Regulatory RNA in cyanobacteria: Developmental decisions, stress responses and a plethora of chromosomally encoded cis-antisense RNAs

The ability for adaptation to vastly different environmental conditions suggests the existence of sophisticated regulatory mechanisms in cyanobacteria. Therefore, various types of regulatory RNA can be expected that interplay with the different signal transduction pathways and stress responses. Indeed, non-coding RNAs (ncRNAs) have been characterized from simple unicellular species with a very compact genome such as Prochlorococcus up to multicelluar forms such as Anabaena with highly complex genome architecture and regulation of gene expression. The model strain Synechocystis PCC6803 expresses more than 300 ncRNAs from free-standing genes, shows massive antisense transcription for at least 800 genes and accumulates sRNAs from three different types of CRISPRs located on plasmid pSYSA. Several of these ncRNAs function in the control of stress responses, photosynthesis, outer cell membrane protein biosynthesis and the differentiation of cells. The cis-antisense RNA IsrR controls accumulation of the light-harvesting protein IsiA under iron limited growth through a co-degradation mechanism with the isiA mRNA. The ncRNA NsiR1 is expressed from an array of direct repeats that consist of a short promoter and the template part for transcription. The expression of NsiR1 is one of the earliest known cell-type specific events in the differentiation of heterocysts and the conservation of location, gene arrangement and sequence among heterocyst-forming cyanobacteria indicates a widely conserved identical and essential function in these species. Modelling the functional interactions of cyanobacterial ncRNAs globally suggests an array of distinct molecular mechanisms that will be discussed.