Stress-dependent coordination of transcriptome and translatome in yeast.
Stress-dependent coordination of transcriptome and translatome in yeast.
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DOI：
10.1371/journal.pbio.1000105
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发表时间：
2009-05
期刊：
影响因子：
9.8
通讯作者：
Gerber AP
中科院分区：
文献类型：
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作者：
Halbeisen RE;Gerber AP
细胞对营养素、激素和药物等环境刺激的反应迅速改变基因表达。在基因表达的强制“重塑”过程中，特定mRNAs水平的变化并不一定与编码蛋白的水平相关，这在一定程度上可能依赖于mRNAs对翻译核糖体的不同招募。为了系统地解决这个问题，我们建立了一种方法，通过亲和纯化内源形成的核糖体并利用DNA微阵列分析相关的mRNAs，快速获得酵母中每个mRNAs的翻译状态。利用这种方法，我们比较了在不同的细胞应激条件下，总mRNA水平(转录组)和核糖体联合(翻译组)的变化。由氨基酸耗尽或渗透休克引起的严重胁迫刺激了高度相关的反应，影响了总RNA水平和翻译组的15%。许多受调控的信息编码与功能相关的蛋白质，因此反映了对特定压力的逻辑反应。相反，添加硫代荧光白和甲萘二酮引起的轻度应激改变了大约1%的消息的翻译组，对总mRNA的影响很小，这表明转录组和翻译组的反应基本上是不相关的。在这些假定的翻译调控信息中，线粒体ATPase的大部分成分。相应信息的多聚体关联增加和治疗后更高的线粒体ATPase活性证实了这种大分子复合体的调节相关性。我们的结果表明，存在高度敏感的翻译调控网络，协调功能相关的信息。这些网络优先被激活，以使细胞快速适应微小的环境扰动。生物体对环境或生理变化的反应是通过改变其适应和生存所必需的特定蛋白质的数量和活性来实现的。重要的是，蛋白质水平可以通过改变信使RNA(mRNA或转录本)的合成速度或稳定性，或蛋白质本身的合成或稳定性来调节。科学家经常在条件变化时测量全球mRNA水平，以识别差异调控的转录本，而且通常假设转录本水平的变化会导致蛋白质水平的相应变化。在这里，我们系统地比较了当酵母细胞暴露在不同的压力下时，整体转录水平(转录组)和转录体核糖体关联水平(翻译组)的整体变化，以确定转录水平和蛋白质水平之间的差异有多大。我们发现，在施加阻止细胞生长的严酷压力后，转录组的变化与翻译组的变化具有很好的相关性。然而，在不影响细胞生长的较温和的压力下，这种相关性通常会消失。在这种情况下，基因表达的重塑主要是通过调节核糖体与mRNA的关联在翻译水平上进行的。作为一个例子，我们表明，线粒体ATPase的许多成分的表达，细胞中的主要能量产生机制，在特定的温和应激条件下，在翻译上被激活，但在转录上不被激活。因此，我们的结果表明，在适应细胞需求的微小变化过程中，蛋白质合成的变化可能是基因表达变化的主要中介。在细胞适应不断变化的生长条件的过程中，转录和翻译调节变化之间的相关性程度因应激的严重程度而不同。
Cells rapidly alter gene expression in response to environmental stimuli such as nutrients, hormones, and drugs. During the imposed “remodeling” of gene expression, changes in the levels of particular mRNAs do not necessarily correlate with those of the encoded proteins, which could in part rely on the differential recruitment of mRNAs to translating ribosomes. To systematically address this issue, we have established an approach to rapidly access the translational status of each mRNA in the yeast Saccharomyces cerevisiae by affinity purification of endogenously formed ribosomes and the analysis of associated mRNAs with DNA microarrays. Using this method, we compared changes in total mRNA levels (transcriptome) with ribosome associations (translatome) after the application of different conditions of cellular stress. Severe stresses, induced by amino acid depletion or osmotic shock, stimulated highly correlated responses affecting about 15% of both total RNA levels and translatome. Many of the regulated messages code for functionally related proteins, thus reflecting logical responses to the particular stress. In contrast, mild stress provoked by addition of Calcofluor-white and menadione altered the translatome of approximately 1% of messages with only marginal effects on total mRNA, suggesting largely uncorrelated responses of transcriptome and translatome. Among these putative translationally regulated messages were most components of the mitochondrial ATPase. Increased polysome associations of corresponding messages and higher mitochondrial ATPase activities upon treatment confirmed the relevance for regulation of this macromolecular complex. Our results suggest the presence of highly sensitive translational regulatory networks that coordinate functionally related messages. These networks are preferentially activated for rapid adaptation of cells to minor environmental perturbations. Organisms respond to environmental or physiological changes by altering the amounts and activities of specific proteins that are necessary for their adaptation and survival. Importantly, protein levels can be modulated by changing either the rate of synthesis or the stability of the messenger RNA (mRNA or transcript), or the synthesis or stability of the protein itself. Scientists often measure global mRNA levels upon changing conditions to identify transcripts that are differentially regulated, and often the assumption is made that changes in transcript levels lead to corresponding changes in protein levels. Here, we systematically compared global transcript levels (transcriptome) with global alterations in the levels of ribosome association of transcripts (translatome) when yeast cells are exposed to different stresses to determine how significant the discrepancy between transcript and protein levels can be. We found that changes in the transcriptome correlate well with those in the translatome after application of harsh stresses that arrest cell growth. However, this correlation is generally lost under more mild stresses that do not affect cell growth. In this case, remodeling of gene expression is mainly executed at the translational level by modulating mRNA association with ribosomes. As one example, we show that expression for many components of the mitochondrial ATPase, the major energy production machinery in cells, is translationally but not transcriptionally activated under a specific mild stress condition. Our results therefore show that alteration of protein synthesis can be the dominant mediator of changes of gene expression during adaptation to minor changes in cellular needs. During cellular adaptation to changing growth conditions, the extent of correlation between changes in transcriptional and translational regulation varies with the severity of the stress.
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