Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae

Degradation of poly(A) RNA by S. cerevisiae Pop2p. (A) Reaction scheme for pre-steady-state exonuclease reaction by Pop2p. (B) Representative PAGE for a pre-steady-state exonuclease reaction with A₃₆. Aliquots were removed at 0.5, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, and 110 min. Numbers indicate the RNA length. (C) Representative PAGE for a pre-steady-state exonuclease reaction with A₃₆ with increased ratio of Pop2p to RNA. Aliquots were removed at 10, 20, 40 sec, 1, 3, 5, 10, 15, and 20 min. (D) Representative PAGE for a pre-steady exonuclease reaction with A₂₄. Aliquots were removed at 10, 20, 40 sec, 1, 3, 5, 10, 15, and 20 min. (E) Representative PAGE for a pre-steady exonuclease reaction with A₁₃. Aliquots were removed at 1, 5, 10, 20, 30, 40, 50, and 60 min. (F) Distribution of k-mers (length of remaining substrate species) at the 20 min time point for pre-steady exonuclease reactions (Pop2p: 1200 nM) with indicated RNA substrates. Data points represent an average of three independent experiments. Error bars show one standard deviation. (G) Time courses for removal of the 3′ nucleotide of the initial substrate degradation for the reactions shown in panels C–E. The curves were fitted to integrated rate for an irreversible first order reaction (k_obs^(A36) = 0.71 ± 0.10 min⁻¹, k_obs^(A24) = 0.47 ± 0.06 min⁻¹, k_obs^(A13) = 0.16 ± 0.01 min⁻¹).