Analysis of Ribosome Biogenesis from Three Standpoints: Investigating the Roles of Ribosomal RNA, Ribosomal Proteins and Assembly Factors

Ribosomes are ubiquitous and abundant molecular machines composed of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins). They play a central role in the cell by translating the genetic code in mRNA to form polypeptides. Because of their large size and the complexity of molecular interactions within ribosomes, we do not still fully understand how they are synthesized in the cell. Yet, a thorough knowledge of ribosome biogenesis is crucial to understand cellular homeostasis and various disease states including ribosomopathies and cancer. In addition, ribosomes serve as an interesting paradigm to understand the principles that dictate the formation and function of the many different ribonucleoprotein particles that play vital roles in the cell. In addition to the rRNA and r-protein components, trans-acting assembly factors play indispensable roles in synthesizing functional ribosomes. Fundamentally, ribosome biogenesis is driven by a network of molecular interactions that evolve in time and space, as assembly progresses from the nucleolus to the cytoplasm. We sought to gain a deeper understanding of ribosome biogenesis in Saccharomyces cerevisiae by investigating the molecular interactions that drive ribosome assembly. Recent structural studies have revealed a number of such molecular interactions at high resolution. Based on these, our investigation was carried out from the perspectives of all three players that are involved in constructing ribosomes, with a specific emphasis on eukaryote-specific elements of rRNAs and r-proteins. From the standpoint of rRNA, we performed the first systematic study to investigate the potential functions of nearly all of the eukaryotic rRNA expansion segments in the yeast large ribosomal subunit. We showed that most of them are indispensable and play vital roles in ribosome biogenesis. Based on the steps of ribosome biogenesis in which each of them participates, we showed that there is neighborhood-specific functional clustering of rRNA and r-protein interactions that drive ribosome assembly. Further, we found evidence for possible functional co-evolution of eukaryotic rRNA and eukaryote-specific elements of r-protein. From the standpoint of r-protein, we used rpL5 as a paradigm for constantly evolving molecular interactions as assembly progresses. Apart from recapitulating Diamond-Blackfan anemia missense mutations in yeast, we characterized interactions formed by specific regions of rpL5 and propose that these interactions potentially govern the loading of 5S RNP en bloc to the nascent large ribosomal subunit, to ensure proper rotation of the 5S RNP during biogenesis, and to further recruit proteins necessary for the test drive of subunits in the cytoplasm. From the standpoint of assembly factors, we analyzed a so-called group of ITS2 cluster proteins, Nop15, Cic1 and Rlp7 and identified the extensive protein-protein interactions and analyzed protein-RNA interactions that they make. Using our data, we were able to localize Rlp7 to the ITS2 spacer in the pre-rRNA and to identify potential mechanisms for their function. Having identified a network of molecular interactions, we suggest that these proteins orchestrate proper folding of rRNA through this network, and stabilize and facilitate the early steps of assembly. Further, based on their location in the preribosome, these factors might serve to ensure proper progression of early steps of assembly to enable subsequent processing of the ITS2 spacer in the middle steps, possibly by recruiting the ATPase Has1. Thus, we have investigated early nucleolar and late nuclear steps of ribosome assembly in the light of molecular interactions formed by rRNA, r-protein and assembly factors that participate in eukaryotic ribosome assembly. Lessons that emerged from this study and tools developed in the process provide a starting point for further investigations pertaining to the roles of eukaryote-specific segments of molecules that participate in ribosome biogenesis, and serve as a paradigm for how a dynamic network of molecular interactions can drive the assembly of complex macromolecular structures.