Characterization of Protein Lysine Propionylation in Escherichia coli: Global Profiling, Dynamic Change, and Enzymatic Regulation

Propionylation at protein lysine residue is characterized to be present in both eukaryotic and prokaryotic species. However, the majority of lysine propionylation substrates still remain largely unknown. Using affinity enrichment and mass-spectrometric-based proteomics, we identified 1467 lysine propionylation sites in 603 proteins in E. coli. Quantitative propionylome analysis further revealed that global lysine propionylation level was drastically increased in response to propionate treatment, a carbon source for many microorganisms and also a common food preservative. The results indicated that propionylation may play a regulatory role in propionate metabolism and propionyl-CoA degradation. In contrast with lysine acetylation and succinylation, our results revealed that the lysine propionylation level of substrates showed an obvious decrease in response to high glucose, suggesting a distinct role of propionylation in bacteria carbohydrate metabolism. This study further showed that bacterial lysine deacetylase CobB and acetyltransferase PatZ could also have regulatory activities for lysine propionylation in E. coli. Our quantitative propionylation substrate analysis between cobB wild-type and cobB knockout strain led to the identification of 13 CobB potentially regulated propionylation sites. Together, these findings revealed the broad propionylation substrates in E. coli and suggested new roles of lysine propionylation in bacterial physiology.