USF1,
a basic region/helix–loop–helix/leucine zipper
(bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen
activator inhibitor) promoter. Two alleles containing the E-box control
PAI-1 transcription; these alleles are termed “4G” and
“5G” based on the G tract flanking E-box. USF1-governed
transcription of PAI-1 is elevated in heritable asthma sufferers:
the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1
uses its basic region to bind E-box, we found that it uses its 12
amino-acid loop to recognize the flanking sequence and discern the
single-nucleotide difference between the alleles. We used the bacterial
one-hybrid and electrophoretic mobility shift assays to assess protein–DNA
recognition, and circular dichroism to examine protein secondary structure.
We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1
bHLHZ K
d values 4.1 ± 0.3 nM and
7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in
stimulated human mast cells showed a preference for 4G. We replaced
the 8 amino-acid loop of transcription factor Max bHLHZ with the 12
amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphismwhile
Max bHLHZ does notconfirming that USF1 differentiation of
the 4G/5G is driven by the loop.