The neurobiology of ribosomal proteins and ribosomal-protein-pseudogenes

In alignment with their evolutionarily conserved role in stress response across various phyla and stress types, we observed the downregulation of ribosomal protein genes (RPGs) and the upregulation of ribosomal protein pseudogenes (RP-pseudogenes) in our preliminary study using murine-based in vivo and in vitro models of neurobiological stress. These models involved exposing mice to chronic variable stress (CVS) and glucocorticoid (GC)-induced stress in primary neurons, respectively. This dysregulation was significantly enriched in neuritic pathways of neurons. Based on these findings, I hypothesize that these alterations in ribosomal infrastructure can modify the stoichiometric composition of ribosomes during stress in a neuron-compartment specific manner. To test this hypothesis, we will utilize GC-stressed primary neurons grown on a microporous membrane to segregate the somatic and neuritic compartments. In Aim 1, I will examine whether downregulated RPGs lead to changes in RP stoichiometry within ribosomes. This will be assessed using a tandem mass tag (TMT)-based semi-quantitative proteomics approach, with results validated through parallel reaction monitoring (PRM)-based absolute quantification. In Aim 2, I will investigate whether upregulated RP-pseudogenes can contribute to altered ribosome composition during stress by potentially translating into paralogs. This will be assessed through integration of ribosome sequencing and RNA-sequencing approaches. The altered stoichiometry of ribosomes can give rise to heterogeneous ribosomes capable of specialized translation of specific mRNA species during stress. Upon identifying the RP contributing to ribosomal heterogeneity, our future research will focus on understanding the specialization induced by these heterogeneous ribosomes.