Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate

The evolution of transcriptional regulatory networks has thus far mostly been studied at the level of cis-regulatory elements. To gain a complete understanding of regulatory network evolution we must also study the evolutionary role of trans-factors, such as transcription factors (TFs). Here, we systematically assess genomic and network-level determinants of TF evolutionary rate in yeast, and how they compare to those of generic proteins, while carefully controlling for differences of the TF protein set, such as expression level. We found significantly distinct trends relating TF evolutionary rate to mRNA expression level, codon adaptation index, the evolutionary rate of physical interaction partners, and, confirming previous reports, to protein-protein interaction degree and regulatory in-degree. We discovered that for TFs, the dominant determinants of evolutionary rate lie in the structure of the regulatory network, such as the median evolutionary rate of target genes and the fraction of species-specific target genes. Decomposing the regulatory network by edge sign, we found that this modular evolution of TFs and their targets is limited to activating regulatory relationships. We show that fast evolving TFs tend to regulate other TFs and niche-specific processes and that their targets show larger evolutionary expression changes than targets of other TFs. We also show that the positive trend relating TF regulatory in-degree and evolutionary rate is likely related to the species-specificity of the transcriptional regulation modules. Finally, we discuss likely causes for TFs' different evolutionary relationship to the physical interaction network, such as the prevalence of transient interactions in the TF subnetwork. This work suggests that positive and negative regulatory networks follow very different evolutionary rules, and that transcription factor evolution is best understood at a network- or systems-level. Transcription factors (TFs) are proteins which regulate the expression of genes by interacting with DNA. Mutations in TF protein sequences can affect the expression levels of regulated genes throughout evolution. In this study, we look into the factors which cause the different TFs in baker's yeast to be more or less tolerant of mutations during recent evolution. This tolerance is measured as the evolutionary rate, defined for each protein as the relative rate of protein-changing DNA mutations over other mutations (Ka/Ks). We found that the typical determinants of protein evolutionary rate, such as expression level and network interactions have a very different influence on TF evolutionary rate. We found that TF evolutionary rate is most highly correlated to the evolutionary properties of the genes which they regulate and specifically genes which they activate. We also show that TF evolutionary rate predicts actual evolutionary expression differences of regulated genes and we discuss some of the features unique to TFs which likely contribute to their different evolutionary trends, such as the types of protein-protein interactions prevalent in the TF subnetwork or TFs' potential role in adaptive evolution.