Genomic and genetic dissection of an archaeal regulon

The extremely halophilic archaeon Halobacterium sp. NRC-1 can grow phototro phically by means of light-driven proton pumping by bacteriorhodopsin in th e purple membrane. Here, we show by genetic analysis of the wild type, and insertion and double-frame shift mutants of Bat that this transcriptional r egulator coordinates synthesis of a structural protein and a chromophore fo r purple membrane biogenesis in response to both light and oxygen. Analysis of the complete Halobacterium sp. NRC-1 genome sequence showed that the re gulatory site, upstream activator sequence (UAS), the putative binding site for Bat upstream of the bacterio-opsin gene (bop), is also present upstrea m to the other Bat-regulated genes. The transcription regulator Bat contain s a photoresponsive cGMP-binding (GAF) domain, and a bacterial AraC type he lix-turn-helix DNA binding motif. We also provide evidence for involvement of the PAS/PAC domain of Bat in redox-sensing activity by genetic analysis of a purple membrane overproducer. Five additional Bat-like putative regula tory genes were found, which together are likely to be responsible for orch estrating the complex response of this archaeon to light and oxygen. Simila rities of the bop-like UAS and transcription factors in diverse organisms, including a plant and a gamma -proteobacterium, suggest an ancient origin f or this regulon capable of coordinating light and oxygen responses in the t hree major branches of the evolutionary tree of life. Finally, sensitivity of four of five regulon genes to DNA supercoiling is demonstrated and corre lated to presence of alternating purine-pyrimidine sequences (RY boxes) nea r the regulated promoters.