When organisms encounter an unfavorable environment, they transition to a physiologically distinct, quiescent state wherein abundant transcripts from the previous active growth state continue to persist, albeit their active transcription is downregulated. In order to generate proteins for the new quiescent physiological state, we hypothesized that the translation machinery must selectively translate upregulated transcripts in an intracellular milieu crowded with considerably higher abundance transcripts from the previous active growth state. Here, we have analyzed genome-wide changes in the transcriptome (RNA sequencing [RNA-seq]), changes in translational regulation and efficiency by ribosome profiling across all transcripts (ribosome profiling [Ribo-seq]), and protein level changes in assembled ribosomal proteins (sequential window acquisition of all theoretical mass spectra [SWATH-MS]) to investigate the interplay of transcriptional and translational regulation in Halobacterium salinarum as it transitions from active growth to quiescence. We have discovered that interplay of regulatory processes at different levels of information processing generates condition-specific ribosomal complexes to translate preferentially pools of low abundance and upregulated transcripts. Through analysis of the gene regulatory network architecture of H. salinarum, Escherichia coli, and Saccharomyces cerevisiae, we demonstrate that this conditional, modular organization of regulatory programs governing translational systems is a generalized feature across all domains of life.

中文翻译：

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盐沼中低丰度和转录本的选择性翻译。

当有机体遇到不利的环境时，它们会过渡到生理上不同的静止状态，其中来自先前活跃生长状态的大量转录本会继续存在，尽管其活跃转录被下调了。为了生成用于新的静态生理状态的蛋白质，我们假设翻译机制必须在细胞内环境中选择性地翻译上调的转录本，该环境中充满了来自先前活跃生长状态的丰度更高的转录本。在这里，我们分析了整个转录组的全基因组变化（RNA测序[RNA-seq]），通过在所有转录物中进行核糖体谱分析（核糖体谱分析[Ribo-seq]）在翻译调控和效率方面的变化，盐盐杆菌从活跃的生长过渡到静止。我们发现，在信息处理的不同层次上，调节过程的相互作用会产生条件特异性的核糖体复合物，从而优先翻译低丰度和上调转录本的库。通过分析H. salinarum，大肠杆菌和酿酒酵母的基因调控网络体系结构，我们证明了这种控制转化系统的调控程序的条件性，模块化组织是生活各个领域的普遍特征。