M. Fernandes et al., FINE-STRUCTURE ANALYSES OF THE DROSOPHILA AND SACCHAROMYCES HEAT-SHOCK FACTOR - HEAT-SHOCK ELEMENT INTERACTIONS, Nucleic acids research, 22(2), 1994, pp. 167-173
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.