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The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain

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The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. / Mandad, Sunit; Rahman, Raza-Ur; Centeno, Tonatiuh Pena; Vidal, Ramon O; Wildhagen, Hanna; Rammner, Burkhard; Keihani, Sarva; Opazo, Felipe; Urban, Inga; Ischebeck, Till; Kirli, Koray; Benito, Eva; Fischer, André; Yousefi, Roya Y; Dennerlein, Sven; Rehling, Peter; Feussner, Ivo; Urlaub, Henning; Bonn, Stefan; Rizzoli, Silvio O; Fornasiero, Eugenio F.

In: SCI REP-UK, Vol. 8, No. 1, 15.11.2018, p. 16913.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Mandad, S, Rahman, R-U, Centeno, TP, Vidal, RO, Wildhagen, H, Rammner, B, Keihani, S, Opazo, F, Urban, I, Ischebeck, T, Kirli, K, Benito, E, Fischer, A, Yousefi, RY, Dennerlein, S, Rehling, P, Feussner, I, Urlaub, H, Bonn, S, Rizzoli, SO & Fornasiero, EF 2018, 'The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain', SCI REP-UK, vol. 8, no. 1, pp. 16913. https://doi.org/10.1038/s41598-018-35277-8

APA

Mandad, S., Rahman, R-U., Centeno, T. P., Vidal, R. O., Wildhagen, H., Rammner, B., Keihani, S., Opazo, F., Urban, I., Ischebeck, T., Kirli, K., Benito, E., Fischer, A., Yousefi, R. Y., Dennerlein, S., Rehling, P., Feussner, I., Urlaub, H., Bonn, S., ... Fornasiero, E. F. (2018). The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. SCI REP-UK, 8(1), 16913. https://doi.org/10.1038/s41598-018-35277-8

Vancouver

Mandad S, Rahman R-U, Centeno TP, Vidal RO, Wildhagen H, Rammner B et al. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. SCI REP-UK. 2018 Nov 15;8(1):16913. https://doi.org/10.1038/s41598-018-35277-8

Bibtex

@article{e088cd9182544f4bb7213dc7843484e9,
title = "The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain",
abstract = "The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.",
keywords = "Journal Article",
author = "Sunit Mandad and Raza-Ur Rahman and Centeno, {Tonatiuh Pena} and Vidal, {Ramon O} and Hanna Wildhagen and Burkhard Rammner and Sarva Keihani and Felipe Opazo and Inga Urban and Till Ischebeck and Koray Kirli and Eva Benito and Andr{\'e} Fischer and Yousefi, {Roya Y} and Sven Dennerlein and Peter Rehling and Ivo Feussner and Henning Urlaub and Stefan Bonn and Rizzoli, {Silvio O} and Fornasiero, {Eugenio F}",
year = "2018",
month = nov,
day = "15",
doi = "10.1038/s41598-018-35277-8",
language = "English",
volume = "8",
pages = "16913",
journal = "SCI REP-UK",
issn = "2045-2322",
publisher = "NATURE PUBLISHING GROUP",
number = "1",

}

RIS

TY - JOUR

T1 - The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain

AU - Mandad, Sunit

AU - Rahman, Raza-Ur

AU - Centeno, Tonatiuh Pena

AU - Vidal, Ramon O

AU - Wildhagen, Hanna

AU - Rammner, Burkhard

AU - Keihani, Sarva

AU - Opazo, Felipe

AU - Urban, Inga

AU - Ischebeck, Till

AU - Kirli, Koray

AU - Benito, Eva

AU - Fischer, André

AU - Yousefi, Roya Y

AU - Dennerlein, Sven

AU - Rehling, Peter

AU - Feussner, Ivo

AU - Urlaub, Henning

AU - Bonn, Stefan

AU - Rizzoli, Silvio O

AU - Fornasiero, Eugenio F

PY - 2018/11/15

Y1 - 2018/11/15

N2 - The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.

AB - The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.

KW - Journal Article

U2 - 10.1038/s41598-018-35277-8

DO - 10.1038/s41598-018-35277-8

M3 - SCORING: Journal article

C2 - 30443017

VL - 8

SP - 16913

JO - SCI REP-UK

JF - SCI REP-UK

SN - 2045-2322

IS - 1

ER -