Lysine acetylome profiling reveals a dual regulatory role in carbon flux redirection and RNA degradation inhibition in Mycobacterium smegmatis

Introduction Mycobacterium tuberculosis in natural environments and host organisms must adapt to constantly changing growth conditions, and its adaptive mechanism for nutrient metabolism represents one response to complex environments. Reversible post-translational protein modifications regulate central metabolic enzymes in M. tuberculosis , thereby governing its adaptation to varying environmental nutrient availability. Methods In this study, we cultured Mycobacterium smegmatis MC 2 155 using Sauton or Middlebrook 7H9 media and applied liquid chromatography–tandem mass spectrometry (LC–MS/MS) to analyze differences in acetylation-modified proteins. We also performed bioinformatic analysis of the acetylated proteins expressed in the different media. Results LC–MS/MS revealed 182 acetylated proteins and 398 sites exclusively in Sauton-medium-cultured strains; whereas 57 acetylated proteins and 141 sites were identified exclusively in nutrient-rich 7H9-medium-cultured strains. Additionally, 302 proteins and 462 sites were differentially acetylated between the Sauton- and 7H9-medium-cultured samples. Our bioinformatics analysis identified differences in whole-protein acetylation modifications in M. smegmatis MC 2 155 under these two culture conditions, primarily reflected in metabolic pathways, including the citrate cycle (TCA cycle), 2-oxocarboxylic acid metabolism, carbon metabolism, RNA degradation, and tryptophan metabolism. Discussion Under the nutrient-limited conditions of Sauton medium culture, multiple sites within isocitrate dehydrogenase exhibited acetylation, leading to reduced enzyme activity. This effect may redirect a greater proportion of carbon flux towards the glyoxylate pathway. Conversely, in 7H9 medium, acetylation at residues K189 and K331 of isocitrate lyase may diminish enzyme activity, thereby channeling increased carbon flux towards the TCA cycle. Acetylation at 3-hydroxyacyl-CoA dehydrogenase (K370) and tryptophan-tRNA synthetase (K200) may reduce fatty acid and protein synthesis, thereby preventing excessive energy expenditure; acetylation at Oligoribonuclease K153 likely diminishes enzyme activity, thereby allowing M. smegmatis to adapt to nutrient limitation by accumulating more c-di-AMP.