Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece.

Abstract

Members of the cyanobacterial genus Cyanothece exhibit considerable variation in physiological and biochemical characteristics. The comparative assessment of the genomes and the proteomes has the potential to provide insights on differences among Cyanothece strains. By applying Sequedex, an annotation-independent method for ascribing gene functions, we confirmed significant species-specific differences of functional genes in different Cyanothece strains, particularly in Cyanothece PCC7425. Using a shotgun proteomics approach based on prefractionation and tandem mass spectrometry, we detected ∼28-48% of the theoretical Cyanothece proteome, depending on the strain. The expression of a total of 642 orthologous proteins was observed in all five Cyanothece strains. These shared orthologous proteins showed considerable correlations in their abundances across different Cyanothece strains. Functional classification indicated that the majority of proteins involved in central metabolic functions such as amino acid, carbohydrate, protein, and RNA metabolism, photosynthesis, respiration, and stress responses were observed to a greater extent in the core proteome, whereas proteins involved in membrane transport, iron acquisition, regulatory functions, flagellar motility, and chemotaxis were observed to a greater extent in the unique proteome. Considerable differences were evident across different Cyanothece strains. Notably, the analysis of Cyanothece PCC7425, which showed the highest number of unique proteins (682), provided direct evidence of evolutionary differences in this strain. We conclude that Cyanothece PCC7425 diverged significantly from the other Cyanothece strains or evolved from a different lineage.