Predicting proteome dynamics using gene expression data

Krzysztof Kuchta, Joanna Towpik, Anna Biernacka, Jan Kutner, Andrzej Kudlicki, Krzysztof Ginalski, Malgorzata Rowicka-Kudlicka

Research output: Contribution to journalArticle

Abstract

While protein concentrations are physiologically most relevant, measuring them globally is challenging. mRNA levels are easier to measure genome-wide and hence are typically used to infer the corresponding protein abundances. The steady-state condition (assumption that protein levels remain constant) has typically been used to calculate protein concentrations, as it is mathematically convenient, even though it is often not satisfied. Here, we propose a method to estimate genome-wide protein abundances without this assumption. Instead, we assume that the system returns to its baseline at the end of the experiment, which is true for cyclic phenomena (e.g. cell cycle) and many time-course experiments. Our approach only requires availability of gene expression and protein half-life data. As proof-of-concept, we predicted proteome dynamics associated with the budding yeast cell cycle, the results are available for browsing online at http://dynprot.cent.uw.edu.pl/. The approach was validated experimentally by verifying that the predicted protein concentration changes were consistent with measurements for all proteins tested. Additionally, if proteomic data are available as well, we can also infer changes in protein half-lives in response to posttranslational regulation, as we did for Clb2, a post-translationally regulated protein. The predicted changes in Clb2 abundance are consistent with earlier observations.

Original languageEnglish (US)
Article number13866
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Proteome
Gene Expression
Proteins
Cell Cycle
Genome
Saccharomycetales
Proteomics
Half-Life
Messenger RNA

ASJC Scopus subject areas

  • General

Cite this

Kuchta, K., Towpik, J., Biernacka, A., Kutner, J., Kudlicki, A., Ginalski, K., & Rowicka-Kudlicka, M. (2018). Predicting proteome dynamics using gene expression data. Scientific Reports, 8(1), [13866]. https://doi.org/10.1038/s41598-018-31752-4

Predicting proteome dynamics using gene expression data. / Kuchta, Krzysztof; Towpik, Joanna; Biernacka, Anna; Kutner, Jan; Kudlicki, Andrzej; Ginalski, Krzysztof; Rowicka-Kudlicka, Malgorzata.

In: Scientific Reports, Vol. 8, No. 1, 13866, 01.12.2018.

Research output: Contribution to journalArticle

Kuchta, K, Towpik, J, Biernacka, A, Kutner, J, Kudlicki, A, Ginalski, K & Rowicka-Kudlicka, M 2018, 'Predicting proteome dynamics using gene expression data', Scientific Reports, vol. 8, no. 1, 13866. https://doi.org/10.1038/s41598-018-31752-4
Kuchta K, Towpik J, Biernacka A, Kutner J, Kudlicki A, Ginalski K et al. Predicting proteome dynamics using gene expression data. Scientific Reports. 2018 Dec 1;8(1). 13866. https://doi.org/10.1038/s41598-018-31752-4
Kuchta, Krzysztof ; Towpik, Joanna ; Biernacka, Anna ; Kutner, Jan ; Kudlicki, Andrzej ; Ginalski, Krzysztof ; Rowicka-Kudlicka, Malgorzata. / Predicting proteome dynamics using gene expression data. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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