Physiologic state modulation by conditional translational complexes

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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.