Specialized Ribosomes: A New Frontier in Gene Regulation, Organismal Biology, & Evolution

The central dogma of molecular biology has for decades served as an explanation for the flow of genetic information within a biological system. In so far as the normal flow of biological information from mRNA to protein, the ribosome has been perceived to decode the genome with essentially machine-like precision; serving as an integral but largely passive participant in the synthesis of all effector proteins across all kingdoms of life. Importantly, a large class of human diseases collectively known as 'ribosomopathies' are characterized by mutations in ribosome components that lead to devastating human conditions including bone marrow failure for which the underlying molecular basis remains poorly understood. In this respect, our research has changed the view that ribosomes carry out largely rote-like functions by demonstrating that not all of the millions of ribosomes within each cell are the same and that ribosome heterogeneity provides a novel means for diversity of the proteins that can be produced in specific cells, tissues, and organisms. I will present our work centered on providing a roadmap for the characterization of ribosome composition at a single cell level and during cellular differentiation. We employed a highly quantitative mass spectrometry-based approach to precisely quantify the abundance of each ribosomal protein (RP) as well as a large cohort of auxiliary ribosome associating factors belonging to actively translating ribosomes within embryonic stem cells. This led to the identification of a subset of ribosomes that are heterogeneous for RP composition. To further address the functional role of ribosome heterogeneity in translational control of the mammalian genome, we employed CRISPR/Cas9 to endogenously tag and purify heterogeneous ribosome populations. We then developed an adapted ribosome profiling method to precisely quantify and characterize the nature of mRNAs translated by distinct heterogenous ribosomes genome-wide. This led to the identification of subpools of transcripts, critical for key cellular processes including cell signaling, metabolism, growth, proliferation and survival, which are selectively translated by specific types of ribosomes. Most remarkably, there are specific metabolic pathways where almost every single component is selectively translated by specialized ribosomes demarcated by a single RP. I will further present recent findings on the mechanisms by which ribosome-mediated control of gene expression is encoded by structured RNA regulons within 5'UTRs. Together, these studies reveal a critical link between ribosome heterogeneity and specialized translational control of the mammalian genome, which adds an important layer of control to the post-transcriptional circuitry of gene regulation and may be critically perturbed in human diseases.