Sequential adaptation to environmental stress needs complex regulation at different cellular levels in cyanobacteria. To uncover the regulatory mechanism in response to
nitrogen starvation, we investigated the genome-wide correlation between
protein abundance and gene expression in a model cyanobacterium Synechocystis sp. PCC 6803 using complementary quantitative iTRAQ proteomics and
RNA-seq transcriptomics. Consistent with the cell growth inhibition, proteomic analysis indicated phase-dependent down-regulation of
proteins related to
nitrogen metabolism, ribosome complexes, glycolysis pathway and
tricarboxylic acid (TCA) cycles by
nitrogen starvation. Transcriptomic analysis also showed that genes related to "Photosynthesis", "
Protein synthesis" and "Energy metabolism" were significantly down-regulated by
nitrogen starvation. Interestingly, the concordance between
protein abundances and their corresponding mRNAs exhibited a functional categories-dependent pattern, with some categories, such as "
Protein synthesis" and "Energy metabolism", having a relatively high correlation, while others even with numerous discordant changes in
protein-
mRNA pairs, indicated divergent regulation of transcriptional and post-transcriptional processes. In particular, an increased abundance of
proteins related to "Photosynthesis" upon
nitrogen starvation was found to be reversely correlated with the down-regulation of their corresponding mRNAs. In addition, two metabolic modules highly correlated with
nitrogen starvation were identified by a co-expression network analysis, and were found to contain mostly photosynthetic
proteins and hypothetical
proteins, respectively. We further confirmed the involvement of the photosynthetic genes in
nitrogen starvation tolerance by constructing and analyzing the psbV gene deletion mutant.