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Nucleic Acids Research, 2003, Vol. 31, No. 15 4391-4400
© 2003 Oxford University Press

Structural and functional homology between the RNAPI subunits A14/A43 and the archaeal RNAP subunits E/F

Hedije Meka, Gregoire Daoust, Kristine Bourke Arnvig1, Finn Werner, Peter Brick and Silvia Onesti*

Department of Biological Sciences, Imperial College, Exhibition Road, London SW7 2AZ, UK and 1 NIMR, The Ridgeway, Mill Hill, London NW7 1AA, UK

*To whom correspondence should be addressed. Tel: +44 20 75947647; Fax: +44 20 75890191; Email: s.onesti{at}imperial.ac.uk

In the archaeal RNA polymerase and the eukaryotic RNA polymerase II, two subunits (E/F and RPB4/RPB7, respectively) form a heterodimer that reversibly associates with the core of the enzyme. Recently it has emerged that this heterodimer also has a counterpart in the other eukaryotic RNA polymerases: in particular two subunits of RNA polymerase I (A14 and A43) display genetic and biochemical characteristics that are similar to those of the RPB4 and RPB7 subunits, despite the fact that only A43 shows some sequence homology to RPB7. We demonstrate that the sequence of A14 strongly suggests the presence of a HRDC domain, a motif that is found at the C-terminus of a number of helicases and RNases. The same motif is also seen in the structure of the F subunit, suggesting a structural link between A14 and the RPB4/C17/subunit F family, even in the absence of direct sequence homology. We show that it is possible to co-express and co-purify large amounts of the recombinant A14/A43 heterodimer, indicating a tight and specific interaction between the two subunits. To shed light on the function of the heterodimer, we performed gel mobility shift assays and showed that the A14/A43 heterodimer binds single-stranded RNA in a similar way to the archaeal E/F complex.


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