Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteria

Oxygenic photosynthesis contains multiple proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Accordingly, its composition is heavily re-organized when iron becomes limiting as a nutrient factor, a situation that is frequently encountered in nature. However, the molecular mechanisms controlling the reorganization of the photosynthetic system upon iron deprivation have remained enigmatic. Here we show that the small regulatory RNA IsaR1 (Iron-stress activated RNA 1) plays a pivotal role in acclimation to low iron conditions. The transcription factor Fur cannot facilitate iron starvation dependent repression of it’s targets because it requires iron for DNA binding. We show that the Fur repressed sRNA IsaR1 fulfills this repressor function in iron homeostasis. The IsaR1 regulon consists of at least 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, the detoxification of anion radicals, citrate cycle, and in tetrapyrrole biogenesis. We demonstrate that IsaR1 is absolutely necessary to maintain physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (i) directly, via posttranscriptional repression of gene expression and indirectly, (ii) via the suppression of Fe/S cluster co-factor and (iii) pigment biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a riboregulator of central importance. These findings provide a new perspective for studies of the regulation of iron homeostasis in photosynthetic organisms. We monitored gene expression of a Synechocystis PCC6083 IsaR1 deletion strain (ΔIsaR1) prior to iron depletion (0h) and 3h, 12h, 24h, 48h and 72h after iron depletion by DFB addition. The gene expression was compared to that of Synechocystis PCC6803 WT cultures which were grown and treated in parallel. The data for the WT iron depletion stress response are already published (PMID: 23275872) and stored in the Geo database (GSE39804). Furthermore, we used a strain expressing IsaR1 (IsaR1OE) under control of the copper inducible petE promoter on the pVZ plasmid. The respective control strain (WT_pVZ) carries a pVZ plasmid with the petE promoter followed by the rho terminator. Both strains were sampled prior to copper addition (0h) and 6h after strong ectopic induction of IsaR1 by copper addition. Each sample was done in two independent biological replicates.