Nucleolar proteome dynamics

Top Cited Papers
Publisher Website
Google Scholar
Abstract
The nucleolus is the cellular organelle that manufactures ribosomes and plays a part in many vital process including cell-cycle regulation and senescence. Using the latest proteomics technologies, Andersen et al. have generated a comprehensive list of nucleolar proteins. Over 690 proteins were found in the in the nucleolar preparation, including Werner's syndrome helicase and various regulatory proteins. The technology also allows analysis of changes in relative levels of proteins as a result of perturbing growth conditions with drugs. This paints a picture of a dynamic proteome: in effect there may be no definitive proteome for the nucleolus or any other organelle, rather there is a series of overlapping proteomes corresponding to different cell states. The nucleolus is a key organelle that coordinates the synthesis and assembly of ribosomal subunits and forms in the nucleus around the repeated ribosomal gene clusters. Because the production of ribosomes is a major metabolic activity, the function of the nucleolus is tightly linked to cell growth and proliferation, and recent data suggest that the nucleolus also plays an important role in cell-cycle regulation, senescence and stress responses1,2,3,4. Here, using mass-spectrometry-based organellar proteomics and stable isotope labelling5, we perform a quantitative analysis of the proteome of human nucleoli. In vivo fluorescent imaging techniques are directly compared to endogenous protein changes measured by proteomics. We characterize the flux of 489 endogenous nucleolar proteins in response to three different metabolic inhibitors that each affect nucleolar morphology. Proteins that are stably associated, such as RNA polymerase I subunits and small nuclear ribonucleoprotein particle complexes, exit from or accumulate in the nucleolus with similar kinetics, whereas protein components of the large and small ribosomal subunits leave the nucleolus with markedly different kinetics. The data establish a quantitative proteomic approach for the temporal characterization of protein flux through cellular organelles and demonstrate that the nucleolar proteome changes significantly over time in response to changes in cellular growth conditions.