The evolution of the GALactose utilization pathway in budding yeasts

The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar galactose for energy and biomass production. The GAL pathway has long served as a model system for understanding how eukaryotic metabolic pathways, including their modes of regulation, evolve. More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering. In this review, we summarize exciting recent work on three different aspects of this iconic pathway's evolution: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.

Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits

Gene regulatory networks (GRNs) drive developmental and cellular differentiation, and variation in their architectures gives rise to morphological diversity. Pioneering studies in Aspergillus fungi, coupled with subsequent work in other filamentous fungi, have shown that the GRN governed by the BrlA, AbaA, and WetA proteins controls the development of the asexual fruiting body or conidiophore. A specific aspect of conidiophore development is the production of phialides, conidiophore structures that are under the developmental control of AbaA and function to repetitively generate spores. Fungal genome sequencing has revealed that some filamentous fungi lack abaA, and also produce asexual structures that lack phialides, raising the hypothesis that abaA loss is functionally linked to diversity in asexual fruiting body morphology. To examine this hypothesis, we carried out an extensive search for the abaA gene across 241 genomes of species from the fungal subphylum Pezizomycotina. We found that abaA was independently lost in four lineages of Eurotiomycetes, including from all sequenced species within the order Onygenales, and that all four lineages that have lost abaA also lack the ability to form phialides. Genetic restoration of abaA from Aspergillus nidulans into Histoplasma capsulatum, a pathogenic species from the order Onygenales that lacks an endogenous copy of abaA, did not alter Histoplasma conidiation morphology but resulted in a marked increase in spore viability. We also discovered that species lacking abaA contain fewer AbaA binding motifs in the regulatory regions of orthologs of some AbaA target genes, suggesting that the asexual fruiting body GRN of organisms that have lost abaA has likely been rewired. Our results provide an illustration of how repeated losses of a key regulatory transcription factor have contributed to the diversity of an iconic fungal morphological trait.

How petals change their spots: cis-regulatory re-wiring in Clarkia (Onagraceae)

A long-standing question in evolutionary developmental biology is how new traits evolve. Although most floral pigmentation studies have focused on how pigment intensity and composition diversify, few, if any, have explored how a pattern element can shift position. In the present study, we examine the genetic changes underlying shifts in the position of petal spots in Clarkia. Comparative transcriptome analyses were used to identify potential candidate genes responsible for spot formation. Co-segregation analyses in F₂ individuals segregating for different spot positions, quantitative PCR, and pyrosequencing, were used to confirm the role of the candidate gene in determining spot position. Transient expression assays were used to identify the expression domain of different alleles. An R2R3Myb transcription factor (CgMyb1) activated spot formation, and different alleles of CgMyb1 were expressed in different domains, leading to spot formation in different petal locations. Reporter assays revealed that promoters from different alleles determine different locations of expression. The evolutionary shift in spot position is due to one or more cis-regulatory changes in the promoter of CgMyb1, indicating that shifts in pattern element position can be caused by changes in a single gene, and that cis-regulatory rewiring can be used to alter the relative position of an existing character.