One third of dynamic protein expression profiles can be predicted by a simple rate equation

Konstantine Tchourine, Christopher S. Poultney, Li Wang, Gustavo M. Silva, Sandhya Manohar, Christian L. Mueller, Richard Bonneau, Christine Vogel

Research output: Contribution to journalArticle

Abstract

Cells respond to environmental stimuli with expression changes at both the mRNA and protein level, and a plethora of known and unknown regulators affect synthesis and degradation rates of the resulting proteins. To investigate the major principles of gene expression regulation in dynamic systems, we estimated protein synthesis and degradation rates from parallel time series data of mRNA and protein expression and tested the degree to which expression changes can be modeled by a simple linear differential equation. Examining three published datasets for yeast responding to diamide, rapamycin, and sodium chloride treatment, we find that almost one-third of genes can be well-modeled, and the estimated rates assume realistic values. Prediction quality is linked to low measurement noise and the shape of the expression profile. Synthesis and degradation rates do not correlate within one treatment, consistent with their independent regulation. When performing robustness analyses of the rate estimates, we observed that most genes adhere to one of two major modes of regulation, which we term synthesis- and degradation-independent regulation. These two modes, in which only one of the rates has to be tightly set, while the other one can assume various values, offer an efficient way for the cell to respond to stimuli and re-establish proteostasis. We experimentally validate degradation-independent regulation under oxidative stress for the heatshock protein Ssa4. This journal is

Original languageEnglish (US)
Pages (from-to)2850-2862
Number of pages13
JournalMolecular BioSystems
Volume10
Issue number11
DOIs
StatePublished - Nov 1 2014

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Diamide
Messenger RNA
Proteins
Gene Expression Regulation
Sirolimus
Heat-Shock Proteins
Sodium Chloride
Proteolysis
Genes
Noise
Oxidative Stress
Yeasts
Datasets

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Medicine(all)

Cite this

Tchourine, K., Poultney, C. S., Wang, L., Silva, G. M., Manohar, S., Mueller, C. L., ... Vogel, C. (2014). One third of dynamic protein expression profiles can be predicted by a simple rate equation. Molecular BioSystems, 10(11), 2850-2862. https://doi.org/10.1039/c4mb00358f

One third of dynamic protein expression profiles can be predicted by a simple rate equation. / Tchourine, Konstantine; Poultney, Christopher S.; Wang, Li; Silva, Gustavo M.; Manohar, Sandhya; Mueller, Christian L.; Bonneau, Richard; Vogel, Christine.

In: Molecular BioSystems, Vol. 10, No. 11, 01.11.2014, p. 2850-2862.

Research output: Contribution to journalArticle

Tchourine, K, Poultney, CS, Wang, L, Silva, GM, Manohar, S, Mueller, CL, Bonneau, R & Vogel, C 2014, 'One third of dynamic protein expression profiles can be predicted by a simple rate equation', Molecular BioSystems, vol. 10, no. 11, pp. 2850-2862. https://doi.org/10.1039/c4mb00358f
Tchourine K, Poultney CS, Wang L, Silva GM, Manohar S, Mueller CL et al. One third of dynamic protein expression profiles can be predicted by a simple rate equation. Molecular BioSystems. 2014 Nov 1;10(11):2850-2862. https://doi.org/10.1039/c4mb00358f
Tchourine, Konstantine ; Poultney, Christopher S. ; Wang, Li ; Silva, Gustavo M. ; Manohar, Sandhya ; Mueller, Christian L. ; Bonneau, Richard ; Vogel, Christine. / One third of dynamic protein expression profiles can be predicted by a simple rate equation. In: Molecular BioSystems. 2014 ; Vol. 10, No. 11. pp. 2850-2862.
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