TY  - JOUR
AU  - Hogl, Sebastian
AU  - van Bebber, Frauke
AU  - Dislich, Bastian
AU  - Kuhn, Peer-Hendrik
AU  - Haass, Christian
AU  - Schmid, Bettina
AU  - Lichtenthaler, Stefan F
TI  - Label-free quantitative analysis of the membrane proteome of Bace1 protease knock-out zebrafish brains.
JO  - Practical proteomics
VL  - 13
IS  - 9
SN  - 1615-9853
CY  - Weinheim
PB  - Wiley VCH69157
M1  - DZNE-2020-03209
SP  - 1519-1527
PY  - 2013
AB  - The aspartyl protease BACE1 cleaves neuregulin 1 and is involved in myelination and is a candidate drug target for Alzheimer's disease, where it acts as the β-secretase cleaving the amyloid precursor protein. However, little is known about other substrates in vivo. Here, we provide a proteomic workflow for BACE1 substrate identification from whole brains, combining filter-aided sample preparation, strong-anion exchange fractionation, and label-free quantification. We used bace1-deficient zebrafish and quantified differences in protein levels between wild-type and bace1 -/- zebrafish brains. Over 4500 proteins were identified with at least two unique peptides and quantified in both wild-type and bace1 -/- zebrafish brains. The majority of zebrafish membrane proteins did not show altered protein levels, indicating that Bace1 has a restricted substrate specificity. Twenty-four membrane proteins accumulated in the bace1 -/- brains and thus represent candidate Bace1 substrates. They include several known BACE1 substrates, such as the zebrafish homologs of amyloid precursor protein and the cell adhesion protein L1, which validate the proteomic workflow. Additionally, several candidate substrates with a function in neurite outgrowth and axon guidance, such as plexin A3 and glypican-1 were identified, pointing to a function of Bace1 in neurodevelopment. Taken together, our study provides the first proteomic analysis of knock-out zebrafish tissue and demonstrates that combining gene knock-out models in zebrafish with quantitative proteomics is a powerful approach to address biomedical questions.
KW  - Amyloid beta-Protein Precursor: genetics
KW  - Amyloid beta-Protein Precursor: metabolism
KW  - Animals
KW  - Animals, Genetically Modified
KW  - Aspartic Acid Endopeptidases: genetics
KW  - Aspartic Acid Endopeptidases: metabolism
KW  - Brain: metabolism
KW  - Chemical Fractionation: methods
KW  - Glypicans: metabolism
KW  - Humans
KW  - Membrane Proteins: analysis
KW  - Membrane Proteins: genetics
KW  - Membrane Proteins: metabolism
KW  - Proteome: genetics
KW  - Proteome: metabolism
KW  - Receptors, Cell Surface: metabolism
KW  - Tandem Mass Spectrometry
KW  - Workflow
KW  - Zebrafish: genetics
KW  - Zebrafish: metabolism
KW  - Zebrafish Proteins: analysis
KW  - Zebrafish Proteins: genetics
KW  - Zebrafish Proteins: metabolism
KW  - Amyloid beta-Protein Precursor (NLM Chemicals)
KW  - Glypicans (NLM Chemicals)
KW  - Membrane Proteins (NLM Chemicals)
KW  - Plxna3 protein, zebrafish (NLM Chemicals)
KW  - Proteome (NLM Chemicals)
KW  - Receptors, Cell Surface (NLM Chemicals)
KW  - Zebrafish Proteins (NLM Chemicals)
KW  - Aspartic Acid Endopeptidases (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:23457027
DO  - DOI:10.1002/pmic.201200582
UR  - https://pub.dzne.de/record/136887
ER  -