Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins

Abstract

Background: The nucleolus is a subnuclear organelle in which rRNAs are transcribed, processed, and assembled with ribosomal proteins into ribosome subunits. Mass spectrometry combined with pulsed incorporation of stable isotopes of arginine and lysine was used to perform a quantitative and unbiased global analysis of the rates at which newly synthesized, endogenous proteins appear within mammalian nucleoli.

Results: Newly synthesized ribosomal proteins accumulated in nucleoli more quickly than other nucleolar components. Studies involving time-lapse fluorescence microscopy of stable HeLa cell lines expressing fluorescent-protein-tagged nucleolar factors also showed that ribosomal proteins accumulate more quickly than other components. Photobleaching and mass-spectrometry experiments suggest that only a subset of newly synthesized ribosomal proteins are assembled into ribosomes and exported to the cytoplasm. Inhibition of the proteasome caused an accumulation of ribosomal proteins in the nucleus but not in the cytoplasm. Inhibition of rRNA transcription prior to proteasomal inhibition further increased the accumulation of ribosomal proteins in the nucleoplasm.

Conclusions: Ribosomal proteins are expressed at high levels beyond that required for the typical rate of ribosome-subunit production and accumulate in the nucleolus more quickly than all other nucleolar components. This is balanced by continual degradation of unassembled ribosomal proteins in the nucleoplasm, thereby providing a mechanism for mammalian cells to ensure that ribosomal protein levels are never rate limiting for the efficient assembly of ribosome subunits. The dual time-lapse strategy used in this study, combining proteomics and imaging, provides a powerful approach for the quantitative analysis of the flux of newly synthesized proteins through a cell organelle.

Figure 1

Measurement of the Rate of Nucleolar Import of RPL27-GFP by Quantitative Microscopy and Proteomics (A) The nuclear GFP fluorescence of HeLa^RPL27-GFP cells was photobleached, and the recovery of fluorescence in the nucleolus and cytoplasm was monitored in the absence (upper panels) and presence (bottom panels) of cycloheximide. (B) Quantitation of the relative fluorescence recovery in the nucleus after photobleaching (average ± SD of three cells) in the absence (green) and presence (red) of cycloheximide. (C) Quantitation of the relative fluorescence recovery in the cytoplasm after photobleaching (average ± SD of three cells) in the absence (green) and presence (red) of cycloheximide. (D) Design of pulse SILAC experiments. HeLa^RPL27-GFP cells were grown in unlabeled SILAC medium (¹²C₆ arginine and ¹²C₆ lysine). Experiments that were time course labeled were initiated by replacement of unlabeled medium with labeling medium (¹³C₆ arginine and ¹³C₆ lysine). Cells were labeled for different lengths of time, and this was followed by isolation of nucleoli. (E) Spectra of the peptide VVLVLAGR from RPL27-GFP, which illustrate the increasing incorporation of ¹³C₆ arginine at m/z 416.79, corresponding to newly synthesized protein relative to the old pool of protein represented by the ¹²C₆ arginine peptide signal at m/z 413.78. (F) Profiles showing increase in nucleoli of the fraction of newly synthesized RPL27 and RPL27-GFP over time were determined from the ¹³C₆/¹²C₆ isotope ratio from multiple peptides.

Figure 2

Global Analysis of Nucleolar-Protein Import by Quantitative Mass Spectrometry (A and B) Profiles of the fraction of labeling of rproteins measured from HeLa^RPL27-GFP cells (A) and from HeLa cells (B) determined as described in Figure 1D. The profiles are color coded in order to emphasize the distinct profiles of RPL5 (yellow) and the differences between 40S (blue) and 60S (green) rproteins. (C) Fraction of newly synthesized nucleolar rproteins (red) and non-rproteins (blue), quantified from nucleoli isolated from HeLa^RPL27-GFP cells labeled for 240 min.

Figure 3

Rates of Synthesis and Import of Nucleolar Proteins (A) Fluorescence-microscopy analysis of cells expressing a GFP-tagged nonribosomal protein (fibrillarin, upper panels) and GFP-tagged ribosomal protein (RPS5, bottom panels) after whole-cell photobleaching. (B) Quantitation of the relative fluorescence recovery in the nucleoli of the photobleached cells expressing GFP-tagged ribosomal proteins. (C) Quantitation of the relative fluorescence recovery in the nucleoli of the photobleached cells expressing GFP-tagged nonribosomal proteins. (D) MS profiles of the fraction of labeling of the endogenous counterpart of proteins in (B) measured by quantitative mass spectrometry. (E) MS profiles of the fraction of labeling of the endogenous counterpart of proteins in (C) measured by quantitative mass spectrometry.

Figure 4

Comparing Rates of Nucleolar Import and Export of RPL27-GFP (A) Two daughter HeLa^RPL27-GFP cells from mitosis were chosen. The GFP fluorescence in the nucleus of the upper cell and the fluorescence in the cytoplasm of the lower cell were photobleached. The two photobleached cells were imaged every 5 min for the next 20 hr, and the fluorescence intensity in the nucleoli and cytoplasm was measured. Scale bars represent 5 μm. (B) Quantitation of the nucleolar (red) and cytoplasmic (green) fluorescence recovery. All data were expressed relative to the fluorescence intensities before photobleaching. (C) HeLa cells were labeled with ¹³C₆¹⁵N₄-arginine and ¹³C₆¹⁵N₂-lysine SILAC medium for 4, 8, and 20 hr (see Figures 1 and 2). Cytoplasmic ribosomes were purified and analyzed by LC-MS. Profiles of the fraction of labeling of rproteins were determined as described in the legend to Figure 2. The profile of nucleolar RPL27 is included as a reference.

Figure 5

Effect of Proteasome Inhibition on RPL27-GFP (A) HeLa^RPL27-GFP cells were treated with epoxomicin (25 μM), and the GFP fluorescence in nucleoli (No), nucleoplasm (Np), and cytoplasm (Cy) was monitored every 5 min for 330 min. (B) Changes in RPL27-GFP fluorescence intensities in nucleoli, the nucleoplasm, and the cytoplasm (relative to the intensities before treatment) after epoxomicin treatment (average ± SD of five cells).

Figure 6

Intranuclear Shuttling of RPL27-GFP (A) Small nucleoplasmic regions (shown as white circles) in live or paraformaldehyde-fixed HeLa^RPL27-GFP cells were photobleached every 4 s for 50 times. The cells were imaged immediately after each bleaching event, and GFP fluorescence in the nucleoli (red circles) was measured. The scale bars represents 5 μm. (B) Quantitation of nucleolar RPL27-GFP fluorescence relative to prebleach levels in live HeLa^RPL27-GFP cells (red), unbleached neighboring HeLa^RPL27-GFP cells in the same experiment (green), and paraformaldehyde-fixed HeLa^RPL27-GFP cells (blue). Average ± SD from five cells in each category. (C and D) Effect of prior treatment with actinomycin D on the response of HeLa^RPL27-GFP cells to proteasome inhibitor MG132. HeLa^RPL27-GFP cells were treated with either 1/5000 (v/v) DMSO (C) or 0.5 μg/ml actinomycin D (stock solution: 2.5mg/ml in DMSO) (D) for 1 hr before the addition of 25 μM MG132. In both cases, the same cell was imaged before (left panel) and 150 min after (right panel) MG132 treatment. The scale bar represents 5 μm. (E) Changes in RPL27-GFP fluorescence intensities in nucleoli, the nucleoplasm, and the cytoplasm (relative to the intensities before treatment. Average ± SD of five cells). Green represents cells pretreated with DMSO before MG132 treatment. Red represents cells pretreated with actinomycin D before MG132 treatment.

Figure 7

FRAP of Nucleolar and Cytoplasmic RPL27-GFP after Drug Treatment (A) Small regions in the nucleolus (left panels) and the cytoplasm (right panels) of a HeLa^RPL27-GFP cell were photobleached, and the recovery of fluorescence was measured. A total of 0.5 μg/ml of actinomycin D was then added to the cells and after an incubation of 1 hr; the same regions of the same cell were photobleached again and measured. A total of 25 μM MG132 was then added, and after an additional incubation of 2 hr, the same regions of these cells were photobleached and measured again. (B) The kinetics of relative fluorescence recovery of nucleolar (left graph) and cytoplasmic (right graph) RPL27-GFP in untreated (blue), actinomycin D-treated (green) and actinomycin D-plus-MG132-treated (red) cells. Each data point shows average ± SD of five cells. The relative recovery of fluorescence in the nucleoplasm of HeLa^RPL27-GFP treated with both actinomycin D and MG132 is shown in yellow. The relative recovery of fluorescence in the nucleoplasm of HeLa^GFP is shown in gray.