Two families of chaperonin: physiology and mechanism

ThehtpABoperon ofLegionella pneumophilacannot be deleted in the presence of thegroEchaperonin operon ofEscherichia coli

HtpB, the chaperonin of the intracellular bacterial pathogen Legionella pneumophila , displays several virulence-related functions in vitro. To confirm HtpB’s role in vivo, host infections with an htpB deletion mutant would be required. However, we previously reported that the htpAB operon (encoding co-chaperonin and chaperonin) is essential. We attempted here to delete htpAB in a L. pneumophila strain carrying the groE operon (encoding the Escherichia coli co-chaperonin and chaperonin). The groE operon was inserted into the chromosome of L. pneumophila Lp02, and then allelic replacement of htpAB with a gentamicin resistance cassette was attempted. Although numerous potential postallelic replacement transformants showed a correct selection phenotype, we still detected htpAB by PCR and full-size HtpB by immunoblot. Southern blot and PCR analysis indicated that the gentamicin resistance cassette had apparently integrated in a duplicated htpAB region. However, we showed by Southern blot that strain Lp02, and the Lp02 derivative carrying the groE operon, have only one copy of htpAB. These results confirmed that the htpAB operon cannot be deleted, not even in the presence of the groE operon, and suggested that attempts to delete htpAB under strong phenotypic selection result in aberrant genetic recombinations that could involve duplication of the htpAB locus.

Structural changes underlying allostery in group II chaperonins

The ATP-dependence of folding chamber closure in the 16-subunit homo-oligomeric chaperonin from archaea Methanococcus maripaludis (Mm-cpn) has been studied by single particle cryo-electron microscopy (Zhang et al., 2011). ATP binding alone causes a rigid body rotation of ~45° and slight closure of the cavity, but full closure requires ATP hydrolysis.

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.

Chaperonins facilitate KNOTTED1 cell-to-cell trafficking and stem cell function

Cell-to-cell communication in plants includes the selective trafficking of transcription factors and other signals through plasmodesmata. The KNOTTED1 (KN1) homeobox (KNOX) family transcription factors, which use this pathway, are essential for stem cell establishment and/or maintenance. Here we show that KN1 trafficking requires the chaperonin complex, which belongs to a group of cytosolic chaperones that fold specific substrate proteins. Genetic and physical interaction data show a functional relevance for chaperonins in KNOX family-dependent stem cell maintenance. Furthermore, tissue-specific complementation assays indicate a mechanistic basis for chaperonin function during the posttranslocational refolding process. Our study shows that chaperonins are essential for the cell-to-cell trafficking of a subset of mobile transcription factors and demonstrates the importance of chaperonin-dependent protein trafficking for plant stem cell function.

Chloroplast β chaperonins from A. thaliana function with endogenous cpn10 homologs in vitro

The involvement of type I chaperonins in bacterial and organellar protein folding has been well-documented. In E. coli and mitochondria, these ubiquitous and highly conserved proteins form chaperonin oligomers of identical 60 kDa subunits (cpn60), while in chloroplasts, two distinct cpn60 α and β subunit types co-exist together. The primary sequence of α and β subunits is ~50% identical, similar to their respective homologies to the bacterial GroEL. Moreover, the A. thaliana genome contains two α and four β genes. The functional significance of this variability in plant chaperonin proteins has not yet been elucidated. In order to gain insight into the functional variety of the chloroplast chaperonin family members, we reconstituted β homo-oligomers from A. thaliana following their expression in bacteria and subjected them to a structure-function analysis. Our results show for the first time, that A. thaliana β homo-oligomers can function in vitro with authentic chloroplast co-chaperonins (ch-cpn10 and ch-cpn20). We also show that oligomers made up of different β subunit types have unique properties and different preferences for co-chaperonin partners. We propose that chloroplasts may contain active β homo-oligomers in addition to hetero-oligomers, possibly reflecting a variety of cellular roles.

Localization of GroEL determined by in vivo incorporation of a fluorescent amino acid

The molecular chaperone GroEL is required for bacterial growth under all conditions, mediating folding assistance, via its central cavity, to a diverse set of cytosolic proteins; yet the subcellular localization of GroEL remains unresolved. An earlier study, using antibody probing of fixed Escherichia coli cells, indicated colocalization with the cell division protein FtsZ at the cleavage furrow, while a second E. coli study of fixed cells indicated more even distribution throughout the cytoplasm. Here, for the first time, we have examined the spatial distribution of GroEL in living cells using incorporation of a fluorescent unnatural amino acid into the chaperone. Fluorescence microscopy indicated that GroEL is diffusely distributed, both under normal and stress conditions. Importantly, the present procedure uses a small, fluorescent unnatural amino acid to visualize GroEL in vivo, avoiding the steric demands of a fluorescent protein fusion, which compromises proper GroEL assembly. Further, this unnatural amino acid incorporation avoids artifacts that can occur with fixation and antibody staining.

Chaperone proteins and winter survival by a freeze tolerant insect

The role of chaperone proteins in the winter survival of insects was evaluated in freeze tolerant gall fly larvae, Eurosta solidaginis. Levels of four heat shock proteins (Hsp110, Hsp70, Hsp60, Hsp40), two glucose-regulated proteins (Grp75, Grp78) and three others (tailless complex polypeptide 1 [TCP-1], αA-crystallin, αB-crystallin) were tracked in outdoor larvae from September to April and, in addition, laboratory experiments assessed chilling, freezing, and anoxia effects on these proteins. Gall fly larvae showed consistent elevation of Hsp110, Hsp70, Hsp40, Grp78 and αB-crystallin over the late autumn and winter months, generally 1.5-2.0-fold higher than September values. This suggests that these proteins contribute to cell preservation over the winter months via protection and stabilization of macromolecules. By contrast, levels of the mitochondrial Hsp60 fell to just 40% of September values by midwinter, paralleling the responses by numerous mitochondrial enzymes and consistent with a reduction in total mitochondria numbers over the winter. None of the proteins were altered when 15°C acclimated larvae were chilled to 3°C for 24h but Hsp70, Hsp40 and Grp75 increased during freezing at -16°C for 24h whereas others (Hsp110, TCP-1 and both crystallins) increased significantly after larvae thawed at 3°C. Anoxia exposure (24h under N2 gas at 15°C) elevated levels of Hsp70, Grp78 and the two crystallins. Levels of active hyperphosphorylated heat shock transcription factor (HSF1) were also analyzed, giving an indication of the state of hsp gene transcription in the larvae. HSF1 was high in September and October but fell to less than 40% of September values in midwinter consistent with suppression of gene transcription in diapause larvae. HSF1 levels responded positively to freezing and increased robustly by 4.9-fold under anoxia. Overall, the data provide strong evidence for the importance of protein chaperones as a mechanism of cell preservation in freeze tolerant insects.

The dimeric structure of the Cpn60.2 chaperonin of Mycobacterium tuberculosis at 2.8 Å reveals possible modes of function

Mycobacterium tuberculosis expresses two proteins (Cpn60.1 and Cpn60.2) that belong to the chaperonin (Cpn) family of heat shock proteins. Studies have shown that the two proteins have different functional roles in the bacterial life cycle and that Cpn60.2 is essential for cell viability and may be involved in M. tuberculosis pathogenicity. Cpn60.2 does not form a tetradecameric double ring, which is typical of other Cpns. We have determined the crystal structure of recombinant Cpn60.2 to 2.8 Å resolution by molecular replacement; the asymmetric unit (AU) contains a dimer, which is consistent with size-exclusion high-performance liquid chromatography and dynamic light-scattering measurements of the soluble recombinant protein. However, we suggest that the actual Cpn60.2 dimer may be different from that identified within the AU on the basis of surface contact stability, solvation free-energy gain, and functional aspects. Unlike the dimer found in the AU, which is formed through apical domain interactions, the dimeric form we propose here provides a free apical domain that is required for normal chaperone activity and may be involved in M. tuberculosis association with macrophages and arthrosclerosis plaque formation. Here we describe in detail the structural aspects that lead to Cpn60.2 dimer formation and prevent the formation of heptameric rings and tetradecameric double rings.

Single-molecule fluorescence polarization study of conformational change in archaeal group II chaperonin

Group II chaperonins found in archaea and in eukaryotic cytosol mediate protein folding without a GroES-like cofactor. The function of the cofactor is substituted by the helical protrusion at the tip of the apical domain, which forms a built-in lid on the central cavity. Although many studies on the change in lid conformation coupled to the binding and hydrolysis of nucleotides have been conducted, the molecular mechanism of lid closure remains poorly understood. Here, we performed a single-molecule polarization modulation to probe the rotation of the helical protrusion of a chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1. We detected approximately 35° rotation of the helical protrusion immediately after photorelease of ATP. The result suggests that the conformational change from the open lid to the closed lid state is responsible for the approximately 35° rotation of the helical protrusion.

Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding

Molecular chaperones are a class of proteins responsible for proper folding of a large number of polypeptides in both prokaryotic and eukaryotic cells. Newly synthesized polypeptides are prone to nonspecific interactions, and many of them make toxic aggregates in absence of chaperones. The eukaryotic chaperonin CCT is a large, multisubunit, cylindrical structure having two identical rings stacked back to back. Each ring is composed of eight different but similar subunits and each subunit has three distinct domains. CCT assists folding of actin, tubulin, and numerous other cellular proteins in an ATP-dependent manner. The catalytic cooperativity of ATP binding/hydrolysis in CCT occurs in a sequential manner different from concerted cooperativity as shown for GroEL. Unlike GroEL, CCT does not have GroES-like cofactor, rather it has a built-in lid structure responsible for closing the central cavity. The CCT complex recognizes its substrates through diverse mechanisms involving hydrophobic or electrostatic interactions. Upstream factors like Hsp70 and Hsp90 also work in a concerted manner to transfer the substrate to CCT. Moreover, prefoldin, phosducin-like proteins, and Bag3 protein interact with CCT and modulate its function for the fine-tuning of protein folding process. Any misregulation of protein folding process leads to the formation of misfolded proteins or toxic aggregates which are linked to multiple pathological disorders.

Chaperonins: two rings for folding

Chaperonins are ubiquitous chaperones found in Eubacteria, eukaryotic organelles (group I), Archaea and the eukaryotic cytosol (group II). They all share a common structure and a basic functional mechanism. Although a large amount of information has been gathered for the simpler group I, much less is known about group II chaperonins. Recent crystallographic and electron microscopy structures have provided new insights into the mechanism of these chaperonins and revealed important differences between group I and II chaperonins, mainly in the molecular rearrangements that take place during the functional cycle. These differences are evident for the most complex chaperonin, the eukaryotic cytosolic CCT, which highlights the uniqueness of this important molecular machine.

The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins

The cytosolic chaperonin CCT is a 1-MDa protein-folding machine essential for eukaryotic life. The CCT interactome shows involvement in folding and assembly of a small range of proteins linked to essential cellular processes such as cytoskeleton assembly and cell-cycle regulation. CCT has a classic chaperonin architecture, with two heterogeneous 8-membered rings stacked back-to-back, enclosing a folding cavity. However, the mechanism by which CCT assists folding is distinct from other chaperonins, with no hydrophobic wall lining a potential Anfinsen cage, and a sequential rather than concerted ATP hydrolysis mechanism. We have solved the crystal structure of yeast CCT in complex with actin at 3.8 Å resolution, revealing the subunit organisation and the location of discrete patches of co-evolving 'signature residues' that mediate specific interactions between CCT and its substrates. The intrinsic asymmetry is revealed by the structural individuality of the CCT subunits, which display unique configurations, substrate binding properties, ATP-binding heterogeneity and subunit-subunit interactions. The location of the evolutionarily conserved N-terminus of Cct5 on the outside of the barrel, confirmed by mutational studies, is unique to eukaryotic cytosolic chaperonins.

The Legionella pneumophila Chaperonin - An Unusual Multifunctional Protein in Unusual Locations

The Legionella pneumophila chaperonin, high temperature protein B (HtpB), was discovered as a highly immunogenic antigen, only a few years after the identification of L. pneumophila as the causative agent of Legionnaires’ disease. As its counterparts in other bacterial pathogens, HtpB did not initially receive further attention, particularly because research was focused on a few model chaperonins that were used to demonstrate that chaperonins are essential stress proteins, present in all cellular forms of life and involved in helping other proteins to fold. However, chaperonins have recently attracted increasing interest, particularly after several reports confirmed their multifunctional nature and the presence of multiple chaperonin genes in numerous bacterial species. It is now accepted that bacterial chaperonins are capable of playing a variety of protein folding-independent roles. HtpB is clearly a multifunctional chaperonin that according to its location in the bacterial cell, or in the L. pneumophila-infected cell, plays different roles. HtpB exposed on the bacterial cell surface can act as an invasion factor for non-phagocytic cells, whereas the HtpB released in the host cell can act as an effector capable of altering organelle trafficking, the organization of actin microfilaments and cell signaling pathways. The road to discover the multifunctional nature of HtpB has been exciting and here we provide a historical perspective of the key findings linked to such discovery, as well as a summary of the experimental work (old and new) performed in our laboratory. Our current understanding has led us to propose that HtpB is an ancient protein that L. pneumophila uses as a key molecular tool important to the intracellular establishment of this fascinating pathogen.

The group II chaperonin Mm-Cpn binds and refolds human γD crystallin

Chaperonins assist in the folding of nascent and misfolded proteins, though the mechanism of folding within the lumen of the chaperonin remains poorly understood. The archeal chaperonin from Methanococcus marapaludis, Mm-Cpn, shares the eightfold double barrel structure with other group II chaperonins, including the eukaryotic TRiC/CCT, required for actin and tubulin folding. However, Mm-Cpn is composed of a single species subunit, similar to group I chaperonin GroEL, rather than the eight subunit species needed for TRiC/CCT. Features of the β-sheet fold have been identified as sites of recognition by group II chaperonins. The crystallins, the major components of the vertebrate eye lens, are β-sheet proteins with two homologous Greek key domains. During refolding in vitro a partially folded intermediate is populated, and partitions between productive folding and off-pathway aggregation. We report here that in the presence of physiological concentrations of ATP, Mm-Cpn suppressed the aggregation of HγD-Crys by binding the partially folded intermediate. The complex was sufficiently stable to permit recovery by size exclusion chromatography. In the presence of ATP, Mm-Cpn promoted the refolding of the HγD-Crys intermediates to the native state. The ability of Mm-Cpn to bind and refold a human β-sheet protein suggests that Mm-Cpn may be useful as a simplified model for the substrate recognition mechanism of TRiC/CCT.

A chaperonin subunit with unique structures is essential for folding of a specific substrate

Type I chaperonins are large, double-ring complexes present in bacteria (GroEL), mitochondria (Hsp60), and chloroplasts (Cpn60), which are involved in mediating the folding of newly synthesized, translocated, or stress-denatured proteins. In Escherichia coli, GroEL comprises 14 identical subunits and has been exquisitely optimized to fold its broad range of substrates. However, multiple Cpn60 subunits with different expression profiles have evolved in chloroplasts. Here, we show that, in Arabidopsis thaliana, the minor subunit Cpn60β4 forms a heterooligomeric Cpn60 complex with Cpn60α1 and Cpn60β1–β3 and is specifically required for the folding of NdhH, a subunit of the chloroplast NADH dehydrogenase-like complex (NDH). Other Cpn60β subunits cannot complement the function of Cpn60β4. Furthermore, the unique C-terminus of Cpn60β4 is required for the full activity of the unique Cpn60 complex containing Cpn60β4 for folding of NdhH. Our findings suggest that this unusual kind of subunit enables the Cpn60 complex to assist the folding of some particular substrates, whereas other dominant Cpn60 subunits maintain a housekeeping chaperonin function by facilitating the folding of other obligate substrates.

Chaperonins assist the folding of some nascent and denatured proteins to their native, functional forms. Each chaperonin consists of a pair of protein complexes resembling two stacked toroids; folding occurs inside the toroid cavity. Chaperonins are ubiquitous in both bacteria and more complex nucleated cells, as well as in the intracellular organelles that have evolved from bacteria by endosymbiosis: mitochondria and, in plants, chloroplasts. They are indispensable for cellular function. Many different chaperonin subunits have evolved in various species of bacteria as well as in most mitochondria and chloroplasts. The physiological and functional relevance of these multiple chaperonin subunits is poorly understood, however. In this study, we have characterized the minor chaperonin subunit Cpn60β4 from Arabidopsis chloroplasts, which differs in structure from other chloroplast chaperonins. When the Cpn60β4 gene is defective, the plants fail to accumulate one protein complex in particular: the chloroplast NADH dehydrogenase-like complex (NDH). We discovered that Cpn60β4 forms a complex with other Cpn60 α and β subunits and that this complex is essential for the folding of the NDH subunit NdhH. Cpn60β4 has a unique protein “tail” that is required for the efficient folding of NdhH. Our findings suggest that Cpn60β4 has evolved with distinctive structural features that facilitate the folding of one specific substrate and that this strategy is used by plants to satisfy their conflicting requirements for chaperonins with both specialized and general functions.

Protein folding in the cytoplasm and the heat shock response

Proteins generally must fold into precise three-dimensional conformations to fulfill their biological functions. In the cell, this fundamental process is aided by molecular chaperones, which act in preventing protein misfolding and aggregation. How this machinery assists newly synthesized polypeptide chains in navigating the complex folding energy landscape is now being understood in considerable detail. The mechanisms that ensure the maintenance of a functional proteome under normal and stress conditions are also of great medical relevance, as the aggregation of proteins that escape the cellular quality control underlies a range of debilitating diseases, including many age-of-onset neurodegenerative disorders.

The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis

The mitosomes of Giardia intestinalis are thought to be mitochondria highly-reduced in response to the oxygen-poor niche. We performed a quantitative proteomic assessment of Giardia mitosomes to increase understanding of the function and evolutionary origin of these enigmatic organelles. Mitosome-enriched fractions were obtained from cell homogenate using Optiprep gradient centrifugation. To distinguish mitosomal proteins from contamination, we used a quantitative shot-gun strategy based on isobaric tagging of peptides with iTRAQ and tandem mass spectrometry. Altogether, 638 proteins were identified in mitosome-enriched fractions. Of these, 139 proteins had iTRAQ ratio similar to that of the six known mitosomal markers. Proteins were selected for expression in Giardia to verify their cellular localizations and the mitosomal localization of 20 proteins was confirmed. These proteins include nine components of the FeS cluster assembly machinery, a novel diflavo-protein with NADPH reductase activity, a novel VAMP-associated protein, and a key component of the outer membrane protein translocase. None of the novel mitosomal proteins was predicted by previous genome analyses. The small proteome of the Giardia mitosome reflects the reduction in mitochondrial metabolism, which is limited to the FeS cluster assembly pathway, and a simplicity in the protein import pathway required for organelle biogenesis.

Histoplasma capsulatum heat-shock 60 orchestrates the adaptation of the fungus to temperature stress

Heat shock proteins (Hsps) are among the most widely distributed and evolutionary conserved proteins. Hsps are essential regulators of diverse constitutive metabolic processes and are markedly upregulated during stress. A 62 kDa Hsp (Hsp60) of Histoplasma capsulatum (Hc) is an immunodominant antigen and the major surface ligand to CR3 receptors on macrophages. However little is known about the function of this protein within the fungus. We characterized Hc Hsp60-protein interactions under different temperature to gain insights of its additional functions oncell wall dynamism, heat stress and pathogenesis. We conducted co-immunoprecipitations with antibodies to Hc Hsp60 using cytoplasmic and cell wall extracts. Interacting proteins were identified by shotgun proteomics. For the cell wall, 84 common interactions were identified among the 3 growth conditions, including proteins involved in heat-shock response, sugar and amino acid/protein metabolism and cell signaling. Unique interactions were found at each temperature [30°C (81 proteins), 37°C (14) and 37/40°C (47)]. There were fewer unique interactions in cytoplasm [30°C (6), 37°C (25) and 37/40°C (39)] and four common interactions, including additional Hsps and other known virulence factors. These results show the complexity of Hsp60 function and provide insights into Hc biology, which may lead to new avenues for the management of histoplasmosis.

Effect of TBCD and its regulatory interactor Arl2 on tubulin and microtubule integrity

Assembly of the α/β tubulin heterodimer requires the participation of a series of chaperone proteins (TBCA-E) that function downstream of the cytosolic chaperonin (CCT) as a heterodimer assembly machine. TBCD and TBCE are also capable of acting in a reverse reaction in which they disrupt native heterodimers. Homologs of TBCA-E exist in all eukaryotes, and the amino acid sequences of α- and β-tubulin isotypes are rigidly conserved among vertebrates. However, the efficiency with which TBCD effects tubulin disruption in vivo depends on its origin: bovine (but not human) TBCD efficiently destroys tubulin and microtubules upon overexpression in cultured cells. Here we show that recombinant bovine TBCD is produced in HeLa cells as a stoichiometric cocomplex with β-tubulin, consistent with its behavior in vitro and in vivo. In contrast, expression of human TBCD using the same host/vector system results in the generation of TBCD that is not complexed with β-tubulin. We show that recombinant human TBCD functions indistinguishably from its nonrecombinant bovine counterpart in in vitro CCT-driven folding reactions, in tubulin disruption reactions, and in tubulin GTPase activating protein assays in which TBCD and TBCC stimulate GTP hydrolysis by β-tubulin at a heterodimer concentration far below that required for polymerization into microtubules. We conclude that bovine and human TBCD have functionally identical roles in de novo tubulin heterodimer assembly, and show that the inability of human TBCD to disrupt microtubule integrity upon overexpression in vivo can be overcome by siRNA-mediated suppression of expression of the TBCD regulator Arl2 (ADP ribosylation factor-like protein).

Insights into chaperonin function from studies on archaeal thermosomes

It is now well understood that, although proteins fold spontaneously (in a thermodynamic sense), many nevertheless require the assistance of helpers called molecular chaperones to reach their correct and active folded state in living cells. This is because the pathways of protein folding are full of traps for the unwary: the forces that drive proteins into their folded states can also drive them into insoluble aggregates, and, particularly when cells are stressed, this can lead, without prevention or correction, to cell death. The chaperonins are a family of molecular chaperones, practically ubiquitous in all living organisms, which possess a remarkable structure and mechanism of action. They act as nanoboxes in which proteins can fold, isolated from their environment and from other partners with which they might, with potentially deleterious consequences, interact. The opening and closing of these boxes is timed by the binding and hydrolysis of ATP. The chaperonins which are found in bacteria are extremely well characterized, and, although those found in archaea (also known as thermosomes) and eukaryotes have received less attention, our understanding of these proteins is constantly improving. This short review will summarize what we know about chaperonin function in the cell from studies on the archaeal chaperonins, and show how recent work is improving our understanding of this essential class of molecular chaperones.

Biochemical and immunological characterization of a cpn60.1 knockout mutant of Mycobacterium bovis BCG

Pathogenic mycobacteria possess two homologous chaperones encoded by cpn60.1 and cpn60.2. Cpn60.2 is essential for survival, providing the basic chaperone function, while Cpn60.1 is not. In the present study, we show that inactivation of the Mycobacterium bovis BCG cpn60.1 (Mb3451c) gene does not significantly affect bacterial growth in 7H9 broth, but that this knockout mutant (Δcpn60.1) forms smaller colonies on solid 7H11 medium than the parental and complemented strains. When growing on Sauton medium, the Δcpn60.1 mutant exhibits a thinner surface pellicle and is associated with higher culture filtrate protein content and, coincidentally, with less protein in its outermost cell envelope in comparison with the parental and complemented strains. Interestingly, in this culture condition, the Δcpn60.1 mutant is devoid of phthiocerol dimycocerosates, and its mycolates are two carbon atoms longer than those of the wild-type, a phenotype that is fully reversed by complementation. In addition, Δcpn60.1 bacteria are more sensitive to stress induced by H(2)O(2) but not by SDS, high temperature or acidic pH. Taken together, these data indicate that the cell wall of the Δcpn60.1 mutant is impaired. Analysis by 2D gel electrophoresis and MS reveals the upregulation of a few proteins such as FadA2 and isocitrate lyase in the cell extract of the mutant, whereas more profound differences are found in the composition of the mycobacterial culture filtrate, e.g. the well-known Hsp65 chaperonin Cpn60.2 is particularly abundant and increases about 200-fold in the filtrate of the Δcpn60.1 mutant. In mice, the Δcpn60.1 mutant is less persistent in lungs and, to a lesser extent, in spleen, but it induces a comparable mycobacteria-specific gamma interferon production and protection against Mycobacterium tuberculosis H37Rv challenge as do the parental and complemented BCG strains. Thus, by inactivating the cpn60.1 gene in M. bovis BCG we show that Cpn60.1 is necessary for the integrity of the bacterial cell wall, is involved in resistance to H(2)O(2)-induced stress but is not essential for its vaccine potential.

Archaeal-like chaperonins in bacteria

Chaperonins (CPN) are ubiquitous oligomeric protein machines that mediate the ATP-dependent folding of polypeptide chains. These chaperones have not only been assigned stress response and normal housekeeping functions but also have a role in certain human disease states. A longstanding convention divides CPNs into two groups that share many conserved sequence motifs but differ in both structure and distribution. Group I complexes are the well known GroEL/ES heat-shock proteins in bacteria, that also occur in some species of mesophilic archaea and in the endosymbiotic organelles of eukaryotes. Group II CPNs are found only in the cytosol of archaea and eukaryotes. Here we report a third, divergent group of CPNs found in several species of bacteria. We propose to name these Group III CPNs because of their distant relatedness to both Group I and II CPNs as well as their unique genomic context, within the hsp70 operon. The prototype Group III CPN, Carboxydothermus hydrogenoformans chaperonin (Ch-CPN), is able to refold denatured proteins in an ATP-dependent manner and is structurally similar to the Group II CPNs, forming a 16-mer with each subunit contributing to a flexible lid domain. The Group III CPN represent a divergent group of bacterial CPNs distinct from the GroEL/ES CPN found in all bacteria. The Group III lineage may represent an ancient horizontal gene transfer from an archaeon into an early Firmicute lineage. An analysis of their functional and structural characteristics may provide important insights into the early history of this ubiquitous family of proteins.

Inactivation of the hereditary spastic paraplegia-associated Hspd1 gene encoding the Hsp60 chaperone results in early embryonic lethality in mice

The mitochondrial Hsp60 chaperonin plays an important role in sustaining cellular viability. Its dysfunction is related to inherited forms of the human diseases spastic paraplegia and hypomyelinating leukodystrophy. However, it is unknown whether the requirement for Hsp60 is neuron specific or whether a complete loss of the protein will impair mammalian development and postnatal survival. In this study, we describe the generation and characterization of a mutant mouse line bearing an inactivating gene-trap insertion in the Hspd1 gene encoding Hsp60. We found that heterozygous mice were born at the expected ratio compared to wild-type mice and displayed no obvious phenotype deficits. Using quantitative reverse transcription PCR, we found significantly decreased levels of the Hspd1 transcript in all of the tissues examined, demonstrating that the inactivation of the Hspd1 gene is efficient. By Western blot analysis, we found that the amount of Hsp60 protein, compared to either cytosolic tubulin or mitochondrial voltage-dependent anion-selective channel protein 1/porin, was decreased as well. The expression of the nearby Hspe1 gene, which encodes the Hsp10 co-chaperonin, was concomitantly down regulated in the liver, and the protein levels in all tissues except the brain were reduced. Homozygous Hspd1 mutant embryos, however, died shortly after implantation (day 6.5 to 7.5 of gestation, Theiler stages 9–10). Our results demonstrate that Hspd1 is an essential gene for early embryonic development in mice, while reducing the amount of Hsp60 by inactivation of one allele of the gene is compatible with survival to term as well as postnatal life.

Analysis of chaperone mRNA expression in the adult mouse brain by meta analysis of the Allen Brain Atlas

The pathology of many neurodegenerative diseases is characterized by the accumulation of misfolded and aggregated proteins in various cell types and regional substructures throughout the central and peripheral nervous systems. The accumulation of these aggregated proteins signals dysfunction of cellular protein homeostatic mechanisms such as the ubiquitin/proteasome system, autophagy, and the chaperone network. Although there are several published studies in which transcriptional profiling has been used to examine gene expression in various tissues, including tissues of neurodegenerative disease models, there has not been a report that focuses exclusively on expression of the chaperone network. In the present study, we used the Allen Brain Atlas online database to analyze chaperone expression levels. This database utilizes a quantitative in situ hybridization approach and provides data on 270 chaperone genes within many substructures of the adult mouse brain. We determined that 256 of these chaperone genes are expressed at some level. Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain. The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families. Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

Cellular strategies for controlling protein aggregation

The aggregation of misfolded proteins is associated with the perturbation of cellular function, ageing and various human disorders. Mounting evidence suggests that protein aggregation is often part of the cellular response to an imbalanced protein homeostasis rather than an unspecific and uncontrolled dead-end pathway. It is a regulated process in cells from bacteria to humans, leading to the deposition of aggregates at specific sites. The sequestration of misfolded proteins in such a way is protective for cell function as it allows for their efficient solubilization and refolding or degradation by components of the protein quality-control network. The organized aggregation of misfolded proteins might also allow their asymmetric distribution to daughter cells during cell division.

Stress response in tardigrades: differential gene expression of molecular chaperones

Semi-terrestrial tardigrades exhibit a remarkable tolerance to desiccation by entering a state called anhydrobiosis. In this state, they show a strong resistance against several kinds of physical extremes. Because of the probable importance of stress proteins during the phases of dehydration and rehydration, the relative abundance of transcripts coding for two alpha-crystallin heat-shock proteins (Mt-sHsp17.2 and Mt-sHsp19.5), as well for the heat-shock proteins Mt-sHsp10, Mt-Hsp60, Mt-Hsp70 and Mt-Hsp90, were analysed in active and anhydrobiotic tardigrades of the species Milnesium tardigradum. They were also analysed in the transitional stage (I) of dehydration, the transitional stage (II) of rehydration and in heat-shocked specimens. A variable pattern of expression was detected, with most candidates being downregulated. Gene transcripts of one Mt-hsp70 isoform in the transitional stage I and Mt-hsp90 in the anhydrobiotic stage were significantly upregulated. A high gene expression (778.6-fold) was found for the small alpha-crystallin heat-shock protein gene Mt-sHsp17.2 after heat shock. We discuss the limited role of the stress-gene expression in the transitional stages between the active and anhydrobiotic tardigrades and other mechanisms which allow tardigrades to survive desiccation.

An in vivo RNA interference screen identifies gene networks controlling Drosophila melanogaster blood cell homeostasis

BACKGROUND

In metazoans, the hematopoietic system plays a key role both in normal development and in defense of the organism. In Drosophila, the cellular immune response involves three types of blood cells: plasmatocytes, crystal cells and lamellocytes. This last cell type is barely present in healthy larvae, but its production is strongly induced upon wasp parasitization or in mutant contexts affecting larval blood cell homeostasis. Notably, several zygotic mutations leading to melanotic mass (or "tumor") formation in larvae have been associated to the deregulated differentiation of lamellocytes. To gain further insights into the gene regulatory network and the mechanisms controlling larval blood cell homeostasis, we conducted a tissue-specific loss of function screen using hemocyte-specific Gal4 drivers and UAS-dsRNA transgenic lines.

RESULTS

By targeting around 10% of the Drosophila genes, this in vivo RNA interference screen allowed us to recover 59 melanotic tumor suppressor genes. In line with previous studies, we show that melanotic tumor formation is associated with the precocious differentiation of stem-cell like blood progenitors in the larval hematopoietic organ (the lymph gland) and the spurious differentiation of lamellocytes. We also find that melanotic tumor formation can be elicited by defects either in the fat body, the embryo-derived hemocytes or the lymph gland. In addition, we provide a definitive confirmation that lymph gland is not the only source of lamellocytes as embryo-derived plasmatocytes can differentiate into lamellocytes either upon wasp infection or upon loss of function of the Friend of GATA cofactor U-shaped.

CONCLUSIONS

In this study, we identify 55 genes whose function had not been linked to blood cell development or function before in Drosophila. Moreover our analyses reveal an unanticipated plasticity of embryo-derived plasmatocytes, thereby shedding new light on blood cell lineage relationship, and pinpoint the Friend of GATA transcription cofactor U-shaped as a key regulator of the plasmatocyte to lamellocyte transformation.

HSP90 at the hub of protein homeostasis: emerging mechanistic insights

Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of a wide range of proteins (known as clients). Clients are enriched in signal transducers, including kinases and transcription factors. Therefore, HSP90 regulates diverse cellular functions and exerts marked effects on normal biology, disease and evolutionary processes. Recent structural and functional analyses have provided new insights on the transcriptional and biochemical regulation of HSP90 and the structural dynamics it uses to act on a diverse client repertoire. Comprehensive understanding of how HSP90 functions promises not only to provide new avenues for therapeutic intervention, but to shed light on fundamental biological questions.

Single-molecule study on the decay process of the football-shaped GroEL-GroES complex using zero-mode waveguides

It has been widely believed that an asymmetric GroEL-GroES complex (termed the bullet-shaped complex) is formed solely throughout the chaperonin reaction cycle, whereas we have recently revealed that a symmetric GroEL-(GroES)(2) complex (the football-shaped complex) can form in the presence of denatured proteins. However, the dynamics of the GroEL-GroES interaction, including the football-shaped complex, is unclear. We investigated the decay process of the football-shaped complex at a single-molecule level. Because submicromolar concentrations of fluorescent GroES are required in solution to form saturated amounts of the football-shaped complex, single-molecule fluorescence imaging was carried out using zero-mode waveguides. The single-molecule study revealed two insights into the GroEL-GroES reaction. First, the first GroES to interact with GroEL does not always dissociate from the football-shaped complex prior to the dissociation of a second GroES. Second, there are two cycles, the "football cycle " and the "bullet cycle," in the chaperonin reaction, and the lifetimes of the football-shaped and the bullet-shaped complexes were determined to be 3-5 s and about 6 s, respectively. These findings shed new light on the molecular mechanism of protein folding mediated by the GroEL-GroES chaperonin system.

Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT

Group II chaperonins, found in eukaryotic and archaeal organisms, recognize substrate proteins through diverse mechanisms that involve either hydrophobic- or electrostatic-dominated interactions. This action is distinct from the universal substrate recognition mechanism of group I chaperonins, which bind a wide spectrum of non-native proteins primarily through hydrophobic interactions. We use computational approaches to pinpoint the substrate protein binding sites of the gamma-subunit of the eukaryotic chaperonin CCT and to identify its interactions with the stringent substrate beta-tubulin. Protein-protein docking methods reveal intrinsic binding sites of CCT comprising a helical (HL) region, homologous to the GroEL-binding site, and the helical protrusion (HP) region. We performed molecular dynamics simulations of the solvated CCTgamma apical domain, beta-tubulin peptide-CCTgamma complexes, and isolated beta-tubulin peptides. We find that tubulin binds to CCTgamma through an extensive interface that spans both the HL region and the HP region. HL interactions involve both hydrophobic and electrostatic contacts, while binding to the HP region is stabilized almost exclusively by a salt bridge network. On the basis of additional simulations of a beta-tubulin-CCTgamma complex that involves a reduced interface, centered onto the HP region, we conclude that this salt bridge network is the minimal stabilizing interaction required. Strong conservation of the charged amino acids that participate in the salt bridge network, Arg306 and Glu271, indicates a general mechanism across the nonidentical CCT subunits and group II chaperonins.

Physicochemical determinants of chaperone requirements

We describe a series of stringent relationships between abundance, solubility and chaperone usage of proteins. Based on these relationships, we show that the need of Escherichia coli proteins for the chaperonin GroEL can be predicted with 86% accuracy. Furthermore, from the observation that the abundance and solubility of proteins depend on the physicochemical properties of their amino acid sequences, we demonstrate that the requirement for GroEL can also be predicted directly from the sequences with 90% accuracy. These results indicate that the physicochemical properties of the amino acid sequences represent an essential component of the cellular quality control system that ensures the maintenance of protein homeostasis in living systems.

A vacuolar-type proton (H+) translocating ATPase alpha subunit encoded by the Hc-vha-6 gene of Haemonchus contortus

In the present study, a full-length cDNA (designated Hc-vha-6) inferred to encode an alpha subunit of a vacuolar-type proton translocating adenosine triphosphatase (V-ATPase) was isolated from the parasitic nematode Haemonchus contortus, and characterized. The transcript for Hc-vha-6 was detected in all developmental stages and both sexes of H. contortus. Elements, including two TATA box (TATAA), two inverted CAAT box (ATTGG), five E box (CANNTG) and six GATA as well as five inverse GATA (TTATC) transcription factor motifs, were identified in the non-coding region upstream of Hc-vha-6. The open reading frame (ORF) of 2601 nucleotides encoded a protein (Hc-VHA-6) of 866 amino acids and a molecular weight of approximately 98.7 kDa. Comparison with a published protein sequence for a homologue (VPH1P) from yeast showed that Hc-VHA-6 had nine transmembrane domains and the 14 essential amino acid residues associated with enzyme activity, assembly, intracellular and/or membrane targeting. Phylogenetic analyses of selected amino acid sequence data revealed Hc-VHA-6 to be most closely related to VHA-6 of Caenorhabditis elegans. A predictive network analysis inferred that vha-6 interacts with at least seven other genes encoding V-ATPase subunits and a small Rab GTPase. This study provides the first insight into a V-ATPase of parasitic nematodes and a sound basis for future functional genomic work.

Denatured proteins facilitate the formation of the football-shaped GroEL-(GroES)2 complex

Controversy exists over whether the chaperonin GroEL forms a GroEL-(GroES)2 complex (football-shaped complex) during its reaction cycle. We have revealed previously the existence of the football-shaped complex in the chaperonin reaction cycle using a FRET (fluorescence resonance energy transfer) assay [Sameshima, Ueno, Iizuka, Ishii, Terada, Okabe and Funatsu (2008) J. Biol. Chem. 283, 23765-23773]. Although denatured proteins alter the ATPase activity of GroEL and the dynamics of the GroEL-GroES interaction, the effect of denatured proteins on the formation of the football-shaped complex has not been characterized. In the present study, a FRET assay was used to demonstrate that denatured proteins facilitate the formation of the football-shaped complex. The presence of denatured proteins was also found to increase the rate of association of GroES to the trans-ring of GroEL. Furthermore, denatured proteins decrease the inhibitory influence of ADP on ATP-induced association of GroES to the trans-ring of GroEL. From these findings we conclude that denatured proteins facilitate the dissociation of ADP from the trans-ring of GroEL and the concomitant association of ATP and the second GroES.

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.

Streptavidin 2D crystal substrates for visualizing biomolecular processes by atomic force microscopy

Flat substrate surfaces are a key to successful imaging of biological macromolecules by atomic force microscopy (AFM). Although usable substrate surfaces have been prepared for still imaging of immobilized molecules, surfaces that are more suitable have recently been required for dynamic imaging to accompany the progress of the scan speed of AFM. In fact, the state-of-the-art high-speed AFM has achieved temporal resolution of 30 ms, a capacity allowing us to trace molecular processes played by biological macromolecules. Here, we characterize three types of streptavidin two-dimensional crystals as substrates, concerning their qualities of surface roughness, uniformity, stability, and resistance to nonspecific protein adsorption. These crystal surfaces are commonly resistant to nonspecific protein adsorption, but exhibit differences in other properties to some extent. These differences must be taken into consideration, but these crystal surfaces are still useful for dynamic AFM imaging, as demonstrated by observation of calcium-induced changes in calmodulin, GroES binding to GroEL, and actin polymerization on the surfaces.

Structure and function of the molecular chaperone Trigger Factor

Newly synthesized proteins often require the assistance of molecular chaperones to efficiently fold into functional three-dimensional structures. At first, ribosome-associated chaperones guide the initial folding steps and protect growing polypeptide chains from misfolding and aggregation. After that folding into the native structure may occur spontaneously or require support by additional chaperones which do not bind to the ribosome such as DnaK and GroEL. Here we review the current knowledge on the best-characterized ribosome-associated chaperone at present, the Escherichia coli Trigger Factor. We describe recent progress on structural and dynamic aspects of Trigger Factor's interactions with the ribosome and substrates and discuss how these interactions affect co-translational protein folding. In addition, we discuss the newly proposed ribosome-independent function of Trigger Factor as assembly factor of multi-subunit protein complexes. Finally, we cover the functional cooperation between Trigger Factor, DnaK and GroEL in folding of cytosolic proteins and the interplay between Trigger Factor and other ribosome-associated factors acting in enzymatic processing and translocation of nascent polypeptide chains.

Generation of a fast maturating red fluorescent protein by a combined approach of elongation mutagenesis and functional salvage screening

Fluorescent proteins that can be useful as indicators or reporters must have rapid maturation time, high quantum yield and photobleaching stability. A red fluorescent protein DsRed that has a high quantum yield and photostability has an innately slow maturation time when compared to other fluorescence proteins. In this study, we combined a functional salvage screen (FSS) and elongation mutagenesis to obtain a DsRed variant that maintained structural features closely linked with a high quantum yield and photostability and evolved to have a rapid maturation time. It is expected that the variant generated here, FmRed (fast maturating red fluorescent protein), will be widely used as an indicator or reporter because it maintained traits superior to that of the wild-type protein and also matured rapidly.