title: MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data.
abstract: 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 information of typical SMB core genes such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). However, no detection method exists for SMB gene clusters that are functional and do not include core SMB genes at present. To advance the exploration of SMB gene clusters, especially those without known core genes, we developed MIDDAS-M, a motif-independent de novodetection algorithm for SMB gene clusters. We integrated virtual gene cluster generation in an annotated genome sequence with highly sensitive scoring of the cooperative transcriptional regulation of cluster member genes. MIDDAS-M accurately predicted 38 SMB gene clusters that have been experimentally confirmed and/or predicted by other motif-based methods in 3 fungal strains. MIDDAS-M further identified a new SMB gene cluster for ustiloxin B, which was experimentally validated. Sequence analysis of the cluster genes indicated a novel mechanism for peptide biosynthesis independent of NRPS. Because it is fully computational and independent of empirical knowledge about SMB core genes, MIDDAS-M allows a large-scale, comprehensive analysis of SMB gene clusters, including those with novel biosynthetic mechanisms that do not contain any functionally characterized genes.
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan.
authors.forename: Myco
authors.initials: M
authors.lastname: Umemura
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Koike
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.
authors.forename: Nozomi
authors.initials: N
authors.lastname: Nagano
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Ishii
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan.
authors.forename: Jin
authors.initials: J
authors.lastname: Kawano
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
authors.forename: Noriko
authors.initials: N
authors.lastname: Yamane
authors.affiliation: Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan.
authors.forename: Ikuko
authors.initials: I
authors.lastname: Kozone
authors.affiliation: Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.
authors.forename: Katsuhisa
authors.initials: K
authors.lastname: Horimoto
authors.affiliation: Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan ; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shin-ya
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
authors.affiliation: Beltsville Agricultural Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
authors.forename: Jiujiang
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, United States of America.
authors.forename: Joan W
authors.initials: JW
authors.lastname: Bennett
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Machida
mesh_terms: D000465:Algorithms; D015415:Biomarkers / Q000378:metabolism; D005658:Fungi / Q000235:genetics*; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D005810:Multigene Family; D059372:Nucleotide Motifs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010453:Peptide Synthases / Q000235:genetics; D048630:Polyketide Synthases / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger; D048630:Polyketide Synthases; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase