During development, metabolic pathways and gene regulation are integrated to orchestrate the events underlying cell-type differentiation. How this occurs at the molecular level involves interactions between proteins and small molecules that are outputs of the metabolic network. In plants, key regulatory proteins that control gene expression include homeodomain leucine zipper (HD-Zip) transcription factors that have steroidogenic acute regulatory-protein (StAR)-related lipid transfer (START) domains. I will present our recent work highlighting START domains and their functions in Class IV HD-Zip transcription factors from Arabidopsis. We are conducting protein-metabolite immunoisolation experiments to reveal putative ligands and we are additionally studying the evolutionary origins of these plant-specific transcription factors in freshwater green algae.