A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus

Abstract

DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases. Initial phylogenetic analysis showed that an EndoQ homolog is found only in the Thermococcales and some of the methanogens in Archaea, and is not present in most members of the domains Bacteria and Eukarya. A better understanding of the distribution of the EndoQ-mediated repair system is, therefore, of evolutionary interest. We showed here that an EndoQ-like polypeptide from Bacillus pumilus, belonging to the bacterial domain, is functional and has similar properties with the archaeal EndoQs.

The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG

“…Such decreased cleavage efficiency towards AP-ssDNA has also been previously described for other characterized EndoQ homologs 32 , 33 . These findings suggest that MacEndoQ possesses endonuclease activity with substrate specificity as observed for EndoQ of the hyperthermophilic order Thermococcales , and the bacterial EndoQ from B. pumilus 32 , 33 . Thus, MacEndoQ appears to be involved in the repair of dU, dI, and AP sites.…”

“…Importantly, our results further suggest that EndoQ also functions in many archaea besides the Thermococcales and may play a key role in maintaining DNA free of uracil in ‘UDG-lacking’ organisms (Fig. 7 and earlier reports 32 , 33 ). Thus, our findings highlight the substantial redundancy in uracil repair proteins in Archaea, raising a new question of what is the advantage of having multiple co-existing repair pathways.…”

“…Based on amino acid sequence homology, the putative EndoQ homologs are present in most of the Euryarchaeota (one of the major phyla of Archaea) and in some limited groups in Bacteria 32 . Similar endonuclease activity was identified from an EndoQ homolog detected in the gram-positive bacterium Bacillus pumilus 33 . This enzyme generates a nick immediately 5′ to uracil, and at the hypoxanthine, xanthine, and AP site in DNA 32 , 33 .…”

“…Similar endonuclease activity was identified from an EndoQ homolog detected in the gram-positive bacterium Bacillus pumilus 33 . This enzyme generates a nick immediately 5′ to uracil, and at the hypoxanthine, xanthine, and AP site in DNA 32 , 33 . Notably, the endonuclease activity toward uracil (and the AP site) is identical between EndoQ and ExoIII.…”

“…Thus, MacEndoQ appears to be involved in the repair of dU, dI, and AP sites. This finding further suggests that other putative EndoQ homologs in Euryarchaeota are most likely to be functional, taking into consideration the high conservation in protein sequences and phyletic analysis of this protein 33 .

Figure 2 MacEndoQ exhibits dU, dI, and AP endonuclease activities.

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