RNA polymerase (Rpo) in archaea consists of a 10-subunit core enzyme plus a dissociable heterodimeric subcomplex, which is composed of two subunits E and F (RpoEF). While the core subunits are devoted to transcribing DNA into RNA, the functional contribution of the RpoEF subunits to the transcription process is not fully understood. The location of RpoEF (near the exit channel for the newly transcribed RNA) on the structure of the intact archaeal Rpo and the presence of a S1 motif in the subunit E suggest that RpoEF's role is to bind RNA.

We have recently shown that the RpoEF from the Antarctic archaeon Methanococcoides burtonii (MbRpoEF) preferentially binds to mRNA of genes whose expression may be important for cellular fitness ⁽¹⁾. These finding is consistent with a previous finding in which MbRpoE had higher abundance at low versus high temperature. To explore the potential of MbRpoEF to specifically bind ssRNA, we are performing Systematic Evolution of Ligands by EXponential enrichment (SELEX) experiments to identify its in vitro RNA target sequence(s). We will characterise the MbRpoEF:ssRNA complex(es) using biophysical methods with the ultimate aim of obtaining high resolution structures by X-ray crystallography.