Physiologic state modulation by conditional translational complexes

基因表达的过程，包括转录和翻译，与细胞生理学密切相关，是地球上所有生物都在进行的。然而，翻译过程及其对细胞生理的影响通常被认为服从于转录调控和翻译后信号传导。尽管转录和信号传递都依赖于蛋白质，因此也依赖于翻译，但这种观点仍然存在。该项目旨在确定基因表达和生理的普遍方面，一直被忽视。这个项目将测试在特定环境条件下所需的蛋白质在暴露于这种条件时优先翻译的新想法。这些研究可能会揭示基因调控的一种新的分子机制，并将极大地促进我们对翻译在控制无数生命过程中的统一、核心作用的理解。此外，该项目还将有助于K-12学生和教师的培训以及高中科学课程的开发。拟议的研究将解决翻译系统组成部分的功能多样性及其转录产生的模块化表达是否调节生物体内大规模的生理状态转变。潜在的假设是，环境依赖的生理细胞状态是由具有可变亚基组成的不同核糖体复合物的有条件的生产、组装和活性产生的。这一假设是基于在系统发育多样性生物的基因调控网络中翻译机制基因的有趣组织。具体来说，核糖体亚基和其他翻译系统蛋白作为多个不同的、重叠的模块，在环境变化中具有不相关的表达模式，有条件地共同调节。本研究将尝试观察某些核糖体亚基的条件关联，以及这种关联是否指导翻译复合体优先翻译编码特定环境相关生理状态功能的转录本。蛋白质（使用SWATH质谱）和核糖体复合物的mRNA（使用RNA-seq）组成将在影响大生理状态转变的环境变化（例如，有氧到厌氧）中进行表征。此外，拟议的研究将通过工程环境响应调节或敲除条件核糖体亚基来可预测地操纵每个生物体的生理状态。特定条件表达核糖体亚基的调节改变应表现出相对于环境变化的不适当的生理状态转变。该假设的一般性将通过使用来自三个生命领域的模式微生物进行研究来评估- H. salinarum（古菌），E. coli（细菌）和S. cerevisiae（真核生物）。这些提议的活动将证明可变翻译复合物是否驱动环境依赖的生理转变。

The process of gene expression, encompassing transcription and translation, is closely interconnected with cellular physiology, and is carried out by all organisms on Earth. Yet, the process of translation and its impact on cellular physiology is generally thought to be subordinate to transcriptional regulation and post-translational signaling. This notion continues despite the fact that both transcription and signaling depend on proteins, and hence on translation. This project seeks to identify a universal aspect of gene expression and physiology that has been overlooked. This project will test the novel idea that proteins needed under particular environmental conditions are preferentially translated when exposed to such conditions. The proposed studies may uncover a new molecular mechanism for gene regulation and will greatly advance our understanding of the unifying, central role of translation in controlling a myriad life processes. In addition, the project will contribute to training of K-12 students and teachers, and high school science curriculum development. The proposed research will address whether functional diversity of components of the translation system and their transcriptionally generated modular expression regulate large-scale physiological state transitions in organisms. The underlying hypothesis is that environment-dependent physiological cell states are generated by the conditional production, assembly, and activity of distinct ribosomal complexes with variable subunit compositions. This hypothesis is based on the intriguing organization of translational machinery genes within gene regulatory networks of phylogenetically diverse organisms. Specifically, ribosomal subunits and other translation system proteins are conditionally co-regulated as multiple distinct, yet overlapping modules with un-correlated expression patterns across environmental shifts. The proposed research will attempt to observe conditional association of certain ribosomal subunits, and whether this association directs the translation complex to preferentially translate transcripts encoding functions for a particular environment-relevant physiological state. Protein (using SWATH mass spectrometry) and mRNA (with RNA-seq) compositions of ribosomal complexes will be characterized across environmental shifts (e.g., aerobic to anaerobic) that effect large physiological state transitions. Additionally, the proposed research will predictably manipulate the physiological state of each organism by engineering environment-responsive regulation or knock outs of conditional ribosomal subunits. Altered regulation of specific conditionally expressed ribosomal subunits should manifest an inappropriate physiological state transition relative to the environmental shift. Generality of the hypothesis will be assessed by performing studies using model microorganisms from the three domains of life - H. salinarum (archaeon), E. coli (bacterium), and S. cerevisiae (eukaryote). These proposed activities will demonstrate whether variable translation complexes drive environment-dependent physiological transitions.