An archaeal transcription factor EnfR with a novel ‘eighth note’ fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA1

Abstract

Thermococcus onnurineus NA1, a hyperthermophilic carboxydotrophic archaeon, produces H2 through CO oxidation catalyzed by proteins encoded in a carbon monoxide dehydrogenase (CODH) gene cluster. TON 1525 with a DNA-binding helix-turn-helix (HTH) motif is a putative repressor regulating the transcriptional expression of the codh gene cluster. The T55I mutation in TON 1525 led to enhanced H2 production accompanied by the increased expression of genes in the codh cluster. Here, TON 1525 was demonstrated to be a dimer. Monomeric TON 1525 adopts a novel ‘eighth note’ symbol-like fold (referred to as ‘eighth note’ fold regulator, EnfR), and the dimerization mode of EnfR is unique in that it has no resemblance to structures in the Protein Data Bank. According to footprinting and gel shift assays, dimeric EnfR binds to a 36-bp pseudo-palindromic inverted repeat in the promoter region of the codh gene cluster, which is supported by an in silico EnfR/DNA complex model and mutational studies revealing the implication of N-terminal loops as well as HTH motifs in DNA recognition. The DNA-binding affinity of the T55I mutant was lowered by ∼15-fold, for which the conformational change of N-terminal loops is responsible. In addition, transcriptome analysis suggested that EnfR could regulate diverse metabolic processes besides H2 production. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.