PXD038842

PXD038842 is an original dataset announced via ProteomeXchange.

Title	Calpain activity is regulated by a KCTD7–cullin 3 complex via non-degradative ubiquitination
Description	Calpains are a class of non-lysosomal cysteine proteases that exert their regulatory functions via limited proteolysis of their substrates. Similar to the lysosomal and proteasomal systems, calpain dysregulation is implicated in the pathogenesis of neurodegenerative disease and cancer. Despite intensive efforts placed on the identification of mechanisms that regulate calpains, however, global regulators of calpains activity have remained elusive. Here we show that calpains are regulated by KCTD7, a cytosolic protein of previously uncharacterized function whose pathogenic mutations result in epilepsy, progressive ataxia, and severe neurocognitive deterioration. We show that KCTD7 works in complex with Cullin-3 and Rbx1 to execute atypical, non-degradative ubiquitination of calpains at specific sites (K398 of calpain 1, and K280 and K674 of calpain 2). Experiments based on single-lysine mutants of ubiquitin determined that KCTD7 mediates ubiquitination of calpain 1 via K6-, K27-, K29-, and K63-linked chains, whereas it uses K6- mediated ubiquitination to modify calpain 2. Loss of KCTD7-mediated ubiquitination of calpains led to calpain hyperactivation, aberrant cleavage of downstream targets, and caspase-3 activation. CRISPR/Cas9-mediated knockout of Kctd7 in mice phenotypically recapitulated human KCTD7 deficiency and resulted in calpain hyperactivation, behavioral impairments, and neurodegeneration. These phenotypes were largely prevented by pharmacological inhibition of calpains, thus demonstrating a major role of calpain dysregulation in KCTD7-associated disease. Finally, we determined that Cullin-3–KCTD7 mediates ubiquitination of all ubiquitous calpains. These results unveil a global mechanism and potential target to restrain calpain activity in human disease and shed light on the molecular pathogenesis of KCTD7-associated disease.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:46:33.613.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Byoung-Kyu Cho
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-14 21:55:50	ID requested
1	2023-05-10 13:23:44	announced
⏵ 2	2023-11-14 08:46:36	announced	2023-11-14: Updated project metadata.

Sharma J, Mulherkar S, Chen UI, Xiong Y, Bajaj L, Cho BK, Goo YA, Leung HE, Tolias KF, Sardiello M, Calpain activity is negatively regulated by a KCTD7-Cullin-3 complex via non-degradative ubiquitination. Cell Discov, 9(1):32(2023) [pubmed]

submitter keyword: Human, PASEF, Calpain

Young Ah Goo
contact affiliation	Mass Spectrometry Technology Access Center at the McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
contact email	ygoo@wustl.edu
lab head
Byoung-Kyu Cho
contact affiliation	Washington University in St. Louis
contact email	byoung-kyu@wustl.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/05/PXD038842

PRIDE project URI

• PRIDE
  1. PXD038842
     1. Label: PRIDE project
     2. Name: Calpain activity is regulated by a KCTD7–cullin 3 complex via non-degradative ubiquitination