Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes

Abstract

We describe an integrated workflow for proteogenomic analysis and global profiling of posttranslational modifications (PTMs) in prokaryotes and use the model cyanobacterium Synechococcus sp. PCC 7002 (hereafter Synechococcus 7002) as a test case. We found more than 20 different kinds of PTMs, and a holistic view of PTM events in this organism grown under different conditions was obtained without specific enrichment strategies. Among 3,186 predicted protein-coding genes, 2,938 gene products (>92%) were identified. We also identified 118 previously unidentified proteins and corrected 38 predicted gene-coding regions in the Synechococcus 7002 genome. This systematic analysis not only provides comprehensive information on protein profiles and the diversity of PTMs in Synechococcus 7002 but also provides some insights into photosynthetic pathways in cyanobacteria. The entire proteogenomics pipeline is applicable to any sequenced prokaryotic organism, and we suggest that it should become a standard part of genome annotation projects.proteogenomics | post-translational modifications | cyanobacteria | photosynthesis | Synechococcus

Proteomic analysis of post translational modifications in cyanobacteria

“…Moreover, the same experimental proteomic datasets are also useful in identifying PTMs on a proteome wide level [100,101]. Our group developed a proteogenomic approach to carry out genome annotation and whole-proteome analysis of PTMs in prokaryotes by employing high resolution and high accuracy MS data, and we used this approach to study the global PTMs in the model cyanobacterium Synechococcus 7002 [27]. We pooled Synechococcus cells that grown to different phases (exponential phase, stationary phase) under different stresses (iron deficiency, phosphate deficiency, nitrogen deficiency, and A5 deficiency) before protein extraction.…”

“…So the development of efficient and specific enriching approaches for more types of PTMs remains an urgent work, especially for those PTMs have already been identified by global PTMs screening [27]. In the future, it is imaginable that rapidly improved MS technology could allow the identify of PTM-bearing peptides without prior enrichment.…”

“…In the future, it is imaginable that rapidly improved MS technology could allow the identify of PTM-bearing peptides without prior enrichment. The novel strategy for whole-proteome analysis of PTMs in prokaryote developed by our group already opens the way for the global profiling of PTMs in any other sequenced cyanobacterium or prokaryote without specific enrichment [27]. This would make it possible to comprehensive analysis of different PTMs simultaneously and will be a hot spot in future PTM study.…”

“…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.…”