Evolution of Transcription Factors and Gene Regulatory Networks

In this contribution I will discuss how the use of resurrected proteins facilitates the analysis of transcription factor protein evolution. The main advantage of the use of resurrected proteins is that experimental tests of the effect of specific amino acid substitutions can not be performed on outgroup proteins because of the strong epistatic interactions with amino acid residues that are apomorphic for the outgroup lineage. By changing ancestral proteins, however, it is often possible to assign a causal role to certain amino acid substitutions in the derived protein activity. I will illustrate this principle with results from the evolution of functional cooperativity between HoxA11 and Foxo1a in regulating PRL in endometrial stromal cells. Functional cooperativity between these proteins evolved in the stem lineage of placental mammals and is associated with many amino acid substitutions. Our results show that there are three amino acid substitutions which affect the intra-molecular regulation of transcriptional activity in HoxA11 as well as the recruitment of p300/CBP. The association with Foxo1a of HoxA11 leads to a phosphorylation of a regulatory peptide, called NP, which in turn relieves a repressive effect on the interaction between HoxA11 and p300/CBP. Overall our results show how transcription factor proteins can evolve context dependent activities and thus likely circumvent the pleiotropy constraint on their evolution.