UC San Diego

Transcription factors regulate gene expression. The coordination of gene expression is fundamental for specifying, determining, and maintaining cell fates. Here I investigate the evolution of a family of developmental transcription factors in the genus of nematodes Caenorhabditis. In the model organism Caenorhabditis elegans, GATA factors primarily function in either endoderm or hypoderm (epidermal) development. The genomes of Caenorhabditis species have diverged extensively however, anatomically these species are barely distinguishable. Which raises the question, have GATA factors evolved while the phenotype of these worms has remained stable? To address this question, Scott Rifkin and I searched for GATA factor orthologs in the proteomes of 58 Caenorhabditis species and two outgroup nematode species using the GATA-type zinc finger domain profile from the PROSITE database. Using maximum likelihood approaches, we estimated the evolutionary history of these GATA-domain-containing sequences. We found that GATA factors have radiated extensively within the Elegans supergroup. For example, the core of the endodermal cell specification network – med-1, med-2, end-3, end-1, and elt-7 – are unique to the Elegans supergroup, suggesting that this expansion rewired Caenorhabditis development. Our phylogenetic analyses, gene structure comparisons, and gene expression studies all support an evolutionary scenario in which a duplication of elt-3 produced the ancestor of elt-7, end-1, and end-3 in the Elegans supergroup ancestor. If this hypothesis is true, it would be an example of subfunctionalization after gene duplication that resulted in at least three Elegans supergroup paralogs that are expressed endoderm-specifically with another, elt-3, only expressed in the hypoderm. These gene duplications coincided with an increase in conserved GATA binding sites in the promoter of another endoderm-specifically expressed GATA factor gene, elt-2, which acts downstream of and is a transcriptional target of elt-7, end-1, and end-3 during endoderm development in C. elegans. One of these sites was found to be necessary for elt-2 expression. Since ELT-2 also regulates itself, there may be a brief time when all four of these GATA factors are expressed and competing for binding to sites in the elt-2 promoter. Using bio-layer interferometry I started quantifying the in vitro binding kinetics of these GATA factors to a functional GATA site and permutations of this site. My preliminary results show subtle differences in binding kinetics and specificity. These findings give insights into how three closely related transcription factors likely partitioned the ancestral role of a single transcription factor in a conserved developmental process.