Supplemental Material for Razzaq, et al., 2021

Figure S1. Regulatory associations of Sfp1 with the tra1_Q3 differentially expressed genes in S. cerevisiae. Sfp1 associations with differentially expressed genes in the tra1_Q3 strain assessed using YEASTRACT+. The experimental evidence underlying each regulatory association (solid lines for DNA-binding evidence; dashed lines for expression evidence), as well as the sign of the interaction—positive (green), negative (red), positive and negative (brown), or undefined (black) are displayed.

Figure S2. Characterization of TRA1 mutant strains. (a) tra1∆/∆ mutants were validated by PCR. Two PCRs (left panel) confirmed the absence of the TRA1 open reading frame (ORF) via primers located inside the ORF, and up- or down-stream of the ORF. Two additional PCRs (right panel) confirmed the integration of the knockout cassette at the TRA1 locus (left side), as well as integration of the CRISPR-Cas9 plasmid in the C. albicans genome (right side). For all PCRs, control strains were added that contain the TRA1 ORF, which include fRS1 (SC5314 wild-type C. albicans), and fRS302 (fRS1 containing a non-targeting Cas9 plasmid integrated in the genome), as well as a no DNA template control. tra1∆/∆ mutant strains ‘1’ and ‘2’ were selected for further phenotypic characterization. (b) The TRA1 deletion strain is severely impaired in growth. Deletion strains and corresponding wild-type strains were grown up overnight in liquid YPD media for 15.5 hours at 37˚C. (c) TRA1 deletion results in severely impaired growth on solid medium. C. albicans strains were serially diluted (1:10 dilutions) and spotted onto solid YPD agar media. (d) tra1_Q3 mutant strains are not defective in overall growth rate. Kinetic growth curves between C. albicans wild-type strain and tra1_Q3 mutant strains indicate no differences in overall growth dynamics over time.

Figure S3. Limited overlap between the Tra1- and Gcn5-regulated genes in C. albicans. (a) Volcano plot showing the distribution of the previously identified 336 differentially expressed genes in gcn5Δ (from (Shivarathri et al. 2019)) within the tra1_Q3 dataset. Genes significantly (log₂ fold change tra1_Q3/TRA1 > 1 and P < 0.05) altered in expression are highlighted in blue (downregulated) and red (upregulated). (b) Differentially regulated Gcn5 targets in tra1_Q3 dataset are listed in the table with both the log₂ fold change within the original gcn5Δ and the tra1_Q3 datasets.