EvoMining reveals the origin and fate of natural products biosynthetic enzymes

Abstract

Natural products, or specialized metabolites, are important for medicine and agriculture alike, as well as for the fitness of the organisms that produce them. Microbial genome mining aims at extracting metabolic information from genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process the likelihood of identifying truly novel biosynthetic systems is low. To overcome this limitation we previously introduced EvoMining, a genome mining approach that incorporates evolutionary principles.Here, we release and use our latest version of EvoMining, which includes novel visualization features and customizable databases, to analyze 42 central metabolic enzyme families conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these enzyme families are lineage specific, opening a new metabolic space related to 'shell' enzymes, which have been overlooked to date. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving microbial adaptive evolution. By defining the origins and fates of metabolic enzymes, EvoMining not only complements traditional genome mining approaches as an unbiased and rule-independent strategy, but it opens the door to gain insights into the evolution of natural products biosynthesis. We anticipate that EvoMining will be broadly used for metabolic evolutionary studies, and to generate genome-mining predictions leading to unprecedented chemical scaffolds and new antibiotics. DATA SUMMARYDatabases have been deposited at Zenodo; DOI: 10.5281/zenodo.1162336 http://zenodo.org/deposit/1219709 Trees and metadata have been deposited in MicroReact GDH Actinobacteria https://microreact.org/project/r1IhjVm6X GDH Cyanobacteria https://microreact.org/project/HyjYUN7pQ) GDH Pseudomonas https://microreact.org/project/rJPC4EQa7 GDH Archaea https://microreact.org/project/ByUcvNmaX ALS Cyanobacteria https://microreact.org/project/B11HkUtdm EvoMining code has been deposited in gitHub https://github/nselem/evomining Docker container in Dockerhub https:// hub.docker.com/r/nselem/evomining/ We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Genomic mining and diversity of assembly line polyketide synthases

“…One selection strategy is guided by the novelty of an assembly line PKS as measured by its distinctness from characterized PKSs. On the protein level, EvoMining reconstructs evolutionary histories of biosynthetic enzymes to find gene clusters that might make molecules with novel chemical structures [56,57]. At the gene cluster level, tools such as BiG-SCAPE, BiG-SliCE, Big-FAM and CORASON enable similarity network analysis to explore chemical diversity [58][59][60].…”

Convergent evolution of Streptomyces protease inhibitors involving a tRNA-mediated condensation-minus NRPS

“…EvoMining (Sélem-Mojica et al 2019) and CORASON (Navarro-Muñoz et al 2020) phylogenomic analyses of actinobacterial L/F transferases allowed us to identify 137 L/F transferase homologs within 1,246 good quality and well annotated actinobacterial genomes. Remarkably, despite the fact that L/F transferases are known to play a central role as housekeeping enzymes involved in proteolytic metabolism (Mogk et al 2007), only 11% of the actinobacterial genomes investigated include a homolog of this gene, suggesting that these organisms may have alternative proteolytic tagging strategies, such as the SsrA (tmRNA) tagging system (Braud et al 2006).…”

“…EvoMining (Cruz-Morales et al 2016;Sélem-Mojica et al 2019) and CORASON (Navarro-Muñoz et al 2020) algorithms were used as previously. S. roseus ATCC31245 was obtained from the ATCC collection, and its genomic DNA was extracted using common protocols (Kieser et al 2000) and sequenced at the genomic sequencing facilities of Langebio, Cinvestav-IPN (Irapuato, Mexico), using an Illumina MiSeq platform in paired-end format with read lengths of 250 bases and insert length of 800 bases.…”

“…The raw reads were filtered using Trimmomatic (Bolger et al 2014) and assembled with velvet (Zerbino and Birney 2008), obtaining a 7.8 Mb assembly in 165 contigs with a coverage of 95 X and a GC content of 72 %. This assembly was annotated using RAST (Aziz et al 2008), antiSMASH (Weber et al 2015) and EvoMining (Sélem-Mojica et al 2019).…”