NaphS2 Gene Expression During Anaerobic Degradation of Naphthalene

Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate. For each experimental set, aRNA from NaphS2 was labelled Cy5 (experiment) or Cy3(control) with three biological replicates hybridized in duplicate. In addition, because of the size of the predicted genome of NaphS2, ORFs were divided into two separate array designs, designated set1 and set2, such that set1 and set2 represent two separate array designs (probe sets) to be treated separately in statistical analysis.

人们对萘等多环芳烃（polycyclic aromatic hydrocarbons, PAHs）的厌氧微生物降解过程尚缺乏系统认知。菌株NaphS2是一类厌氧硫酸盐还原型海洋δ-变形菌，可在硫酸盐存在条件下，以萘、芳香化合物苯甲酸及丙酮酸作为电子供体进行生长。为鉴定参与萘降解通路的功能基因，本研究比较了NaphS2在三种不同生长底物组合下的基因表达差异：苯甲酸与丙酮酸、萘与丙酮酸，以及萘与苯甲酸。针对每组实验，我们将NaphS2的扩增RNA（aRNA）分别用Cy5（实验组）或Cy3（对照组）进行荧光标记，共设置三个生物学重复，每个重复的样品均开展两次杂交实验。此外，鉴于NaphS2的预测基因组规模较大，我们将其开放阅读框（open reading frames, ORFs）划分为两套独立的芯片探针组，分别命名为set1与set2；这两套探针组需在后续统计分析中单独进行处理。