Okubo Yoko, Skovran Elizabeth, Guo Xiaofeng, Sivam Dhileep, Lidstrom Mary E
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
OMICS. 2007 Winter;11(4):325-40. doi: 10.1089/omi.2007.0027.
Microarrays are an important tool for understanding global gene expression changes, and the resulting data sets can be used to direct physiologic and metabolic studies. To take advantage of this technology, 60-mer oligonucleotide microarrays were designed for Methylobacterium extorquens AM1 to study gene expression changes that occur under differing physiological conditions. The carbon utilization pathways for methanol and succinate have been well characterized, and growth with these substrates was chosen as the condition used to validate the microarray data. The data were analyzed using two different methods and compared to previously obtained experimental data. The array data processed using the Significance Analysis of Microarrays followed by p-value assessment, correlated best to the experimental data. In addition to validating the microarrays, these studies uncovered possible connections between methylotrophy, iron, and sulfur homeostasis, bacteriochlorophyll production and polyketide synthesis, and will likely aid in uncovering further metabolic networks and genes required for methylotrophy.
微阵列是了解全球基因表达变化的重要工具，所产生的数据集可用于指导生理学和代谢研究。为了利用这项技术，设计了用于嗜甲基甲基杆菌AM1的60聚体寡核苷酸微阵列，以研究在不同生理条件下发生的基因表达变化。甲醇和琥珀酸的碳利用途径已得到充分表征，选择以这些底物进行生长作为用于验证微阵列数据的条件。使用两种不同方法分析数据，并与先前获得的实验数据进行比较。使用微阵列显著性分析随后进行p值评估处理的阵列数据与实验数据相关性最佳。除了验证微阵列外，这些研究还揭示了甲基营养、铁和硫稳态、细菌叶绿素产生和聚酮合成之间可能的联系，并可能有助于揭示甲基营养所需的进一步代谢网络和基因。
