Abstract: Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation

Abstract: 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

Abstract: Abstract The OmpR-type transcription factor RpaB (for regulator of phycobilisome association B), or Ycf27/Rre26, in the cyanobacterium Synechocystis sp. PCC 6803 controls the expression of genes encoding proteins related to photosystems I and II, electron transport, certain other proteins and the regulatory small RNA PsrR1, with which it forms a type-4 coherent feed forward loop in the post-transcriptional control of photosynthesis. The basis for regulation through RpaB is the HLR1 element, a bipartite binding motif that consists of two octameric repeats separated by two random nucleotides. Depending on the distance between HLR1 and the start site of transcription, RpaB can activate or repress transcription. RpaB itself is part of a two-component system with Hik33 (NblS in Synechococcus elongatus PCC 7942) and might be redox controlled by the thioredoxin system. The rpaB gene cannot be deleted, i.e., it is essential in cyanobacteria. Orthologs of rpaB are ubiquitous in cyanobacteria and exist in the chloroplast genomes of red algae, of Glaucophyta, Cryptophyta, Haptophyta, and Raphidophyta, and the charophyte alga Chlorokybus atmophyticus, which exhibit stunning conservation of domains and residues known to serve as elements for signaling input and functionality. However, RpaB was lost during the early evolution of land plants, raising questions as to whether it became replaced by another mechanism