The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry

Human Genetics
Matthea R SandersonRachel Wevrick

Abstract

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder caused by the loss of function of a set of imprinted genes on chromosome 15q11-15q13. One of these genes, NDN, encodes necdin, a protein that is important for neuronal differentiation and survival. Loss of Ndn in mice causes defects in the formation and function of the nervous system. Necdin is a member of the melanoma-associated antigen gene (MAGE) protein family. The functions of MAGE proteins depend highly on their interactions with other proteins, and in particular MAGE proteins interact with E3 ubiquitin ligases and deubiquitinases to form MAGE-RING E3 ligase-deubiquitinase complexes. Here, we used proximity-dependent biotin identification (BioID) and mass spectrometry (MS) to determine the network of protein-protein interactions (interactome) of the necdin protein. This process yielded novel as well as known necdin-proximate proteins that cluster into a protein network. Next, we used BioID-MS to define the interactomes of necdin proteins carrying coding variants. Variant necdin proteins had interactomes that were distinct from wildtype necdin. BioID-MS is not only a useful tool to identify protein-protein interactions, but also to analyze the effects of variants...Continue Reading

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Citations

Jul 16, 2021·The Journal of Biological Chemistry·Matthea R SandersonRachel Wevrick
Aug 3, 2021·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Kazuaki Yoshikawa
Nov 12, 2021·Nucleic Acids Research·Noemi Del ToroHenning Hermjakob

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Datasets Mentioned

BETA
PXD018962

Methods Mentioned

BETA
ubiquitination
confocal microscopy
two-hybrid
affinity capture
co-immunoprecipitation
deubiquitination
transfection
exome sequencing
two hybrid
PAR-CLIP

Software Mentioned

Pymol
gnomAD
BioID
Polyphen
SIFT
ClueGo
PANTHER
MAPPIT
CADD
MS

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