groE Operon Research Articles

A bioinformatics approach to identifying Wolbachia infections in arthropods.

Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host’s reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.

Enhanced butyric acid tolerance and production by Class I heat shock protein-overproducing Clostridium tyrobutyricum ATCC 25755.

The response of Clostridium tyrobutyricum to butyric acid stress involves various stress-related genes, and therefore overexpression of stress-related genes can improve butyric acid tolerance and yield. Class I heat shock proteins (HSPs) play an important role in the process of protecting bacteria from sudden changes of extracellular stress by assisting protein folding correctly. The results of quantitative real-time PCR indicated that the Class I HSGs grpE, dnaK, dnaJ, groEL, groES, and htpG were significantly upregulated under butyric acid stress, especially the dnaK and groE operons. Overexpression of groESL and htpG could significantly improve the tolerance of C. tyrobutyricum to butyric acid, while overexpression of dnaK and dnaJ showed negative effects on butyric acid tolerance. Acid production was also significantly promoted by increased GroESL expression levels; the final butyric acid and acetic acid concentrations were 28.2 and 38% higher for C. tyrobutyricum ATCC 25755/groESL than for the wild-type strain. In addition, when fed-batch fermentation was carried out using cell immobilization in a fibrous-bed bioreactor, the butyric acid yield produced by C. tyrobutyricum ATCC 25755/groESL reached 52.2g/L, much higher than that for the control. The improved butyric acid yield is probably attributable to the high GroES and GroEL levels, which can stabilize the biosynthetic machinery of C. tyrobutyricum under extracellular butyric acid stress.

Genetic and transcriptional organization of the groEL operon containing trxA in Gemella morbillorum

Gemella morbillorum, a low G+C content Gram-positive bacterium, is considered to be a commensal organism in humans but occasionally causes endocarditis or other diseases. We determined the sequences of groESL, dnaK and their flanking regions in G. morbillorum. Sequence analysis revealed the presence of putative CtsR binding sites in both groE and dnaK operons, but the lack of CIRCE in groE and the presence of CIRCE in dnaK. This finding suggests in addition to the known regulatory systems for the class I heat shock protein genes, there may be another model in G. morbillorum. Furthermore, an unusual organization of the groE operon as groES-groEL-trxA was found. Genome sequence on GenBank database and southern blot indicate that there is only one copy of trxA in G. morbillorum. Sequencing of the groE locus from other Gemella species and clinical isolates revealed the same genetic structure, suggesting the conservation of the structure in Gemella species. Northern hybridization revealed that there were two transcripts, a large transcript, groES-groEL-trxA and a small transcript, trxA, in groE operon. Treatment of heat or diamide increased the transcription level of groES-groEL-trxA, whereas these two stresses did not affect the small trxA transcript. Thus, this study reveals that the trxA is co-transcribed with the groE operon, and most possibly under the control of the CtsR.

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.

A Novel Genetic Organization of the groE Operon Containing trxA Gene in Gemella morbillorum

A Novel Genetic Organization of the groE Operon Containing trxA Gene in Gemella morbillorum

Reduction-sensitive and cysteine residue-mediated Streptococcus pneumoniae HrcA oligomerization in vitro.

In both gram-positive and several gram-negative bacteria, the transcription of dnaK and groE operons is negatively regulated by HrcA; however, the mechanism modulating HrcA protein activity upon thermal stress remains elusive. Here, we demonstrate that HrcA is modulated via reduction and oligomerization in vitro. Native-PAGE analysis was used to reveal the oligomeric structure of HrcA. The oligomeric HrcA structure became monomeric following treatment with the reducing agent dithothreitol, and this process was reversed by treatment with hydrogen peroxide. Moreover, the mutant HrcA C118S exhibited reduced binding to CIRCE elements and became less oligomerized, suggesting that cysteine residue 118 is important for CIRCE element binding as well as oligomerization. Conversely, HrcA mutant C280S exhibited increased oligomerization. An HrcA double mutant (C118S, C280S) was monomeric and exhibited a level of oligomerization and CIRCE binding similar to wild type HrcA, suggesting that cysteine residues 118 and 280 may function as checks to one another during oligomer formation. Biochemical fractionation of E. coli cells overexpressing HrcA revealed the presence of HrcA in the membrane fraction. Together, these results suggest that the two HrcA cysteine residues at positions 118 and 280 function as reduction sensors in the membrane and mediate oligomerization upon stress.

Molecular Phylogeny ofWolbachiaStrains in Arthropod Hosts Based ongroE-Homologous Gene Sequences

Wolbachia is a genus of maternally inherited, intracellular, alpha-Proteobacteria which are widespread among arthropods and cause various reproductive alterations such as cytoplasmic incompatibility and feminization. Wolbachia strains in arthropods have been phylogenetically divided into two supergroups, A and B. Here, we determined the phylogenetic relationships among Wolbachia strains harbored by insects and isopod crustaceans by using groE operon sequences, which encode highly conserved bacterial heat shock proteins. This study includes the first survey for Wolbachia in isopods from a Southeast Asian country, i.e., Thailand. Two isopod species from different parts of Thailand were found to be infected by Wolbachia. Their groE sequences were also included in the phylogenetic analysis. Our results showed clearly that 19 strains from tropical insects, 11 strains from French isopods, and two strains from Thai isopods were in the B supergroup, and 15 strains from tropical insects were in the A supergroup. This is the first report of phylogenetic analysis of a large data set comprising Wolbachia groE sequences from both insects and isopod crustaceans.

Dual regulation of dnaK and groE operons by HrcA and Ca++ in Streptococcus pneumoniae

The dnaK and groE operons in Streptococcus pneumoniae are repressed by HrcA in the presence of Ca(++). However, it is unclear how HrcA and Ca(++) regulate the dnaK and groE operons. This study examined the dual regulation of the dnaK and groE operons in S. pneumoniae by HrcA and Ca(++). At 30 degrees C, the hrcA mutant showed a constitutively higher level of dnaK expression at both the protein and mRNA levels than that of the wild type whereas the level of groEL expression was relatively unchanged. On the other hand, the levels of both dnaK and groEL transcripts were increased after heat shock but the hrcA mutant was not sensitive to heat shock. Immunoblot analysis of the cells pretreated with the Ca(++) chelator, BAPTA-AM, revealed the induction of HrcA and GroEL at both 30 degrees C and 42 degrees C. However, at longer preincubation time with BAPTA-AM, GroEL was further induced but the level of HrcA decreased suggesting that Ca(++) regulates the dnaK and groE operons differently. Overall, Ca(++) and HrcA differentially regulate the transcription of the dnaK and groE operons in S. pneumoniae. These results are expected to contribute to resolving the relationship between DnaK/GroEL expression and the pathogenesis in S. pneumoniae.

Homologous cpn60 genes in Rhizobium leguminosarum are not functionally equivalent

Many bacteria possess 2 or more genes for the chaperonin GroEL and the cochaperonin GroES. In particular, rhizobial species often have multiple groEL and groES genes, with a high degree of amino-acid similarity, in their genomes. The Rhizobium leguminosarum strain A34 has 3 complete groE operons, which we have named cpn.1, cpn.2 and cpn.3. Previously we have shown the cpn. 1 operon to be essential for growth, but the two other cpn operons to be dispensable. Here, we have investigated the extent to which loss of the essential GroEL homologue Cpn60.1 can be compensated for by expression of the other two GroEL homologues (Cnp60.2 and Cpn60.3). Cpn60.2 could not be overexpressed to high levels in R. leguminosarum, and was unable to replace Cpn60.1. A strain that overexpressed Cpn60.3 grew in the absence of Cpn60.1, but the complemented strain displayed a temperature-sensitive phenotype. Cpn60.1 and Cpn60.3, when coexpressed in Escherichia coli, preferentially selfassembled rather than forming mixed heteroligomers. We conclude that, despite their high amino acid similarity, the GroEL homologues of R. leguminosarum are not functionally equivalent in vivo.

Distinct mechanisms regulate expression of the two major groEL homologues in Rhizobium leguminosarum

We investigated the regulation of the two of the three groE operons (cpn.1 and cpn.2) of the root-nodulating bacterium R. leguminosarum strain A34. Both are heat inducible, and both have a CIRCE sequence in their upstream regions, suggesting regulation by an HrcA repressor. Mutagenesis of the CIRCE sequence upstream of cpn.1 led to an increase in the levels of cpn.1 mRNA, and knock-out of the hrcA gene increased the level of Cpn60.1 protein (the GroEL homologue encoded by the cpn.1 operon). Inactivation of the hrcA gene also caused increased expression of a 29 kDa protein that was identified as RhiA, a component of a quorum-sensing system. However, neither loss of the upstream CIRCE sequence, nor loss of HrcA function, had any effect on expression from the cpn.2 promoter. Further analysis of the cpn.2 upstream region suggested regulation could be mediated by an RpoH system, and this was confirmed by deleting the rpoH gene from the chromosome, which led to a decreased level of Cpn60.2 expression. Inactivation of RpoH led to a reduction in growth rate which could be partly compensated for by inactivation of HrcA, indicating an overlap in the in vivo function of the proteins regulated by these two systems.

Hydrophobic surface exposure-mediated CIRCE repression by the Ca 2+-sensor, HrcA, in Streptococcus pneumoniae

Heat shock-induced expression of the CIRCE ( controlling inverted repeat of chaperone expression) regulon in Streptococcus pneumoniae was examined in the presence of Ca 2+. In the presence of the Ca 2+, thermo-resistance and expression of the CIRCE regulon of S. pneumoniae were significantly repressed. In addition, hydrophobicity of the HrcA was increased in the presence of the metal ion suggesting that Ca 2+ induces conformational changes such as exposure of the hydrophobic surfaces of HrcA, which facilitate binding to GroEL. This in turn enhances access to CIRCE and leads to repression of the dnaK and groE operons.

Organization of heat shock dnaK and groE operons of the nosocomial pathogen Enterococcus faecium

Enterococcus faecium is a frequently antibiotic-resistant opportunistic pathogen that is commonly recovered from hospitalized patients. The genetic organization of the dnaK operon was analyzed and was shown to consist of at least four heat shock genes, hrcA–grpE–dnaK–dnaJ. The dnaK/J intergenic region was 140 bp shorter than in E. faecalis. The dnaK operon was expressed from a putative σ A-type promoter (PhrcA) upstream of the hrcA start codon and was preceded by two conserved CIRCE sequences. Northern hybridization revealed the presence of multiple mRNAs in the dnaK operon. Conversely, the groE operon was transcribed as a single mRNA. Induction of dnaK and groEL genes occurred in response to either heat shock or exposure to other stress agents.

Crystal Structure of a Heat-inducible Transcriptional Repressor HrcA from Thermotoga maritima: Structural Insight into DNA Binding and Dimerization

All cells have a defense mechanism against a sudden heat-shock stress. Commonly, they express a set of proteins that protect cellular proteins from being denatured by heat. Among them, GroE and DnaK chaperones are representative defending systems, and their transcription is regulated by a heat-shock repressor protein HrcA. HrcA repressor controls the transcription of groE and dnaK operons by binding the palindromic CIRCE element, presumably as a dimer, and the activity of HrcA repressor is modulated by GroE chaperones. Here, we report the first crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima at 2.2A resolution. The Tm_HrcA protein crystallizes as a dimer. The monomer is composed of three domains: an N-terminal winged helix-turn-helix domain (WH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. The Tm_HrcA dimer structure is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains. In the overall dimer structure, the two WH domains are exposed, but the conformation of these two domains seems to be incompatible with DNA binding. We suggest that our structure may represent an inactive form of the HrcA repressor. Structural implication on how the inactive form of HrcA may be converted to the active form by GroEL binding to a conserved C-terminal sequence region of HrcA is discussed.

Two of the three groEL homologues in Rhizobium leguminosarum are dispensable for normal growth

Although many bacteria contain only a single groE operon encoding the essential chaperones GroES and GroEL, examples of bacteria containing more than one groE operon are common. The root-nodulating bacterium Rhizobium leguminosarum contains at least three operons encoding homologues to Escherichia coli GroEL, referred to as Cpn60.1, Cpn60.2 and Cpn60.3, respectively. We report here a detailed analysis of the requirement for and relative levels of these three proteins. Cpn60.1 is present at higher levels than Cpn60.2, and Cpn60.3 protein could not be detected under any conditions although the cpn60.3 gene is transcribed under anaerobic conditions. Insertion mutations could not be constructed in cpn60.1 unless a complementing copy was present, showing that this gene is essential for growth under the conditions used here. Both cpn60.2 and cpn60.3 could be inactivated with no loss of viability, and a double cpn60.2 cpn60.3 mutant was also constructed which was fully viable. Thus only Cpn60.1 is required for growth of this organism.

Ca2+‐dependent expression of the CIRCE regulon inStreptococcus pneumoniae

DnaK and GroEL play a pivotal role in protein folding, and promote cell proliferation and survival. In Gram-positive and several Gram-negative bacteria, HrcA represses the transcription of dnaK and groE operons by binding to the highly conserved CIRCE (controlling inverted repeat of chaperone expression) operator sequence in the presence of GroEL. HrcA may respond to environmental stress and various other factors that modulate the transcription of the dnaK and groE operons. However, the mechanisms by which these factors modulate the activity of HrcA remain elusive. Here, we show that the thermoresistance of Streptococcus pneumoniae is significantly repressed in the presence of Ca2+. Furthermore, heat shock-induced expression of the CIRCE regulon in S. pneumoniae is repressed in the presence of Ca2+, although to a lesser degree than in the hrcA mutant, strongly suggesting that HrcA inhibits expression of the CIRCE regulon in a Ca2+-dependent manner. Although HrcA does not bind directly to Ca2+, its hydrophobicity is increased in the presence of the metal ion. Taken together, our observations suggest that Ca2+ induces conformational changes, such as exposure of the hydrophobic surfaces of HrcA, which facilitate binding to GroEL. Alternatively, the presence of Ca2+ may facilitate GroEL in interacting freely with HrcA. This, in turn, enhances access to CIRCE and leads to repression of the dnaK and groE operons in S. pneumoniae.

Male‐killing Wolbachia in the butterfly Hypolimnas bolina

AbstractSome lines of the butterfly Hypolimnas bolina L. (Lepidoptera: Nymphalidae) are characterized by their female‐biased sex ratio. In these lines, most males die before reaching the middle larval stage. However, the cause of the bias remains unclear. We detected the proteobacterium Wolbachia in all individuals in the female‐biased butterfly lines and in some of the lines with a normal sex ratio. Tetracycline treatment of adult females of a female‐biased line led to a significant increase in both the hatch rate of their eggs (F1) and the male‐to‐female ratio of F1 pupae. In addition, certain assays of tetracycline treatment on mother butterflies significantly increased the male to female ratio of F1 adults. Known bacterial sex ratio distorters other than Wolbachia were not detected by diagnostic PCR assay, nor by the sequencing of 16S rDNA amplified using general prokaryotic 16S rDNA primers. These results strongly suggest that the distortion of the sex ratio is due to the killing of males by the inherited Wolbachia. Sequences of the 16S rDNA amplified using Wolbachia‐specific primers, the cell division protein gene (ftsZ), the molecular chaperone groE genes (groE operon), and the Wolbachia surface protein gene (wsp) from Wolbachia in lines belonging to three subspecies of the butterfly (bolina, jacintha, and philippensis) revealed no variation among lines nor between female‐biased lines and a normal one.

Analysis of orthologoushrcAgenes inEscherichia coliandBacillus subtilis

The hrcA gene codes for a transcriptional repressor protein interacting with the CIRCE operator thereby reducing expression of the groE operon of more than 120 bacterial species. At least in Bacillus subtilis, the activity of the HrcA protein is modulated by the GroE chaperonin system. We amplified the hrcA gene from five different bacterial species and analyzed its activity in Escherichia coli and Bacillus subtilis. While those from Clostridium acetobutylicum and Staphylococcus aureus turned out to be active, those of Helicobacter pylori, Lactococcus lactis and Thermotoga maritima were inactive in E. coli, but that of T. maritima turned out to repress expression of the reporter gene in B. subtilis. All these results strongly suggest to us a specific recognition of HrcA by the GroE chaperonin system.

Analysis of orthologous hrcA genes in Escherichia coli and Bacillus subtilis

The hrcA gene codes for a transcriptional repressor protein interacting with the CIRCE operator thereby reducing expression of the groE operon of more than 120 bacterial species. At least in Bacillus subtilis, the activity of the HrcA protein is modulated by the GroE chaperonin system. We amplified the hrcA gene from five different bacterial species and analyzed its activity in Escherichia coli and Bacillus subtilis. While those from Clostridium acetobutylicum and Staphylococcus aureus turned out to be active, those of Helicobacter pylori, Lactococcus lactis and Thermotoga maritima were inactive in E. coli, but that of T. maritima turned out to repress expression of the reporter gene in B. subtilis. All these results strongly suggest to us a specific recognition of HrcA by the GroE chaperonin system.

Transcriptional analysis of the groE and dnaK heat-shock operons of Enterococcus faecalis

Enterococcus faecalis is able to survive in extremely adverse conditions, and its ability to resist stress is considered a key virulence attribute. Here, we conducted a detailed transcriptional analysis of the groE and dnaK operons of E. faecalis. The dnaK operon is comprised of four genes ( hrcA– grpE– dnaK– dnaJ) preceded by two conserved CIRCE sequences. The dnaK operon is expressed from a σ A-type promoter located upstream of hrcA and multiple transcripts are detectable, possibly due to mRNA processing. The groE operon ( groES– groEL) is transcribed as a single mRNA from a σ A-type promoter located immediately upstream of a CIRCE element. Induction of dnaK and groEL occurs in response to heat shock and exposure to NaCl, SDS and H 2O 2.

Identification of a helix-turn-helix motif of Bacillus thermoglucosidasius HrcA essential for binding to the CIRCE element and thermostability of the HrcA-CIRCE complex, indicating a role as a thermosensor.

In the heat shock response of bacillary cells, HrcA repressor proteins negatively control the expression of the major heat shock genes, the groE and dnaK operons, by binding the CIRCE (controlling inverted repeat of chaperone expression) element. Studies on two critical but yet unresolved issues related to the structure and function of HrcA were performed using mainly the HrcA from the obligate thermophile Bacillus thermoglucosidasius KP1006. These two critical issues are (i) identifying the region at which HrcA binds to the CIRCE element and (ii) determining whether HrcA can play the role of a thermosensor. We identified the position of a helix-turn-helix (HTH) motif in B. thermoglucosidasius HrcA, which is typical of DNA-binding proteins, and indicated that two residues in the HTH motif are crucial for the binding of HrcA to the CIRCE element. Furthermore, we compared the thermostabilities of the HrcA-CIRCE complexes derived from Bacillus subtilis and B. thermoglucosidasius, which grow at vastly different ranges of temperature. The thermostability profiles of their HrcA-CIRCE complexes were quite consistent with the difference in the growth temperatures of B. thermoglucosidasius and B. subtilis and, thus, suggested that HrcA can function as a thermosensor to detect temperature changes in cells.