Figure 4. Low-glucose Rap1 targets contain Sko1, Sut1, or Mig1 binding sites and a weak Rap1 consensus motif.

A) The specificity of sequence motifs for low-glucose versus static targets was determined using ROVER⁴¹ with a site p-value cutoff of 0.001. The value of each motif in predicting Rap1 binding was determined using the area under (AUC) the receiver operator characteristic (ROC) plot⁴², with each promoter represented by the motif score generated by the MatrixScan module of BioProspector³⁷. Motif scores encapsulate the similarity of DNA sequences at each locus to the specified position weight matrix (PWM). ROC plots show how low-glucose targets (true positives) were captured in relation to non-low-glucose targets (false positives) for a given motif score. A motif that had no predictive value would have an AUC of about 0.5; higher values are better (maximum = 1). B) Overrepresented DNA sequence motifs for static and low-glucose Rap1 targets were determined using MDscan and BioProspector³⁷,³⁸. The motif found for the static targets is the archetypical Rap1 binding motif. The most significant motif discovered for the low-glucose targets is very similar to the Sut1 binding motif². We identified the Rap1-weak motif through a directed search using a degenerate Rap1-Strong PWM (methods). All PWMs are displayed as sequence logos⁴⁰. C) Rap1 in vitro binding affinity for low-glucose-, static-, and non-Rap1 targets was enumerated using published protein binding microarray data²⁹. “Protein binding microarray” is a technique that determines a protein's in vitro DNA-binding specificity for a set of arrayed loci or DNA sequences.