dRNA-seq-based analysis of the Thermococcus kodakarensis KOD1 transcriptional landscape to identify growth-regulated small regulatory RNAs

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Amongst others, the advent of high throughput sequencing technologies revolutionized the characterization of RNA populations from microbe to humans; however, no members of the hyperthermophilic euryarchaeota have yet been analyzed. The proposed research project aims to gain a more detailed insight into the (s)RNA population of Thermococcus kodadarensis KOD1. A recently developed differential method for high throughput sequencing of cDNA libraries (dRNA-seq) will be applied to analyse the T. kodadarensis transcriptome in response to the growth phase. Besides the transcriptome-analysis, the experiments will focus on the genetic, biocomputational and biochemical characterization of selected sRNAs in order to unravel their biological function and identify potential interacting (m)RNAs. With regard to this, a unique reporter system will be established to verify potential interactions in vivo. Further experiments will concentrate on the functional role of the RNA-chaperone Lsm. For this purpose, tagging of the Lsm protein for co-immunoprecipitation, or of stable RNAs, will be used to identify potential interactions in vitro and in vivo. Together, this will lead to a better understanding of the role of regulatory sRNAs in the archaeal domain.