N-terminal COFRADIC on cytosolic proteins of HEK293T cells - UniProt search

ABSTRACT: N-terminal proteoforms stem from the same gene but differ at their N-terminus, and most of these are found to be truncated, though some are N-terminally extended caused by ribosomes starting translation from codons in the annotated 5’UTR, and/or carry modified N-termini different from those of the canonical protein. Biological functions of N-terminal proteoforms are emerging, however, it remains unknown to what extend N-terminal proteoforms further expand the functional complexity. To address this in a more global manner, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. For this, we first generated an in-depth catalogue of N-terminal proteoforms in the cytosol of HEK293T cells. As the N-terminal region is the part that differs between the proteoforms, we performed N-terminal enrichment via COFRADIC on the cytosol of HEK293T cells. We combined three digestion enzymes to increase the depth of analysis. Data was searched twise: once with a regular UniProt database and a second time with a custom database (combining the sequences of UniProt proteins, UniProt isoforms and publicly available Ribo-seq data). Data was filtered and this resulted in a catalogue of 3,306 N-termini from which 20 pairs of canonical protein and N-terminal proteoform(s) were selected for interactome analysis. Our analysis of these pairs revealed that the overlap of the interactomes for both proteoforms is in general high, showing their functional relation. However, for all pairs tested we do report differences as well. We show that N-terminal proteoforms can be engaged in new/different interactions and as well can lose several interactions compared to the canonical protein.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Annelies Bogaert  

LAB HEAD: Kris Gevaert

PROVIDER: PXD039392 | Pride | 2023-06-08

REPOSITORIES: Pride