(Georgia Institute of Technology, 2022-04-28)
Fakhretaha Aval, Sara
The ribosome is the most abundant assembly within cells on the earth. The mRNA biological codes are translated to proteins by ribosomes for approximately 4 billion years. All ribosomes are composed of ribosomal RNA and ribosomal proteins. Sequence and structural analysis of ribosomal RNA show that all cytoplasmic ribosomes share a conserved common core. However, eukaryotic ribosomal RNAs obtain more structural complexities by accretion of RNA helices onto the ribosomal common core. The inserted RNA helices are called ribosomal RNA expansion segments. As a result, ribosomal RNA structural complexity develops functional complexity in the ribosome, particularly the human ribosome, which possesses the longest expansion segments among all living organisms. In this dissertation, we investigate the structure and function of rRNA expansion segments in three domains of life. Here, we first show that elongated expansion segments were present in ancient ribosomes of the last Asgard and Eukarya common ancestor. We predicted and validated the secondary structures of Asgard ribosomal expansion segments using covariation analysis and chemical footprinting technique. We then explored the structures and functions of expansion segments in mammals. We showed human expansion segments interact with proteins known to interact with G-quadruplexes, and ribonucleoprotein granules, suggesting a critical role in the molecular transport system. The results suggest that human ribosomes can form ribonucleoprotein granules through expansion segments. In addition, we demonstrated that expansion segments form liquid condensates through G-quadruplexes multivalent interactions in vitro. Moreover, we showed that ribosomes can traffic between human cells which is not mediated by mRNA-ribosome association. In addition, we explored the correlation between the complexity of brain and ribosomal RNA in Eukarya. The length of ribosomal RNA, expansion segments 7, and expansion segment 27 correlate with the number of neurons in brains. Furthermore, we investigated the correlation between the presence of G-Quadruplexes and number of neurons in brains. The results show that organisms with more complex brains have more G-quadruplexes on the surface of ribosomal RNA. In summary, we proposed a model for ribosomal trafficking. In this model, the tentacles of expansion segments interact with granule-associated proteins, promote liquid granule formation through phase separation, and mediate ribosome trafficking. This model is applicable to neuronal axons, nanotubes between cells, and probably in other circumstances. Finally, we discussed in detail the preparation of an RT-qPCR assay to diagnose SARS-CoV-2 in academic laboratories and describe the implementation of environmental testing across campus.