Holliday junction-resolving enzymes from eight hyperthermophilic archaea differ in reactions with cruciform DNA

Holliday junction-resolving enzymes have been identified in a broad variety of organisms and tissues. In this study, six new Holliday junction-cleaving enzymes (Hjcs) were obtained from hyperthermophilic crenarchaeal and euryarchaeal species, including Pyrococcus horikoshii, Pyrococcus abyssi, Methanococcus jannaschii, Methanobacterium thermautotrophicum, Archaeoglobus fulgidus, and Aeropyrum pernix. The genes were cloned and overexpressed in Escherichia coli, and the respective proteins were purified from crude extracts to homogeneity. For an initial characterization of the enzymatic activities, synthetic heat-stable fixed and mobile cruciform DNA substrates were used at 75 degrees C. The Hjcs from Pyrococcus furiosus, Sulfolobus solfataricus, and the archaeal virus SIRV2 were included in the study for comparison. Despite their sequence homology, the enzymes showed marked differences in their reactions with individual cruciform DNAs. While the fixed cruciform structure was cleaved by all enzymes at only one major position, the mobile cruciform structure displayed different cleavage patterns for individual Hjcs, each with several cleavage positions. Furthermore, a strong bias for cleavage of one direction across the junction was observed with the fixed cruciform DNA for all enzymes. In contrast, the mobile cruciform DNA displayed different preferences, depending on the enzyme used.