Gene expression-based comparison of PQQ and known transcriptional regulators

Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ. Gene expression changes for PQQ supplemented (EC50 ~ 3 nmol PQQ/Kg diet) or deficient rats were assayed by expression microarray analysis and compared to those for known transcriptional regulators (epicatechin; Epi; dexamethasone, Dex; clofibrate, Clo; phenobarbital, Pb). Two principal expression clusters were observed; one for Dex and another for Pb, Epi, Clo, and PQQ. Within the latter, a PQQ subcluster containing a unique group of genes for cell signaling and transport functions. Next, short and long term PQQ depletion and repletion protocols (48 or 36 h, respectively) were performed, leading to changes in hepatic gene expression for both time periods. Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status. PQQ deprivation generally caused down regulation of genes associated with mitochondriogenesis, cell differentiation, and immune function. These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms. Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets. To establish if the changes in gene expression in response to PQQ exposure will follow a similar pattern as other xenobiotics, the responses to PQQ exposure were contrasted with those from exposure to epicatechin (Epi), dexamethasone (Dex), clofibrate (Clo), or phenobarbital (Pb). Dietary conditions were also chosen to clarify the response to short- and longer-term PQQ deprivation. A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ. Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, the gene expression profiles of Sprague Dawley (SD) rats treated with different xenobiotics were compared to the gene expression profile of PQQ treated SD rats.吡咯并喹啉醌（Pyrroloquinoline quinone, PQQ）是一种天然存在的化合物，研究表明其添加至缺乏PQQ的啮齿动物饲料中时，可改善动物的生长与繁殖性能。为阐明其作用机制，本研究检测了饲喂添加或不添加PQQ饲料的大鼠肝脏基因表达变化。对补充PQQ（半数效应浓度EC50约3 nmol PQQ/kg饲料）或PQQ缺乏的大鼠，通过表达微阵列（microarray）分析检测基因表达变化，并与已知的转录调节因子（表儿茶酚epicatechin, Epi；地塞米松dexamethasone, Dex；氯贝丁酯clofibrate, Clo；苯巴比妥phenobarbital, Pb）的表达变化进行对比。 研究观察到两个主要的基因表达簇：一个对应地塞米松处理组，另一个对应苯巴比妥、表儿茶酚、氯贝丁酯及PQQ处理组。在后一簇中，存在一个PQQ亚簇，其包含一组参与细胞信号转导与转运功能的独特基因。随后，本研究开展了短期与长期PQQ剥夺及补充方案（分别为48小时与36小时），检测了两个时间周期内大鼠肝脏基因表达的变化。在分析的约10000个基因与表达序列标签（Expressed Sequence Tag, EST）中，4.7%的转录本对膳食PQQ水平变化敏感。PQQ剥夺通常会下调与线粒体生成、细胞分化及免疫功能相关的基因。这些基因表达变化可解释此前已发表的多数与PQQ缺乏及药理剂量PQQ给药相关的功能观察结果。 为评估PQQ的潜在功能，本研究通过微阵列技术开展基因表达谱分析，作为综合识别潜在通路与作用机制的研究手段之一。鉴于PQQ缺乏的全身效应受微摩尔级膳食摄入水平的调控，本研究使用高纯化饲料以降低其他生物活性因子与外源性化学物（xenobiotics，如典型啮齿动物饲料中常见的此类物质）的干扰。为验证PQQ暴露诱导的基因表达变化是否与其他外源性化学物具有相似模式，本研究将PQQ暴露的应答与表儿茶酚（Epi）、地塞米松（Dex）、氯贝丁酯（Clo）及苯巴比妥（Pb）暴露的应答进行了对比。本研究还设置了不同膳食条件以明确短期与长期PQQ剥夺的应答特征。本研究的目标之一是确定是否可通过特定膳食方案或模式，识别对PQQ功能发挥至关重要的基因。已有研究表明线粒体相关功能受PQQ调控，因此本研究提出假设：与脂肪酸、氨基酸代谢及线粒体功能相关的关键基因，同样会受膳食PQQ水平的影响。 本整体研究包含两项实验。本特定实验中，我们比较了经不同外源性化学物处理的斯普拉格-道利（Sprague Dawley, SD）大鼠的基因表达谱，与经PQQ处理的斯普拉格-道利大鼠的基因表达谱。