Dynamic Changes in the Proteome of Synechocystis 6803 in Response to CO2 Limitation Revealed by Quantitative Proteomics

Cyanobacteria developed efficient carbon concentrating mechanisms which significantly improve the photosynthetic performance and survival of cells under limiting CO2 conditions. Dynamic changes of the Synechocystis proteome to CO2 limitation were investigated using shotgun LC-MS/MS approach with isobaric tag for relative and absolute quantification (iTRAQ) technique. Synechocystis cells grown at high (3%) CO2 were shifted to air-level CO2 followed by protein extraction after 6, 24, and 72 h. About 19% of the cyanobacterial proteome was identified and the expression changes were quantified for 17% of theoretical ORFs. For 76 proteins, up- or down-regulation was found to be significant (more than 1.5 or less than 0.7). Major changes were observed in proteins participating in inorganic carbon uptake, CO2 fixation, nitrogen transport and assimilation, as well as in the protection of the photosynthetic machinery from excess of light. Further, a number of hypothetical proteins with unknown functions were discovered. In general, the cells appear to acclimate to low CO2 without a significant stress since the stress-related molecular chaperones were down-regulated and only a minor decline was detected for proteins of phycobilisomes, photosynthetic complexes, and translation machinery. The results of iTRAQ experiment were validated by the Western blot analysis for selected proteins.