The chaperonins: perspectives from the Archaea

Functional diversity in archaeal Hsp60: a molecular mosaic of Group I and Group II chaperonin

External stress disrupts the balance of protein homeostasis, necessitating the involvement of heat shock proteins (Hsps) in restoring equilibrium and ensuring cellular survival. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, lacks the conventional Hsp100, Hsp90, and Hsp70, relying solely on a single ATP-dependent Group II chaperonin, Hsp60, comprising three distinct subunits (α, β, and γ) to refold unfolded substrates and maintain protein homeostasis. Hsp60 forms three different complexes, namely Hsp60αβγ, Hsp60αβ, and Hsp60β, at temperatures of 60 °C, 75 °C, and 90 °C, respectively. This study delves into the intricacies of Hsp60 complexes in S. acidocaldarius, uncovering their ability to form oligomeric structures in the presence of ATP. The recognition of substrates by Hsp60 involves hydrophobic interactions, and the subsequent refolding process occurs in an ATP-dependent manner through charge-driven interactions. Furthermore, the Hsp60β homo-oligomeric complex can protect the archaeal and eukaryotic membrane from stress-induced damage. Hsp60 demonstrates nested cooperativity in ATP hydrolysis activity, where MWC-type cooperativity is nested within KNF-type cooperativity. Remarkably, during ATP hydrolysis, Hsp60β, and Hsp60αβ complexes exhibit a mosaic behavior, aligning with characteristics observed in both Group I and Group II chaperonins, adding a layer of complexity to their functionality.

DNA damage and molecular level effects induced by polystyrene (PS) nanoplastics (NPs) after Chironomus riparius (Diptera) larvae

In this work, we analyzed the early molecular effects of polystyrene (PS) nanoplastics (NPs) on an aquatic primary consumer (larvae of Chironomus riparius, Diptera) to evaluate their potential DNA damage and the transcriptional response of different genes related to cellular and oxidative stress, endocrine response, developmental, oxygen transport, and immune response. After 24-h exposures of larvae to doses of PS NPs close to those currently found in the environment, the results revealed a large genotoxic effect. This end was evidenced after significant increases in DNA strand breaks of C. riparius larvae quantified by the comet assay, together with results obtained when analyzing the expression of four genes involved in DNA repair (xrrc1, ATM, DECAY and NLK) and which were reduced in the presence of these nanomaterials. Consequently, this reduction trend is likely to prevent the repair of DNA damage caused by PS NPs. In addition, the same tendency to reduce the expression of genes involved in cellular stress, oxidative stress, ecdysone pathway, development, and oxygen transport was observed. Taken together, these results suggest that PS NPs reduce the expression of hormonal target genes and a developmental gene. We show, for the first time, effects of PS NPs on the endocrine system of C. riparius and suggest a possible mechanism of blocking ecdysteroid hormones in insects. Moreover, the NPs were able to inhibit the expression of hemoglobin (Hb C), a protein involved in oxygen transport, and activate a gene of the humoral immune system. These data reveal for the first time the genomic effects of PS NPs in the aquatic invertebrate C. riparius, at the base of the food chain.

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

Behcet’s disease: from heat shock proteins to infections

Background: Behcet’s disease (BD) is a chronic, inflammatory multisystemic condition of unknown etiology. Although the cause of BD is not clear, it is believed to be the result of an autoimmune process triggered by an infectious or environmental agent (possibly local to a geographic region) in a genetically predisposed individual.

Objective: To detail current knowledge of the role of microorganisms in the pathogenesis of BD and review the infectious etiology of this disease.

Methods: The review based on publication in SCOPUS, Science direct, and PubMed.

Results: A microbial infection has been implicated in the development of the disease to explain the strong inflammatory reactions observed, the activation of monocytes and macrophages, and the induction of proinflammatory cytokines and chemokines detected. Common factors linking some of the possible pathogenetic agents are extrinsically induced tissue stress or heat shock proteins, which react with host tissues and elicit significant T-helper type 1 cell responses.

Conclusion: Based on collected data, we conclude that the microorganisms discussed seem to participate and, at least in part, act as triggers during the course of BD. By clarifying the microbial associations of BD and finding its etiology, particularly the causative antigens leading to BD, it would be easier to suggest more effective treatment and preventive strategies for this disease.

OMICS in ecology: systems level analyses of Halobacterium salinarum reveal large-scale temperature-mediated changes and a requirement of CctA for thermotolerance

Halobacterium salinarum is an extremely halophilic archaeon that inhabits high-salinity aqueous environments in which the temperature can range widely, both daily and seasonally. An OMICS analysis of the 37°C and 49°C proteomes and transcriptomes for revealing the biomodules affected by temperature is reported here. Analysis of those genes/proteins displaying dramatic changes provided a clue to the coordinated changes in the expression of genes within five arCOG biological clusters. When proteins that exhibited minor changes in their spectral counts and insignificant p values were also examined, the apparent influence of the elevated temperatures on conserved chaperones, metabolism, translation, and other biomodules became more obvious. For instance, increases in all eight conserved chaperones and three arginine deiminase pathway enzymes and reductions in most tricarboxylic acid (TCA) cycle enzymes and ribosomal proteins suggest that complex system responses occurred as the temperature changed. When the requirement for the four proteins that showed the greatest induction at 49°C was analyzed, only CctA (chaperonin subunit α), but not Hsp5, DpsA, or VNG1187G, was essential for thermotolerance. Environmental stimuli and other perturbations may induce many minor gene expression changes. Simultaneous analysis of the genes exhibiting dramatic or minor changes in expression may facilitate the detection of systems level responses.

Cumulative impact of chaperone-mediated folding on genome evolution

Molecular chaperones support protein folding and unfolding along with assembly and translocation of protein complexes. Chaperones have been recognized as important mediators between an organismal genotype and phenotype as well as important maintainers of cellular fitness under environmental conditions that induce high mutational loads. Here we review recent studies revealing that the folding assistance supplied by chaperones is evident in genomic sequences implicating chaperone-mediated folding as an influential factor during protein evolution. Interaction of protein with chaperones ensures a proper folding and function, yet an adaptation to obligatory dependence on such assistance may be irreversible, representing an evolutionary trap. A correlation between the requirement for a chaperone and protein expression level indicates that the evolution of substrate-chaperone interaction is bounded by the required substrate abundance within the cell. Accumulating evidence suggests that the utility of chaperones is governed by a delicate balance between their help in mitigating the risks of protein misfolding and aggregate formation on one hand and the slower rate of protein maturation and the energetic cost of chaperone synthesis on the other.

The possible role of HSPs on Behçet's disease: a bioinformatic approach

Current evidence lends increasing support to immunoinflammatory mechanisms as one of the prime pathogenic processes involved in the development and progression of Behçet's disease (BD). It has been observed that most human beings have cellular and humoral reactions against microbial heat shock proteins (HSPs). The observation that eukaryotic and prokaryotic HSPs have high sequence similarity promoted the hypothesis that HSPs might be potential candidates for molecular mimicry and could act as potentially dangerous autoantigens. In this study, using bioinformatics tools, we examined the hypothesis that HSPs (evolutionarily conserved proteins), which are present in pathogenic and commensal organisms and their hosts, provide the stimulus that initiates BD in susceptible individuals. In this regards, the nucleotide and amino acid sequences of the human HSP 60 kDa and bacterial HSP 60 kDa deposited in the NCBI and PDB databases were subjected to analysis using bioinformatics tools, including The CLC Sequence Viewer and MEGA softwares. These data showed that the sequence homology between bacterial and self HSPs (leading to cross-reactivity and molecular mimicry phenomenon) may be associated with the development of the disease; and suggesting that microbial HSPs, which cross-react with host tissues and elicit significant immune responses are possible pathogenetic agents involved in the development and progression of BD.

Remarkable in vitro bactericidal activity of bismuth(III) sulfonates against Helicobacter pylori

Four new tris-substituted bismuth(III) sulfonates of general formula [Bi(O(3)SR)(3)] (R = phenyl 1, p-tolyl 2, 2,4,6-mesityl 3 and S-(+)-10-camphoryl 4) have been synthesised and characterised. Their synthesis by solvent-free (SF) and solvent-mediated (SM) methods has been explored and their activity against Helicobacter pylori has been investigated. The compounds 1-4 display a remarkable in vitro activity against three laboratory strains of H. pylori (B128, 26,695 and 251) with minimum inhibitory concentration (MIC) values as low as 0.049 μg mL(-1) for the strains B128 and 26,695, and 0.781 μg mL(-1) for the clinical isolate 251. This places most MIC values in the nano-molar region and demonstrates the strong influence of the sulfonate group on the bactericidal properties. The novel solid state structure [Bi(8)(O(3)SMes)(20)(SO(4))(2)(H(2)O)(6)]·(C(7)H(8))(7)5·(C(7)H(8))(7), derived from the SM reaction under reflux conditions, is presented and the incorporation of the two inorganic sulfate anions in the centre of the wheel-like bismuth sulfonate cluster explained.

Successful immunotherapy of canine flea allergy with injected Actinomycetales preparations

AIMS

Can heat-killed, borate-buffered suspensions of Gordonia bronchialis, Rhodococcus coprophilus or Tsukamurella inchonensis be used to treat canine flea allergy?

MATERIALS & METHODS

Organisms cultured on Sauton's medium into stationary phase were autoclaved in borate-buffered saline and stored at 10 mg wet weight/ml. Intradermal injections of 0.1 ml containing 1 mg of bacilli were administered on the first and 20th days of the study. G. bronchialis and R. coprophilus were most effective in a pilot study of a small number of dogs with flea allergy. A larger number of affected dogs were then randomized to receive placebo or either of the two selected reagents. The extent and severity of allergic signs and symptoms were scored and blood samples were collected just before the first injection and 28 days after the second.

RESULTS

Both selected reagents reduced the extent and severity of lesions (p < 0.001) and reduced scratching. Eosinophil numbers were reduced (p < 0.0001) between the first and second assessment.

CONCLUSIONS

Injections of G. bronchialis or R. coprophilus effectively reduce the signs and symptoms of flea allergy in dogs.

Identification of Proteins Related to Nickel Homeostasis in Helicobater pylori by Immobilized Metal Affinity Chromatography and Two-Dimensional Gel Electrophoresis

Helicobacter pylori (H. pylori) is a widespread human pathogen causing peptic ulcers and chronic gastritis. Maintaining nickel homeostasis is crucial for the establishment of H. pylori infection in humans. We used immobilized-nickel affinity chromatography to isolate Ni-related proteins from H. pylori cell extracts. Two-dimensional gel electrophoresis and mass spectrometry were employed to separate and identify twenty two Ni-interacting proteins in H. pylori. These Ni-interacting proteins can be classified into several general functional categories, including cellular processes (HspA, HspB, TsaA, and NapA), enzymes (Urease, Fumarase, GuaB, Cad, PPase, and DmpI), membrane-associated proteins (OM jhp1427 and HpaA), iron storage protein (Pfr), and hypothetical proteins (HP0271, HP jhp0216, HP jhp0301, HP0721, HP0614, and HP jhp0118). The implication of these proteins in nickel homeostasis is discussed.

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.

Chaperonin-dependent accelerated substitution rates in prokaryotes

Many proteins require the assistance of molecular chaperones in order to fold efficiently. Chaperones are known to mask the effects of mutations that induce misfolding because they can compensate for the deficiency in spontaneous folding. One of the best studied chaperones is the eubacterial GroEL/GroES system. In Escherichia coli, three classes of proteins have been distinguished based on their degree of dependency on GroEL for folding: 1) those that do not require GroEL, 2) those that require GroEL in a temperature-dependent manner, and 3) those that obligately require GroEL for proper folding. The buffering effects of GroEL have so far been observed in experimental regimens, but their effect on genomes during evolution has not been examined. Using 446 sequenced proteobacterial genomes, we have compared the frequency of amino acid replacements among orthologs of 236 proteins corresponding to the three categories of GroEL dependency determined for E. coli. Evolutionary rates are significantly correlated with GroEL dependency upon folding with GroEL dependency class accounting for up to 84% of the variation in amino acid substitution rates. Greater GroEL dependency entails increased evolutionary rates with GroEL obligatory proteins (Class III) evolving on average up to 15% faster than GroEL partially dependent proteins (Class II) and 35% faster than GroEL-independent proteins (Class I). Moreover, GroEL dependency class correlations are strictly conserved throughout all proteobacteria surveyed, as is a significant correlation between folding class and codon bias. The results suggest that during evolution, GroEL-dependent folding increases evolutionary rate by buffering the deleterious effects of misfolding-related mutations.

Two chaperonin systems in bacterial genomes with distinct ecological roles

Bacterial chaperonins are essential to cell viability and have a role in endosymbiosis, which leads to increased biological complexity. However, the extent to which chaperonins promote ecological innovation is unknown. We screened 622 bacterial genomes for genes encoding chaperonins, and found archaeal-like chaperonins in bacteria that inhabit archaeal ecological niches. We found that chaperonins encoded in pathogenic bacteria are the most functionally divergent. We identified the molecular basis of the dramatic structural changes in mitochondrial GROEL, a highly derived chaperonin gene. Our analysis suggests that chaperonins are important capacitors of evolutionary and ecological change.

Tubeimoside-1 exerts cytotoxicity in HeLa cells through mitochondrial dysfunction and endoplasmic reticulum stress pathways

Traditional Chinese herbal medicines are a great source of cancer chemotherapeutic agents. Tubeimoside-1 (TBMS1) is a triterpenoid saponin extracted from Bolbostemma paniculatum (Maxim.) Franquet (Cucurbitaceae), a Chinese herb with anticancer potential named as "Tu Bei Mu". In the present study, we used proteomics to examine the cytotoxic effects of TBMS1 on HeLa cells. Protein profiling of TBMS1-treated HeLa cells revealed profound protein alterations related to energy metabolism and protein synthesis and folding, suggesting that mitochondria and endoplasmic reticulum (ER) play a role in TBMS1-initiated apoptosis. TBMS1 induced the depletion of mitochondrial transmembrane potential (DeltaPsi(m)), leading to the activation of caspase-dependent apoptotic cell death. Unfolded Protein Response (UPR) signaling pathways are also activated after TBMS1 treatment and these changes were accompanied by increased expression of GADD153/CHOP, a transcription factor associated with growth arrest and apoptosis in the event of prolonged ER stress. Salubrinal (Sal), a selective inhibitor for ER stress, partially abrogated the TBMS1-related cell death. These results suggest that TBMS1 exerts cytotoxicity in HeLa cells through both mitochondrial dysfunction and ER stress cell death pathways.

Expression profiles and physiological roles of two types of molecular chaperonins from the hyperthermophilic archaeon Thermococcus kodakarensis

Thermococcus kodakarensis possesses two chaperonins, CpkA and CpkB, and their expression is induced by the downshift and upshift, respectively, of the cell cultivation temperature. The expression levels of the chaperonins were examined by using specific antibodies at various cell growth temperatures in the logarithmic and stationary phases. At 60 degrees C, CpkA was highly expressed in both the logarithmic and stationary phases; however, CpkB was not expressed in either phase. At 85 degrees C, CpkA and CpkB were expressed in both phases; however, the CpkA level was decreased in the stationary phase. At 93 degrees C, CpkA was expressed only in the logarithmic phase and not in the stationary phase. In contrast, CpkB was highly expressed in both phases. The results of reverse transcription-PCR experiments showed the same growth phase- and temperature-dependent profiles as observed in immunoblot analyses, indicating that the expression of cpkA and cpkB is regulated at the mRNA level. The cpkA or cpkB gene disruptant was then constructed, and its growth profile was monitored. The cpkA disruptant showed poor cell growth at 60 degrees C but no significant defects at 85 degrees C and 93 degrees C. On the other hand, cpkB disruption led to growth defects at 93 degrees C but no significant defects at 60 degrees C and 85 degrees C. These data indicate that CpkA and CpkB are necessary for cell growth at lower and higher temperatures, respectively. The logarithmic-phase-dependent expression of CpkA at 93 degrees C suggested that CpkA participates in initial cell growth in addition to lower-temperature adaptation. Promoter mapping and quantitative analyses using the Phr (Pyrococcus heat-shock regulator) gene disruptant revealed that temperature-dependent expression was achieved in a Phr-independent manner.

Proteomic approach to study the cytotoxicity of dioscin (saponin)

Dioscin, extracted from the root of Polygonatum zanlanscianense pamp, exhibits cytotoxicity towards human myeloblast leukemia HL-60 cells. Proteomic analysis revealed that the expression of mitochondrial associated proteins was substantially altered in HL-60 cells corresponding to the dioscin treatment, suggesting that mitochondria are the major cellular target of dioscin. Mitochondrial functional studies validated that mitochondrial apoptotic pathway was initiated by dioscin treatment. Changes in proteome other than mitochondrial related proteins implicate that other mechanisms were also involved in dioscin-induced apoptosis in HL-60 cells, including the activity impairment in protein synthesis, alterations of phosphatases in cell signaling, and deregulation of oxidative stress and cell proliferation. Current study of protein alterations in dioscin-treated HL-60 cells suggested that dioscin exerts cytotoxicity through multiple apoptosis-inducing pathways.

The Haloferax volcanii FtsY homolog is critical for haloarchaeal growth but does not require the A domain

The targeting of many Sec substrates to the membrane-associated translocation pore requires the cytoplasmic signal recognition particle (SRP). In Eukarya and Bacteria it has been shown that membrane docking of the SRP-substrate complex occurs via the universally conserved SRP receptor (Sralpha/beta and FtsY, respectively). While much has been learned about the archaeal SRP in recent years, few studies have examined archaeal Sralpha/FtsY homologs. In the present study the FtsY homolog of Haloferax volcanii was characterized in its native host. Disruption of the sole chromosomal copy of ftsY in H. volcanii was possible only under conditions where either the full-length haloarchaeal FtsY or an amino-terminally truncated version of this protein lacking the A domain, was expressed in trans. Subcellular fractionation analysis of H. volcanii ftsY deletion strains expressing either one of the complementing proteins revealed that in addition to a cytoplasmic pool, both proteins cofractionate with the haloarchaeal cytoplasmic membrane. Moreover, membrane localization of the universally conserved SRP subunit SRP54, the key binding partner of FtsY, was detected in both H. volcanii strains. These analyses suggest that the H. volcanii FtsY homolog plays a crucial role but does not require its A domain for haloarchaeal growth.

Predicted highly expressed genes in archaeal genomes

Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription/translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription/translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during high-speed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.