Regulation of the U3 small subunit processome and associated RNA-binding proteins

Abstract

The rate of ribosome biogenesis regulates the growth rate of the cell and is believed to be linked to the cell’s proliferative potential. Moreover, ribosome production is down-regulated in terminally differentiated cells and up-regulated in the majority of cancers. rRNA transcription is regulated in these processes although much remains unclear about the regulation of rRNA processing. In eukaryotes, 18S ribosomal RNA (rRNA) processing is mediated by the small subunit (SSU) processome. This is composed of the U3 small nucleolar (sno)RNP, many sub-complexes and a range of putative rRNA binding and modifying proteins. It is not clear however, which proteins bind or cleave the pre-rRNA, with the exception of NOB1. Moreover, the majority of research to date has been conducted in the yeast Saccharomyces cerevisiae whereas the human SSU processome remains largely unstudied. Here we report that U3 snoRNP accumulation and function are regulated through the U3-specific hU3-55k protein. We demonstrate that U3 snoRNP levels are specifically down-regulated during human lung (CaLu-3) and colon (CaCo-2) epithelial cell differentiation and that this is likely mediated through regulating hU3- 55k levels. Moreover, CaCO-2 adenocarcinoma cells are believed to revert to their pre-cancerous phenotype during differentiation, suggesting that U3 snoRNP levels increase during tumourogenesis. We also show that phosphorylation of hU3-55k is likely to be essential for U3 snoRNP function; being required for the initial cleavage of the pre-rRNA. We therefore demonstrate two independent mechanisms that may regulate ribosome biogenesis through hU3-55k. We also demonstrate that the human and yeast SSU processomes contain many orthologous proteins. However, components responsible for 3’ pre-18S rRNA processing may function at temporally and spatially different points to their counterparts in yeast. Nonetheless, PNO1 and NOB1 are closely associated, with their nucleocytoplasmic shuttling affected by blocking pre-rRNA transcription, CRM1 mediated export and the mTOR pathway, likely preventing pre-40S export to the cytoplasm. This suggests yet another level of regulation to ribosome biogenesis through pre-rRNA processing