Large-scale systems biology analysis of secondary metabolites

As the antimicrobial resistance crisis becomes evident, there is a strong need to search for novel antibiotics and design engineered cell factories for improved production of antibiotics. However, strain engineering for many antibiotics roducing microorganisms, such as streptomycetes or other actinomycetes, remains challenging, as we know little about their global metabolism and regulation. Fortunately, microbial whole-genome sequence availability has opened new avenues to understand microbial metabolism through large-scale system biology analysis, for example, using genome-scale metabolic models. Fully sequenced microbial genomes also prove crucial to discover novel secondary metabolites with antibiotic properties among other medicinal and industrial applications. Thus, genome-scale science ushers a new era for antibiotics discovery and production, demanding integrated computational workflows for genome analysis.

This thesis presents a comprehensive genome analytics workflow for secondary metabolite producers, integrating many systems biology tools such as comparative genomics, genome mining, and genome-scale metabolic models (chapter 2.1). This workflow was used for the comprehensive characterization of the genome and phenome of non-model streptomycetes like Streptomyces griseofuscus (chapter 2.2) and genome reduced Streptomyces collinus strains (chapter 2.3). The workflow also investigated the BGC, genome, and phenome potential of the rare actinomycete Streptoalloteichus sp. NAI 85712 (chapter 2.4). A high-quality genome-scale metabolic model of E. coli Nissle 1917 was reconstructed, describing detailed biosynthetic pathways of five secondary metabolites. The presented workflow provides a platform for studying global metabolism and guiding the future engineering of antibiotics producers.

This thesis further expanded the computational workflows to investigate BGCs and genomes across larger datasets. A comparative study of three different producers of the antibiotic pyracrimycin detected a BGC responsible for its biosynthesis (chapter 3.1). Next, a large-scale study involving the integrated phylogenetic analysis and BGC comparison highlighted the evolutionary distribution of BGCs and variations among particular BGCs across the Bacillus subtilis complex group (chapter 3.2). Further, a large-scale BGC comparison provided insights into the global distribution of diverse BGCs across enterobacteria and detected associated genes of particular BGC using pangenome analysis.

The findings of this work will guide the future engineering of microbes for the production of antibiotics and other secondary metabolites. The developed integrated workflows can lead to future applications of large-scale genome mining and genome analytics in large drug discovery screening programs across the world.