Clp ATPases and their role in protein unfolding and degradation

ClpL Chaperone as a Possible Component of the Disaggregase Activity of Limosilactobacillus fermentum U-21

The L. fermentum U-21 strain, known for secreting chaperones into the extracellular milieu, emerges as a promising candidate for the development of novel therapeutics termed disaggregases for Parkinson's disease. Our study focuses on characterizing the secreted protein encoded by the C0965_000195 locus in the genome of this strain. Through sequence analysis and structural predictions, the protein encoded by C0965_000195 is identified as ClpL, homologs of which are known for their chaperone functions. The chaperone activity of ClpL from L. fermentum U-21 is investigated in vivo by assessing the refolding of luciferases with varying thermostabilities from Aliivibrio fischeri and Photorhabdus luminescens within Escherichia coli cells. The results indicate that the clpL gene from L. fermentum U-21 can compensate for the absence of the clpB gene, enhancing the refolding capacity of thermodenatured proteins in clpB-deficient cells. In vitro experiments demonstrate that both spent culture medium containing proteins secreted by L. fermentum U-21 cells, including ClpL, and purified heterologically expressed ClpL partially prevent the thermodenaturation of luciferases. The findings suggest that the ClpL protein from L. fermentum U-21, exhibiting disaggregase properties against aggregating proteins, may represent a key component contributing to the pharmabiotic attributes of this strain.

Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

Germin (GER) and germin-like proteins (GLPs) play an important role in various plant processes. Zea mays contains 26 germin-like protein genes (ZmGLPs) located on chromosomes 2, 4, and 10; most of which are functionally unexplored. The present study aimed to characterize all ZmGLPs using the latest computational tools. All of them were studied at a physicochemical, subcellular, structural, and functional level, and their expression was predicted in plant development, against biotic and abiotic stresses using various in silico approaches. Overall, ZmGLPs showed greater similarity in their physicochemical properties, domain architecture, and structure, mostly localized in the cytoplasmic or extracellular regions. Phylogenetically, they have a narrow genetic background with a recent history of gene duplication events on chromosome 4. Functional analysis revealed novel enzymatic activities of phosphoglycolate phosphatase, adenosylhomocysteinase, phosphoglycolate phosphatase-like, osmotin/thaumatin-like, and acetohydroxy acid isomeroreductase largely mediated by disulfide bonding. Expression analysis revealed their crucial role in the root, root tips, crown root, elongation and maturation zones, radicle, and cortex with the highest expression being observed during germination and at the maturity levels. Further, ZmGLPs showed strong expression against biotic (Aspergillus flavus, Colletotrichum graminicola, Cercospora zeina, Fusarium verticillioides, and Fusarium virguliforme) while limited expression was noted against abiotic stresses. Concisely, our results provide a platform for additional functional exploration of the ZmGLP genes against various environmental stresses.

Expression and function of clpS and clpA in Xanthomonas campestris pv. campestris

ATP-dependent proteases (FtsH, Lon, and Clp family proteins) are ubiquitous in bacteria and play essential roles in numerous regulatory cell processes. Xanthomonas campestris pv. campestris is a Gram-negative pathogen that can cause black rot diseases in crucifers. The genome of X. campestris pv. campestris has several clp genes, namely, clpS, clpA, clpX, clpP, clpQ, and clpY. Among these genes, only clpX and clpP is known to be required for pathogenicity. Here, we focused on two uncharacterized clp genes (clpS and clpA) that encode the adaptor (ClpS) and ATPase subunit (ClpA) of the ClpAP protease complex. Transcriptional analysis revealed that the expression of clpS and clpA was growth phase-dependent and affected by the growth temperature. The inactivation of clpA, but not of clpS, resulted in susceptibility to high temperature and attenuated virulence in the host plant. The altered phenotypes of the clpA mutant could be complemented in trans. Site-directed mutagenesis revealed that K223 and K504 were the amino acid residues critical for ClpA function in heat tolerance. The protein expression profile shown by the clpA mutant in response to heat stress was different from that exhibited by the wild type. In summary, we characterized two clp genes (clpS and clpA) by examining their expression profiles and functions in different processes, including stress tolerance and pathogenicity. We demonstrated that clpS and clpA were expressed in a temperature-dependent manner and that clpA was required for the survival at high temperature and full virulence of X. campestris pv. campestris. This work represents the first time that clpS and clpA were characterized in Xanthomonas.

Identification of Essential Genes Associated With Prodigiosin Production in Serratia marcescens FZSF02

Prodigiosin is a promising secondary metabolite produced mainly by Serratia strains. To study the global regulatory mechanism of prodigiosin biosynthesis, a mutagenesis library containing 23,000 mutant clones was constructed with the EZ-Tn5 transposon, and 114 clones in the library showed altered prodigiosin production ability. For 37 of the 114 clones, transposon insertion occurred on the prodigiosin biosynthetic cluster genes; transposon inserted genes of the 77 clones belonged to 33 different outside prodigiosin biosynthetic cluster genes. These 33 genes can be divided into transcription-regulating genes, membrane protein-encoding genes, and metabolism enzyme-encoding genes. Most of the genes were newly reported to be involved in prodigiosin production. Transcriptional levels of the pigA gene were significantly downregulated in 22 mutants with different inserted genes, which was in accordance with the phenotype of decreased prodigiosin production. Functional confirmation of the mutant genes involved in the pyrimidine nucleotide biosynthesis pathway was carried out by adding orotate and uridylate (UMP) into the medium. Gene complementation confirmed the regulatory function of the EnvZ/OmpR two-component regulatory system genes envZ and ompR in prodigiosin production.

Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans

Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.

Kinetics of the thermal inactivation and the refolding of bacterial luciferases in Bacillus subtilis and in Escherichia coli differ

Here we present a study of the thermal inactivation and the refolding of the proteins in Gram positive Bacillus subtilis. To enable use of bacterial luciferases as the models for protein thermal inactivation and refolding in B. subtilis cells, we developed a variety of bright luminescent B. subtilis strains which express luxAB genes encoding luciferases of differing thermolability. The kinetics of the thermal inactivation and the refolding of luciferases from Photorhabdus luminescens and Photobacterium leiognathi were compared in Gram negative and Gram positive bacteria. In B. subtilis cells, these luciferases are substantially more thermostable than in Escherichia coli. Thermal inactivation of the thermostable luciferase P. luminescens in B. subtilis at 48.5°С behaves as a first-order reaction. In E.coli, the first order rate constant (Kt) of the thermal inactivation of luciferase in E. coli exceeds that observed in B. subtilis cells 2.9 times. Incubation time dependence curves for the thermal inactivation of the thermolabile luciferase of P. leiognathi luciferase in the cells of E. coli and B. subtilis may be described by first and third order kinetics, respectively. Here we shown that the levels and the rates of refolding of thermally inactivated luciferases in B. subtilis cells are substantially lower that that observed in E. coli. In dnaK-negative strains of B. subtilis, both the rates of thermal inactivation and the efficiency of refolding are similar to that observed in wild-type strains. These experiments point that the role that DnaKJE plays in thermostability of luciferases may be limited to bacterial species resembling E. coli.

The effect of mutation in the clpX gene on the synthesis of N-acyl-homoserine lactones and other properties of Burkholderia cenocepacia 370

In order to study the regulation of N-acyl-homoserine lactones synthesis (AHLs, the signal molecules of Quorum Sensing regulation) in Burkholderia cenocepacia strain 370 we obtained mutants with increased AHL production. One of the mutants, named BC-B6, was obtained by TnMod-RKm(r) plasposon mutagenesis. The plasposon insertion was located within the clpX gene encoding the ATPase subunit ClpX of the ClpXP protease. The mutation reduced bacterial virulence in mice intranasal infection. The results of proteomic analysis demonstrated that the expression of at least 19 proteins differed not less than 2-fold between the parental and mutant strains. 18 of the proteins were upregulated in the mutant, and one protein was downregulated. The proteins included those that involved in protein synthesis and modification, in energy production, in general metabolism, in transport and regulation. To check the effect of the clpX mutation on the AHL synthesis, a mutant with inactivated clpX gene (BC-clpX:Km(r)) was constructed by gene replacement method. This mutant also exhibited increased AHLs production. A swarming motility of both mutants was reduced compared to the original strain. Thus, the obtained results show that the clpX gene was involved in the regulation of AHL production and a number of cellular processes in B. cenocepacia 370.

Degradation of some polyubiquitinated proteins requires an intrinsic proteasomal binding element in the substrates

Lysine 48-linked polyubiquitin chains usually target proteins for 26 S proteasomal degradation; however, this modification is not a warrant for destruction. Here, we found that efficient degradation of a physiological substrate UbcH10 requires not only an exogenous polyubiquitin chain modification but also its unstructured N-terminal region. Interestingly, the unstructured N-terminal region of UbcH10 directly binds the 19 S regulatory complex of the 26 S proteasome, and it mediates the initiation of substrate translocation. To promote ubiquitin-dependent degradation of the folded domains of UbcH10, its N-terminal region can be displaced by exogenous proteasomal binding elements. Moreover, the unstructured N-terminal region can initiate substrate translocation even when UbcH10 is artificially cyclized without a free terminus. Polyubiquitinated circular UbcH10 is completely degraded by the 26 S proteasome. Accordingly, we propose that degradation of some polyubiquitinated proteins requires two binding interactions: a polyubiquitin chain and an intrinsic proteasomal binding element in the substrates (likely an unstructured region); moreover, the intrinsic proteasomal binding element initiates substrate translocation regardless of its location in the substrates.

Studying chaperone-proteases using a real-time approach based on FRET

Chaperone-proteases are responsible for the processive breakdown of proteins in eukaryotic, archaeal and bacterial cells. They are composed of a cylinder-shaped protease lined on the interior with proteolytic sites and of ATPase rings that bind to the apical sides of the protease to control substrate entry. We present a real-time FRET-based method for probing the reaction cycle of chaperone-proteases, which consists of substrate unfolding, translocation into the protease and degradation. Using this system we show that the two alternative bacterial ClpAP and ClpXP complexes share the same mechanism: after initial tag recognition, fast unfolding of substrate occurs coinciding with threading through the chaperone. Subsequent slow substrate translocation into the protease chamber leads to formation of a transient compact substrate intermediate presumably close to the chaperone-protease interface. Our data for ClpX and ClpA support the mechanical unfolding mode of action proposed for these chaperones. The general applicability of the designed FRET system is demonstrated here using in addition an archaeal PAN-proteasome complex as model for the more complex eukaryotic proteasome.

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

Background

The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins.

Method

In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B) are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out.

Results

Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s) for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified.

Conclusion

The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome.

The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from the parasite that could provide leads to identify novel drug targets against malaria.

The flexible attachment of the N-domains to the ClpA ring body allows their use on demand

ClpA is an Hsp100 chaperone that uses the chemical energy of ATP to remodel various protein substrates to prepare them for degradation. It comprises two AAA+ modules and the N-domain, which is attached N-terminally to the first AAA+ module through a linker. On the basis of cryo-electron microscopic and X-ray crystallographic data it has been suggested that the linker confers mobility to the N-domain. In order to define the role of the N-domain in ClpAP-dependent substrate degradation we have generated a Delta N variant at the protein level by introducing a protease cleavage site. The ClpA molecule generated in this way lacks the N-domain and the associated linker but is impaired only slightly in the processing of substrates that are degraded independently of ClpS. In fact, it shows increased catalytic efficiency in the degradation of ssrA-tagged GFP compared to ClpAwt. The role of the linker attaching the N-domain to the bulk of the molecule was probed by characterizing variants with different lengths of the linker. The degradation efficiency of a ClpS-dependent N-end rule substrate, FRliGFP, is reduced for linkers that are shorter or longer than natural linkers but remains the same for the variant where the linker is replaced by an engineered sequence of equivalent length. These results suggest that the flexible attachment of the N-domains to ClpA allows their recruitment to the pore on demand for certain substrates, while allowing them to move out of the way for substrates binding directly to the pore.

Protein targeting to ATP-dependent proteases

ATP-dependent proteases control diverse cellular processes by degrading specific regulatory proteins. Recent work has shown that protein substrates are specifically transferred to ATP-dependent proteases through different routes. These routes can function in parallel or independently. In all of these targeting mechanisms, it can be useful to separate two steps: substrate binding to the protease and initiation of degradation.

Evolutionary relationships and structural mechanisms of AAA+ proteins

Complex cellular events commonly depend on the activity of molecular "machines" that efficiently couple enzymatic and regulatory functions within a multiprotein assembly. An essential and expanding subset of these assemblies comprises proteins of the ATPases associated with diverse cellular activities (AAA+) family. The defining feature of AAA+ proteins is a structurally conserved ATP-binding module that oligomerizes into active arrays. ATP binding and hydrolysis events at the interface of neighboring subunits drive conformational changes within the AAA+ assembly that direct translocation or remodeling of target substrates. In this review, we describe the critical features of the AAA+ domain, summarize our current knowledge of how this versatile element is incorporated into larger assemblies, and discuss specific adaptations of the AAA+ fold that allow complex molecular manipulations to be carried out for a highly diverse set of macromolecular targets.

Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone

The ClpXP ATPase-protease complex is a major component of the protein quality control machinery in the cell. A ClpX subunit consists of an N-terminal zinc binding domain (ZBD) and a C-terminal AAA+ domain. ClpX oligomerizes into a hexamer with the AAA+ domains forming the base of the hexamer and the ZBDs extending out of the base. Here, we report that ClpX switches between a capture and a feeding conformation. ZBDs in ClpX undergo large nucleotide-dependent block movement towards ClpP and into the AAA+ ring. This motion is modulated by the ClpX cofactor, SspB. Evidence for this movement was initially obtained by the surprising observation that an N-terminal extension on ClpX is clipped by bound ClpP in functional ClpXP complexes. Protease-protection, crosslinking, and light scattering experiments further support these findings.

Two peptide sequences can function cooperatively to facilitate binding and unfolding by ClpA and degradation by ClpAP

Clp/Hsp100 proteins comprise a large family of AAA(+) ATPases. Some Clp proteins function alone as molecular chaperones, whereas others act in conjunction with peptidases, forming ATP-dependent proteasome-like compartmentalized proteases. Protein degradation by Clp proteases is regulated primarily by substrate recognition by the Clp ATPase component. The ClpA and ClpX ATPases of Escherichia coli generally recognize short amino acid sequences that are located near the N or C terminus of a substrate. However, both ClpAP and ClpXP are able to degrade proteins in which the end containing the recognition signal is fused to GFP such that the signal is in the interior of the primary sequence of the substrate. Here, we tested whether the internal ClpA recognition signal was the sole element required for targeting the substrate to ClpA. The results show that, in the absence of a high-affinity peptide recognition signal at the terminus, two elements are important for recognition of GFP-RepA fusion proteins by ClpA. One element is the natural ClpA recognition signal located at the junction of GFP and RepA in the fusion protein. The second element is the C-terminal peptide of the fusion protein. Together, these two elements facilitate binding and unfolding by ClpA and degradation by ClpAP. The internal site appears to function similarly to Clp adaptor proteins but, in this case, is covalently attached to the polypeptide containing the terminal tag and both the "adaptor" and "substrate" modules are degraded.

ClpXP controls the expression of LEE genes in enterohaemorrhagic Escherichia coli

Enterohaemorrhagic Escherichia coli (EHEC) contains a 36-kb pathogenicity island termed the locus of enterocyte effacement (LEE), which encodes a type III secretion system (TTSS) and virulence proteins. In this paper, we show that the O157:H7 Sakai clpPX mutant strongly impaired the secretion of virulence proteins by TTSS and repressed transcription from all the LEE promoters. The rpoS mutation in O157:H7 Sakai enhanced the transcription from all the LEE promoters and the secretion of virulence proteins, and it could partially suppress the defects of the clpPX mutation. These data indicate that the O157:H7 Sakai ClpXP protease is a positive regulator for LEE expression and that this regulation occurs by two pathways: the sigma(S)-dependent and -independent pathways.

Roles of the N-domains of the ClpA Unfoldase in Binding Substrate Proteins and in Stable Complex Formation with the ClpP Protease

The hexameric cylindrical Hsp100 chaperone ClpA mediates ATP-dependent unfolding and translocation of recognized substrate proteins into the coaxially associated serine protease ClpP. Each subunit of ClpA is composed of an N-terminal domain of approximately 150 amino acids at the top of the cylinder followed by two AAA+ domains. In earlier studies, deletion of the N-domain was shown to have no effect on the rate of unfolding of substrate proteins bearing a C-terminal ssrA tag, but it did reduce the rate of degradation of these proteins (Lo, J. H., Baker, T. A., and Sauer, R. T. (2001) Protein Sci. 10, 551-559; Singh, S. K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J., Steven, A. C., and Maurizi, M. R. (2001) J. Biol. Chem. 276, 29420-29429). Here we demonstrate, using both fluorescence resonance energy transfer to measure the arrival of substrate at ClpP and competition between wild-type and an inactive mutant form of ClpP, that this effect on degradation is caused by diminished stability of the ClpA-ClpP complex during translocation and proteolysis, effectively disrupting the targeting of unfolded substrates to the protease. We have also examined two larger ssrA-tagged substrates, CFP-GFP-ssrA and luciferase-ssrA, and observed different behaviors. CFP-GFP-ssrA is not efficiently unfolded by the truncated chaperone whereas luciferase-ssrA is, suggesting that the former requires interaction with the N-domains, likely via the body of the protein, to stabilize its binding. Thus, the N-domains play a key allosteric role in complex formation with ClpP and may also have a critical role in recognizing certain tag elements and binding some substrate proteins.

Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation

The cylindrical Hsp100 chaperone ClpA mediates ATP-dependent unfolding of substrate proteins bearing "tag" sequences, such as the 11-residue ssrA sequence appended to proteins translationally stalled at ribosomes. Unfolding is coupled to translocation through a central channel into the associating protease, ClpP. To explore the topology and mechanism of ClpA action, we carried out chemical crosslinking and functional studies. Whereas a tag from RepA protein crosslinked proximally to the flexible N domains, the ssrA sequence in GFP-ssrA crosslinked distally in the channel to a segment of the distal ATPase domain (D2). Single substitutions placed in this D2 loop, and also in two apparently cooperating proximal (D1) loops, abolished binding of ssrA substrates and unfolded proteins lacking tags and blocked unfolding of GFP-RepA. Additionally, a substitution adjoining the D2 loop allowed binding of ssrA proteins but impaired their translocation. This loop, as in homologous nucleic-acid translocases, may bind substrates proximally and, coupled with ATP hydrolysis, translocate them distally, exerting mechanical force that mediates unfolding.

Cytoplasmic degradation of ssrA-tagged proteins

Degradation of ssrA-tagged proteins is a central feature of protein-quality control in all bacteria. In Escherichia coli, the ATP-dependent ClpXP and ClpAP proteases are thought to participate in this process, but their relative contributions to degradation of ssrA-tagged proteins in vivo have been uncertain because two adaptor proteins, ClpS and SspB, can modulate proteolysis of these substrates. Here, intracellular levels of these protease components and adaptors were determined during exponential growth and as cells entered early stationary phase. Levels of ClpA and ClpP increased about threefold during this transition, whereas ClpX, ClpS and SspB levels remained nearly constant. Using GFP-ssrA expressed from the chromosome as a degradation reporter, the effects of altered concentrations of different protease components or adaptor proteins were explored. Both ClpXP and ClpAP degraded GFP-ssrA in the cell, demonstrating that wild-type levels of SspB and ClpS do not inhibit ClpAP completely. Upon entry into stationary phase, increased levels of ClpAP resulted in increased degradation of ssrA-tagged substrates. As measured by maximum turnover rates, ClpXP degradation of GFP-ssrA in vivo was significantly more efficient than in vitro. Surprisingly, ClpX-dependent ClpP-independent degradation of GFP-ssrA was also observed. Thus, unfolding of this substrate by ClpX appears to enhance intracellular degradation by other proteases.

Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation

ClpX and related AAA+ ATPases of the Clp/Hsp100 family are able to denature native proteins. Here, we explore the role of protein stability in ClpX denaturation and subsequent ClpP degradation of model substrates bearing ssrA degradation tags at different positions. ClpXP degraded T. thermophilus RNase-H* with a C-terminal ssrA tag very efficiently, despite the very high global stability of this thermophilic protein. In fact, global thermodynamic stability appears to play little role in susceptibility to degradation, as a far less stable RNase-H*-ssrA mutant was degraded more slowly than wild type by ClpXP and a completely unfolded mutant variant was degraded less than twice as fast as the wild-type parent. When ssrA peptide tags were covalently linked to surface cysteines at positions 114 or 140 of RNase-H*, the conjugates were proteolyzed very slowly. This resistance to degradation was not caused by inaccessibility of the ssrA tag or an inability of ClpXP to degrade proteins with side-chain linked ssrA tags. Our results support a model in which ClpX denatures proteins by initially unfolding structural elements attached to the degradation tag, suggest an important role for the position of the degradation tag and direction of force application, and correlate well with the mapping of local protein stability within RNase-H* by native-state hydrogen exchange.

Evolutionary history and higher order classification of AAA+ ATPases

The AAA+ ATPases are enzymes containing a P-loop NTPase domain, and function as molecular chaperones, ATPase subunits of proteases, helicases or nucleic-acid-stimulated ATPases. All available sequences and structures of AAA+ protein domains were compared with the aim of identifying the definitive sequence and structure features of these domains and inferring the principal events in their evolution. An evolutionary classification of the AAA+ class was developed using standard phylogenetic methods, analysis of shared sequence and structural signatures, and similarity-based clustering. This analysis resulted in the identification of 26 major families within the AAA+ ATPase class. We also describe the position of the AAA+ ATPases with respect to the RecA/F1, helicase superfamilies I/II, PilT, and ABC classes of P-loop NTPases. The AAA+ class appears to have undergone an early radiation into the clamp-loader, DnaA/Orc/Cdc6, classic AAA, and "pre-sensor 1 beta-hairpin" (PS1BH) clades. Within the PS1BH clade, chelatases, MoxR, YifB, McrB, Dynein-midasin, NtrC, and MCMs form a monophyletic assembly defined by a distinct insert in helix-2 of the conserved ATPase core, and additional helical segment between the core ATPase domain and the C-terminal alpha-helical bundle. At least 6 distinct AAA+ proteins, which represent the different major clades, are traceable to the last universal common ancestor (LUCA) of extant cellular life. Additionally, superfamily III helicases, which belong to the PS1BH assemblage, were probably present at this stage in virus-like "selfish" replicons. The next major radiation, at the base of the two prokaryotic kingdoms, bacteria and archaea, gave rise to several distinct chaperones, ATPase subunits of proteases, DNA helicases, and transcription factors. The third major radiation, at the outset of eukaryotic evolution, contributed to the origin of several eukaryote-specific adaptations related to nuclear and cytoskeletal functions. The new relationships and previously undetected domains reported here might provide new leads for investigating the biology of AAA+ ATPases.

Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease

The SspB adaptor enhances ClpXP degradation by binding the ssrA degradation tag of substrates and the AAA+ ClpX unfoldase. To probe the mechanism of substrate delivery, we engineered a disulfide bond between the ssrA tag and SspB and demonstrated otherwise normal interactions by solving the crystal structure. Although the covalent link prevents adaptor.substrate dissociation, ClpXP degraded GFP-ssrA that was disulfide bonded to the adaptor. Thus, crosslinked substrate must be handed directly from SspB to ClpX. The ssrA tag in the covalent adaptor complex interacted with ClpX.ATPgammaS but not ClpX.ADP, suggesting that handoff occurs in the ATP bound enzyme. By contrast, SspB alone bound ClpX in both nucleotide states. Similar handoff mechanisms will undoubtedly be used by many AAA+ adaptors and enzymes, allowing assembly of delivery complexes in either nucleotide state, engagement of the recognition tag in the ATP state, and application of an unfolding force to the attached protein following hydrolysis.

Binding and degradation of heterodimeric substrates by ClpAP and ClpXP

ClpA and ClpX function both as molecular chaperones and as the regulatory components of ClpAP and ClpXP proteases, respectively. ClpA and ClpX bind substrate proteins through specific recognition signals, catalyze ATP-dependent protein unfolding of the substrate, and when in complexes with ClpP translocate the unfolded polypeptide into the cavity of the ClpP peptidase for degradation. To examine the mechanism of interaction of ClpAP with dimeric substrates, single round binding and degradation experiments were performed, revealing that ClpAP degraded both subunits of a RepA homodimer in one cycle of binding. Furthermore, ClpAP was able to degrade both protomers of a RepA heterodimer in which only one subunit contained the ClpA recognition signal. In contrast, ClpXP degraded both subunits of a dimeric substrate only when both protomers contained a recognition signal. These data suggest that ClpAP and ClpXP may recognize and bind substrates in significantly different ways.

Sculpting the proteome with AAA(+) proteases and disassembly machines

Machines of protein destruction-including energy-dependent proteases and disassembly chaperones of the AAA(+) ATPase family-function in all kingdoms of life to sculpt the cellular proteome, ensuring that unnecessary and dangerous proteins are eliminated and biological responses to environmental change are rapidly and properly regulated. Exciting progress has been made in understanding how AAA(+) machines recognize specific proteins as targets and then carry out ATP-dependent dismantling of the tertiary and/or quaternary structure of these molecules during the processes of protein degradation and the disassembly of macromolecular complexes.

The DnaK-DnaJ-GrpE chaperone system activates inert wild type pi initiator protein of R6K into a form active in replication initiation

The plasmid R6K is an interesting model system for investigating initiation of DNA replication, not only near the primary binding sites of the initiator protein pi but also at a distance, caused by pi -mediated DNA looping. An important milestone in the mechanistic analysis of this replicon was the development of a reconstituted replication system consisting of 22 different highly purified proteins (Abhyankar, M. A., Zzaman, S., and Bastia, D. (2003) J. Biol. Chem. 278, 45476-45484). Although the in vitro reconstituted system promotes ori gamma-specific initiation of replication by a mutant form of the initiator called pi*, the wild type (WT) pi is functionally inert in this system. Here we show that the chaperone DnaK along with its co-chaperone DnaJ and the nucleotide exchange factor GrpE were needed to activate WT pi and caused it to initiate replication in vitro at the correct origin. We show further that the reaction was relatively chaperone-specific and that other chaperones, such as ClpB and ClpX, were incapable of activating WT pi. The molecular mechanism of activation appeared to be a chaperone-catalyzed facilitation of dimeric inert WT pi into iteron-bound monomers. Protein-protein interaction analysis by enzyme-linked immunosorbent assay revealed that, in the absence of ATP, DnaJ directly interacted with pi but its binary interactions with DnaK and GrpE and with ClpB and ClpX were at background levels, suggesting that pi is recruited by protein-protein interaction with DnaJ and then fed into the DnaK chaperone machine to promote initiator activation.

The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis

Measurements of overall protein degradation rates in wild-type and clpP mutant Bacillus subtilis cells revealed that stress- or starvation-induced bulk protein turnover depends virtually exclusively on the ClpP peptidase. ClpP is also essential for intracellular protein quality control, and in its absence newly synthesized proteins were highly prone to aggregation even at 37 degrees C. Proteomic comparisons between the wild type and a DeltaclpP mutant showed that the absence of ClpP leads to severe perturbations of "normal" physiology, complicating the detection of ClpP substrates. A pulse-chase two-dimensional gel approach was therefore used to compare wild-type and clpP mutant cultures that had been radiolabeled in mid-exponential phase, by quantifying changes in relative spot intensities with time. The results showed that overall proteolysis is biased toward proteins with vegetative functions which are no longer required (or are required at lower levels) in the nongrowing state. The identified substrate candidates for ClpP-dependent degradation include metabolic enzymes and aminoacyl-tRNA synthetases. Some substrate candidates catalyze the first committed step of certain biosynthetic pathways. Our data suggest that ClpP-dependent proteolysis spans a broad physiological spectrum, with regulatory processing of key metabolic components and regulatory proteins on the one side and general bulk protein breakdown at the transition from growing to nongrowing phases on the other.

Bivalent Tethering of SspB to ClpXP Is Required for Efficient Substrate Delivery

SspB homodimers deliver ssrA-tagged substrates to ClpXP for degradation. SspB consists of a substrate binding domain and an unstructured tail with a ClpX binding module (XB). Using computational design, we engineered an SspB heterodimer whose subunits did not form homodimers. Experiments with the designed molecule and variants lacking one or two tails demonstrate that both XB modules are required for strong binding and efficient substrate delivery to ClpXP. Assembly of stable SspB-substrate-ClpX delivery complexes requires the coupling of weak tethering interactions between ClpX and the SspB XB modules as well as interactions between ClpX and the substrate degradation tag. The ClpX hexamer contains three XB binding sites, one per N domain dimer, and thus binds strongly to just one SspB dimer at a time. Because different adaptor proteins use the same tethering sites in ClpX, those which employ bivalent tethering, like SspB, will compete more effectively for substrate delivery to ClpXP.

The N-terminal zinc binding domain of ClpX is a dimerization domain that modulates the chaperone function

Clp ATPases are unique chaperones that promote protein unfolding and subsequent degradation by proteases. The mechanism by which this occurs is poorly understood. Here we demonstrate that the N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lambdaO and MuA but not GFP-SsrA. Furthermore, experiments indicate that ZBD contains a primary binding site for the lambdaO substrate and for the cofactor SspB. Removal of ZBD from the ClpX sequence renders the ATPase activity of ClpX largely insensitive to the presence of ClpP, substrates, or the SspB cofactor. All these results indicate that ZBD plays an important role in the ClpX mechanism of function and that ATP binding and/or hydrolysis drives a conformational change in ClpX involving ZBD.

Solution Structure of the Dimeric Zinc Binding Domain of the Chaperone ClpX

ClpX (423 amino acids), a member of the Clp/Hsp100 family of molecular chaperones and the protease, ClpP, comprise a multimeric complex supporting targeted protein degradation in Escherichia coli. The ClpX sequence consists of an NH2-terminal zinc binding domain (ZBD) and a COOH-terminal ATPase domain. Earlier, we have demonstrated that the zinc binding domain forms a constitutive dimer that is essential for the degradation of some ClpX substrates such as gammaO and MuA but is not required for the degradation of other substrates such as green fluorescent protein-SsrA. In this report, we present the NMR solution structure of the zinc binding domain dimer. The monomer fold reveals that ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions. However, the dimeric ZBD structure is not related to any protein structure in the Protein Data Bank. A trimer-of-dimers model of ZBD is presented, which might reflect the closed state of the ClpX hexamer.

Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation

ClpS is a small protein, usually encoded immediately upstream of ClpA in the genomes of proteobacteria. Recent results show that it is a molecular adaptor for substrate recognition by ClpA in Escherichia coli. We analyzed ClpS by bioinformatic methods and found that ClpS homologs are also found in organisms that lack ClpA, such as actinobacteria, cyanobacteria, and plant chloroplasts. Furthermore, ClpS is homologous to a domain in the eukaryotic E3 ubiquitin ligase, N-recognin. This domain has previously been described as responsible for the recognition of type 2 N-end rule substrates. Despite very low levels of sequence similarity to proteins of known structure, there appears to be substantial structural similarity between ClpS and the C-terminal domain of ribosomal protein L7/12 (1CTF).