Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn’s disease

Abstract

Lysine acetylation (Kac), an abundant post-translational modification (PTM) in prokaryotes, regulates various microbial metabolic pathways. However, no studies have examined protein Kac at the microbiome level, and it remains unknown whether Kac level is altered in patient microbiomes. Herein, we use a peptide immuno-affinity enrichment strategy coupled with mass spectrometry to characterize protein Kac in the microbiome, which successfully identifies 35,200 Kac peptides from microbial or human proteins in gut microbiome samples. We demonstrate that Kac is widely distributed in gut microbial metabolic pathways, including anaerobic fermentation to generate short-chain fatty acids. Applying to the analyses of microbiomes of patients with Crohn's disease identifies 52 host and 136 microbial protein Kac sites that are differentially abundant in disease versus controls. This microbiome-wide acetylomic approach aids in advancing functional microbiome research.

Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

“…Lysine acetylation might be an important factor that affects obesity by regulating energy homeostasis [55]. Zhang et al [56] reported that most acetylphosphate-generating enzymes are derived from Firmicutes that have higher lysine acetylome-to-metaproteome ratios than other bacterial phyla. Threonine levels were higher in the serum from the control group.…”

Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics

“…The study of PTMs using proteomics typically requires an enrichment or depletion step, and a limited number of studies have profiled PTMs in the human gut environment from intestinal biopsies or stool samples. For example, a pioneering study has used a peptide immuno-affinity enrichment strategy to profile an abundant PTM in prokaryotes, lysine acetylation, in the gut microbiome [92] . The study identified lysine-acetylated sites on both host and microbial proteins that were differentially abundant in patients with Crohn's disease and healthy controls.…”

Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

“…This microbiomewide acetylome approach claried that aberrant Kac protein changes in the microbiome might be related to CD development. 21 By using titanium dioxide (TiO 2 ) for the efficient enrichment of phosphopeptides, He et al used MS to analyze and quantitate the phosphoproteomic changes in a HBx-transgenic mouse model of hepatocellular carcinoma (HCC), leading to the proling of 22 539 phosphorylation sites in 5431 proteins, and revealing elevated kinase activities of Src family kinases (SFKs), protein kinase C (PKCs), mitogen-activated protein kinases (MAPKs), and Rho-associated kinases (e.g., ROCK2) in HCC. 22 By identifying the main kinases in various tumor tissues and the corresponding para-tissues, kinase activity can be targeted and extended to personalized medicine, and appropriate drug combinations can be used to benet individual patients.…”