Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates

Abstract

ClpX, an archetypal proteolytic AAA+ unfoldase, must engage the ssrA tags of appropriate substrates prior to ATP-dependent unfolding and translocation of the denatured polypeptide into ClpP for degradation. Here, specificity-transplant and disulfide-crosslinking experiments reveal that the ssrA tag interacts with different loops that form the top, middle, and lower portions of the central channel of the ClpX hexamer. Our results support a two-step binding mechanism, in which the top loop serves as a specificity filter and the remaining loops form a binding site for the peptide tag relatively deep within the pore. Crosslinking experiments suggest a staggered arrangement of pore loops in the hexamer and nucleotide-dependent changes in pore-loop conformations. This mechanism of initial tag binding would allow ATP-dependent conformational changes in one or more pore loops to drive peptide translocation, force unfolding, and mediate threading of the denatured protein through the ClpX pore.

Figure 1

Three pore loops of ClpX are involved in ssrA-tag binding. (A) The RKH loops are colored gold, the pore-1 loops red, and the pore-2 loops blue in a ClpX hexamer model based on the subunit structure of H. pylori ClpX and the structure of the HslU hexamer (Kim and Kim, 2003; Bochtler et al., 2000). Three subunits of the hexamer were removed to allow visualization of the pore loops. These loops are not resolved in the crystal structure and the conformations shown are hypothetical. (B) A variant of human ClpX (hClpX^RKH/pore-2; 0.3 μM) containing the RKH and pore-2 loops of E. coli ClpX supported efficient degradation of CM-titin-ssrA by human ClpP (0.9 μM). Values of K_M and V_max derived from Michaelis-Menten analysis were 5μM and 2.7 min⁻¹ enz⁻¹ for hClpX^RKH/pore-2, and 1μM and 4.4 min⁻¹ enz⁻¹ for E. coli ClpXP. At equivalent enzyme concentrations, hClpX or variants with just the RKH loop (hClpX^RKH) or the pore-2 loop (hClpX^pore-2) from E. coli ClpX supported only slow hClpP degradation of the ssrA-tagged substrate. V_max may be lower for hClpX^eRKH/pore-2/hClpP than for E. coli ClpXP because the E. coli pore-2 loops do not interact properly with human ClpP. For example, E. coli ClpP binding represses the ATPase activity of E. coli ClpX in a pore-2 dependent manner (Martin et al., 2007), whereas the ATPase activity of hClpX^eRKH/pore-2 was not affected by hClpP binding (data not shown).

Figure 2

Crosslinking of ssrA peptides to ClpX pore loops. (A) Cartoon depicting disulfide crosslinking between a cysteine-containing ssrA peptide and a cysteine introduced into a pore loop of ClpX. Peptides contained a single cysteine in the ssrA-tag portion of the molecule (red), a biotinylated residue (b) in an N-terminal extension (yellow), and a N-terminal fluorescein (f). The avidin-biotin complex mimics a native protein substrate and orients the ssrA peptide for binding to ClpX. (B) Non-reducing SDS-PAGE of fluorescent cysteine-substituted ssrA peptides crosslinked the single-chain ClpX hexamer E^C200EREER with a cysteine in the pore-2 loop. Peptides with residues 1–9 of the ssrA tag individually replaced by cysteine were crosslinked to ClpX in the presence of ATPγS (upper panel) or in the absence of nucleotide to test for non-specific crosslinking (lower panel). Peptides A10C and A11C did not bind ClpX. (C) Bar graphs show the relative amounts of crosslinked product formed between cysteine-substituted ssrA peptides and a cysteine in the RKH loop (top panel), pore-1 loop (middle panel), or pore-2 loop (bottom panel) of a ClpX subunit trapped in the ATP state (E^CEREER, red bars) or empty state (R^CEREER, blue bars). Yellow bars show the intensities of non-specific crosslinking for each mutant in the absence of ATPγS. All intensities are averages from three independent crosslinking reactions; the highest mean intensity was assigned a value of 10. Standard deviations are not shown but were less than 10% of the mean.

Figure 3

Interaction of SspB•ssrA complexes with ClpX pore loops. (A) Binding of ClpX or ClpX-Δpore2 to a fluorescein-labeled disulfide-bonded SspB-ssrA complex (25 nM) was assayed by fluorescence anisotropy. The dashed binding curve for wild-type ClpX is from Bolon et al. (2004a). The solid binding curve for ClpX-Δpore2 reveals an approximate 65-fold decrease in affinity, implicating the pore-2 loop in SspB-mediated substrate delivery. (B) Surface-exposed positions around the ssrA-binding site in SspB were mutated individually to cysteine to probe potential disulfide crosslinking with ClpX. Most of the structure shown is based on the 1OU9 cocrystal structure (Levchenko et al., 2003), but the C-terminal six residues of the extended ssrA + 2 peptide were modeled. (C) Disulfide crosslinking between cysteine-substituted variants of SspB and single-chain variants of ClpX (E^CEREER) with cysteines at position 228 (RKH loop), 153 (pore-1 loop), or 200 (pore-2 loop) was performed in the presence or absence of GFP-ssrA+2. Crosslinked products were detected by anti-SspB western blotting (middle and right panels) or by coomassie staining (left panel) after non-reducing SDS-PAGE. Crosslinking reactions contained 1μM cysteine-substituted single-chain ClpX, 10μM cysteine-substituted SspB, and 4 μM GFP-ssrA + 2. (D) In this model of ClpX (green; two subunits removed to allow visualization of the pore), equivalent pore-loops (pore-1 red; pore-2 blue) are at the same axial level (Bochtler et al., 2000; Kim and Kim, 2003) and SspB (purple) with a bound ssrA tag (yellow) enters the upper part of the ClpX channel. This model accounts well for direct SspB handoff of ssrA-tagged substrate to ClpX and for the role of the pore-2 loop in recognition of SspB•ssrA complexes, but it is difficult to rationalize strong crosslinking between the pore-2 loops and SspB.

Figure 4

Two-step model for ssrA-tag binding to the ClpX pore. The cartoons show a schematic ClpX complex with two subunits in ATP-bound or empty nucleotide states and their associated RKH loops (gold), pore-1 loops (red), and pore-2 loops (blue). (A) The -carboxylate of ssrA is attracted by transient electrostatic interactions with the positively charged RKH loop at the entrance of the ClpX channel. (B) Binding of the LAA motif to the pore-1 and pore-2 loops moves the ssrA tag deep into the pore. (C) ATP-hydrolysis driven conformational changes in the loops and/or entire subunits (“up” conformation in ATP state; “down” conformation in empty state) translocate the ssrA tag, unfold the substrate, and thread the unfolded chain through the ClpX pore. (D) SspB delivery of ssrA-tagged substrate. A staggered orientation of equivalent loops in different subunits may allow SspB to access the pore-2 loop for direct substrate handoff.