6S RNA of cyanobacteria – an old issue became green

6S RNA is indicative of small-non-coding RNAs (sRNA) which implement complex regulatory networks among diverse bacteria. More than 30 years after sequencing of 6S RNA from E. coli, their function as an inhibitor of transcription based on interaction with RNA polymerase holoenzyme (RNAP) during stationary growth was verified. However, there are limited informations about this RNA from other groups of bacteria.

The homolog of 6S RNA became identified in the freshwater cyanobacteria Synechococcus elongates PCC 6301 and Synechocystis sp. PCC 6803 as one of the very first cyanobacterial sRNAs. Recently we could show the accumulation of distinct 6S RNA molecules of different lengths in Prochlorococcus MED4 (1). For the first time we reported the regulation of sRNA levels during growth and the diel cycle. Coordination of biological activities through an internal circadian clock within prokaryotes is confined to cyanobacteria. Therefore, their gene expression system, including the functional role of 6S RNA must have adapted accordingly.

As a first step towards understanding the function of this small-non-coding RNA in a unicellular cyanobacterium we started to accomplish well described in vitro transcription systems of E. coli. We observed an interaction of the 6S RNA of Synechocystis sp. PCC6803 to RNAP of E. coli by gel retardation. The absorbing ability to act as a template for a specific de novo transcript described for E. coli (2) could be replicated with the cyanobacterial sRNA in vitro. Otherwise the melting point of the 6S RNA of Synechocystis sp. PCC6803 is more than 10 °C lower than determined for E. coli. First results of expression analysis in vivo compound a potentially varied behaviour of 6S RNA in cyanobacteria compared to enterobacteria.