SYNTERUPTOR: mining genomic islands for non-classical specialised metabolite gene clusters

Haas, D.; Barba, M.; Vicente, C. M.; Nezbedova, S.; Garenaux, A.; Bury-Mone, S.; Lorenzi, J.-N.; Hotel, L.; Laureti, L.; Thibessard, A.; Le Goff, G.; Ouazzani, J.; Leblond, P.; Aigle, B.; Pernodet, J.-L.; Lespinet, O.; Lautru, S.

doi:10.1101/2024.01.03.573040

bioRxiv · 10.1101/2024.01.03.573040

SYNTERUPTOR: mining genomic islands for non-classical specialised metabolite gene clusters

Haas, D.·Barba, M.·Vicente, C. M.·Nezbedova, S.·Garenaux, A.·Bury-Mone, S.·Lorenzi, J.-N.·Hotel, L.·Laureti, L.·Thibessard, A.·Le Goff, G.·Ouazzani, J.·Leblond, P.·Aigle, B.·Pernodet, J.-L.·Lespinet, O.·Lautru, S.

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Abstract

Microbial specialised metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for under characterised enzymes. Here we present SYNTERUPTOR (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by earlier versions of antiSMASH, and experimentally demonstrated that it directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. SYNTERUPTOR is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.

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Haas, D., Barba, M., Vicente, C. M., Nezbedova, S., Garenaux, A., Bury-Mone, S., Lorenzi, J.-N., Hotel, L., Laureti, L., Thibessard, A., Le Goff, G., Ouazzani, J., Leblond, P., Aigle, B., Pernodet, J.-L., Lespinet, O., Lautru, S.. 2024-01-03. SYNTERUPTOR: mining genomic islands for non-classical specialised metabolite gene clusters. https://doi.org/10.1101/2024.01.03.573040

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