Mayer Kimberly M, Ford Jermaine, Macpherson Gordon R, Padgett David, Volkmann-Kohlmeyer Brigitte, Kohlmeyer Jan, Murphy Colleen, Douglas Susan E, Wright Jonathan M, Wright Jeffrey L C
Center for Marine Science, University of North Carolina at Wilmington, 5600 Marvin Moss Lane, Wilmington, NC 28409, USA.
Can J Microbiol. 2007 Feb;53(2):291-302. doi: 10.1139/W06-131.
Using an approach based on polymerase chain reaction (PCR), we examined the diversity of polyketide synthase (PKS) genes present in 160 marine fungal isolates, representing 142 species. We obtained ketosynthase (KS) domain PCR products from 99 fungal isolates, representing Dothideomycetes, Sordariomycetes, Eurotiomycetes, and incertae sedis. Sequence similarity searches and phylogenetic analysis of 29 marine partial-KS-encoding sequences revealed domains predicted to encode reducing, nonreducing, and 6-methylsalicylic acid PKSs. Bioinformatic analysis of an alignment of the KS sequences from marine-derived fungi revealed no unique motifs in this region. However, several specificity-determining positions were apparent between fungal 6-methylsalicylic acid PKSs as compared with either reducing or nonreducing PKSs. Evaluation of these positions in the context of a modelled three-dimensional protein structure highlighted their potential use as PKS classification markers. Evaluating primer-binding sites was necessary to obtain KS domain fragments from putative PKSs while maintaining a level of sequence information adequate to properly classify and characterize them.
我们采用基于聚合酶链反应（PCR）的方法，检测了160株海洋真菌分离株（代表142个物种）中存在的聚酮合酶（PKS）基因的多样性。我们从99株真菌分离株中获得了酮合成酶（KS）结构域PCR产物，这些分离株代表座囊菌纲、粪壳菌纲、散囊菌纲和分类地位不确定的真菌。对29个海洋来源的部分KS编码序列进行序列相似性搜索和系统发育分析，结果显示这些序列中存在预测可编码还原型、非还原型和6-甲基水杨酸聚酮合酶的结构域。对来自海洋真菌的KS序列比对进行生物信息学分析，结果显示该区域没有独特的基序。然而，与还原型或非还原型聚酮合酶相比，真菌6-甲基水杨酸聚酮合酶之间有几个明显的特异性决定位点。在三维蛋白质结构模型的背景下对这些位点进行评估，突出了它们作为聚酮合酶分类标记的潜在用途。评估引物结合位点对于从假定的聚酮合酶中获得KS结构域片段很有必要，同时要保持足够的序列信息水平，以便对它们进行正确分类和表征。
