Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi.

Valentina Del Olmo Toledo,J Christian Pérez,Robert Puccinelli,Polly M Fordyce,Geraldine Butler

doi:10.1371/journal.pgen.1007884

Abstract

The Sterol Regulatory Element Binding Proteins (SREBPs) are basic-helix-loop-helix transcription regulators that control the expression of sterol biosynthesis genes in higher eukaryotes and some fungi. Surprisingly, SREBPs do not regulate sterol biosynthesis in the ascomycete yeasts (Saccharomycotina) as this role was handed off to an unrelated transcription regulator in this clade. The SREBPs, nonetheless, expanded in fungi such as the ascomycete yeasts Candida spp., raising questions about their role and evolution in these organisms. Here we report that the fungal SREBPs diversified their DNA binding preferences concomitantly with an expansion in function. We establish that several branches of fungal SREBPs preferentially bind non-palindromic DNA sequences, in contrast to the palindromic DNA motifs recognized by most basic-helix-loop-helix proteins (including SREBPs) in higher eukaryotes. Reconstruction and biochemical characterization of the likely ancestor protein suggest that an intrinsic DNA binding promiscuity in the family was resolved by alternative mechanisms in different branches of fungal SREBPs. Furthermore, we show that two SREBPs in the human commensal yeast Candida albicans drive a transcriptional cascade that inhibits a morphological switch under anaerobic conditions. Preventing this morphological transition enhances C. albicans colonization of the mammalian intestine, the fungus’ natural niche. Thus, our results illustrate how diversification in DNA binding preferences enabled the functional expansion of a family of eukaryotic transcription regulators.

Highlights

Evolutionary changes in gene expression patterns constitute a major source of phenotypic diversity [1,2,3,4]
We show that in C. albicans two of its SREBPs act in concert to inhibit a morphological switch under anaerobic conditions
A distinctive feature of this family—which distinguishes them from other bHLH proteins—is the presence of a tyrosine residue instead of an arginine in the first helix of the DNA binding domain (Fig 1A). Using this hallmark as the main criterion for inclusion, we assembled a comprehensive phylogeny of the fungal SREBPs based on a manually curated alignment of the DNA binding domain of ~200 proteins (S1 Table; models and computational procedures used for phylogenetic reconstruction are described under Materials and Methods)

Summary

Introduction

Evolutionary changes in gene expression patterns constitute a major source of phenotypic diversity [1,2,3,4]. The primary step through which all cells regulate expression of their genes is the binding of transcription regulators to cis-regulatory sequences. Changes in the transcription regulators themselves are important sources of evolutionary rewiring [13,14,15,16,17], relatively few examples of how these proteins change are understood in molecular detail. Little is known about how different DNA binding preferences arise within a family of transcription regulators and whether such variation results in the functional diversification of the family. We address this question here studying the SREBP (sterol regulatory element binding protein) family of transcription regulators (reviewed in [18,19,20]). While the SREBPs have been traditionally associated with the regulation of sterol biosynthesis genes, several members of this family appear to govern cellular processes unrelated to lipid synthesis

Methods

Results

Discussion

Conclusion