Translation regulation by molecular switch RNA-binding protein LARP1

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The goal of this research program is to uncover the molecular mechanisms underlying RNA-binding protein (RBP) regulation of the decisive stage of gene expression, translation. To maintain homeostasis, signaling pathways direct the cell’s translational output by relaying information about its environment through RBPs; RBPs ultimately repress or stimulate the translation of associated mRNAs depending on whether the cell needs the protein product it encodes. At the molecular level, signals are transduced by RBP conformational changes, ranging from subtle to large-scale. Such changes alter RBP surface chemistry and shape, in turn strengthening or weakening their interactions with RNA and other proteins. These shifting molecular interactions shunt RNAs down the appropriate pathway: translation, storage, or decay. Some RBPs can guide target RNAs to opposing endpoints, thereby acting as molecular switches. Surprisingly, the principles guiding such fundamental decisions by the cell are surprisingly understudied. The specific and nonspecific interactions that RBPs have with their target RNAs are tunable on several levels. First, most RBPs have multiple RNA-binding domains (RBDs), the relative orientations of which are maintained by linker regions and can change based on RNA and protein binding partners. Second, most RBPs receive input from signaling pathways that describe the cellular environment and, in response, actuate gene expression changes; different pathways culminate in different post-translational modifications (PTMs) that can lead to divergent translational outcomes via the same RBP. Third, RNAs receive co- and post-transcriptional modifications that signal various messages to their RBP partners; these marks can thereby induce RBP conformational change, altering interactors and translational outcome. The interplay among these signaling inputs and translational output is not well understood. We propose to use the RBP La-related protein 1 (LARP1) as a model system for understanding how cells integrate information from multi-RBD RBPs, PTMs, and post-transcriptional mRNA modifications to direct the translation of specific transcripts. We will use biochemistry, biophysics, and structural biology to address these fundamental questions of translation regulation. We will examine how the three LARP1 RBDs—two separated by 400 amino acids in primary structure—communicate their binding statuses through space to regulate the translation of associated transcripts. We will also investigate how post-translational modifications affect the RNA- and protein-binding activities of LARP1 to manage the translation of distinct classes of mRNAs. Since LARP1 recognizes co- and post-transcriptional RNA modifications, we will also utilize this system to understand how RBPs respond to information from RNA targets to adjust structure-function relationships. Our work will propel LARP1 biology forward and also yield conceptual advances that are applicable to many, if not all, translation regulator RBPs.