Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E99-107. doi: 10.1073/pnas.1205532110. Epub 2012 Dec 17.
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.
真菌次生代谢物的生物合成途径目前正处于深入研究阶段，旨在阐明这些化合物的遗传基础，因为它们在药物和合成生物学方面具有巨大的潜力。首选方法是系统地基因缺失，以逐个鉴定关键合酶的支持酶。在这项研究中，我们设计并应用了一种 Aspergillus nidulans 的 DNA 表达阵列，并结合传统数据，形成了一个全面的基因表达纲要。我们采用基于关联的有罪推定分析来预测我们实验条件下 58 个有效合酶的生物合成簇的范围。与传统数据的比较表明，该方法在 16 个已知簇中的 13 个中是准确的，在其余 3 个簇中几乎准确。此外，我们应用了一种数据聚类方法，该方法可以识别物理上分离的基因簇（超级簇）之间的交叉化学性质，并通过预测和验证由合酶 AN1242 和 prenyltransferase AN11080 组成的超级簇，以及鉴定产物化合物 nidulanin A，来验证该方法。我们之所以选择 Aspergillus nidulans 进行方法开发和验证，是因为它有丰富的生化数据，但该方法可以应用于任何具有测序和组装基因组的真菌，从而支持真菌王国中进一步的次生代谢途径阐明。
