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首页> 外文期刊>Journal of Experimental Botany >Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)
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Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)

机译：常见冰厂Mesembryanthemum crystallinum中的大规模mRNA表达谱，进行C 3 光合作用和十字绣果酸代谢（CAM）

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The common ice plant (Mesembryanthemum crystallinum L.) has emerged as a useful model for molecular genetic studies of Crassulacean acid metabolism (CAM) because CAM can be induced in this species by water deficit or salinity stress. Non-redundant sequence information from expressed sequence tag data was used to fabricate a custom oligonucleotide microarray to compare large-scale mRNA expression patterns in M. crystallinum plants conducting C3 photosynthesis versus CAM. Samples were collected every 4 h over a 24 h time period at the start of the subjective second day from plants grown under constant light and temperature conditions in order to capture variation in mRNA expression due to salinity stress and circadian clock control. Of 8455 genes, a total of 2343 genes (∼28%) showed a significant change as judged by analysis of variance (ANOVA) in steady-state mRNA abundance at one or more time points over the 24 h period. Of these, 858 (10%) and 599 (7%) exhibited a greater than two-fold ratio (TFR) increase or decrease in mRNA abundance, respectively. Functional categorization of these TFR genes revealed that many genes encoding products that function in CAM-related C4 acid carboxylation/decarboxylation, glycolysis/gluconeogenesis, polysaccharide, polyol, and starch biosynthesis/degradation, protein degradation, transcriptional activation, signalling, stress response, and transport facilitation, and novel, unclassified proteins exhibited stress-induced increases in mRNA abundance. In contrast, salt stress resulted in a significant decrease in transcript abundance for genes encoding photosynthetic functions, protein synthesis, and cellular biogenesis functions. Many genes with CAM-related functions exhibited phase shifts in their putative circadian expression patterns following CAM induction. This report establishes an extensive catalogue of gene expression patterns for future investigations aimed at understanding the complex, transcriptional hierarchies that govern CAM-specific expression patterns. A novel graph-theoretic approach called ‘Max Clique Builder’ is introduced that identifies and organizes sets of coordinately regulated genes, such as those encoding subunits of the vacuolar H+-ATPase complex, into tighter functionally related clusters with more similar expression patterns compared with standard hierarchical clustering methods.
机译：普通制冰厂（Mesembryanthemum crystallinum L.）已成为Crassulacean酸代谢（CAM）的分子遗传研究的有用模型，因为该物种可通过缺水或盐分胁迫诱导CAM。利用表达的序列标签数据中的非冗余序列信息来构建定制的寡核苷酸微阵列，以比较在进行C 3 光合作用与CAM的结晶植物中的大规模mRNA表达模式。在主观第二天开始时，在主观第二天开始的24小时内，每4小时从在恒定光照和温度条件下生长的植物中收集样品，以捕获由于盐度胁迫和昼夜节律控制而产生的mRNA表达变化。根据24小时周期内一个或多个时间点稳态mRNA丰度的方差分析（ANOVA）判断，在8455个基因中，共有2343个基因（约28％）显示出显着变化。其中，858（10％）和599（7％）分别显示出mRNA丰度大于或等于两倍（TFR）的增加或减少。这些TFR基因的功能分类表明，许多编码产物的基因在CAM相关的C 4 酸羧化/脱羧，糖酵解/糖异生，多糖，多元醇和淀粉的生物合成/降解，蛋白质降解，转录中起作用激活，信号，应激反应和运输便利化，和新的，未分类的蛋白质表现出应激诱导的mRNA丰度增加。相反，盐胁迫导致编码光合功能，蛋白质合成和细胞生物发生功能的基因的转录丰度大大降低。 CAM诱导后，许多具有CAM相关功能的基因在其假定的昼夜节律表达模式中表现出相移。该报告建立了广泛的基因表达模式目录，以供将来研究，旨在了解控制CAM特定表达模式的复杂转录层次结构。引入了一种称为“ Max Clique Builder”的新颖的图论方法，该方法可以识别并组织协调调控的基因组，例如编码液泡H + -ATPase复合物亚基的基因，并整合为功能更紧密的簇与标准的层次聚类方法相比，具有更多相似的表达模式。

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