N⁶-formylation of lysine : a pathological secondary modification of proteins

Abstract

There is increasing recognition that aberrant protein modifications play an important role in the pathophysiology of inflammation and oxidative stress in cells. We recently discovered that N⁶-formylation of lysine is an abundant endogenous modification of histone and chromatin proteins. The high abundance of N⁶-formyllysine in histone proteins and its chemical similarity to the biologically important N⁶- acetyllysine has raised questions about its mechanisms of formation and biological consequences. Using novel ultrasensitive and specific liquid chromatography-coupled tandem mass spectrometry methods (LC-MS/MS) to quantify N⁶-formyllysine lesions in proteins, we aimed to investigate the sources as well as the fate of this abundant endogenous protein modification. We present evidence that endogenous formaldehyde is a major source of N⁶-formyllysine and that this adduct is widespread among proteins in all cellular compartments. We observed in vitro as well as in vivo that formaldehyde exposure leads to a dose-dependent increase in N⁶-formyllysine protein adducts, with the use of isotopically-labeled formaldehyde to dissect endogenous from exogenous formaldehyde as sources of the adduct. Further, other isotope labeling studies revealed that lysine demethylation in histone proteins is not a source of N⁶-formyllysine. With regard to N⁶-formyllysine persistence in cells, our investigation of histone deacetylases revealed that despite chemical similarity of N⁶-formyllysine to N⁶-acetyllysine, the former is refractory to removal by histone deacetylases, which suggests that they will persist throughout the life of individual histone proteins. If not repaired, lysine formylation could accumulate to significant levels. The resemblance of N⁶-formyllysine to N⁶-acetyllysine, together with recent studies that mapped its location on many conserved lysine acetylation and methylation sites along histone proteins, support the idea that this abundant protein modification could interfere with normal regulation of gene expression, potentially leading to an epigenetic mechanism of disruption of cell function.