Carbone Ignazio, Ramirez-Prado Jorge H, Jakobek Judy L, Horn Bruce W
Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA.
BMC Evol Biol. 2007 Jul 9;7:111. doi: 10.1186/1471-2148-7-111.
The biosynthesis of aflatoxin (AF) involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST) and O-methylsterigmatocystin (OMST), the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A. nidulans that synthesizes only ST, A. flavus that makes predominantly AF, and A. parasiticus that generally produces either AF or OMST. Whether these differences are important in the evolutionary/ecological processes of species adaptation and diversification is unknown. Equally unknown are the specific genomic mechanisms responsible for ordering and clustering of genes in the AF pathway of Aspergillus.
To elucidate the mechanisms that have driven formation of these clusters, we performed systematic searches of aflatoxin cluster homologs across five Aspergillus genomes. We found a high level of gene duplication and identified seven modules consisting of highly correlated gene pairs (aflA/aflB, aflR/aflS, aflX/aflY, aflF/aflE, aflT/aflQ, aflC/aflW, and aflG/aflL). With the exception of A. nomius, contrasts of mean Ka/Ks values across all cluster genes showed significant differences in selective pressure between section Flavi and non-section Flavi species. A. nomius mean Ka/Ks values were more similar to partial clusters in A. fumigatus and A. terreus. Overall, mean Ka/Ks values were significantly higher for section Flavi than for non-section Flavi species.
Our results implicate several genomic mechanisms in the evolution of ST, OMST and AF cluster genes. Gene modules may arise from duplications of a single gene, whereby the function of the pre-duplication gene is retained in the copy (aflF/aflE) or the copies may partition the ancestral function (aflA/aflB). In some gene modules, the duplicated copy may simply augment/supplement a specific pathway function (aflR/aflS and aflX/aflY) or the duplicated copy may evolve a completely new function (aflT/aflQ and aflC/aflW). Gene modules that are contiguous in one species and noncontiguous in others point to possible rearrangements of cluster genes in the evolution of these species. Significantly higher mean Ka/Ks values in section Flavi compared to non-section Flavi species indicate increased positive selection acting in the evolution of genes in OMST and AF gene clusters.
黄曲霉毒素（AF）的生物合成涉及复杂聚酮途径中的20多种酶促反应，该途径将乙酸盐和丙二酸盐转化为中间产物柄曲霉素（ST）和O - 甲基柄曲霉素（OMST），它们分别是AF的倒数第二个和最终前体。尽管这些前体在化学和结构上非常相似，但它们在曲霉菌种水平上的积累情况有所不同。显著的例子有仅合成ST的构巢曲霉、主要产生AF的黄曲霉以及通常产生AF或OMST的寄生曲霉。这些差异在物种适应和多样化的进化/生态过程中是否重要尚不清楚。同样未知的是负责曲霉AF途径中基因排序和聚类的具体基因组机制。
为了阐明驱动这些基因簇形成的机制，我们对五个曲霉基因组中的黄曲霉毒素基因簇同源物进行了系统搜索。我们发现了高水平的基因重复，并鉴定出由高度相关基因对组成的七个模块（aflA/aflB、aflR/aflS、aflX/aflY、aflF/aflE、aflT/aflQ、aflC/aflW和aflG/aflL）。除了nomius曲霉外，所有基因簇基因的平均Ka/Ks值对比显示，黄曲霉群和非黄曲霉群物种之间在选择压力上存在显著差异。nomius曲霉的平均Ka/Ks值与烟曲霉和土曲霉中的部分基因簇更为相似。总体而言，黄曲霉群的平均Ka/Ks值显著高于非黄曲霉群物种。
我们的结果表明了几种基因组机制参与了ST、OMST和AF基因簇基因的进化。基因模块可能源于单个基因的重复，其中重复前基因的功能保留在副本中（aflF/aflE），或者副本可能分担祖先功能（aflA/aflB）。在一些基因模块中，重复副本可能只是增强/补充特定途径功能（aflR/aflS和aflX/aflY），或者重复副本可能进化出全新功能（aflT/aflQ和aflC/aflW）。在一个物种中相邻而在其他物种中不相邻的基因模块表明这些物种进化过程中基因簇基因可能发生了重排。与非黄曲霉群物种相比，黄曲霉群中显著更高的平均Ka/Ks值表明在OMST和AF基因簇基因的进化中存在增加的正选择作用。
