We recently showed that in biotin starvation in yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans and rat Rattus norvegicus, despite abundant glucose provision, the expression of genes for glucose utilization and lipogenesis were lowered, and for fatty acid β-oxidation and gluconeogenesis were raised, and glycolytic/fermentative flow was reduced. This work explored the mechanisms of these results. We show that they are associated with ATP deficit and activation of the energy stress sensor AMP kinase (AMPK; Snf1 in yeast). Analysis of microarray results revealed extensive changes of transcripts for signal transduction pathways and transcription factors AMPK, SREBP-1c, ChREBP, NAMPT, PGC-1α, mTORC1 in rat, and their homologs in worm. In yeast the altered factor transcripts were Adr1, Cat8, Sip4, Mig1, HXK2, and Rgt1. The insulin pathway was negatively enriched (in rat and worm), whereas the adiponectins and JAK/STAT pathways were increased (present only in the rat; they activate AMPK). Together, all these changes explain the effects of biotin starvation on glucose utilization, energy status and carbon metabolism gene expression in a coherent manner across three phylogenetically distant eukaryotes and may have clinical significance in humans, since the effects are reminiscent of insulin resistance. We propose a general model for integrating these results in regulatory circuitries, according to the biology of each species, based on impaired anaplerosis due to pyruvate carboxylase deficiency, that have a basic underlying logic. In a preliminary test in yeast, aspartate corrects all the alterations produced by biotin starvation.