Abstract
BackgroundProtein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. Staphylococcus aureus is the third most important foodborne pathogen worldwide. Nonetheless, substrates and biological roles of malonylation are still poorly understood in this pathogen.ResultsUsing anti-malonyl-lysine antibody enrichment and high-resolution LC-MS/MS analysis, 440 lysine-malonylated sites were identified in 281 proteins of S. aureus strain. The frequency of valine in position − 1 and alanine at + 2 and + 4 positions was high. KEGG pathway analysis showed that six categories were highly enriched, including ribosome, glycolysis/gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA), valine, leucine, isoleucine degradation, and aminoacyl-tRNA biosynthesis. In total, 31 malonylated sites in S. aureus shared homology with lysine-malonylated sites previously identified in E. coli, indicating malonylated proteins are highly conserved among bacteria. Key rate-limiting enzymes in central carbon metabolic pathways were also found to be malonylated in S. aureus, namely pyruvate kinase (PYK), 6-phosphofructokinase, phosphoglycerate kinase, dihydrolipoyl dehydrogenase, and F1F0-ATP synthase. Notably, malonylation sites were found at or near protein active sites, including KH domain protein, thioredoxin, alanine dehydrogenase (ALD), dihydrolipoyl dehydrogenase (LpdA), pyruvate oxidase CidC, and catabolite control protein A (CcpA), thus suggesting that lysine malonylation may affect the activity of such enzymes.ConclusionsData presented herein expand the current knowledge on lysine malonylation in prokaryotes and indicate the potential roles of protein malonylation in bacterial physiology and metabolism.
Highlights
Protein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria
A total of 440 Kmal sites were identified in 281 proteins of S. aureus (Supplementary Table S1), which were less than the number of malonylated proteins recently identified in E. coli and B. amyloliquefaciens [14], but more than in S. erythraea [15] and Toxoplasma gondii [27]
Lysine malonylation was found on certain proteins of the 50S ribosomal family (L1, L9, L3, L6, L30), and five Kmal sites were identified in heat shock protein 70 (Hsp70)
Summary
A novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. The emerging advancements in high-sensitive mass spectrometry and high-quality pan-anti-acyl-lysine antibody have revealed post-translational modifications (PTMs) in the bacterial gene expression, virulence, and protein (2021) 19:1 bacteria, such as Bacillus subtilis and Geobacillus kaustophilus [6, 7]. Recent studies have described a novel post-translational modification, namely lysine-2-hydroxyisobutyrylation (Khib), on histones of eukaryotic cells with potential involvement in cell transcription and metabolism. It is speculated that both protein acetylation and malonylation are reversibly regulated by lysine acetyltransferases (KATs) and KDACs in mammalian cells. There has been an increasing interest in exploring the regulatory roles of lysine malonylation (Kmal) in several microbial species, such as Escherichia coli [13], Bacillus amyloliquefaciens [14], and Saccharopolyspora erythraea [15]. Little is known about the substrates and biological roles of Kmal in S. aureus
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