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A quantitative spatial proteomics analysis of proteome turnover in human cells.

Boisvert FM, Ahmad Y, Gierliński M, Charrière F, Lamont D, Scott M, Barton G, Lamond AI - Mol. Cell Proteomics (2011)

Bottom Line: Using quantitative mass spectrometry and stable isotope labeling with amino acids in cell culture, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualized using specialized software tools developed in PepTracker.Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear, and nucleolar compartments.This strongly correlated with subunits of large, multiprotein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization, and turnover rates, on a whole proteome level remains a major challenge in the postgenome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labeling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation, and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and stable isotope labeling with amino acids in cell culture, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualized using specialized software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear, and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was ~20 h. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxyl terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multiprotein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

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Pulse SILAC method.A, HeLa cells are cultured in different SILAC media containing either “light” (L), or “medium” (M) arginines and lysines until full incorporation of the amino acids. The medium of the cells growing with the “medium” amino acids is then changed for a “heavy” (H) medium. Cells are then harvested at different times, along with the equivalent cells growing in the “light” medium. Equal amounts of cells are then combined and separate cytoplasmic, nuclear, and nucleolar fractions were isolated from each time point. The resulting ratios: M/L isotopes over time measures the rate of protein degradation B, increase in the ratio: of H/L measures new protein synthesis C, and the change in the H/M ratio measures the rate of net protein turnover D.
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Figure 1: Pulse SILAC method.A, HeLa cells are cultured in different SILAC media containing either “light” (L), or “medium” (M) arginines and lysines until full incorporation of the amino acids. The medium of the cells growing with the “medium” amino acids is then changed for a “heavy” (H) medium. Cells are then harvested at different times, along with the equivalent cells growing in the “light” medium. Equal amounts of cells are then combined and separate cytoplasmic, nuclear, and nucleolar fractions were isolated from each time point. The resulting ratios: M/L isotopes over time measures the rate of protein degradation B, increase in the ratio: of H/L measures new protein synthesis C, and the change in the H/M ratio measures the rate of net protein turnover D.

Mentions: HeLa cells were grown in media containing arginine and lysine, either with the normal light isotopes of carbon, hydrogen and nitrogen (i.e.12C14N) (light – “L”), or else with l-arginine-13C614N4 and l-lysine-2H4 (medium – “M”) for at least five cell divisions, resulting in >99% incorporation of the M amino acids (Fig. 1A). The culture media with the M amino acids is then replaced with media containing l-arginine- 13C6-15N4 and l-lysine-13C6-15N2 (heavy –“H”). H amino acids are pulsed into cells with M-labeled proteins for varying times, from 30 min to 48 h. For each peptide at each time point the fraction of H amino acids incorporated replacing the pre-existing M amino acids is determined by MS.


A quantitative spatial proteomics analysis of proteome turnover in human cells.

Boisvert FM, Ahmad Y, Gierliński M, Charrière F, Lamont D, Scott M, Barton G, Lamond AI - Mol. Cell Proteomics (2011)

Pulse SILAC method.A, HeLa cells are cultured in different SILAC media containing either “light” (L), or “medium” (M) arginines and lysines until full incorporation of the amino acids. The medium of the cells growing with the “medium” amino acids is then changed for a “heavy” (H) medium. Cells are then harvested at different times, along with the equivalent cells growing in the “light” medium. Equal amounts of cells are then combined and separate cytoplasmic, nuclear, and nucleolar fractions were isolated from each time point. The resulting ratios: M/L isotopes over time measures the rate of protein degradation B, increase in the ratio: of H/L measures new protein synthesis C, and the change in the H/M ratio measures the rate of net protein turnover D.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3316722&req=5

Figure 1: Pulse SILAC method.A, HeLa cells are cultured in different SILAC media containing either “light” (L), or “medium” (M) arginines and lysines until full incorporation of the amino acids. The medium of the cells growing with the “medium” amino acids is then changed for a “heavy” (H) medium. Cells are then harvested at different times, along with the equivalent cells growing in the “light” medium. Equal amounts of cells are then combined and separate cytoplasmic, nuclear, and nucleolar fractions were isolated from each time point. The resulting ratios: M/L isotopes over time measures the rate of protein degradation B, increase in the ratio: of H/L measures new protein synthesis C, and the change in the H/M ratio measures the rate of net protein turnover D.
Mentions: HeLa cells were grown in media containing arginine and lysine, either with the normal light isotopes of carbon, hydrogen and nitrogen (i.e.12C14N) (light – “L”), or else with l-arginine-13C614N4 and l-lysine-2H4 (medium – “M”) for at least five cell divisions, resulting in >99% incorporation of the M amino acids (Fig. 1A). The culture media with the M amino acids is then replaced with media containing l-arginine- 13C6-15N4 and l-lysine-13C6-15N2 (heavy –“H”). H amino acids are pulsed into cells with M-labeled proteins for varying times, from 30 min to 48 h. For each peptide at each time point the fraction of H amino acids incorporated replacing the pre-existing M amino acids is determined by MS.

Bottom Line: Using quantitative mass spectrometry and stable isotope labeling with amino acids in cell culture, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualized using specialized software tools developed in PepTracker.Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear, and nucleolar compartments.This strongly correlated with subunits of large, multiprotein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

ABSTRACT
Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization, and turnover rates, on a whole proteome level remains a major challenge in the postgenome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labeling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation, and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and stable isotope labeling with amino acids in cell culture, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualized using specialized software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear, and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was ~20 h. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxyl terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multiprotein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.

Show MeSH
Related in: MedlinePlus