Integrated proteomic and metabolomic characterization of a novel two-component response regulator Slr1909 involved in acid tolerance in Synechocystis sp. PCC 6803.

Low pH is recognized as a major environmental stress to cyanobacteria that play a pivotal role in the global carbon cycling. Although several cellular mechanisms in response to acid stress were proposed, the regulatory mechanism related to acid stress has not been fully elucidated. By screening gene knockout mutants for all 44 putative response regulator (RR)-encoding genes of Synechocystis sp. PCC 6803 grown under acid stress, we found that a mutant of slr1909 (previously known as rre9), which encoded an orphan RR, grew poorly in BG11 medium at pH6.2-6.5 when compared with the wild type. Using a quantitative iTRAQ-LC-MS/MS proteomics approach coupled with GC-MS based metabolomics and quantitative real-time reverse transcription-PCR (RT-qPCR), we further determined the possible acid response network mediated by Slr1909. The results showed that the signal transduction pathway mediated by Slr1909 may be independent from that mediated by SphS-SphR previously discovered, as none of the proteins and their coding genes regulated by SphS-SphR were differentially regulated in the ∆slr1909 mutant grown under acid stress. Only 24 and 10 proteins were up- and down-regulated in the ∆slr1909 mutant when compared with the wild type under acid stress condition, respectively. Notably, three proteins, Slr1259, Slr1260 and Slr1261 whose encoding genes seem located in an operon, were down-regulated upon the knockout of the slr1909 gene, suggesting their roles in acid tolerance. In addition, metabolomic analysis allowed identification of a dozen metabolites important for the discrimination of the ∆slr1909 mutant and the wild type under acid stress, including several monosaccharide and fatty acids. The study provided a proteomic and metabolomic characterization of the acid-response network mediated by an orphan regulator Slr1909 in Synechocystis. BIOLOGICAL SIGNIFICANCE: Low pH is recognized as a major environmental stress to cyanobacteria that play a pivotal role in the global carbon cycling. Although several cellular mechanisms in response to acid stress were proposed, the regulatory mechanism related to acid stress is still far from being fully elucidated. In a previous work, one two-component signal transduction system SphS-SphR was found involved in acid stress in Synechocystis. In this work, by screening gene knockout mutants for all 44 putative response regulator (RR)-encoding genes grown under acid stress, we found that a novel two-component response regulator Slr1909 was also involved in acid tolerance in Synechocystis. Moreover, the analysis showed that the signal transduction pathway mediated by Slr1909 may be independent from that mediated by SphS-SphR. Using a quantitative iTRAQ-LC-MS/MS proteomics and coupled with GC-MS based metabolomics and quantitative real-time reverse transcription-PCR (RT-qPCR), we further determined the possible acid response network mediated by Slr1909. The study provided a proteomic and metabolomic characterization of a novel acid-response network mediated by an orphan regulator Slr1909 in Synechocystis, and valuable new insight for better understanding of stress responses to acidity in cyanobacteria.