Applied force reveals mechanistic and energetic details of transcription termination

Abstract

Transcription termination by bacterial RNA polymerase (RNAP) occurs at sequences coding for a GC-rich RNA hairpin followed by a U-rich tract. We used single-molecule techniques to investigate the mechanism by which three representative terminators (his, t500, and tR2) destabilize the elongation complex (EC). For his and tR2 terminators, loads exerted to bias translocation did not affect termination efficiency (TE). However, the force-dependent kinetics of release and the force-dependent TE of a mutant imply a forward translocation mechanism for the t500 terminator. Tension on isolated U-tracts induced transcript release in a manner consistent with RNA:DNA hybrid shearing. We deduce that different mechanisms, involving hypertranslocation or shearing, operate at terminators with different U-tracts. Tension applied to RNA at terminators suggests that closure of the final 2-3 hairpin bases destabilizes the hybrid and that competing RNA structures modulate TE. We propose a quantitative, energetic model that predicts the behavior for these terminators and mutant variants.

Figure 1. Intrinsic Terminators and Single-Molecule DNA-pulling Assay

(A) Sequences and expected secondary structure for the three intrinsic hairpin terminators and U-tracts used in this study. Underlined bases indicate the transcript termination positions. (B) Experimental geometry for the DNA-pulling dumbbell assay (not to scale). Two polystyrene beads (light blue) are held in two separate optical traps (pink). RNAP (green) is attached to the smaller of the two beads via a biotin-avidin linkage (yellow and black), and the DNA template (dark blue) is attached to the larger bead via a digoxigenin-antidigoxigenin linkage (purple and orange). The RNA transcript (red) emerges co-transcriptionally from RNAP and is untethered. The direction of transcription is shown (green arrow); in this particular orientation of the DNA template, the applied tension assists RNAP translocation. (C) Twelve representative records of RNAP elongation on the his terminator template under 18 pN of assisting load. Nine records terminated within ±40 nm of the expected position of the terminator (shaded gray area), whereas three ran through the terminator position.

Figure 2. TE and Kinetics as a Function of Force Applied to the DNA

Termination efficiency and terminal dwell lifetimes (mean ± SEM) are plotted as functions of the load applied between the DNA template and the RNAP; positive force values correspond to loads assisting RNAP translocation. (A) TE for the his terminator (dark blue circles), tR2 terminator (red squares), and his U-tract (light blue triangles). Fits of each data set to a constant are displayed (dotted lines): 78 ± 3% (his), 31 ± 3% (tR2), and 7 ± 3% (his U-tract). (B) TE for the t500 terminator (light green triangles) and t500 stem mutant (dark green circles). The force-dependence of the t500 stem mutant terminator was fit by Equations 2,3 (dark green dotted line), yielding a distance parameter of 0.49 ± 0.13 nm (~1.4 bp). The inset shows substitutions made to the base of the hairpin stem for the t500 mutant. (C) Average terminal dwell times at the t500 terminator (light green triangles). Data were fit to Equation 1 (light green dotted line) giving a force-dependent distance parameter of 0.52 ± 0.10 nm. Inset: Three groups of three representative, aligned records that terminated at the t500 sequence under loads of -10 pN (red), -4 pN (black), and +10 pN (blue).

Figure 3. Single-Molecule RNA-pulling Transcription Assay

(A) Experimental geometry for the RNA-pulling dumbbell assay. The nascent RNA (red) is hybridized to a 25-nt overhang of a 3 kb DNA handle (dark blue), which is attached at its distal end to a polystyrene bead (light blue) through a biotin-avidin linkage (yellow and black). (B) Ten representative records of RNAP elongation on the his U-tract template under 30 pN assisting load. Eight records terminated within ±50 nm of the expected position of the his U-tract (shaded gray area), whereas two ran through this region. (C) Record of RNA extension (blue) on the his U-tract template at both high and low loads (red). Initially, elongation took place under 25 pN load along the nascent transcript. At 32 sec, the force was dropped to 10 pN, causing a decrease in the apparent tether extension. Under 10 pN of load, the record shows that RNAP continues transcription at very nearly the same rate at that observed at 25 pN. At 55 sec, the tether ruptured. Using the average rate of elongation at 25 pN and extrapolating from the extension of the tether immediately prior to the drop in force, we can accurately estimate the template position at which the RNA was released (dotted line). In this record, the extrapolated termination location occurred within ±50 nm of the expected position of the his U-tract (shaded gray area).

Figure 4. Force Applied Along RNA Affects TE and an Energetic Model of Termination

(A)-(C) Termination efficiency (mean ± SEM) plotted as a function of the load applied between the nascent RNA and RNAP. (A) The complete his terminator (dark blue) and associated U-tract alone (light blue), (B) the complete t500 terminator (dark green) and associated U-tract alone (light green), (C) the complete tR2 terminator (dark red) and associated U-tract alone (light red). For each complete terminator, two values for TE at F = 0 are plotted: the TE determined in bulk solution using a gel-based assay (black filled circles) and the TE measured in the same fashion, but in the presence of a complementary oligo that prevents secondary structure from forming in the upstream region (the endogenous TE, shown by the open, colored circle at F = 0). Solid light-colored lines show global fits to Equations 2 & 4, solid dark-colored lines show fits to Equations 2 & 5. (D) An energy landscape representation of the quantitative model for termination. The TE is determined by the difference, ΔE_total, between energy barriers to elongation (right) and termination (left). The portion of the landscape depicted in red represents the barrier to termination for terminator U-tracts, which can be modulated by force on the RNA, lowering it by ~F ×·δ_hybrid (dotted red line; the exact expression for modulation of this barrier includes corrections for the mechanical properties of ssRNA, not shown here; see Supplemental Materials and Equation 4) The inclusion of a hairpin stem lowers the termination barrier by E_stem (solid green line). Force on RNA biases against folding of the terminator hairpin, raising the barrier to termination by ~F ×·δ_stem (dotted green line). The overall TE is related to ΔE_total through Equation 2. (E) Table of global best-fit parameters, obtained by fitting the TE for all three terminators and associated U-tracts at all forces to Equation 2 & 5.

Figure 5. Model Prediction for TE of Mutant Terminators

Sequences and expected secondary structures for 4 mutant terminator constructs based on his, t500, and tR2 (mutated bases are shown in red). Model predictions (TE_pred) for the endogenous TE were calculated from Equation 2 & 5 at F =0, using previously determined values for E_hybrid (Figure 4) and computing E_stem from MFOLD predictions for the energy difference in pairing nucleotides at the base of the hairpin stem between the mutant and unmodified terminators. Experimental values (TE_actual) for the endogenous TE were measured in solution in the presence of saturating concentrations of complementary oligos designed to block competing upstream secondary structure.

Figure 6. Model of the Termination Pathway

The pathways to termination or transcriptional run-through for the his, t500, and tR2 terminators. Upon reaching an intrinsic terminator, a fraction of terminators hairpins fail to fold due to kinetic competition with upstream secondary structure, resulting in run-through. For the fraction that fold, the subsequent decision to terminate is set by a competition between the energy barriers for termination and elongation (Figure 4D). The his and t500 terminators are energetically biased to terminate with high probability once the hairpin folds, whereas the tR2 terminator terminates only ~65% of the time. Once the decision to terminate is made, the his and tR2 terminators terminate without forward translocation, likely by a shearing motion of the RNA:DNA hybrid through ~1.4 bp. At the t500 terminator, RNAP first forward translocates by ~1.4 bp along DNA to reach a state that is committed to termination (the 3’ end of the transcript has been removed from the RNAP active-site, blocking further elongation). The existence of this committed intermediate leads to a terminal dwell prior to termination. A second translocation step of ~1.5 bp is required for complete complex dissociation.