Functional Equivalence of HMGA- and Histone H1-Like Domains in a Bacterial Transcriptional Factor

Histone H1 and high-mobility group A (HMGA) proteins compete dynamically to modulate chromatin structure and regulate DNA transactions in eukaryotes. In prokaryotes, HMGA-like domains are known only in Myxococcus xanthus CarD and its Stigmatella aurantiaca ortholog. These have an N-terminal module absent in HMGA that interacts with CarG (a zinc-associated factor that does not bind DNA) to form a stable complex essential in regulating multicellular development light-induced carotenogenesis, and other cellular processes. An analogous pair, $CarD_{Ad} $ and $CarG_{Ad} $, exists in another myxobacterium, Anaeromyxobacter dehalogenans. Intriguingly, the $CarD_{Ad} $ C terminus lacks the hallmark HMGA DNA-binding AT-hooks and instead resembles the C-terminal region (CTR) of histone H1. We find that $CarD_{Ad} $ alone could not replace CarD in M. xanthus. By contrast, when introduced with $CarG_{Ad,} \,Car_{Ad} $ functionally replaced CarD in regulating not just 1 but 3 distinct processes in M. xanthus, despite the lower DNA-binding affinity of $CarG_{Ad} $ versus CarD in vitro. The ability of the cognate $CarD_{Ad} - CarG_{Ad} $ pair to interact, but not the noncognate $CarD_{Ad} - CarG_{Ad} $, rationalizes these data. Thus, in chimeras that conserve CarD-CarG interactions, the H1-like CTR of $CarD_{Ad} $ could replace the CarD HMGA AT-hooks with no loss of function in vivo. More tellingly, even chimeras with the CarD AT-hook region substituted by human histone H1 CTR or full-length H1 functioned in M. xanthus. Our domain-swap analyses showing functional equivalence of HMGA AT-hooks and H1 CTR in prokaryotic transcriptional regulation provide molecular insights into possible modes of action underlying their biological roles.