Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase [Dataset] (doi:10.11588/data/Q3TSLH)

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Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase [Dataset]

doi:10.11588/data/Q3TSLH

heiDATA

2021-04-16

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Kong, Ka-Yiu Edwin; Fischer, Bernd; Meurer, Matthias; Kats, Ilia; Li, Zhaoyan; Rühle, Frank; Barry, Joseph D.; Kirrmaier, Daniel; Chevyreva, Veronika; San Luis, Bryan-Joseph; Costanzo, Michael; Huber, Wolfgang; Andrews, Brenda J.; Boone, Charles; Knop, Michael; Khmelinskii, Anton, 2021, "Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase [Dataset]", https://doi.org/10.11588/data/Q3TSLH, heiDATA, V1

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase [Dataset]

doi:10.11588/data/Q3TSLH

Kong, Ka-Yiu Edwin (Institute of Molecular Biology (IMB), Mainz, Germany)

Fischer, Bernd (Computational Genome Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany)

Meurer, Matthias (Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany)

Kats, Ilia (Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany)

Li, Zhaoyan (Institute of Molecular Biology (IMB), Mainz, Germany)

Rühle, Frank (Institute of Molecular Biology (IMB), Mainz, Germany)

Barry, Joseph D. (Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany)

Kirrmaier, Daniel (Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany)

Chevyreva, Veronika (Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany)

San Luis, Bryan-Joseph (The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto and Department of Molecular Genetics, University of Toronto, Toronto, Canada)

Costanzo, Michael (The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto and Department of Molecular Genetics, University of Toronto, Toronto, Canada)

Huber, Wolfgang (Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany)

Andrews, Brenda J. (The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto and Department of Molecular Genetics, University of Toronto, Toronto, Canada)

Boone, Charles (The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto and Department of Molecular Genetics, University of Toronto, Toronto, Canada)

Knop, Michael (Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany)

Khmelinskii, Anton (Institute of Molecular Biology (IMB), Mainz, Germany)

heiDATA

Khmelinskii, Anton

Knop, Michael

https://doi.org/10.11588/data/Q3TSLH

Medicine, Health and Life Sciences

Data accompanying the paper "Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase".

Ka-Yiu Edwin Kong, Bernd Fischer, Matthias Meurer, Ilia Kats, Zhaoyan Li, Frank Rühle, Joseph D. Barry, Daniel Kirrmaier, Veronika Chevyreva, Bryan-Joseph San Luis, Michael Costanzo, Wolfgang Huber, Brenda J. Andrews, Charles Boone, Michael Knop, Anton Khmelinskii, Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase, Molecular Cell, Volume 81, Issue 11, 2021, Pages 2460-2476.e11, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2021.04.018. (https://www.sciencedirect.com/science/article/pii/S1097276521003233) Abstract: Summary Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation. Keywords: selective protein degradation; ubiquitin-proteasome system; proteostasis; protein quality control; fluorescent timers; N-degron pathways; GID ubiquitin ligase

10.1016/j.molcel.2021.04.018

Ka-Yiu Edwin Kong, Bernd Fischer, Matthias Meurer, Ilia Kats, Zhaoyan Li, Frank Rühle, Joseph D. Barry, Daniel Kirrmaier, Veronika Chevyreva, Bryan-Joseph San Luis, Michael Costanzo, Wolfgang Huber, Brenda J. Andrews, Charles Boone, Michael Knop, Anton Khmelinskii, Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase, Molecular Cell, Volume 81, Issue 11, 2021, Pages 2460-2476.e11, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2021.04.018. (https://www.sciencedirect.com/science/article/pii/S1097276521003233) Abstract: Summary Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation. Keywords: selective protein degradation; ubiquitin-proteasome system; proteostasis; protein quality control; fluorescent timers; N-degron pathways; GID ubiquitin ligase

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