Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants

Martin Grønbæk-Thygesen; Vasileios Voutsinos; Kristoffer E. Johansson; Thea K. Schulze; Matteo Cagiada; Line Pedersen; Lene Clausen; Snehal Nariya; Rachel L. Powell; Amelie Stein; Douglas M. Fowler; Kresten Lindorff-Larsen; Rasmus Hartmann-Petersen

doi:10.1038/s41467-024-48481-0

Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants

Martin Grønbæk-Thygesen
, Vasileios Voutsinos
, Kristoffer E. Johansson
, Thea K. Schulze
, Matteo Cagiada
, Line Pedersen
, Lene Clausen
, Snehal Nariya
, Rachel L. Powell
, Amelie Stein
, Douglas M. Fowler
, Kresten Lindorff-Larsen^*
, Rasmus Hartmann-Petersen

^*Corresponding author af dette arbejde

Biomolecular Sciences

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Abstract

Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 ( ~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.

Originalsprog	Engelsk
Artikelnummer	4026
Tidsskrift	Nature Communications
Vol/bind	15
Udgave nummer	1
Antal sider	18
ISSN	2041-1723
DOI	https://doi.org/10.1038/s41467-024-48481-0
Status	Udgivet - 2024

Bibliografisk note

Funding Information:
We acknowledge the use of the FACS, sequencing,\u00A0microscopy, bioinformatics, and computing core facilities at the Biotech Research & Innovation Centre and the Department of Biology, University of Copenhagen. We thank Vibe H. Oestergaard, Michael Lisby, Leonor Rib, Nick Popp, Sofie V. Nielsen, S\u00F8ren Lindemose, and Anne-Marie Lauridsen for technical support. Figures\u00A01A, Fig.\u00A05B, Supplementary Fig.\u00A011C, created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license. The work was funded by the Novo Nordisk Foundation (https://novonordiskfonden.dk) challenge program PRISM (to K.L.-L., A.S., D.M.F. & R.H.-P.), the Novo Nordisk Foundation NNF21OC0071057 (to R.H.P.), the Lundbeck Foundation (https://www.lundbeckfonden.com) R272-2017-452 and R209-2015-3283 (to A.S.), and R249-2017-510 (to L.C.), and the Danish Council for Independent Research (Det Frie Forskningsr\u00E5d) (https://dff.dk) https://doi.org/10.46540/2032-00007B (to R.H.P.).

Publisher Copyright:
© The Author(s) 2024.

Finansiering

We acknowledge the use of the FACS, sequencing,\u00A0microscopy, bioinformatics, and computing core facilities at the Biotech Research & Innovation Centre and the Department of Biology, University of Copenhagen. We thank Vibe H. Oestergaard, Michael Lisby, Leonor Rib, Nick Popp, Sofie V. Nielsen, S\u00F8ren Lindemose, and Anne-Marie Lauridsen for technical support. Figures\u00A01A, Fig.\u00A05B, Supplementary Fig.\u00A011C, created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license. The work was funded by the Novo Nordisk Foundation (https://novonordiskfonden.dk) challenge program PRISM (to K.L.-L., A.S., D.M.F. & R.H.-P.), the Novo Nordisk Foundation NNF21OC0071057 (to R.H.P.), the Lundbeck Foundation (https://www.lundbeckfonden.com) R272-2017-452 and R209-2015-3283 (to A.S.), and R249-2017-510 (to L.C.), and the Danish Council for Independent Research (Det Frie Forskningsr\u00E5d) (https://dff.dk) https://doi.org/10.46540/2032-00007B (to R.H.P.).

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Grønbæk-Thygesen, M., Voutsinos, V., Johansson, K. E., Schulze, T. K., Cagiada, M., Pedersen, L., Clausen, L., Nariya, S., Powell, R. L., Stein, A., Fowler, D. M., Lindorff-Larsen, K., & Hartmann-Petersen, R. (2024). Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants. Nature Communications, 15(1), Artikel 4026. https://doi.org/10.1038/s41467-024-48481-0

Grønbæk-Thygesen, M, Voutsinos, V , Johansson, KE, Schulze, TK, Cagiada, M , Pedersen, L, Clausen, L, Nariya, S, Powell, RL, Stein, A, Fowler, DM, Lindorff-Larsen, K & Hartmann-Petersen, R 2024, 'Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants', Nature Communications, bind 15, nr. 1, 4026. https://doi.org/10.1038/s41467-024-48481-0

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title = "Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants",

abstract = "Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 (\textasciitilde{} 98\%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.",

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T1 - Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants

AU - Grønbæk-Thygesen, Martin

AU - Voutsinos, Vasileios

AU - Johansson, Kristoffer E.

AU - Schulze, Thea K.

AU - Cagiada, Matteo

AU - Pedersen, Line

AU - Clausen, Lene

AU - Nariya, Snehal

AU - Powell, Rachel L.

AU - Stein, Amelie

AU - Fowler, Douglas M.

AU - Lindorff-Larsen, Kresten

AU - Hartmann-Petersen, Rasmus

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N2 - Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 (~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.

AB - Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 (~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.

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