Sequence-specific RNA binding by Bicoid

Abstract

It has recently been reported that the bicoid protein (Bcd), a homeodomain-containing protein which forms an anterior-to-posterior gradient during early Drosophila embryogenesis, can bind messenger RNA encoding the caudal protein (Cad) and repress its translation¹,². This may be mediated by direct interactions between the homeodomain and a discrete RNA sequence in the untranslated 3′ region of the cad transcript, the Bcd response element(BRE)¹,². The evidence for direct and specific homeodomain-RNA interactions depends principally on the results of competition experiments¹ but these could not be reproduced under the conditions originally reported³. Here we present competition experiments performed under different conditions confirming that direct, sequence-specific interactions can occur between the Bcd homeodomain and the cad BRE. We also extend previous evidence¹ that site-specific RNA binding by the Bcd homeodomain depends on the lysine at position 9 of helix III, an amino-acid that mediates site-specific DNA binding^4,5,6.