Metabolic gene clusters or biosynthetic gene clusters are tightly linked sets of mostly non-homologous genes participating in a common, discrete metabolic pathway. The genes are in physical vicinity to each other on the genome, and their expression is often coregulated.[1][2][3] Metabolic gene clusters are common features of bacterial[4] and most fungal[5] genomes. They are less often found in other[6] organisms. They are most widely known for producing secondary metabolites, the source or basis of most pharmaceutical compounds, natural toxins, chemical communication, and chemical warfare between organisms. Metabolic gene clusters are also involved in nutrient acquisition, toxin degradation,[7] antimicrobial resistance, and vitamin biosynthesis.[5] Given all these properties of metabolic gene clusters, they play a key role in shaping microbial ecosystems, including microbiome-host interactions. Thus several computational genomics tools have been developed to predict metabolic gene clusters.
- ^ Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, et al. (April 2017). "Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants". Plant Physiology. 173 (4): 2041–2059. doi:10.1104/pp.16.01942. PMC 5373064. PMID 28228535.
- ^ Miller BL, Miller KY, Roberti KA, Timberlake WE (January 1987). "Position-dependent and -independent mechanisms regulate cell-specific expression of the SpoC1 gene cluster of Aspergillus nidulans". Molecular and Cellular Biology. 7 (1): 427–34. doi:10.1128/MCB.7.1.427. PMC 365085. PMID 3550422.
- ^ Banf M, Zhao K, Rhee SY (September 2019). "METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters". Bioinformatics. 35 (17): 3178–3180. doi:10.1093/bioinformatics/btz021. PMC 6735823. PMID 30657869.
- ^ Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. (July 2014). "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters". Cell. 158 (2): 412–421. doi:10.1016/j.cell.2014.06.034. PMC 4123684. PMID 25036635.
- ^ a b Slot JC (2017). "Fungal Gene Cluster Diversity and Evolution". Fungal Phylogenetics and Phylogenomics. Advances in Genetics. Vol. 100. pp. 141–178. doi:10.1016/bs.adgen.2017.09.005. ISBN 978-0-12-813261-6. PMID 29153399.
- ^ Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A (May 2017). "A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants". The Plant Cell. 29 (5): 944–959. doi:10.1105/tpc.17.00009. PMC 5466033. PMID 28408660.
- ^ Gluck-Thaler E, Slot JC (June 2018). "Specialized plant biochemistry drives gene clustering in fungi". The ISME Journal. 12 (7): 1694–1705. Bibcode:2018ISMEJ..12.1694G. doi:10.1038/s41396-018-0075-3. PMC 6018750. PMID 29463891.