Genome Mining for antibiotics biosynthesis pathways with antiSMASH 3

Tilmann Weber, Hyun Uk Kim, Kai Blin, Eriko Takano, Rainer Breitling, Marnix Medema

Research output: Chapter in Book/Report/Conference proceedingConference abstract in proceedingsResearchpeer-review

Abstract

Microorganisms are the most important source of natural products with antimicrobial or antitumor activity. These natural products are the main source for anti-­‐infectives; 80% of antibiotics currently in medical use are derived from this class of compounds. In the past, functional screenings aiming directly to the substances or to putative targets were the only possibility to identify and isolate such compounds. With the recent progress of sequencing technologies, genome mining has become a very important method to complement the laborious and expensive experimental approach and to broaden the biological sources for novel drug candidates. For high-­‐throughput genome mining, sophisticated software is required, which allows the prediction of putative biosynthetic products based on genomic data. Here, we present the new version 3 of the software antiSMASH (http://antismash.secondarymetabolites.org). antiSMASH3 currently is the most comprehensive automated genome mining platform for natural product biosynthetic pathways. It automatically screens genomic data of bacteria and fungi for the presence of 24 different types of secondary metabolite biosynthetic pathways. For different classes of secondary metabolites, detailed analyses on domain organization, enzyme active sites, and substrate specificities are integrated in the pipeline and allow the prediction of the biosynthetic core-­‐products of the pathways. In addition to tools focusing on the enzymes of the pathways, the identified gene clusters are searched compared against different integrated databases to identify homologous (often uncharacterized) gene clusters in other microorganisms, genes encoding the biosynthesis of conserved precursors or related experimentally validated gene clusters. A new module of antiSMASH3 now also provides a direct integration of metabolic modeling platform covering primary and secondary metabolism.
Original languageEnglish
Title of host publicationAbstract Book - DTU Sustain Conference 2014
Number of pages1
Place of PublicationKgs. Lyngby
PublisherTechnical University of Denmark
Publication date2014
Publication statusPublished - 2014
EventDTU Sustain Conference 2014 - Technical University of Denmark, Lyngby, Denmark
Duration: 17 Dec 201417 Dec 2014
http://www.sustain.dtu.dk/

Conference

ConferenceDTU Sustain Conference 2014
LocationTechnical University of Denmark
CountryDenmark
CityLyngby
Period17/12/201417/12/2014
Internet address

Cite this

Weber, T., Kim, H. U., Blin, K., Takano, E., Breitling, R., & Medema, M. (2014). Genome Mining for antibiotics biosynthesis pathways with antiSMASH 3. In Abstract Book - DTU Sustain Conference 2014 Technical University of Denmark.