The molecular origin of various DNA-repair quantum yield in photolyases.

Abstract

Photolyases is a blue-light-activated flavoenzyme that use FADH− as the catalytic cofactor to repair UV-induced DNA lesions including cyclobutene pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4 PP). Different classes of CPD photolyases show diverse genetic sequences but have similar folding structure. Class I CPD photolyases from bacteria have much higher repair quantum yields than class II CPD photolyases from plants. The difference mainly comes from a bifurcation in initial electron transfer: class I CPD photolyases mainly use a tunnelling pathway (electron from the isoalloxazine ring directly tunnels to the CPD substrate), while class II CPD photolyases mainly use a two-step hopping pathway (electron first jumps to the adenine and then jumps to the CPD substrate). In this study, we switched two key residues in the active sites of class I (N341, R342 in EcPL from Escherichia coli) and class II photolyases (G381, F382 in AtPL from Arabidopsis thaliana). Steady-state repair quantum yield measurements show dramatic lower repair quantum yields in EcPL mutants compared to EcPL while a different trend is observed in AtPL and its mutants. To reveal how these residues affect the repair reaction, ultrafast laser spectroscopy was used to determine the reaction rates of seven electron-transfer reactions in 10 elementary steps. We found that the repair quantum yields can be tuned by favoring either electron tunnelling or hopping channel, and thus adjusting the quantum yield of electron injection to the CPD substrate. Photolyases evolved to have high affinity and specificity towards DNA lesion with reasonably repair quantum yield. Solely increasing repair quantum yield by single mutation may disrupt the delicate balance between substrate binding and CPD repair.