Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803

Abstract

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.

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Chlorosis as a Developmental Program in Cyanobacteria: The Proteomic Fundament for Survival and Awakening

“…Today, gel-free sample preparations together with stable isotope labeling strategies set the standard for studying dynamic responses of the proteome and its post-translational modifications on global levels. Following this, the application of isobaric tags for relative and absolute quantitation (iTRAQ) represents the most common labeling strategy in cyanobacterial proteome studies (40), and references in (41). By applying dimethylation labeling as an alternative quantitation strategy (26) …”

Dynamics of Photosynthesis in a Glycogen-Deficient glgC Mutant of Synechococcus sp. Strain PCC 7002

“…When nitrogen availability is limiting for cell growth and proliferation, a defined sequence of stress responses is deployed in most cyanobacteria. The immediate response is to increase the expression of genes associated with nitrogen uptake and assimilation (1)(2)(3)(4). This is followed within hours by the cessation of growth and the mobilization of internal nitrogen stores through the degradation of the light-harvesting phycobilisomes, which contain nitrogen-rich phycobiliproteins and phycocyanin (5-7).…”

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