Integration Of Proteomic And Transcriptomic Reveals Varying Pattern Of Gene Expression In Synechocystis Sp. PCC6803under Salt Stress And Nitrogen Starvation

“Omics” technology has been widely applied to uncover molecular varying patternand responsive mechanism present in cell under different environment. To uncoverthe regulatory mechanism in response to salt stress and nitrogen starvation incyanobacteria, we investigated the genome-wide correlation between proteinabundance and gene expression in model cyanobacterium Synechocystis sp. PCC6803using complementary quantitative iTRAQ proteomics and RNA-seqtranscriptomics.Proteomic data analysis showed that salt stress had a great impact on ribosomeproteins, also proteins involved in “energy metabolism”,“fatty acid and phospholipidmetabolism” and some regulators have changed significantly. Meanwhile largeamounts hypothetical proteins were up-regulated in salt acclimation period that showsthere are diversity regulation mechanisms in Synechocystis under salt stress. RNA-seqtranscriptomic analysis also showed that genes involved in the same function categoryresponded to salt stress in a phase-dependent pattern. In addition this showedcyanobacyteria cells may employ a combination of cell membrane and envelopemodifcations, and induction of multiple transporters as protection mechanismsagainst salt stress. Our complementary proteome and transcriptome analysis showedthat concordance between protein abundances and their corresponding mRNAs variedsignificantly between various gene-protein pairs, indicating divergent regulation oftranscriptional and post-transcriptional processes during salt stress adaptation inSynechocystis. Notably, a gene encoding CO2uptake related protein (CupA) and threegenes encoding hypothetical proteins were induced at protein levels after long-termhigh salinity stress. Gene knockout and comparative growth analysis demonstratedthat these genes were involved in salt tolerance in Synechocystis.Proteomic analysis indicated phase-dependent down-regulation of proteins relatedto nitrogen transport and assimilation, ribosome complex, glycolysis and TCA cyclesin Synechocystis under nitrogen starvation. Interestingly some regulators andphotosynthetic proteins were up-regulated and this indicated comprehensiveregulatory strategies present in Synechocystis. Transcriptomic analysis also showedthat functional categories such as “photosynthesis”,“protein synthesis” and “nitrogenmetabolism” were significantly altered by nitrogen starvation. Also some transportersand transposase genes were up-regulated at all three stages that showed cells may employ multilevel responsive mechanisms to cope with nitrogen starvation. Twometabolic modules highly correlated with nitrogen starvation were identified by aco-expression network analysis, and were found containing mostly photosyntheticproteins and hypothetic proteins, respectively. The concordance between theabundances of proteins and their corresponding mRNAs for some genes involved inprotein synthesis is high, but for some genes involved in photosyntheis it is reversible.We further confirmed the involvement of the photosynthetic genes in nitrogenstarvation tolerance by constructing and analyzing the psbV gene deletion mutant.This study showed the genome-wide changes of biomacromolecules inSynechocystis under salt stress and nitrogen starvation, and identified several keygenes involved in salt and nitrogen starvation response. It will shed light in modifyingthe cyanobacteria into salt-tolerance and efficiently biofuel-producing single cellfactories.