Mining the Genomes of Lichen Associated Bacteria for Biosynthetic Gene Clusters Encoding New Secondary Metabolites
Microbial secondary metabolites have made a remarkable contribution to the therapeutics on the market today, particularly in the development of new antimicrobials. The majority of currently employed antimicrobial drugs are either directly biosynthesised by microorganisms or based on the structures of microbial metabolites. The discovery of the antibiotic penicillin in 1928 launched the golden age of antimicrobials. Since that time, bioactive natural products have helped us double our lifespans. They have greatly reduced the mortality and morbidity associated with infectious diseases and revolutionised the pharmaceutical industry. Unfortunately, the introduction of novel antimicrobial drugs into clinical practice has almost always led to resistance to those drugs, which dramatically decreases the useful lifespans of the drugs.
To address this challenge, researchers began to explore new sources for natural product screening, from the traditional phenotypic screening of soil samples to other ecological niches. The microbial assemblages in lichens have become increasingly recognised as an underestimated repertoire of bioactive compounds. This study examined the biosynthetic and chemical diversity of actinobacteria isolated from New Zealand lichen samples using ‘dry lab’ and ‘wet lab’ approaches.
More than 500 actinobacteria were isolated during the course of this study, and an in-house high-throughput NGS library preparation platform was developed to sequence these isolates. Multidimensional analyses were then conducted to explore the phylogenetic and functional divergence in our sequencing datasets. Eight biosynthetic pathways mined from our datasets were cloned and/or refactored. These constructs were then transferred to different heterologous expression hosts and screened for the production of new metabolites using a python-assisted GNPS (Global Natural Product Social Molecular Networking) platform that was developed as part of this work. Four heterologous expression systems were identified as good leads and subjected to further study, leading to the identification and characterisation of chemical entities that have not previously been reported. This thesis validated that the New Zealand lichens are a novel genetic and chemical reservoir for natural product biosynthesis study. Analysis of over 300 genomes reconstructed from lichen sourced isolates uncovered the phylogenetic divergence and function novelty, shed light on biosynthetic dark matter, and provided a promising direction for future study.