Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria

Abstract

As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 50% of the total primary production on Earth. Previously, we reported the lysine acetylome in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Here we performed the first proteomic survey of lysine malonylation in Synechocystis using highly accurate tandem mass spectrometry in combination with affinity purification. We identified 598 lysine malonylation sites on 339 proteins with high confidence in total. A bioinformatic analysis suggested that these malonylated proteins may play various functions and were distributed in diverse subcellular compartments. Among them, many malonylated proteins were involved in cellular metabolism. The functional significance of lysine malonylation in the metabolic enzyme activity of phosphoglycerate kinase (PGK) was determined by site-specific mutagenesis and biochemical studies. Interestingly, 27 proteins involved in photosynthesis were found to be malonylated for the first time, suggesting that lysine malonylation may be involved in photosynthesis. Thus our results provide the first lysine malonylome in a photosynthetic organism and suggest a previously unexplored role of lysine malonylation in the regulation of metabolic processes and photosynthesis in Synechocystis as well as in other photosynthetic organisms.

Global Proteomic Analysis of Lysine Malonylation in Toxoplasma gondii

“…Overall, 506 Kmal sites across 326 proteins were detected. The number of Kmal proteins in T. gondii was higher than that reported in common wheat, S. erythraea (Xu et al, 2016;Liu et al, 2018), but was lower than that detected in E. coli (Qian et al, 2016), rhizobacterium Bacillus amyloliquefaciens FZB42 (Fan et al, 2017) and mammals (Colak et al, 2015), however was close to the number of malonylated proteins identified in Cyanobacteria (Ma et al, 2017). As shown in Figure 1B, a total of 326 proteins were modified/malonylated at more than two lysine residues.…”

“…Lysine malonylation was firstly observed in mammalian cells and bacterial cells (Lin et al, 2012). Since then, there have been growing interests in exploring the regulatory roles of Kmal in various microbial species, such as Escherichia coli (Qian et al, 2016), Cyanobacteria (Ma et al, 2017), and Saccharopolyspora erythraea (Xu et al, 2016). Although Kmal can regulate many crucial and diverse cellular processes (He et al, 2012), its existence and function in T. gondii remain unknown.…”

Systematic analysis of the lysine malonylome in common wheat

“…In recent years, as a result of advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS), a large number of lysine-acetylated proteins have been identified [ 2 ]. However, compared to these acetylation profiles, only a few organisms have been studied with respect to lysine malonylation, including Bacillus amyloliquefaciens [ 4 ], Escherichia coli [ 5 ], Saccharopolyspora erythraea [ 10 ], cyanobacteria ( Synechocystis ) [ 11 ], rice [ 12 ], HeLa cells [ 9 ], and mice [ 7 , 13 ].…”

Protein lysine de-2-hydroxyisobutyrylation by CobB in prokaryotes

“…Ksucc regulated the activity of acetyl-coenzyme A synthetase (Acs) in Mycobacterium tuberculosis ( 33 ). Lysine malonylation was involved in metabolism in E. coli and photosynthesis in Cyanobacteria ( 9 , 34 ) . Given the important biological significance of the above-listed lysine PTMs in prokaryotes, it is conceivable to anticipate that Khib also likely regulates the protein function and thereby modulates the physiological processes in prokaryotes.…”