Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi
Secondary metabolites are produced mostly by clustered genes that are essential to their
biosynthesis. The transcriptional expression of these genes is often cooperatively regulated
by a transcription factor located inside or close to a cluster. Most of the secondary
metabolism biosynthesis (SMB) gene clusters identified to date contain so-called core genes
with distinctive sequence features, such as polyketide synthase (PKS) and non-ribosomal
peptide synthetase (NRPS). Recent efforts in sequencing fungal genomes have revealed far …
biosynthesis. The transcriptional expression of these genes is often cooperatively regulated
by a transcription factor located inside or close to a cluster. Most of the secondary
metabolism biosynthesis (SMB) gene clusters identified to date contain so-called core genes
with distinctive sequence features, such as polyketide synthase (PKS) and non-ribosomal
peptide synthetase (NRPS). Recent efforts in sequencing fungal genomes have revealed far …
MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data
Many bioactive natural products are produced as “secondary metabolites” by plants,
bacteria, and fungi. During the middle of the 20th century, several secondary metabolites
from fungi revolutionized the pharmaceutical industry, for example, penicillin, lovastatin, and
cyclosporine. They are generally biosynthesized by enzymes encoded by clusters of
coordinately regulated genes, and several motif-based methods have been developed to
detect secondary metabolite biosynthetic (SMB) gene clusters using the sequence …
bacteria, and fungi. During the middle of the 20th century, several secondary metabolites
from fungi revolutionized the pharmaceutical industry, for example, penicillin, lovastatin, and
cyclosporine. They are generally biosynthesized by enzymes encoded by clusters of
coordinately regulated genes, and several motif-based methods have been developed to
detect secondary metabolite biosynthetic (SMB) gene clusters using the sequence …
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