Transcriptome Analysis Reveals IsiA-Regulatory Mechanisms Underlying Iron Depletion and Oxidative-Stress Acclimation in Synechocystis sp. Strain PCC 6803

Abstract

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. strain PCC 6803. In this study, the ΔisiA 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 transcriptome sequencing (RNA-seq) analysis of the WT strain and the ΔisiA mutant 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 the WT strain and ΔisiA mutant, 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 coexpression network analysis (WGCNA) demonstrated three functional modules in which the turquoise module was negatively correlated with superoxide dismutase (SOD) activity. Coexpression network analysis identified several hub genes of each module. Cotranscriptional 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 cotranscriptional 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.

A global transcriptional activator involved in the iron homeostasis in cyanobacteria

“…The significantly up-regulated genes have been summarized in Table 1. Consistent with the previous studies (57)(58)(59), isiA (sll0247) and isiB (sll0248), which are considered the marker genes for Fe deficiency, were significantly up-regulated (198.21 times and 64.72 times, respectively) under Fe-deplete conditions, as compared to Fe-replete conditions. Besides, genes related to Fe uptake were also up-regulated to some extent.…”

Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714

“… 15 The mRNA coverage extended beyond the isiABC genes and included the genes, ssl0461 and dfp , encoding a DUF2555 domain-containing protein and the coenzyme A biosynthesis bifunctional protein CoaBC. It has been suggested independently that these five genes belong to this operon, 48 while ssl0461 has recently been renamed to isiD. 49 …”

Deciphering the genetic landscape of enhanced poly-3-hydroxybutyrate production in Synechocystis sp. B12

“…6 ). Its transcription is known to be induced by iron starvation [ 65 ] but also other stress conditions [ 90 , 91 ]. Over the years, extensive research was done on these genes, showing that the isiA product probably protects PSI from excessive excitation, but their function has not been clearly determined [ 66 , 92 – 94 ].…”