Proteogenomic has been applied to the identification of previously unidentified genes and the correction and validation of predicted genes in various organisms. The same experimental proteomic datasets are also useful in identifying posttranslational modifications (PTMs) on a proteome wide level. Synechococcus sp. PCC 7002 is a unicellular, marine cyanobacterium and a model organism for studying photosynthetic carbon fixation and the development of biofuels. Because a large portion (1,210 out of 3,186) of protein-coding genes are annotated as hypothetical proteins, a comprehensive analysis is needed to provide experimental support for the genome annotation so as to facilitate systems-level analysis.   

The research groups led by Dr. GE Feng and Dr. LI Tao at Institute of Hydrobiology (IHB), Chinese Academy of Sciences (CAS) performed systematic investigation to characterize the proteogenomic analysis of Synechococcus sp. PCC 7002. By using MS data and Synechococcus sp. PCC 7002 as a test case, researchers developed a proteogenomic approach to carry out genome annotation and whole-proteome analysis of PTMs in prokaryotes.    

In their study, a total of 2,938 Synechococcus proteins (>92% coverage) with high confidence were identified by using the whole-proteome analysis. The results exceed those obtained in most published cases. Researchers further integrated the proteomic data with the transcriptome determined by RNA-Seq to facilitate the validation of the proteomic results. The results showed that 118 previously unidentified protein-coding regions were discovered and the annotation of 38 existing gene models was revised.       

More importantly, researchers for the first time identified 23 different PTM types on 6,704 unique peptides from 2,230 Synechococcus proteins that may play important roles in cellular functions, based on the proteomic data. The entire proteogenomics pipeline is also applicable to any sequenced prokaryotic organism.   

Relevant results were published in Proceedings of the National Academy of Sciences of the United States of America (PNAS) entitled “Proteogenomic Analysis and Global Discovery of Post-Translational Modifications in Prokaryotes”.   

Overview of the PTM events involved in the photosynthesis process (Image by Prof. GE feng’s group)