The notion of a “plurifunctional” nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of ∼350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes.

Significance: Translational control is a cornerstone of gene-expression regulation in physiological and pathological contexts. The contribution of nonribosomal factors, including messenger RNAs (mRNAs) and mRNA-bound factors, to translational control have been extensively studied. Recently, the hypothesis of a ribosome-mediated regulation emerged, which proposes that cells produce ribosomes of different composition and displaying different translational properties. This work reveals that ribosomal RNA 2′-O-methylation can be modulated in human ribosomes, including at key functional sites for translation, and that changes in the 2′-O-methylation pattern control the intrinsic capabilities of ribosomes to translate mRNAs. This work directly demonstrates the existence of composition-modified ribosomes and their associated change in translational activity as conceptualized by the specialized ribosome concept.

Protein synthesis is a fundamental cell process and ribosomes - particularly through the ribosomal RNA that display ribozyme activity - are the main effectors of this process. Ribosome biogenesis is a very complex process involving transcriptional as well as many post-transcriptional steps to produce functional ribosomes. It is now well demonstrated that ribosome production is enhanced in cancer cells and that ribosome biogenesis plays a crucial role in tumor progression. However, at present there is an important lack of data to determine whether the entire process of ribosome biogenesis and ribosome assembly is modified during tumor progression and what could be the potential impact on the dysregulation of translational control that is observed in cancer cells. In breast cancer cells displaying enhanced aggressivity, both in vitro and in vivo, we have analyzed the major steps of ribosome biogenesis and the translational capacity of the resulting ribosome. We show that increased tumorigenicity was associated with modifications of nucleolar morphology and profound quantitative and qualitative alterations in ribosomal biogenesis and function. Specifically cells with enhanced tumor aggressivity displayed increased synthesis of 45S pre-rRNA, with activation of an alternative preRNA synthetic pathway containing a 43S precursor and enhanced post-transcriptional methylation of specifc sites located in the 28S rRNA. While the global translational activity was not modified, IRES-initiated translation, notably that of p53 mRNA, was less efficient and the control of translational fidelity was importantly reduced in cells with increased aggressivity. These results suggest that acquisition of enhanced tumor aggressivity can be associated with profound qualitative alterations in ribosomal control, leading to reduced quality control of translation in cancer cells

Nucleolin is one of the major nonribosomal proteins of the nucleolus. Through its four RNA-binding domains, nucleolin interacts specifically with pre-rRNA as soon as synthesis begins, but it is not found in mature cytoplasmic ribosomes. Nucleolin is able to shuttle between the cytoplasm and the nucleus. These data suggest that nucleolin might be involved in the nucleolar import of cytoplasmic components and in the assembly of pre-ribosomal particles. Here we show, using two-dimensional blots in a ligand blotting assay, that nucleolin interacts with 18 ribosomal proteins from rat (14 and 4 from the large and small subunit, respectively). The C-terminal domain of nucleolin (p50) interacts with 10 of these identified ribosomal proteins. In vitro binding assays show that the glycine-arginine rich domain of nucleolin (RGG domain) is sufficient for the interaction with one of these proteins. Interestingly, most of the proteins that interact with p50 belong to the core ribosomal proteins, which are resistant to extraction with high salt concentration. These findings suggest that nucleolin might be involved in the nucleolar targeting of some ribosomal proteins and in their assembly within pre-ribosomal particles.