ClpX(P) generates mechanical force to unfold and translocate its protein substrates

Abstract

AAA(+) unfoldases denature and translocate polypeptides into associated peptidases. We report direct observations of mechanical, force-induced protein unfolding by the ClpX unfoldase from E. coli, alone, and in complex with the ClpP peptidase. ClpX hydrolyzes ATP to generate mechanical force and translocate polypeptides through its central pore. Threading is interrupted by pauses that are found to be off the main translocation pathway. ClpX's translocation velocity is force dependent, reaching a maximum of 80 aa/s near-zero force and vanishing at around 20 pN. ClpX takes 1, 2, or 3 nm steps, suggesting a fundamental step-size of 1 nm and a certain degree of intersubunit coordination. When ClpX encounters a folded protein, it either overcomes this mechanical barrier or slips on the polypeptide before making another unfolding attempt. Binding of ClpP decreases the slip probability and enhances the unfolding efficiency of ClpX. Under the action of ClpXP, GFP unravels cooperatively via a transient intermediate.

Figure 1. Unfolding and Translocation of GFP-Titin Fusion Proteins by ClpX and ClpXP

(A) The geometry of our single-molecule assay in dual-trap optical tweezers: ClpX(P) complexes were immobilized on a streptavidin polystyrene bead (SA) via a biotin tag on ClpX. The GFP-titin fusion substrate is covalently linked to a 3 kbp dsDNA handle with a Dig tag that binds to an antibody-coated polystyrene bead (AD). All substrates included one or two GFP molecules (green) fused to a Ti_cm-ssrA moiety (red and black). The blue flexible linker corresponds to the ybbR tag. (B–D) GFP unfolding (red arrowheads), motor slips (black arrowheads) and translocation trajectories for three different substrates obtained at ~7 pN. (B) Single GFP-titin substrate. (C) Double GFP substrate with a short linker (10 aa) between the GFP molecules. (D) Double GFP substrate with a long flexible linker of 200 aa corresponding to two Ti_cm domains (red) between the GFP molecules. (E) Basic features of our single-molecule trajectories. The rip corresponding to a GFP unfolding is preceded by a pause (orange). After GFP is unfolded, ClpX translocates the unfolded polypeptide chain (green) with occasional pauses (orange). In all cases the raw data were filtered and decimated to 1000 Hz (in gray) or 2.5 Hz (in red). For the protocol describing the attachment of the dsDNA handle to the fusion substrates, see Figure S3. In the presence of ATP-γ-S, none of the unfolding or translocation events described in (B)–(E) were observed (Figure S5).

Figure 2. Motor Properties and Mechanochemical Cycle of ClpX(P)

(A) Extension translocation velocity (mean ± SEM in nm/s) as a function of external force for ClpX (red symbols) and ClpXP (blue symbols). The dotted curves represent phenomenological fits to the data. (B) Contour length translocation velocity (mean ± SEM in aa/s) as a function of external force for ClpX (red symbols) and ClpXP (blue symbols). The dotted lines extrapolate velocity to zero-external force. (C) Histograms of extension velocity for ClpX (red) and ClpXP (blue) at forces below 13 pN, where velocity is force independent. (D) The pause density (or frequency) during ClpX(P) translocation (mean ± SEM) as a function of force. (E) Correlation plot between ClpX(P) pause density (mean ± SEM) versus translocation velocity, when velocity is force independent (<13 pN). (F) The proposed minimal mechanochemical cycle for ClpX(P) during translocation, including associated force-dependent rates. X(P)_n-1, X(P)_n, and X(P)_n+1 refer to consecutive steps of ClpX(P) during translocation. The translocation rate (k_f) and pause entry (k_p), reflected by the pause-free velocity and pause density, respectively, are force dependent whereas the exit from a pause (k_-p) is independent of force. For additional information on pause desnsity and duration, see Table S2.

Figure 3. ClpXP Translocation Stepping Displays Coordination between Subunits

(A) Fragment of a ClpXP translocation region at ~10 pN displaying stepping periodicity of 1.0 nm. Raw data filtered and decimated to 500 Hz are shown in gray, and the raw data boxcar-filtered to 20 Hz are shown in blue. (B) The pairwise distance distribution for the trace in (A) shows a 1 nm periodicity (black arrows). (C) Side view of the nucleotide-bound ClpX hexamer (Glynn et al., 2009) with three subunits removed to allow visualization of the pore 1 loops (red) with the critical Tyr153 (stick representation) shows distinct staggering relative to the pore axis. The loop of the nucleotide-free subunit 1 is close to the top of the pore, whereas the loops of the nucleotide-bound subunits 2 and 3 are in an intermediate and bottom position, respectively. The distances between Tyr153 in each of these staggered positions are ~1 nm. (D and E) Fragment of a ClpXP translocation region at ~14 pN displaying a stepping periodicity of 2.2 and 3.0 nm, respectively. (F) The pairwise distance distribution for the traces in (D) and (E) shows the 2.2 and 3.0 nm periodicity (upper and lower panels, respectively). For data comparing the ATP hydrolysis rates of ClpX and ClpXP, see Table S1 and Figure S4.

Figure 4. Unraveling of GFP by ClpX(P) Shows a Well-Defined Structural Transition and Reveals a Single-Unfolding Intermediate

(A) The distribution of rip sizes (in aa) for all observed GFP unfolding events (red, n = 107) and slips (light red, n = 250) in ClpX and ClpXP traces. (B) ClpX trace containing the unfolding of the first GFP in the double GFP construct with the long linker (Figure 1D). The unfolding event is followed by the translocation of the unfolded GFP and the long linker. Raw data filtered and decimated to 800 Hz. (C) A detailed view of the short-lived GFP unfolding intermediate (black arrow in panel B). (D) Histogram of the first rip size during GFP unfolding. (E) The distribution of GFP unfolding intermediate lifetimes is well described by a single exponential. Dashed lines represent 95% confidence interval of the fit. (F) Histogram of the second rip size during GFP unfolding. For the rip size distribution before the long translocation marker (panel B), see Figure S1, and for side-by-side comparison of ClpX and ClpXP unfolding of GFP, see Figure S2.

Figure 5. A Schematic Representation of GFP Unfolding via a Short-Lived Intermediate

(F), (I), and (U) denote the folded, intermediate, and unfolded conformations of GFP. ΔX quantities correspond to experimentally observed extension changes (obs). X^F and X^I are the dimensions of the folded and intermediate states of GFP, estimated from structural data (struct). X^U1 and X^U2 are the true extensions (true) corresponding to the unfolding of the first and second portions of GFP (shown as flexible chains in green and purple, respectively). The true extension of the entire unfolded GFP molecule is X^U1 + X^U2. The table provides reference values estimated for 6–10 pN. Bottom right panel displays a characteristic “rip-transition-rip” during GFP unfolding.

Figure 6. ClpXP Is a More Robust Motor with Higher Unfolding Efficiency and Lower Slipping Frequency than ClpX Alone

(A and B) The dwell time before each ClpX- or ClpXP-mediated unfolding event is exponentially distributed. Dashed lines represent 95% confidence interval of the fit. (C) Slip size histograms for ClpX (red) and ClpXP (blue). (D) The slip entry rate (mean ± SEM) for ClpX (red) and ClpXP (blue). Slip entry rate is the inverse of the average waiting time before a slip occurs.

Figure 7. Model for the Mechanical Unfolding of GFP by ClpX(P)

(A) A two-dimensional representation of the folded GFP topology: β strands 11→7 are shown in green, and β strands 6→1 in purple. The ybbR tag is in blue. (B) A schematic diagram of GFP (green/purple) unfolding by a ClpX hexamer (orange) in complex with ClpP (blue). The left panel shows the entire complex with an intact GFP molecule before unfolding. The center-left panel shows the unfolding intermediate (in purple). The center-right panel shows the fully unfolded GFP after the spontaneous unfolding of the intermediate. The right panel shows ClpXP toward the end of unfolded GFP translocation. The GFP structure has been enlarged by ~53 for display purposes. (C) Assignment of the stages of GFP unfolding and translocation by ClpXP (in C-to-N direction) to a typical single-molecule trajectory. After several unfolding attempts (1), ClpXP unravels β strands 11→7 of GFP, generating a short-lived intermediate (2). After the spontaneous unfolding of the remaining GFP structure (β strands 6→1), ClpXP translocates the unfolded polypeptide through its central pore into ClpP (3). Note that ClpXP commenced translocation while the GFP unfolding intermediate was still present (2). The number labeling (1–3) scheme is the same as in panel B.