Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes

Research output: Contribution to journalJournal articlepeer-review

Standard

Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. / Poulsen, Jon W; Madsen, Christian Toft; Young, Clifford; Kelstrup, Christian D; Grell, Heidi C; Henriksen, Peter; Jensen, Lars Juhl; Nielsen, Michael Lund.

In: Journal of Proteomics, Vol. 75, No. 13, 2012, p. 3886-97.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Poulsen, JW, Madsen, CT, Young, C, Kelstrup, CD, Grell, HC, Henriksen, P, Jensen, LJ & Nielsen, ML 2012, 'Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes', Journal of Proteomics, vol. 75, no. 13, pp. 3886-97. https://doi.org/10.1016/j.jprot.2012.04.055

APA

Poulsen, J. W., Madsen, C. T., Young, C., Kelstrup, C. D., Grell, H. C., Henriksen, P., Jensen, L. J., & Nielsen, M. L. (2012). Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. Journal of Proteomics, 75(13), 3886-97. https://doi.org/10.1016/j.jprot.2012.04.055

Vancouver

Poulsen JW, Madsen CT, Young C, Kelstrup CD, Grell HC, Henriksen P et al. Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. Journal of Proteomics. 2012;75(13):3886-97. https://doi.org/10.1016/j.jprot.2012.04.055

Author

Poulsen, Jon W ; Madsen, Christian Toft ; Young, Clifford ; Kelstrup, Christian D ; Grell, Heidi C ; Henriksen, Peter ; Jensen, Lars Juhl ; Nielsen, Michael Lund. / Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. In: Journal of Proteomics. 2012 ; Vol. 75, No. 13. pp. 3886-97.

Bibtex

@article{70c3e92f006b47c6afc017443be1a203,
title = "Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes",
abstract = "Deubiquitylating enzymes (DUBs) are a large group of proteases that regulate ubiquitin-dependent metabolic pathways by cleaving ubiquitin-protein bonds. Here we present a global study aimed at elucidating the effects DUBs have on protein abundance changes in eukaryotic cells. To this end we compare wild-type Saccharomyces cerevisiae to 20 DUB knock-out strains using quantitative proteomics to measure proteome-wide expression of isotope labeled proteins, and analyze the data in the context of known transcription-factor regulatory networks. Overall we find that protein abundances differ widely between individual deletion strains, demonstrating that removing just a single component from the complex ubiquitin system causes major changes in cellular protein expression. The outcome of our analysis confirms many of the known biological roles for characterized DUBs such as Ubp3p and Ubp8p, and we demonstrate that Sec28p is a novel Ubp3p substrate. In addition we find strong associations for several uncharacterized DUBs providing clues for their possible cellular roles. Hierarchical clustering of all deletion strains reveals pronounced similarities between various DUBs, which corroborate current DUB knowledge and uncover novel functional aspects for uncharacterized DUBs. Observations in our analysis support that DUBs induce both direct and indirect effects on protein abundances.",
author = "Poulsen, {Jon W} and Madsen, {Christian Toft} and Clifford Young and Kelstrup, {Christian D} and Grell, {Heidi C} and Peter Henriksen and Jensen, {Lars Juhl} and Nielsen, {Michael Lund}",
note = "Copyright {\textcopyright} 2012 Elsevier B.V. All rights reserved.",
year = "2012",
doi = "10.1016/j.jprot.2012.04.055",
language = "English",
volume = "75",
pages = "3886--97",
journal = "Journal of Proteomics",
issn = "1874-3919",
publisher = "Elsevier",
number = "13",

}

RIS

TY - JOUR

T1 - Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes

AU - Poulsen, Jon W

AU - Madsen, Christian Toft

AU - Young, Clifford

AU - Kelstrup, Christian D

AU - Grell, Heidi C

AU - Henriksen, Peter

AU - Jensen, Lars Juhl

AU - Nielsen, Michael Lund

N1 - Copyright © 2012 Elsevier B.V. All rights reserved.

PY - 2012

Y1 - 2012

N2 - Deubiquitylating enzymes (DUBs) are a large group of proteases that regulate ubiquitin-dependent metabolic pathways by cleaving ubiquitin-protein bonds. Here we present a global study aimed at elucidating the effects DUBs have on protein abundance changes in eukaryotic cells. To this end we compare wild-type Saccharomyces cerevisiae to 20 DUB knock-out strains using quantitative proteomics to measure proteome-wide expression of isotope labeled proteins, and analyze the data in the context of known transcription-factor regulatory networks. Overall we find that protein abundances differ widely between individual deletion strains, demonstrating that removing just a single component from the complex ubiquitin system causes major changes in cellular protein expression. The outcome of our analysis confirms many of the known biological roles for characterized DUBs such as Ubp3p and Ubp8p, and we demonstrate that Sec28p is a novel Ubp3p substrate. In addition we find strong associations for several uncharacterized DUBs providing clues for their possible cellular roles. Hierarchical clustering of all deletion strains reveals pronounced similarities between various DUBs, which corroborate current DUB knowledge and uncover novel functional aspects for uncharacterized DUBs. Observations in our analysis support that DUBs induce both direct and indirect effects on protein abundances.

AB - Deubiquitylating enzymes (DUBs) are a large group of proteases that regulate ubiquitin-dependent metabolic pathways by cleaving ubiquitin-protein bonds. Here we present a global study aimed at elucidating the effects DUBs have on protein abundance changes in eukaryotic cells. To this end we compare wild-type Saccharomyces cerevisiae to 20 DUB knock-out strains using quantitative proteomics to measure proteome-wide expression of isotope labeled proteins, and analyze the data in the context of known transcription-factor regulatory networks. Overall we find that protein abundances differ widely between individual deletion strains, demonstrating that removing just a single component from the complex ubiquitin system causes major changes in cellular protein expression. The outcome of our analysis confirms many of the known biological roles for characterized DUBs such as Ubp3p and Ubp8p, and we demonstrate that Sec28p is a novel Ubp3p substrate. In addition we find strong associations for several uncharacterized DUBs providing clues for their possible cellular roles. Hierarchical clustering of all deletion strains reveals pronounced similarities between various DUBs, which corroborate current DUB knowledge and uncover novel functional aspects for uncharacterized DUBs. Observations in our analysis support that DUBs induce both direct and indirect effects on protein abundances.

U2 - 10.1016/j.jprot.2012.04.055

DO - 10.1016/j.jprot.2012.04.055

M3 - Journal article

C2 - 22634085

VL - 75

SP - 3886

EP - 3897

JO - Journal of Proteomics

JF - Journal of Proteomics

SN - 1874-3919

IS - 13

ER -

ID: 40289650