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Promoter region binding of Efg1 in diverse C. albicans clinical isolates.
There is extensive variation in the Efg1-responsive transcriptome among five C. albicans clinical isolates (13). These isolates represent five different clades and vary in ability to produce hyphae and biofilm (11, 13). Genome sequence analysis by Hirakawa et al. (11) indicated that the average genome-wide nucleotide diversity between any two isolates is ~0.37%. To increase confidence in gene expression differences among these isolates, we repeated triplicate RNA-seq assays for the five clinical isolates and efg1Δ/Δ derivatives after hyphal induction for 4 h in RPMI plus fetal bovine serum (RPMI+FBS) at 37°C (see Data Set S1 in the supplemental material, all genes). Analysis of the pooled data sets defined a set of 200 genes that presented significant Efg1-responsive RNA levels in all strains (>2-fold change between efg1Δ/Δ and WT; adjusted P < 0.05). We refer to these 200 genes as core Efg1-responsive genes (see Data Set S1, down and up data). Data set comparisons also identified 1,051 genes with Efg1-responsive RNA levels in only one or a few strains. We refer to these 1,051 genes as strain-limited Efg1-responsive genes (see Data Set S1, down and up); they represent natural variation in the Efg1 regulatory circuit. We sought to determine the basis for this natural variation.
One possible explanation for variation in Efg1-responsive genes is that Efg1 binds to distinct genomic loci in each strain. Differences in the binding spectrum would lead to different consequences for loss of Efg1. To identify loci to which Efg1 binds, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) analysis of epitope-tagged Efg1-hemagglutinin (Efg1-HA) in each clinical isolate background. Samples were prepared after hyphal induction for 4 h in RPMI+FBS at 37°C. Efg1-HA presented consistent binding loci in all five clinical isolates (Fig. 1A; see also Data Set S2). Pearson's coefficients for 500-bp bins across the genome indicated that samples correlated strongly, with R values ranging from 0.85 to 1.00 (Fig. 1B). Computed Efg1 binding motifs for each clinical isolate showed that bound regions were associated with the canonical Efg1 binding motif, 5′-TGCAT-3′ (Fig. 1C). These results argue that Efg1-target binding is largely uniform among the five C. albicans isolates.

Efg1 core network of direct target genes.
We merged RNA-seq and ChIP-seq data to identify genes that were both differentially expressed in efg1Δ/Δ mutants and bound by Efg1. This analysis showed that 218 to 299 genes were regulated directly by Efg1 in each clinical isolate, and 110 genes were regulated directly by Efg1 in all five clinical isolates (Fig. 2; see also Table S1, Efg1 direct target gene ID and core direct Efg1 targets). The 110 genes, which we call core direct Efg1 targets, included 85 Efg1-activated genes and 25 Efg1-repressed genes (Fig. 3A). Core direct targets were enriched for functions related to adhesion and biofilm formation (adhesion of symbiont to host, P = 1.48e−06; single-species biofilm formation, P = 8.87e−06), in keeping with the observation that Efg1 is required for biofilm formation in all clinical isolates tested (13).
Examination of binding peaks surrounding specific genes indicated that Efg1 binding differences were not the cause of regulatory differences among strains. For example, core direct targets UME6, ALS3, and HGC1 were under positive control by Efg1 in all strains examined (Fig. 3B; see also Table S1, core direct Efg1 targets). The 5′ regions of these genes were uniformly bound by Efg1 (Fig. 1D). In contrast, AAF1, ALS7, and ECM331 were regulated by Efg1 in some strains and not in others (Fig. 3B; see also Table S1, differential expression). The 5′ regions of these genes were also uniformly bound by Efg1 (Fig. 1E). Therefore, differences in Efg1-responsive expression of genes cannot be explained by differences in Efg1-promoter region binding.

Strain-limited promoter response to Efg1.
To determine whether strain differences in Efg1-responsive gene expression reflect sequence differences in promoter or regulatory regions, we focused on the CHT2 gene. Its RNA levels were repressed by Efg1 in strain SC5314 but activated slightly by Efg1 in strain P75010 (see Table S1, differential expression). To assay activity of the same promoter sequence in both strains, we fused a 1,743-bp fragment from the SC5314 CHT2 5′ region to a lacZ reporter gene and introduced the construct into each wild type (WT) and its derived efg1Δ/Δ mutant (Fig. 4A and B). Measurement of β-galactosidase indicated that the reporter gene was repressed by Efg1 in strain SC5314 and unaffected by Efg1 in strain P75010 (Fig. 4C). These assays were conducted after hyphal induction for 24 h in RPMI+FBS at 37°C, allowing time for β-galactosidase to accumulate. Repression required the CHT2 promoter region (Fig. 4C). These results showed that identical C. albicans promoter sequences respond differently to Efg1 in these two strain backgrounds.

Sculpting of Efg1 transcriptional target space by partner TFs.
To explore the basis for strain variation in Efg1-responsive gene expression, we focused on the two strains SC5314 and P75010. SC5314 is the type strain for C. albicans and was isolated from a patient with a generalized Candida infection (http://www.candidagenome.org/Strains.shtml). P75010 is a bloodstream isolate (14). We hypothesized that differences in expression or activity of TFs that are functionally related to Efg1 may explain natural variation in the Efg1 regulatory response (Fig. 5A). TF genes that were expressed at higher levels in SC5314 than in P75010 (Fig. 5B; see also Table S2) included WOR1 (regulator of white-opaque switching), ZFU2 (regulator of cell adherence), ADR1 (regulator of carbon metabolism), and TEC1 and BRG1 (regulators of biofilm and hyphal formation). We increased dosages of individual TF genes in P75010 to test whether their increased expression altered Efg1-responsive gene expression.
Each TF gene, PCR-amplified from strain P75010, was integrated into the genome in P75010 EFG1+/+ and efg1Δ/Δ strains. Integration was targeted to the MDR1 locus. (An mdr1Δ/Δ mutation lacking an inserted TF gene did not alter gene regulation in our assays [Fig. 5C, P75010+empty; see also Table S3, ectopic strains efg1 versus EFG1.]) Gene expression was assayed after hyphal induction for 4 h in RPMI+FBS at 37°C (Fig. 5C; see also Table S3). Dosage increases yielded 2- to 10-fold increased TF gene expression (see Table S3, WOR1-BRG1-TEC1 relationship). Increased dosage of the known biofilm and hyphal regulatory gene BRG1 in strain P75010 caused Efg1-responsive regulation of ECM331, HGT1, ECE1, and HYR1 to resemble more closely that in strain SC5314. Increased dosage of the biofilm and hyphal regulatory gene TEC1 had similar effects on ECE1 and HYR1. Increased dosage of ZFU2 and ADR1 had little effect (see Table S3, ADR1-ZFU2 data). Increased dosage of WOR1 in P75010 also caused Efg1-responsive regulation to resemble that in SC5314 (Fig. 5C; see also Table S3, ectopic strains efg1 versus EFG1). For example, ECM331 and HYR1 were under negative control by Efg1 in P75010 but under positive control in SC5314 and the increased-dosage strain, P75010+WOR1. Conversely, CHT2 was under positive control by Efg1 in P75010 but under negative control in SC5314 and P75010+WOR1. Although the range of genes assayed was limited, increased dosage of WOR1, BRG1, or TEC1 in strain P75010 caused features of Efg1-dependent gene regulation to resemble those in strain SC5314.
To determine whether the gene expression effects of increased TF gene dosage depend upon Efg1, we compared gene dosage impact in P75010 EFG1+/+ and efg1Δ/Δ backgrounds (Fig. 6; see also Table S3, ectopic strains versus empty). Increased BRG1 dosage had significant effects on 10 genes (adjusted P < 0.05; excluding BRG1 itself) in the EFG1+/+ background, and those effects were abolished in the efg1Δ/Δ background. Therefore, effects of increased BRG1 dosage on these genes depend upon Efg1. Increased TEC1 dosage had significant effects on 15 genes (excluding TEC1) in an EFG1+/+ background, and only some of those effects were abolished in an efg1Δ/Δ background. Therefore, effects of increased TEC1 dosage are partially independent of Efg1. Increased WOR1 dosage had significant effects on 10 genes (excluding WOR1) in the EFG1+/+ background, and those effects were abolished in the efg1Δ/Δ background. Therefore, effects of increased WOR1 dosage on these genes depend upon Efg1.

Positive control of biofilm formation by Wor1 in P75010.
We hypothesized that the gene expression impact of increased WOR1, BRG1, or TEC1 dosage may translate into biological phenotype. Strain SC5314 is a stronger biofilm former than P75010 (13). We observed that increased dosage of WOR1, BRG1, or TEC1 in P75010 drove greater biofilm production (Fig. 7A), based upon either depth or volume (Fig. 7C). We concluded that differences in WOR1, BRG1, or TEC1 expression levels between strains can account for differences in both biofilm formation ability and Efg1-responsive gene expression.
The Efg1-Wor1 physical interaction in vitro depends upon the Wor1 PrLD, a region that is required for Wor1 function in the white-opaque switch (10). We hypothesized that the Efg1-Wor1 functional interaction in gene expression and biofilm formation may also be PrLD dependent. In our increased dosage assay, PrLD-disrupted WOR1 mutants (DE-to-A or YF-to-S) had much less impact than wild-type WOR1 in Efg1-responsive regulation of ECM331, HGT1, ECE1, CHT2, or HYR1 (Fig. 5D; see also Table S3, ectopic strains efg1 versus EFG1) or biofilm production (Fig. 7B and C). Therefore, integrity of the Wor1 PrLD is required for Wor1 to impact both Efg1-responsive gene expression and biofilm formation.
If Wor1 promotes biofilm formation through interaction with Efg1, then an efg1Δ/Δ mutation should abrogate the stimulation of biofilm formation by increased WOR1 dosage. We observed that an efg1Δ/Δ mutation blocked biofilm formation in strain P75010 regardless of increased WOR1 dosage (see Fig. S1). Therefore, the impact of WOR1 dosage on biofilm formation, like its impact on Efg1-responsive gene expression, depends upon Efg1.
In order to understand the scope of the impact of WOR1 gene expression, we conducted RNA-seq analysis on P75010+empty vector and P75010+WOR1 strains. Increased WOR1 dosage altered expression of 396 genes (293 upregulated, 103 downregulated; fold change, >2; adjusted P < 0.05 [see Data Set S3]). Upregulated genes were enriched for adhesion functions and included many genes associated with biofilm or hyphal growth (ALS1, HYR1, SAP4-SAP5-SAP6, and UME6). The 396 genes with significantly altered expression were enriched for Efg1-bound genes (P < 10−5, Fisher’s exact test [see Fig. S1]). EFG1 RNA levels were not significantly affected (see Data Set S3). Therefore, increased WOR1 dosage has a narrow effect on gene expression under these growth conditions. Based on WOR1 dosage effects on gene expression and biofilm formation, our findings support the model that Wor1 acts in part through Efg1 to modulate gene expression.