Acetylome Analysis Reveals the Involvement of Lysine Acetylation in Photosynthesis and Carbon Metabolism in the Model Cyanobacterium Synechocystis sp. PCC 6803

Abstract

Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC−MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.

Proteomic analysis of post translational modifications in cyanobacteria

“…PTM events are also reported to exist in photosynthesis apparatus, including photosystem I [35], photosystem II [36], phycobiliproteins [37,38] and cytochrome b6f complex [39]. Classes of PTMs that have already been reported in cyanobacteria include protein splicing [40][41][42][43][44], phosphorylation [22,[24][25][26], acetylation [23], methylation [11], biotinylation [45][46][47], persulfide [48][49][50], ADP-ribosylation [51], glutathionylation [28], prenylation [52], palmitoylation [32], Histidine Hydroxyl Modification [53] and carboxylterminalprocessing [54,55].…”

“…Then this approach has become a standard procedure in bacterial acetylome analyses [79][80][81][82]. Our group provides the first extensive data on lysine acetylation in cyanobacterium Synechocystis 6803 based on this method, which is also the first study of protein lysine acetylation reported in cyanobacteria [23]. Synechocystis 6803 cells exposed to three different stresses (nitrogen-deficient, heterotrophic condition, and high light condition) were harvested and pooled before protein extraction.…”

“…The interplay between two PTMs was studied in both prokaryote and eukaryote [127,128], which suggested that cross-talk between different PTMs was extensive and remained to be discovered. The large-scale PTM proteomics data revealed that PTM cross-talk may also exist in cyanobacteria since many proteins were discovered to have more than one PTM [23,25,27]. Histone PTM cross-talk networks have been systematically discovered in Saccharomyces cerevisiae [129].…”

“…Therefore, systematic investigation of PTMs could contribute to the holistic and comprehensive description of protein species and to elucidate potential biological roles of each protein species in cyanobacteria. Although the proteomics studies of PTMs carried out in cyanobacteria were limited [22][23][24][25][26][27][28], these studies provided clues to elucidate the complex signal transduction network and the biochemical processes that contribute to their ecological success. Here we provide a snapshot of the PTM proteomic studies, including the current status, the progresses have been made, and the main challenges.…”

Advances in proteomics for production strain analysis

“…Despite the enrichment strategies required for identifying these low abundance features, it is possible to assess PTMs on a systems level . Three pioneering studies have been conducted in the last two years, cataloguing system-wide PTM responses in Synechocystis and demonstrating their role in regulation of photosynthesis and central metabolic pathways [19,30,31].…”