Positional proteomics reveals differences in N‐terminal proteoform stability
Daria Gawron, Elvis Ndah, Kris Gevaert, Petra Van Damme
Author Affiliations
Daria Gawron 1,2, Elvis Ndah 1,2,3, Kris Gevaert 1,2 and Petra Van Damme*, 1, 2
1Department of Medical Protein Research, VIB, Ghent, Belgium
2Department of Biochemistry, Ghent University, Ghent, Belgium
3Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
↵*Corresponding author. Tel: +32 92649279; Fax: +32 92649496; E‐mail: petra.vandamme@vib-ugent.be
View Abstract
DOI 10.15252/msb.20156662 | Published online 18.02.2016
Molecular Systems Biology (2016) 12: 858
Abstract
To understand the impact of alternative translation initiation on a proteome, we performed a proteome‐wide study on protein turnover using positional proteomics and ribosome profiling to distinguish between N‐terminal proteoforms of individual genes. By combining pulsed SILAC with N‐terminal COFRADIC, we monitored the stability of 1,941 human N‐terminal proteoforms, including 147 N‐terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine. N‐terminally truncated proteoforms were less abundant than canonical proteoforms and often displayed altered stabilities, likely attributed to individual protein characteristics, including intrinsic disorder, but independent of N‐terminal amino acid identity or truncation length. We discovered that the removal of initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms, while susceptibility for N‐terminal acetylation did not seem to influence protein turnover rates. Taken together, our findings reveal differences in protein stability between N‐terminal proteoforms and point to a role for alternative translation initiation and co‐translational initiator methionine removal, next to alternative splicing, in the overall regulation of proteome homeostasis.
Synopsis
Alternative translation initiation and co‐translational initiator methionine removal contribute to the increased complexity of the human proteome by generating multiple N‐terminal proteoforms that can show differences in cellular stability.
Complementary use of positional proteomics and ribosome profiling aids in the characterization of the human N‐terminome.
N‐terminally truncated proteoforms are less abundant than canonical proteoforms, but may display altered stabilities.
The removal of the initiator methionine by methionine aminopeptidases generally reduces the stability of processed proteoforms.
Alternative Translation Initiation Initiator Methionine Processing N‐Terminal Proteoform Protein Stability Ribosome Profiling
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