The RRM domain-containing protein Rbp3 interacts with ribosomes and the 3’ ends of mRNAs encoding photosynthesis proteins

Gene expression changes were monitored in cultures of the cyanobacterium Synechocystis sp. PCC 6803 at 30 min after a shift from cultivation under standard light conditions (50 µmol photons m-2 s-1) to high light (HL; 250 µmol photons m-2 s-1) and 1 h after a shift from the standard growth temperature of 30°C to 20°C (cold). Acclimation to shifts in light and temperature is critical for photoautotrophic organisms such as cyanobacteria. The RRM domain proteins Rbp2 and Rpb3 are RNA-binding proteins that bind specific mRNAs and are involved in the localization of these mRNAs to the thylakoid membrane. Here, we investigated the effects of Rpb2 and Rbp3 on gene expression changes during the acclimation responses to an increase in light intensity and a decrease in temperature. We analyzed cultures of the wild-type (WT) and of the Δrbp2Δrbp3 double mutant, which lacks Rbp2 and Rbp3. We found that the transcript levels of psaA and psaB genes were significantly decreased in cells of the Δrbp2Δrbp3 double mutant upon cold stress and 30 min of high light compared to wild type. In addition, the transcript levels of Rbp1, another RRM domain-containing protein, were greatly increased. Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type, and the Δrbp2Δrbp3 double mutant, which lacks Rbp2 and Rbp3. Samples were taken in biological duplicates. Total RNA was DNase-treated using TURBO DNase (Thermo Fisher Scientific). 2 µg DNase-treated RNA were labeled with Cy3 using the ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech). A high-resolution microarray manufactured by Agilent (Design ID 075764, format 8 × 60 K, slide Layout = IS-62976-8-V2) was used. 600 ng labeled RNA were used for hybridization for 17 h at 65 °C, per array.