Chloroplastic Hsp100 chaperones ClpC2 and ClpD interact in vitro with a transit peptide only when it is located at the N-terminus of a protein
© Bruch et al.; licensee BioMed Central Ltd. 2012
Received: 3 October 2011
Accepted: 30 April 2012
Published: 30 April 2012
Clp/Hsp100 chaperones are involved in protein quality control. They act as independent units or in conjunction with a proteolytic core to degrade irreversibly damaged proteins. Clp chaperones from plant chloroplasts have been also implicated in the process of precursor import, along with Hsp70 chaperones. They are thought to pull the precursors in as the transit peptides enter the organelle. How Clp chaperones identify their substrates and engage in their processing is not known. This information may lie in the position, sequence or structure of the Clp recognition motifs.
We tested the influence of the position of the transit peptide on the interaction with two chloroplastic Clp chaperones, ClpC2 and ClpD from Arabidopsis thaliana (AtClpC2 and AtClpD). The transit peptide of ferredoxin-NADP+ reductase was fused to either the N- or C-terminal end of glutathione S-transferase. Another fusion with the transit peptide interleaved between two folded proteins was used to probe if AtClpC2 and AtClpD could recognize tags located in the interior of a polypeptide. We also used a mutated transit peptide that is not targeted by Hsp70 chaperones (TP1234), yet it is imported at a normal rate. The fusions were immobilized on resins and the purified recombinant chaperones were added. After a washing protocol, the amount of bound chaperone was assessed. Both AtClpC2 and AtClpD interacted with the transit peptides when they were located at the N-terminal position of a protein, but not when they were allocated to the C-terminal end or at the interior of a polypeptide.
AtClpC2 and AtClpD have a positional preference for interacting with a transit peptide. In particular, the localization of the signal sequence at the N-terminal end of a protein seems mandatory for interaction to take place. Our results have implications for the understanding of protein quality control and precursor import in chloroplasts.
KeywordsHsp100 chaperones Clp Chloroplasts Protein import Transit peptide
Clp/Hsp100 proteins are a class of hexameric molecular chaperones from the ever-growing family of AAA + (ATPases associated with diverse cellular activities) ATPases. They possess a wide range of functional roles, including protein folding assistance, protein degradation, disaggregation of denatured polypeptides and assembly of large molecular complexes [1–3]. Most (if not all) Clp/Hsp100 proteins act as independent chaperones but some associate with oligomeric barrel-shaped proteases to degrade irreversibly damaged proteins [4, 5]. Notable examples are ClpA and ClpX from Escherichia coli and ClpC from Bacillus subtilis and Synechococcus elongatus, which couple to their respective ClpP protease [6–8].
In plants, the diversity of the Clp family is greater than in any other organism. The model plant A. thaliana has at least 23 members . Hsp100 chaperones from the ClpX family (ClpX1-3) are found in mitochondria while those from the ClpC (ClpC1 and ClpC2) and ClpD subtype are chloroplastic. The ClpPR proteolytic core is represented by six different proteins (ClpP1-6) and four ClpR proteins (ClpR1-4). Three modulator/adaptor proteins (ClpT1, ClpT2 and ClpS) are thought to regulate substrate recognition and binding.
Recombinant AtClpC2 and AtClpD have been recently characterized . AtClpD was consistently obtained as two forms, one being the full-length protein and the other corresponding to a C-terminus-processed variant. The proteins displayed ATPase and foldase activity and self-assembled into hexamers. Clp/Hsp100 chaperones are constitutively expressed and are highly conserved among different plant species . Knockout plants in the Atclpc1 gene are pale green and show retarded growth, while Atclpc1/Atclpc2 double mutants are not viable . All this evidence suggests that chloroplastic Clp proteins are key members in the process of protein quality control in the chloroplast.
In addition to their proposed housekeeping duties, ClpC proteins from plants have been implicated in the import of nuclear-encoded proteins into chloroplasts. Proteins destined to the organelle are synthesized as higher molecular mass precursors containing an N-terminal extension called transit peptide (TP). It acts as a signal that is recognized by the translocon channel, a bipartite complex with central pores through which precursors penetrate into the plastid stroma [13, 14]. A fraction of ClpC is localized in the stromal side of the chloroplast inner membrane and interacts with the import machinery when a precursor is being translocated [10, 15]. In A. thaliana, chloroplasts isolated from insertional mutants in the clpc1 gene show a diminished rate of import [12, 16, 17]. The current model of protein import into chloroplasts place Hsp100 chaperones (specifically, members of the ClpC subfamily) as motors pulling precursors by their TPs. Yet many aspects of this scenario are still to be elucidated, such as TP recognition by the chaperone, threading of the polypeptide through the Hsp100 ring and interplay with the Hsp70 network, which was also shown to interact with precursors .
The step of substrate recognition has been studied in ClpA from E. coli. This chaperone can recognize tags located at the N- or C-terminal end (e.g., the RepA tag and the SsrA tag, respectively) [19, 20]. Though the amino acid composition of these tags is well characterized, consensus sequences are still not defined, as many other untagged proteins are substrates of ClpA . It is thought that short exposed segments with hydrophobic amino acids and little (if any) tridimensional structure are recognized, like is the case for the substrates of Lon protease and the chaperones GroEL, DnaK, Trigger Factor and many others . However, it is not known which specific attributes are recognized by the Hsp100 chaperones associated with the translocation channel. Furthermore, since only a handful of Hsp100 targets have been identified, no obvious sequence pattern is available to analyze if a given TP could be an Hsp100 substrate.
The aim of this work was to elucidate some aspects of the process of TP recognition by Clp/Hsp100 chaperones. Several fusion proteins were constructed in which TPs were placed at different positions in a polypeptide. Then, binding to these probes by purified recombinant AtClpC2 and AtClpD was analyzed. Using this in vitro system, we found that AtClpC2 and AtClpD only interacted with the fusions that have the TPs in the natural location (i.e., at the N-terminus).
Results and discussion
AtClpC2 and AtClpD interact with transit peptides located in the N-terminal end
The interaction of AtClpC2 and AtClpD with a TP located at N-terminal end of a given protein was rather expected. This situation is present in protein translocation across membranes, where the N-termini of precursors enter the organelle and may be met by AtClpC1/2 (and possibly AtClpD) that pull them in. The fact that only the C-terminal processed variant of AtClpD interacted with the fusions suggests that this would be the active form, at least under these conditions. However, no evidence exists about chaperone activity regulation by C-terminal processing. This could represent a novel mechanism to adjust the quantity of active AtClpD.
We also used TP1234-GST in this study to investigate why TP1234-bearing proteins are efficiently imported to chloroplasts, considering that they are not targeted by Hsp70 chaperones . Su et al. postulated that Hsp100 and Hsp70 chaperones associate to precursors independently rather than cooperatively . They arrived at this conclusion after noting that A. thaliana double mutant plants in the dominant paralogs of Hsp70 and Hsp100 (cpHsc70-1 and ClpC1, respectively) showed additive import defects. The fact that the chaperones readily associated with TP1234-GST supports this model: since Hsp70 chaperones do not interact with TP1234, then AtClpC1 or AtClpC2 (and possibly AtClpD) provide the driving force for its import, without the aid of another chaperone system.
AtClpC2 and AtClpD cannot recognize a transit peptide with blocked termini
For internally tagged substrates, AtClpC2 and AtClpD chaperones behave as their bacterial counterparts, i.e., they do not recognize the tags when located between two proteins . This lack of recognition rules out two probable scenarios. First, it could be possible that a loop containing the recognition sequence is targeted by the chaperones, since the central pore present in Clp hexamers is wide enough to accommodate two polypeptide chains simultaneously . In this case, the presence of a free end would not be necessary. A second possibility would be that dimers of the Clp chaperones continuously scan for targets and upon finding them, the hexamer would form over the sequence. This situation would also avoid the requirement for a free end. Yet, our results and those of others do not support these models, at least in vitro. The situation in vivo may be somewhat different. Other proteins may aid in substrate presentation or in the assembly and disassembly of the hexamers, making the above hypotheses still plausible.
AtClpC2 and AtClpD cannot recognize transit peptides located at the C-terminal end of a protein
Taken together, our results show that tag position seems to be important for substrate recognition by Clp chaperones from plants, as observed for the TP of pea FNR. By contrast, bacterial Clp chaperones such as ClpA and ClpX from E. coli do not discriminate against the position of the sequence tag [28, 31]. For example, the first 15 amino acids of the ClpA-substrate RepA are sufficient to tag any protein for degradation by ClpP. When this ClpA-recognition motif is allocated to the C-terminal end, efficient degradation by ClpAP ensues. Moreover, when the RepA tag was placed at the C-terminal end of the green fluorescent protein but in an inverse orientation, the tagged protein was still unfolded by ClpA as judged by a loss in fluorescence. Other experiments were carried out using a ClpX-specific tag (the last ten amino acids of its substrate MuA) with similar results. These reports from the Wickner lab showed that bacterial Clp chaperones promote substrate unfolding, regardless of the position and orientation of the tag. Why this different mode of action between plant and bacterial chaperones exists is not clear. Precursors may represent a subset of Clp/Hsp100 substrates with particular recognition rules. More work is needed to fully understand how stromal chaperones bind to precursors and other targets.
In this work, we show that AtClpC2 and AtClpD from A. thaliana interact with the transit peptide of pea FNR located at the N-terminal end of a polypeptide. Its relocation to the C-terminal end or to the interior of a protein abolishes the interaction. The chaperones could also bind to a mutated TP not recognizable by Hsp70 chaperones, explaining why fusion proteins bearing this TP are efficiently imported into chloroplasts. Altogether, our results agree with the role of Clp/Hsp100 chaperones in the binding and pulling of incoming proteins into the chloroplastic stroma.
The DNA coding sequence of TP and TP1234 of pea FNR were amplified by PCR from the plasmids pGF202b and pGF202b-1234 . The primers contained an NcoI and a SacI restriction sites that allowed directional cloning into a modified pET32 vector called pETGEXCT , resulting in plasmids pETGEX-TP and pETGEX-TP1234. These expression vectors produce each TP fused to the N-terminal end of GST. Construction of plasmids pGF202 and pGF205, which express GST fused to the N-terminal end of the FNR precursor (fusion GST-TP-FNR) or mature FNR (fusion GST-FNR), respectively, has been described elsewhere [33, 34]. Plasmids pDR52 and pDR52b  encode the proteins GST-TP and GST-TP1234, respectively, where the TPs are fused to the C-terminal region of GST. All constructs used in this study were checked by DNA sequencing.
Protein expression and purification
The plasmids were used to transform the E. coli strain BL21(DE3). Transformed cells were grown in Luria-Bertani medium containing the corresponding antibiotics at 37°C until the suspension reached an optical density of 0.7 at 600 nm. Afterwards, the cells were cooled to 18°C, induced by adding 0.5 mM isopropyl-β-D-thiogalactopyranoside and grown for 16 hours at 18°C. Cells were collected by centrifugation, resuspended in cold lysis buffer (50 mM Tris–HCl, pH 8.0, 150 mM NaCl, 1 mM phenylmethylsulfonyl fluoride, 1 mM benzamidine, 1 mM dithiothreitol, 5 mM EDTA, 10% v/v glycerol) in a 20:1 ratio (culture:lysis buffer) and sonicated in an ice-water bath. All subsequent steps were performed at 4°C. The soluble fraction was obtained by centrifugation (30000 × g, 1 h) and incubated with glutathione-agarose resin (35 μl resin/ml soluble extract) for 30 min. Then, the beads were washed 3 times with 10 volumes of lysis buffer, 3 times with 3 volumes of lysis buffer containing 5 mM ATP and 0.15 mg/ml E. coli denatured proteins , and finally, 3 times with 10 volumes of P buffer (50 mM Tris–HCl, pH 8.0, 100 mM NaCl, 10 mM MgCl2, 10% v/v glycerol). This procedure removes DnaK contamination from TP-containing fusions. For limited proteolysis assays, the fusion proteins were eluted using P buffer + 10 mM glutathione and used immediately.
Protein samples were subjected to gel electrophoresis in denaturing conditions according to Laemmli , using 12% polyacrylamide gels. Samples were also analyzed by Western blotting. Polyacrylamide gels were transferred overnight to nitrocellulose sheets. After transfer, proteins were detected with the corresponding antibody followed by an anti-rabbit alkaline phosphatase-conjugated antibody (GE Healthcare, USA). Detection with the chromogenic substrates 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium chloride was carried out as recommended by the suppliers. Band quantification was performed by scanning the blots and by subsequent analysis of the data with GelPro Analyzer software (Media Cybernetics, USA).
The antibodies against GST, FNR and AtClpD were obtained by us. Antibodies against AtClpC2 were purchased from Agrisera AB (Sweden).
The different fusion proteins were bound to glutathione-agarose beads from cell lysates as described above. Then, 500 μl of the corresponding loaded matrix were added to 500 μl of AtClpC2 or AtClpD in the presence of 5 mM ATP and incubated for 30 min at 25°C. Beads were then pelleted by mild centrifugation and resuspended in 500 μl of P buffer. A 100-μl aliquot was taken from the mixture and centrifugated to collect the resin. The beads were boiled in 50 μl of 2X loading buffer and analyzed by SDS-polyacryamide gels and immunoblotting with antibodies raised against each chaperone. P buffer was added to the remaining resin in an equal volume and the washing procedure was performed as described. This method was repeated three more times. Resin without recombinant proteins or loaded with GST served as controls.
Limited proteolysis assays
For each assay, 5 μg of the fusion protein GST-TP-FNR were incubated with 2 ng of thermolysin in buffer T (20 mM Tris–HCl, pH 8.0, 400 mM NaCl, 8 mM CaCl2). Aliquots corresponding to 1 μg of the fusion protein were taken at 0, 10, 20, 60 and 180 minutes after the addition of the protease. The samples were boiled for 5 minutes with an adequate amount of 2X loading buffer and analyzed by SDS-polyacryamide gels or by immunoblotting using antibodies against GST or FNR.
EAC is a staff member and GLR and EMB are Fellows of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina). This study was supported by grants from CONICET and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT, Argentina).
- Neuwald AF, Aravind L, Spouge JL, Koonin EV: AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 1999, 9: 27-43.PubMedGoogle Scholar
- Ogura T, Wilkinson AJ: AAA + superfamily ATPases: common structure–diverse function. Genes Cells. 2001, 6: 575-597. 10.1046/j.1365-2443.2001.00447.x.PubMedView ArticleGoogle Scholar
- Snider J, Thibault G, Houry WA: The AAA + superfamily of functionally diverse proteins. Genome Biol. 2008, 9: 216-10.1186/gb-2008-9-4-216.PubMedPubMed CentralView ArticleGoogle Scholar
- Maurizi MR, Xia D: Protein binding and disruption by Clp/Hsp100 chaperones. Structure. 2004, 12: 175-183.PubMedView ArticleGoogle Scholar
- Schirmer EC, Glover JR, Singer MA, Lindquist S: HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem Sci. 1996, 21: 289-296.PubMedView ArticleGoogle Scholar
- Stanne TM, Pojidaeva E, Andersson FI, Clarke AK: Distinctive types of ATP-dependent Clp proteases in cyanobacteria. J Biol Chem. 2007, 282: 14394-14402. 10.1074/jbc.M700275200.PubMedView ArticleGoogle Scholar
- Porankiewicz J, Wang J, Clarke AK: New insights into the ATP-dependent Clp protease: Escherichia coli and beyond. Mol Microbiol. 1999, 32: 449-458. 10.1046/j.1365-2958.1999.01357.x.PubMedView ArticleGoogle Scholar
- Gottesman S, Roche E, Zhou Y, Sauer RT: The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 1998, 12: 1338-1347. 10.1101/gad.12.9.1338.PubMedPubMed CentralView ArticleGoogle Scholar
- Adam Z, Rudella A, van Wijk KJ: Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Curr Opin Plant Biol. 2006, 9: 234-240. 10.1016/j.pbi.2006.03.010.PubMedView ArticleGoogle Scholar
- Rosano GL, Bruch EM, Ceccarelli EA: Insights into the CLP/HSP100 chaperone system from chloroplasts of Arabidopsis thaliana. J Biol Chem. 2011, 286: 29671-29680. 10.1074/jbc.M110.211946.PubMedPubMed CentralView ArticleGoogle Scholar
- Zheng B, Halperin T, Hruskova-Heidingsfeldova O, Adam Z, Clarke AK: Characterization of Chloroplast Clp proteins in Arabidopsis: Localization, tissue specificity and stress responses. Physiol Plant. 2002, 114: 92-101. 10.1034/j.1399-3054.2002.1140113.x.PubMedView ArticleGoogle Scholar
- Kovacheva S, Bedard J, Wardle A, Patel R, Jarvis P: Further in vivo studies on the role of the molecular chaperone, Hsp93, in plastid protein import. Plant J. 2007, 50: 364-379. 10.1111/j.1365-313X.2007.03060.x.PubMedView ArticleGoogle Scholar
- Li HM, Chiu CC: Protein transport into chloroplasts. Annu Rev Plant Biol. 2010, 61: 157-180. 10.1146/annurev-arplant-042809-112222.PubMedView ArticleGoogle Scholar
- Strittmatter P, Soll J, Bolter B: The chloroplast protein import machinery: a review. Methods Mol Biol. 2010, 619: 307-321. 10.1007/978-1-60327-412-8_18.PubMedView ArticleGoogle Scholar
- Nielsen E, Akita M, vila-Aponte J, Keegstra K: Stable association of chloroplastic precursors with protein translocation complexes that contain proteins from both envelope membranes and a stromal Hsp100 molecular chaperone. EMBO J. 1997, 16: 935-946. 10.1093/emboj/16.5.935.PubMedPubMed CentralView ArticleGoogle Scholar
- Kovacheva S, Bedard J, Patel R, Dudley P, Twell D, Rios G, Koncz C, Jarvis P: In vivo studies on the roles of Tic110, Tic40 and Hsp93 during chloroplast protein import. Plant J. 2005, 41: 412-428.PubMedView ArticleGoogle Scholar
- Constan D, Froehlich JE, Rangarajan S, Keegstra K: A stromal Hsp100 protein is required for normal chloroplast development and function in Arabidopsis. Plant Physiol. 2004, 136: 3605-3615. 10.1104/pp.104.052928.PubMedPubMed CentralView ArticleGoogle Scholar
- Su PH, Li HM: Stromal Hsp70 is important for protein translocation into pea and Arabidopsis chloroplasts. Plant Cell. 2010, 22: 1516-1531. 10.1105/tpc.109.071415.PubMedPubMed CentralView ArticleGoogle Scholar
- Levchenko I, Luo L, Baker TA: Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev. 1995, 9: 2399-2408. 10.1101/gad.9.19.2399.PubMedView ArticleGoogle Scholar
- Wickner S, Gottesman S, Skowyra D, Hoskins J, McKenney K, Maurizi MR: A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc Natl Acad Sci U S A. 1994, 91: 12218-12222. 10.1073/pnas.91.25.12218.PubMedPubMed CentralView ArticleGoogle Scholar
- Tobias JW, Shrader TE, Rocap G, Varshavsky A: The N-end rule in bacteria. Science. 1991, 254: 1374-1377. 10.1126/science.1962196.PubMedView ArticleGoogle Scholar
- Sauer RT, Baker TA: AAA + Proteases: ATP-Fueled Machines of Protein Destruction. Annu Rev Biochem. 2011, 80: 587-612. 10.1146/annurev-biochem-060408-172623.PubMedView ArticleGoogle Scholar
- Rial DV, Arakaki AK, Ceccarelli EA: Interaction of the targeting sequence of chloroplast precursors with Hsp70 molecular chaperones. Eur J Biochem. 2000, 267: 6239-6248. 10.1046/j.1432-1327.2000.01707.x.PubMedView ArticleGoogle Scholar
- Rial DV, Ottado J, Ceccarelli EA: Precursors with altered affinity for Hsp70 in their transit peptides are efficiently imported into chloroplasts. J Biol Chem. 2003, 278: 46473-46481. 10.1074/jbc.M306684200.PubMedView ArticleGoogle Scholar
- Guo F, Maurizi MR, Esser L, Xia D: Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J Biol Chem. 2002, 277: 46743-46752. 10.1074/jbc.M207796200.PubMedView ArticleGoogle Scholar
- Creighton TE: Proteins: Structures and Molecular Properties. W. H.Freeman; Second Edition; 2011.Google Scholar
- Fitzkee NC, Rose GD: Reassessing random-coil statistics in unfolded proteins. Proc Natl Acad Sci U S A. 2004, 101: 12497-12502. 10.1073/pnas.0404236101.PubMedPubMed CentralView ArticleGoogle Scholar
- Hoskins JR, Wickner S: Two peptide sequences can function cooperatively to facilitate binding and unfolding by ClpA and degradation by ClpAP. Proc Natl Acad Sci U S A. 2006, 103: 909-914. 10.1073/pnas.0509154103.PubMedPubMed CentralView ArticleGoogle Scholar
- Burton RE, Siddiqui SM, Kim YI, Baker TA, Sauer RT: Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J. 2001, 20: 3092-3100. 10.1093/emboj/20.12.3092.PubMedPubMed CentralView ArticleGoogle Scholar
- Gur E, Sauer RT: Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev. 2008, 22: 2267-2277. 10.1101/gad.1670908.PubMedPubMed CentralView ArticleGoogle Scholar
- Hoskins JR, Yanagihara K, Mizuuchi K, Wickner S: ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence. Proc Natl Acad Sci U S A. 2002, 99: 11037-11042. 10.1073/pnas.172378899.PubMedPubMed CentralView ArticleGoogle Scholar
- Sharrocks AD: A T7 expression vector for producing N- and C-terminal fusion proteins with glutathione S-transferase. Gene. 1994, 138: 105-108. 10.1016/0378-1119(94)90789-7.PubMedView ArticleGoogle Scholar
- Serra EC, Krapp AR, Ottado J, Feldman MF, Ceccarelli EA, Carrillo N: The precursor of pea ferredoxin-NADP + reductase synthesized in Escherichia coli contains bound FAD and is transported into chloroplasts. J Biol Chem. 1995, 270: 19930-19935. 10.1074/jbc.270.34.19930.PubMedView ArticleGoogle Scholar
- Serra EC, Carrillo N, Krapp AR, Ceccarelli EA: One-step purification of plant ferredoxin-NADP + oxidoreductase expressed in Escherichia coli as fusion with glutathione S-transferase. Protein Expr Purif. 1993, 4: 539-546. 10.1006/prep.1993.1071.PubMedView ArticleGoogle Scholar
- Rial DV, Ceccarelli EA: Removal of DnaK contamination during fusion protein purifications. Protein Expr Purif. 2002, 25: 503-507. 10.1016/S1046-5928(02)00024-4.PubMedView ArticleGoogle Scholar
- Rosano GL, Ceccarelli EA: Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain. Microb Cell Fact. 2009, 8: 41-10.1186/1475-2859-8-41.PubMedPubMed CentralView ArticleGoogle Scholar
- Laemmli UK: Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970, 227: 680-685. 10.1038/227680a0.PubMedView ArticleGoogle Scholar