Transcriptome analysis reveals IsiA regulatory mechanisms underlying iron depletion and oxidative stress acclimation in Synechocystis sp. PCC 6803.

Microorganisms in nature are commonly exposed to various stresses in parallel. The isiA gene encodes an iron stress-induced chlorophyll-binding protein which is significantly induced under iron starvation and oxidative stress. Acclimation of oxidative stress and iron deficiency was investigated using a regulatory mutant of the Synechocystis sp. PCC 6803. In this study, the DeltaisiA mutant grew more slowly in oxidative stress and iron depletion conditions compared to the wild type (WT) counterpart under the same conditions. Thus, we performed RNA-seq analysis of WT and DeltaisiA under double stress conditions to obtain a comprehensive view of isiA-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed significant differences between WT and DeltaisiA, mainly related to photosynthesis and the iron-sulfur cluster. The deletion of isiA affects the expression of various genes that are involved in cellular processes and structures, such as photosynthesis, phycobilisome and the proton-transporting ATPase complex. Weighted gene co-expression network analysis (WGCNA) demonstrated three functional modules, in which the turquoise module was negatively correlated with superoxide dismutase activity. Co-expression network analysis identified several hub genes of each module. Co-transcriptional PCR and reads coverage using the Integrative Genomics Viewer demonstrated that isiA, isiB, isiC, ssl0461, and dfp belonged to the isi operon. Three sRNAs related to oxidative stress were identified. This study enriches our knowledge of IsiA regulatory mechanisms under iron deficiency and oxidative stress.IMPORTANCE This study analyzed the impact of isiA deletion on the transcriptomic profile of Synechocystis The isiA gene encodes an iron stress-induced chlorophyll-binding protein, which is significantly induced under iron starvation. The deletion of isiA affects the expression of various genes that are involved in photosynthesis and ABC transporters. WGCNA revealed three functional modules in which the blue module was correlated with oxidative stress. We further demonstrated that the isi operon contained the following five genes: isiA, isiB, isiC, ssl0461, and dfp by co-transcriptional PCR. Three sRNAs were identified that were related to oxidative stress. This study enhances our knowledge of IsiA regulatory mechanisms under iron deficiency and oxidative stress.