Biocomputational Analyses and Experimental Validation Identify the Regulon Controlled by the Redox-Responsive Transcription Factor RpaB

• Published in: iScience Vol. 15; pp. 316 - 331
• Main Authors: Riediger, Matthias, Kadowaki, Taro, Nagayama, Ryuta, Georg, Jens, Hihara, Yukako, Hess, Wolfgang R.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 31.05.2019; Elsevier
• Subjects: Bioinformatics; Cell Biology; Molecular Biology; Plant Biology; Plant Biology; Molecular Biology; Bioinformatics; Cell Biology
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2019.04.033

Oxygenic photosynthesis requires the coordination of environmental stimuli with the regulation of transcription. The transcription factor RpaB is conserved from the simplest unicellular cyanobacteria to complex eukaryotic algae, representing more than 1 billion years of evolution. To predict the RpaB-controlled regulon in the cyanobacterium Synechocystis, we analyzed the positional distribution of binding sites together with high-resolution mapping data of transcriptional start sites (TSSs). We describe more than 150 target promoters whose activity responds to fluctuating light conditions. Binding sites close to the TSS mediate repression, whereas sites centered ∼50 nt upstream mediate activation. Using complementary experimental approaches, we found that RpaB controls genes involved in photoprotection, cyclic electron flow and state transitions, photorespiration, and nirA and isiA for which we suggest cross-regulation with the transcription factors NtcA or FurA. The deep integration of RpaB with diverse photosynthetic gene functions makes it one of the most important and versatile transcriptional regulators. [Display omitted] •RpaB controls a complex regulon, widely beyond the photosynthetic machinery•The expression of the RNA regulators IsrR, PsrR1, and others depends on RpaB•RpaB exhibits cross-regulations with other transcription factors, NtcA and Fur•RpaB is a crucial transcriptional regulator in a photosynthetic microorganism Bioinformatics; Cell Biology; Molecular Biology; Plant Biology