Systems Biology Strategies and Technologies for Understanding Microbes, Plants, and Communities Analytical Strategies for the Study of Plants, Microbes, and Microbial Communities

corresponding to 2,369 unique proteins, covering 65% of the predicted proteins. Quantitative analysis of changes in protein abundance under environmental perturbations has led to the identification of the key proteins required for the maintenance of cellular fitness necessary for cell survival. We also examined the impact of diurnal rhythms on the protein level of Cyanothece 51142. We identified a total of 3,616 proteins with high confidence, which accounts for ~68% of the predicted proteins based on the completely sequenced Cyanothece 51142 genome. About 77% of identi- fied proteins could be assigned to functional categories. Quantitative proteome analysis uncovered that ~3% of the proteins exhibit oscillations in their abundance under alter- nating light-dark conditions. The majority of these cyclic proteins are associated to central intermediary metabolism, photosynthesis as well as biosynthesis of cofactors. Our data also suggest that diurnal changes in activities of several enzymes are mainly controlled by turnover of related cofac- tors and key players but not entire protein complexes. While Cyanothece sp. ATCC 51142 continues to represent a model organism for proteomics investigations, six additional Cyanothece either have finished, or draft genome sequences. This number of strains, having genome sequences, allows for comparison of Cyanothece at the level of the core genome and core proteome. While the core genome predicts the