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Protein Cysteines Map to Functional Networks According to Steady-state Level of Oxidation

Young-Mi Go, Duc M. Duong, Junmin Peng and Dean P. Jones

The cysteine (Cys) proteome serves critical roles in protein structure, function and regulation, and includes key targets in oxidative mechanisms of disease. Thioredoxins maintain Cys residues in thiol forms, and previous research shows that the redox potential of thioredoxin in mitochondria and nuclei is more reduced than cytoplasm, suggesting that proteins in these compartments may have different steady-state oxidation. This study measured fractional oxidation of 641 peptidyl Cys residues from 333 proteins in HT29 cells by mass spectrometry. Average oxidation of cytoplasmic, nuclear and mitochondrial proteins was similar (15.8, 15.5, 14%, respectively). Pathway analysis showed that more reduced cytoplasmic Cys were in proteins associated with the cytoskeleton, more reduced nuclear Cys with Ran signaling and RNA post-transcriptional modification, and more reduced mitochondrial Cys with energy metabolism, cell growth and cell proliferation. More oxidized cytoplasmic Cys included associations with PI3/Akt, Myc-mediated apoptosis and 14-3-3-mediated signaling. Weaker associations of oxidized nuclear and mitochondrial Cys occurred with granzyme B signaling and intermediary metabolism, respectively. Thus, steady-state peptidyl Cys oxidation is associated with functional pathways rather than simply with organellar distribution. This suggests that oxidative mechanisms of disease could target functional pathways or networks rather than individual proteins or subcellular compartments.