The evolution of sequence specificity in a DNA binding protein family

Transcriptional regulation enables bacteria to adjust to its environment. This is driven by transcription factors (TFs), which display DNA site recognition specificity with some flexibility built-in. TFs however are not considered essential to a minimal cellular life. How do they evolve? It has been hypothesised that TFs evolve by gaining specificity (and other functions) on a background of non-specific chromosome structuring proteins. We used the IHF/HU family of DNA binding proteins, in which IHF binds DNA in a sequence specific manner whereas HU binds more indiscriminately, to test this hypothesis. We show that neither protein was present in the last common bacterial ancestor, and that HU evolved first in early-branching clades. By reconstructing ancestral sequences in-silico on a rooted phylogeny of IHF/HU we show that the common ancestor of this family was probably HU-like and therefore non-specific in binding DNA. Various residues characteristic of IHF and shown to be involved in specific sequence recognition (at least in E. coli ) evolved gradually with several gains and losses along the phylogeny. Finally, we suggest that the evolution of the IHF/HU from a HU-like ancestor to IHF, and by inference the evolution of DNA site specificity in this family, was driven by selection.