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Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets

View ORCID ProfileOmkar S. Mohite, View ORCID ProfileColton J. Lloyd, View ORCID ProfileJonathan M. Monk, View ORCID ProfileTilmann Weber, Bernhard O. Palsson
doi: https://doi.org/10.1101/781328
Omkar S. Mohite
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Colton J. Lloyd
2Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Jonathan M. Monk
2Department of Bioengineering, University of California, San Diego, La Jolla, USA
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Tilmann Weber
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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  • For correspondence: palsson@eng.ucsd.edu tiwe@biosustain.dtu.dk
Bernhard O. Palsson
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
2Department of Bioengineering, University of California, San Diego, La Jolla, USA
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  • For correspondence: palsson@eng.ucsd.edu tiwe@biosustain.dtu.dk
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Abstract

The growing number of sequenced genomes enables the study of secondary metabolite biosynthetic gene clusters (BGC) in phyla beyond well-studied soil bacteria. We mined 2627 enterobacterial genomes to detect 8604 BGCs, including nonribosomal peptide synthetases, siderophores, polyketide-nonribosomal peptide hybrids, and 60 other BGC types, with an average of around 3.3 BGCs per genome. These BGCs represented 212 distinct BGC families, of which only 20 have associated products in the MIBiG standard database with functions such as siderophores, antibiotics, and genotoxins. Pangenome analysis identified genes associated with a specific BGC encoding for colon cancer-related colibactin. In one example, we associated genes involved in the type VI secretion system with the presence of a colibactin BGC in Escherichia. This richness of BGCs in enterobacteria opens up the possibility to discover novel secondary metabolites, their physiological roles and provides a guide to identify and understand PKS associated gene sets.

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Posted September 25, 2019.
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Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets
Omkar S. Mohite, Colton J. Lloyd, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson
bioRxiv 781328; doi: https://doi.org/10.1101/781328
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Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets
Omkar S. Mohite, Colton J. Lloyd, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson
bioRxiv 781328; doi: https://doi.org/10.1101/781328

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