FINE-STRUCTURE ANALYSES OF THE DROSOPHILA AND SACCHAROMYCES HEAT-SHOCK FACTOR - HEAT-SHOCK ELEMENT INTERACTIONS

Heat shock genes are activated by the binding of the heat shock transc ription factor (HSF) to heat shock elements (HSEs), consisting of arra ys of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the conserved, central trinucleoti de GAA reduce the relative binding affinity of both HSFs. In addition, the base at position 1 (N1) also influences binding, with a strong pr eference for an A at this position. Methylation interference initially indicated that HSF contacts A1 in the minor groove, but interacts wit h the immediately adjacent base G2 in the major groove. Further charac terization of this apparently abrupt minor to major groove transition by substitution of A1 with an inosine, shows that HSF contacts A1 in t he major groove. We offer an explanation for this apparent contradicti on and propose that HSF recognizes the HSE primarily through contacts within the major groove of the DNA helix. Finally, based on these obse rvations and a re-evaluation of the base frequencies and criteria for consensus sequence assignment, we propose that the sequence AGAAN more accurately represents the consensus HSE motif.