Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TF) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here, we identified, characterized, and compared the function of the RosR TF across three related hypersaline-adapted archaeal model species. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (hsRosR). Here, we use functional genomics and quantitative phenotyping to demonstrate that, despite strong sequence conservation of RosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii (hvRosR) and Haloferax mediterranei (hmRosR) regulates genes whose products function in motility and the membrane, leading to significant defects in motility when RosR is deleted. Given weak conservation and degeneration in cis-regulatory sequences recognized by the RosR TF across species, we hypothesize that the RosR regulatory network is readily rewired during evolution across related species of archaea.