Efficient processing of DNA ends during yeast nonhomologous end joining - Evidence for a DNA polymerase beta (POL4)-dependent pathway

Repair of DNA double strand breaks by nonhomologous end joining (NHEJ) requ ires enzymatic processing beyond simple ligation when the terminal bases ar e damaged or not fully compatible. We transformed yeast with a series of li nearized plasmids to examine the role of Pol4 (Pol IV, DNA polymerase beta) in repair at a variety of end configurations. Mutation of POL4 did not imp air DNA polymerase-independent religation of fully compatible ends and led to at most a a-fold reduction in the frequency of joins that require only D NA polymerization, In contrast, the frequency of joins that also required r emoval of a 5'- or S'-terminal mismatch was markedly reduced in pol4 (but n ot rev3, exo1, apn1, or rad1) yeast. In a chromosomal double strand break a ssay, pol4 mutation conferred a marked increase in sensitivity to HO endonu clease in a rad52 background, due primarily to loss of an NHEJ event that a nneals with a 3'-terminal mismatch. The NHEJ activity of Pol4 was dependent on its nucleotidyl transferase function, as well as its unique amino termi nus. Paradoxically, in vitro analyses with oligonucleotide substrates demon strated that although Pol4 fills gaps with displacement of mismatched but n ot matched 5' termini, it lacks both 5'- and 3'-terminal nuclease activitie s. Pol4 is thus specifically recruited to perform gap-filling in an NHEJ pa thway that must also involve as yet unidentified nucleases.