Ubiquitin is a carbon dioxide–binding protein

The identification of CO(2)-binding proteins is crucial to understanding CO(2)-regulated molecular processes. CO(2) can form a reversible posttranslational modification through carbamylation of neutral N-terminal α-amino or lysine ε-amino groups. We have previously developed triethyloxonium (TEO) ion as a chemical proteomics tool for covalent trapping of carbamates, and here, we deploy TEO to identify ubiquitin as a mammalian CO(2)-binding protein. We use (13)C-NMR spectroscopy to demonstrate that CO(2) forms carbamates on the ubiquitin N terminus and ε-amino groups of lysines 6, 33, 48, and 63. We demonstrate that biologically relevant pCO(2) levels reduce ubiquitin conjugation at lysine-48 and down-regulate ubiquitin-dependent NF-κB pathway activation. Our results show that ubiquitin is a CO(2)-binding protein and demonstrates carbamylation as a viable mechanism by which mammalian cells can respond to fluctuating pCO(2).