ArticleProceedings of the National Academy of Sciences of the United States of America2013
Accurate prediction of secondary metabolite gene clusters in filamentous fungi.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers, 1 of them a synthesis that pooled it.
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Who cites it
125 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.Nucleic acids research · 2019Pooled it
- Dual-functionMicrobiology spectrum · 2026Article
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- Systematic over-expression of secondary metabolism transcription factors to reveal the pharmaceutical potential of Aspergillus nidulans.Communications biology · 2025Article
- Strain and contact-dependent metabolomic reprogramming reveals distinct interaction strategies between Laccaria bicolor and Trichoderma.Fungal biology and biotechnology · 2025Article
- Regulation and induction of fungal secondary metabolites: a comprehensive review.Archives of microbiology · 2025Review
- Engineering of Global Transcriptional Regulators (GTRs) inJournal of fungi (Basel, Switzerland) · 2025Review
- Section-level genome sequencing and comparative genomics ofStudies in mycology · 2025Article
- AFED, a comprehensive resource for Aspergillus flavus gene expression profiling.Database : the journal of biological databases and curation · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Heterologous Biosynthesis of Prenylflavonoids inACS omega · 2025Article
- Comparative genome analysis of patulin-producingPeerJ · 2025Article
- Transcription Factor Engineering inJournal of natural products · 2024Article
- Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites inJournal of fungi (Basel, Switzerland) · 2024Article
- Epigenetic Regulation of Fungal Secondary Metabolism.Journal of fungi (Basel, Switzerland) · 2024Review
- Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies.Molecular genetics and genomics : MGG · 2024Article
- The Near-GaplessJournal of fungi (Basel, Switzerland) · 2024Article
- Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2.BMC genomics · 2024Article
- Article
- Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in hostFrontiers in plant science · 2024Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.
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