to further collaborate with NCIMB Ltd and fully exploit its bacterial resources in a larger scale (8000 strains) of gene-based survey for PA discovery by applying IUK feasibility grant (i.e. industrial biotechnology catalyst-technical feasibility studies) or BBSRC-funded programme.

Biosurfactant production by yeasts belonging to the genus Pseudozyma – Ian Roberts – Institute of Food Research

Project partners – Doug Cossar – Croda Europe Ltd

Abstract

Yeast biodiversity has enormous potential for innovative natural products bioengineering. Several different yeast species, in addition to the well-known brewing and baking yeasts, have already proved of considerable value to bioindustry. They are valuable both as sources of novel natural products and as industrial-scale production vehicles for known compounds. Since 1948, the UK National Collection of Yeast Cultures (NCYC) has been collecting diverse yeasts from widely different habitats worldwide and is recognised internationally as one of the largest, most biologically diverse and best-characterised yeast collections in the world. More recently, it has begun an ambitious project to genome sequence all 4,000 strains in the collection. Mining yeast genomes computationally generates new knowledge of species diversity and its origins. Linking genomic knowledge to high-throughput robotic screens allows us to uncover and understand novel yeast properties, leading to innovations of high commercial value. In this project we will seek to expand knowledge of yeast variants using the comprehensive biological resources of the NCYC. We will focus on variation in biosurfactant producing yeasts belonging to Pseudozyma. In particular we will investigate what Mannosylerythritol Lipid (MEL) surfactants are produced by a novel species discovered within the NCYC collection, what additional functional variation can be uncovered by looking at a wider range of Pseudozyma species, and how functional variation is related to genetic variation discovered via whole genome sequencing. In the longer term we will utilise this new knowledge in strain improvement programmes aimed at producing MELs with novel, commercially desirable structure/activity relationships. The project is innovative as it brings together yeast taxonomy, genomics and metabolic engineering to yield environmentally-friendly biosurfactants with improved properties.