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Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells.

Ly T, Endo A, Lamond AI - Elife (2015)

Bottom Line: Previously, we analyzed protein abundance changes across a 'minimally perturbed' cell cycle by using centrifugal elutriation to differentially enrich distinct cell cycle phases in human NB4 cells (Ly et al., 2014).For example, we show most cells arrested in G2 by CDK1 inhibition express abnormally high levels of replication and origin licensing factors and are likely poised for genome re-replication.The protein data are available in the Encyclopedia of Proteome Dynamics (

View Article: PubMed Central - PubMed

Affiliation: Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom.

ABSTRACT
Previously, we analyzed protein abundance changes across a 'minimally perturbed' cell cycle by using centrifugal elutriation to differentially enrich distinct cell cycle phases in human NB4 cells (Ly et al., 2014). In this study, we compare data from elutriated cells with NB4 cells arrested at comparable phases using serum starvation, hydroxyurea, or RO-3306. While elutriated and arrested cells have similar patterns of DNA content and cyclin expression, a large fraction of the proteome changes detected in arrested cells are found to reflect arrest-specific responses (i.e., starvation, DNA damage, CDK1 inhibition), rather than physiological cell cycle regulation. For example, we show most cells arrested in G2 by CDK1 inhibition express abnormally high levels of replication and origin licensing factors and are likely poised for genome re-replication. The protein data are available in the Encyclopedia of Proteome Dynamics (

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Related in: MedlinePlus

Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.(A) Proteins involved in generating precursor or secondarymetabolites are shown grouped by metabolic pathway. Fold changes are shown inred in parentheses. (B) The cholesterol biosynthesis pathway isshown schematically (Espenshade and Hughes,2007) with enzymes shown as circles and arrows indicating progressivesteps in the pathway from acetyl-CoA to cholesterol. Fold changes are indicatedby shading and are explicitly provided when greater than twofold.(C) Network analysis of chromatin-associated proteins thatchange in abundance in response to serum starvation. The colour indicates thedirection of the change (red: up, blue: down), and the shading indicates themagnitude.DOI:http://dx.doi.org/10.7554/eLife.04534.004
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fig3: Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.(A) Proteins involved in generating precursor or secondarymetabolites are shown grouped by metabolic pathway. Fold changes are shown inred in parentheses. (B) The cholesterol biosynthesis pathway isshown schematically (Espenshade and Hughes,2007) with enzymes shown as circles and arrows indicating progressivesteps in the pathway from acetyl-CoA to cholesterol. Fold changes are indicatedby shading and are explicitly provided when greater than twofold.(C) Network analysis of chromatin-associated proteins thatchange in abundance in response to serum starvation. The colour indicates thedirection of the change (red: up, blue: down), and the shading indicates themagnitude.DOI:http://dx.doi.org/10.7554/eLife.04534.004

Mentions: To explore this further, we examined the protein networks and signaling pathways thatchanged specifically upon each cell cycle arrest. Most of the proteins whose abundanceschange upon serum starvation do not show cell cycle stage variations in abundance inelutriated cells. Changes specific to the serum starvation arrest protocol include adramatic increase in the levels of proteins involved in cellular metabolism (Figure 3A). Many are involved in catabolic pathwaysand in the generation of precursor and/or secondary metabolites. For example, theFAHD2A, GCDH, and BCKDHB genes all encode proteins important for the catabolism of aminoacids.10.7554/eLife.04534.004Figure 3.Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.


Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells.

Ly T, Endo A, Lamond AI - Elife (2015)

Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.(A) Proteins involved in generating precursor or secondarymetabolites are shown grouped by metabolic pathway. Fold changes are shown inred in parentheses. (B) The cholesterol biosynthesis pathway isshown schematically (Espenshade and Hughes,2007) with enzymes shown as circles and arrows indicating progressivesteps in the pathway from acetyl-CoA to cholesterol. Fold changes are indicatedby shading and are explicitly provided when greater than twofold.(C) Network analysis of chromatin-associated proteins thatchange in abundance in response to serum starvation. The colour indicates thedirection of the change (red: up, blue: down), and the shading indicates themagnitude.DOI:http://dx.doi.org/10.7554/eLife.04534.004
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383314&req=5

fig3: Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.(A) Proteins involved in generating precursor or secondarymetabolites are shown grouped by metabolic pathway. Fold changes are shown inred in parentheses. (B) The cholesterol biosynthesis pathway isshown schematically (Espenshade and Hughes,2007) with enzymes shown as circles and arrows indicating progressivesteps in the pathway from acetyl-CoA to cholesterol. Fold changes are indicatedby shading and are explicitly provided when greater than twofold.(C) Network analysis of chromatin-associated proteins thatchange in abundance in response to serum starvation. The colour indicates thedirection of the change (red: up, blue: down), and the shading indicates themagnitude.DOI:http://dx.doi.org/10.7554/eLife.04534.004
Mentions: To explore this further, we examined the protein networks and signaling pathways thatchanged specifically upon each cell cycle arrest. Most of the proteins whose abundanceschange upon serum starvation do not show cell cycle stage variations in abundance inelutriated cells. Changes specific to the serum starvation arrest protocol include adramatic increase in the levels of proteins involved in cellular metabolism (Figure 3A). Many are involved in catabolic pathwaysand in the generation of precursor and/or secondary metabolites. For example, theFAHD2A, GCDH, and BCKDHB genes all encode proteins important for the catabolism of aminoacids.10.7554/eLife.04534.004Figure 3.Serum starvation induces changes to cellular metabolism and chromatinremodeling proteins.

Bottom Line: Previously, we analyzed protein abundance changes across a 'minimally perturbed' cell cycle by using centrifugal elutriation to differentially enrich distinct cell cycle phases in human NB4 cells (Ly et al., 2014).For example, we show most cells arrested in G2 by CDK1 inhibition express abnormally high levels of replication and origin licensing factors and are likely poised for genome re-replication.The protein data are available in the Encyclopedia of Proteome Dynamics (

View Article: PubMed Central - PubMed

Affiliation: Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom.

ABSTRACT
Previously, we analyzed protein abundance changes across a 'minimally perturbed' cell cycle by using centrifugal elutriation to differentially enrich distinct cell cycle phases in human NB4 cells (Ly et al., 2014). In this study, we compare data from elutriated cells with NB4 cells arrested at comparable phases using serum starvation, hydroxyurea, or RO-3306. While elutriated and arrested cells have similar patterns of DNA content and cyclin expression, a large fraction of the proteome changes detected in arrested cells are found to reflect arrest-specific responses (i.e., starvation, DNA damage, CDK1 inhibition), rather than physiological cell cycle regulation. For example, we show most cells arrested in G2 by CDK1 inhibition express abnormally high levels of replication and origin licensing factors and are likely poised for genome re-replication. The protein data are available in the Encyclopedia of Proteome Dynamics (

Show MeSH
Related in: MedlinePlus