ClusterMine360: a database of microbial PKS/NRPS biosynthesis

Abstract

ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information.

Minimum Information about a Biosynthetic Gene cluster

“…For example, the MIBiG-curated dataset has already been integrated into the antiSMASH tool in the form of a new module 26 that compares any identified BGCs with the full MIBiG-compliant dataset of known BGCs. Moreover, a full-fledged database is currently under development that will be tightly integrated with antiSMASH and will build on the previously published ClusterMine360 framework 12 . Additionally, MIBiG-compliant data will be integrated into the recently released Integrated Microbial Genomes Atlas of Biosynthetic Clusters (IMG-ABC) database from the Joint Genome Institute (https://img.jgi.doe.gov/ABC/) 27 .…”

“…Currently, the situation is far from ideal, with information on natural product biosynthetic pathways scattered across hundreds of scientific articles in a wide variety of journals; it requires in-depth reading of papers to confidently discern which of the molecular functions associated with a gene cluster or pathway have been experimentally verified and which have been predicted solely on the basis of biosynthetic logic or bioinformatic algorithms. Although some valuable existing manually curated databases have data models in place to store some of this information 12,13,14 , all are specialized towards certain subcategories of BGCs and include just a limited number of parameters defined by the interests of a subset of the scientific community. To enable the future development of databases with universal value, a generally applicable community standard is required that specifies the exact annotation and metadata parameters agreed upon by a wide range of scientists, as well as the possible types of evidence that are associated with each variable in publications and/or patents.…”

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

“…This observation has spurred interest in leveraging bacterial genome sequence data for natural product discovery (3)(4)(5)(6)(7)(8)(9). Several tools have been developed to integrate genomic data toward the genome-guided discovery of modular, assembly line-derived natural products, including polyketides and nonribosomal peptides, by applying the biosynthetic logic elucidated from the study of model pathways (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). However, few systematic strategies target other important classes of natural products, including ribosomally synthesized natural products.…”

Marine Microbial Secondary Metabolites

“…Many of these earlier algorithms have been refined in more recent tools, e.g. anti-SMASH (Blin et al, 2013;Medema et al, 2011) and the findings consolidated into specific databases such as ClusterMine360 (Conway & Boddy, 2013).…”