A functional carbohydrate chip platform for analysis of carbohydrate-protein interaction

A carbohydrate chip based on glass or other transparent surfaces has been suggested as a potential tool for high-throughput analysis of carbohydrate-protein interactions. Here we proposed a facile, efficient, and cost-effective method whereby diverse carbohydrate types are modified in a single step and directly immobilized onto a glass surface, with retention of functional orientation. We modified various types of carbohydrates by reductive amination, in which reducing sugar groups were coupled with 4-(2-aminoethyl)aniline, which has di-amine groups at both ends. The modified carbohydrates were covalently attached to an amino-reactive NHS-activated glass surface by formation of stable amide bonds. This proposed method was applied for efficient construction of a carbohydrate microarray to analyze carbohydrate-protein interactions. The carbohydrate chip prepared using our method can be successfully used in diverse biomimetic studies of carbohydrates, including carbohydrate-biomolecule interactions, and carbohydrate sensor chip or microarray development for diagnosis and screening.

Comparison between a TaqMan polymerase chain reaction assay and a culture method for ctx-positive Vibrio cholerae detection

The main objective of the present work was to evaluate a real-time polymerase chain reaction (PCR) method to detect toxigenic Vibrio cholerae in Pangasius hypophthalmus, a freshwater fish cultured mainly in South East Asia. A FDA traditional culture method and a real-time PCR method of the ctx gene were used for detection of V. cholerae in spiked samples of pangasius fish. After an overnight enrichment of samples at 37 degrees C in alkaline peptone water, 2 cfu/25 g of fish was detected with both methods. Although both methods were very sensitive, obtaining results with culture methods may take several days, while real-time PCR takes only a few hours. Furthermore, with traditional methods, complementary techniques such as serotyping, although not available for all serogroups, are needed to identify toxigenic V. cholerae. However, with real-time PCR, toxigenic serogroups are detected in only one step after overnight enrichment.

Cholesterol specificity of some heptameric beta-barrel pore-forming bacterial toxins: structural and functional aspects

Apart from the thiol-specific/cholesterol-dependent cytolysin family of toxins (see Chapter 20) there are a number of other unrelated bacterial toxins that also have an affinity for plasma membrane cholesterol. Emphasis is given here on the Vibrio cholerae cytolysin (VCC) and the cytolysins from related Vibrio species. The inhibition of the cytolytic activity of these toxins by prior incubation with extracellular cholesterol or low density lipoprotein emerges as a unifying feature, as does plasma membrane cholesterol depletion. Incubation of VCC with cholesterol produces a heptameric oligomer, which is not equivalent to the pre-pore since it is unable to penetrate the plasma membrane. In structural terms, the precise sequence of VCC monomer binding to membrane, oligomer formation and pore insertion through the bilayer has yet to be fully defined. Several other bacterial toxins have a dependency for cholesterol, although the available data is limited in most cases.

Cholera toxin: A paradigm for multi-functional engagement of cellular mechanisms (Review)

Cholera toxin (Ctx) from Vibrio cholerae and its closely related homologue, heat-labile enterotoxin (Etx) from Escherichia coli have become superb tools for illuminating pathways of cellular trafficking and immune cell function. These bacterial protein toxins should be viewed as conglomerates of highly evolved, multi-functional elements equipped to engage the trafficking and signalling machineries of cells. Ctx and Etx are members of a larger family of A-B toxins of bacterial (and plant) origin that are comprised of structurally and functionally distinct enzymatically active A and receptor-binding B sub-units or domains. Intoxication of mammalian cells by Ctx and Etx involves B pentamer-mediated receptor binding and entry into a vesicular pathway, followed by translocation of the enzymatic A1 domain of the A sub-unit into the target cell cytosol, where covalent modification of intracellular targets leads to activation of adenylate cyclase and a sequence of events culminating in life-threatening diarrhoeal disease. Importantly, Ctx and Etx also have the capacity to induce a wide spectrum of remarkable immunological processes. With respect to the latter, it has been found that these toxins activate signalling pathways that modulate the immune system. This review explores the complexities of the cellular interactions that are engaged by these bacterial protein toxins, and highlights some of the new insights to have recently emerged.

Structural and kinetic features of family I inorganic pyrophosphatase from Vibrio cholerae

In this paper, kinetic properties of a soluble inorganic pyrophosphatase of family I from Vibrio cholerae (V-PPase), intestinal pathogen and causative agent of human cholera, are characterized in detail, and the crystal structure of a metal-free enzyme is reported. Hydrolytic activity of V-PPase has been studied as a function of pH, concentration of metal cofactors (Mg2+ or Mn2+), and ionic strength. It has been found that, despite the high conservation of amino acid sequences for the known bacterial PPases of family I, V-PPase differs from the other enzymes of the same family in a number of parameters. Dissociation constants of V-PPase complexed with Mg2+ or Mn2+ were essentially the same as for Escherichia coli PPase (E-PPase). However, the pH optimum of MgPP(i) hydrolysis by V-PPase was shifted to more alkaline pH due to higher values of the pK(a) of ionizable groups for both the free enzyme and the enzyme-substrate complex. The stability of a hexameric form of V-PPase has been studied as a function of pH. The corresponding pK(a) of a group that controls the stability of the hexamer at pH below 6 (pK(a) = 4.4) was significantly lower than in the other hexameric PPases. The crystal structure reported here is analyzed and compared with the structure of E-PPase. The location of amino acid residues that differ in V-PPase and E-PPase is discussed. Since V-PPase has been found to retain its hydrolytic activity in high ionic strength media, the observed structural and kinetic features are analyzed in view of the possible osmoadaptation of this protein.

[Analysis of exoproteins of El Tor Vibrio cholerae by 2DE and MALDI-TOF-MS/MS]

OBJECTIVE

Our aim is to analyze the exoproteins of the epidemic strain and nonepidemic strain of El Tor Vibrio cholerae.

METHODS

We separated the exoproteins of two El Tor strains, one epidemic strain N16961 and one nonepidemic strain 92-3, by two dimension electrophoresis. All protein spots were identified by MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight) mass spectrometry and database referencing.

RESULTS

We identified 49 exoproteins from 206 protein spots in epidemic strain and 42 exoproteins from 236 protein spots in nonepidemic strain. Sixty-eight exoproteins were totally identified in two strains, and the proteins with signal peptides were about 55.88% in total. We classified the exoproteins into 10 subgroups according to their functions. Among them were metabolic enzymes, protein maintenance and folding, protein synthesis and signal transduction proteins, which accounted for 36.76% of all the proteins identified. We identified 11 hypothetical proteins and 2 unknown function proteins with signal peptides at the first time, accounting for 19.12%. Transporter, flagellum components, degradation enzymes, outer membrane proteins and toxin accounted for 14.71%, 11.76%, 10.29%, 5.88%, 1.47% separately.

CONCLUSION

We obtained the exoprotein profiles of epidemic strain and nonepidemic strain of El Tor Vibrio cholerae. The reasons of why the flagellum components without signal peptides that are associated closely with virulence could be released out of the bacteria, and why with high hemagglutinin/protease secretion in nonepidemic strains should be analyzed in the future.

[Analysis of molecular biological characteristic of the gene and its flanking sequences, similar with transposase in Vibrio cholerae pathogenicity island, among V. alginolyticus strains]

OBJECTIVE

To investigate whether the gene similar with transposase gene (vpiT) from pathogenicity island of Vibrio cholerae exists in V. alginolyticus strains, and to analyze molecular biological characteristic of the gene and its flanking sequences.

METHODS

PCR detection of the gene, similar with vpiT in pathogenicity island of V. cholerae was done among 94 strains of V. alginolyticus. PCR products from positive strains were directly sequenced. Based on acquired partial sequences, we designed primers for reverse PCR, and got the amplification fragment containing complete gene (valT) from V. alginolyticus E0601, which was similar with vpiT gene. The reverse PCR product was cloned and sequenced, and the acquired sequence was analyzed with bioinformatic methods.

RESULTS

We found that among 94 V. alginolyticus strains, only V. alginolyticus E0601 and E0612, from east coastal areas of Guangdong province, produced predicted positive amplification fragments in PCR detection. Sequencing indicated that amplification fragments from V. alginolyticus E0601 and E0612 had identical DNA sequence (named valT-S1). Sequence valT-S3 from V. alginolyticus E0601, containing complete valT gene and flanking segments, was finally obtained through reverse PCR, cloning, and sequencing. Bioinformatic analysis on valT-S3 suggested that valT was transposase gene, highly similar with vpiT in V. cholerae VPI.

CONCLUSION

According to above result and related references, we believe that valT and its flanking segments were acquired from heterogenous bacteria, and VPI or its component probably transfers among Vibrio species including V. alginolyticus.

Vibrio cholerae hemolysin is apoptogenic to peritoneal B-1a cells but its oligomer shepherd the cells for IgA response

Vibrio cholerae hemolysin (HlyA) can exist as a monomer with hemolytic activity and an oligomer that agglutinates erythrocytes. Biochemical differences accompanying the change in state of aggregation led us to weigh possible differences between the two forms from mucosal immunoregulation perspective. HlyA oligomer-treated murine B-1a cells up-regulated TLR2 and involved the signaling molecules MyD88, TRAF6 and NF-kappaB. The cells subsequently expressed IgM and IgA. HlyA monomer treatment although resulted in TLR2 up-regulation, could not induce these effects. Apoptosis was detected in majority of the monomer-treated cells that involved caspase-9 and caspase-3. This study shows for the first time that two forms of the same protein could drive the host immune cell to two different outcomes, one of death and the other towards activation.

Flexibility in the ABC transporter MsbA: Alternating access with a twist

ATP-binding cassette (ABC) transporters are integral membrane proteins that translocate a wide variety of substrates across cellular membranes and are conserved from bacteria to humans. Here we compare four x-ray structures of the bacterial ABC lipid flippase, MsbA, trapped in different conformations, two nucleotide-bound structures and two in the absence of nucleotide. Comparison of the nucleotide-free conformations of MsbA reveals a flexible hinge formed by extracellular loops 2 and 3. This hinge allows the nucleotide-binding domains to disassociate while the ATP-binding half sites remain facing each other. The binding of the nucleotide causes a packing rearrangement of the transmembrane helices and changes the accessibility of the transporter from cytoplasmic (inward) facing to extracellular (outward) facing. The inward and outward openings are mediated by two different sets of transmembrane helix interactions. Altogether, the conformational changes between these structures suggest that large ranges of motion may be required for substrate transport.

Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles

We report enhancement in the fluorescent signal of the carbocyanine dye Cy5 by using an engineered virus as a scaffold to attach >40 Cy5 reporter molecules at fixed locations on the viral capsid. Although cyanine dye loading is often accompanied by fluorescence quenching, our results demonstrate that organized spatial distribution of Cy5 reporter molecules on the capsid obviates this commonly encountered problem. In addition, we observe energy transfer from the virus to adducted dye molecules, resulting in a highly fluorescent viral nanoparticle. We have used this enhanced fluorescence for the detection of DNA-DNA hybridization. When compared with the most often used detection methods in a microarray-based genotyping assay for Vibrio cholerae O139, these viral nanoparticles markedly increased assay sensitivity, thus demonstrating their applicability for existing DNA microarray protocols.

Simultaneous direct detection of toxigenic and non-toxigenic Vibrio cholerae from rectal swabs and environmental samples by sandwich ELISA

A mAb-based simple, specific and rapid two-tip dipstick ELISA was developed for simultaneous detection of toxin- and non-toxin-producing strains ofVibrio cholerae, and for direct detection ofV. choleraefrom rectal swabs of patients and from environmental water samples. Rabbit polyclonal antibodies and murine mAbs were raised against recombinant protein (r-protein) antigens of cholera toxin B (CtxB) and outer membrane protein W (OmpW). Rabbit polyclonal antibodies to both r-proteins were coated individually onto the tips of nitrocellulose (NC) membranes of a two-tipped NC dipstick as capture antibodies and a mixture of two mAbs was used for the detecting antibodies. The test was found to be specific forV. choleraestrains O1, O139, non-O1 and non-O139, and did not show any cross-reaction to closely related bacterial strains. The test was evaluated on rectal swabs collected at the bedside of 75 hospitalized diarrhoeal patients and on 50 environmental water samples after enrichment for 4 h in alkaline peptone water. The mAb two-tip dipstick ELISA detectedV. choleraein 52/75 rectal swabs and 2/50 environmental water samples for CtxB antigen, and in 1/50 environmental water samples for the non-toxin OmpW antigen ofV. choleraewithin 1.5 h. These findings were identical to those observed using PCR and conventional culture methods. Thus, this mAb-based two-tip dipstick ELISA could be used for early and reliable simultaneous detection of toxigenic and non-toxigenic strains ofV. choleraefrom clinical and environmental water samples.

GM1-functionalized liposomes in a microtiter plate assay for cholera toxin in Vibrio cholerae culture samples

Vibrio cholerae, the causative agent for cholera, infects its host by expressing a protein consisting of two subunits: the pentameric cholera toxin B (CTB) and cholera toxin A (CTA). CTB frequently is used as an indicator of the presence of pathogenic V. cholerae and typically is detected using enzyme-linked immunosorbent assays (ELISAs). In lieu of an enzyme-linked detection method, we have developed GM(1) ganglioside-functionalized fluorescent dye-encapsulating liposomes for the detection of CTB produced by V. cholerae in a simple microtiter plate assay. Liposomes were compared with fluorescein-labeled antibodies and enzyme-linked secondary antibodies for quantification of purified CTB. A limit of detection for CTB using the liposomes was 340pg/ml, which was comparable to that using the ELISA but 18 times lower than that using the fluorescein-labeled anti-CTB antibodies for the same purpose. The sensitivity of the assay provided by the liposomes was substantial, and the working range improved when compared with that of the fluorescein-labeled antibodies and the ELISA. In addition, the liposomes required shorter assay times, exhibited greater precision, and were less expensive compared with the ELISA. The liposomes were optimized with respect to phospholipid and ganglioside concentrations. The optimized liposomes were then used to probe culture supernatants from V. cholerae El Tor C6706 grown in Dulbecco's modified Eagle's medium and AKI medium for the presence of CTB.

Structural studies on Vibrio cholerae ToxR periplasmic and cytoplasmic domains

The transcription activator ToxR controls the expression of cholera toxin, pilus colonization factor and outer membrane protein in Vibrio cholerae. It binds to the 5'-TTTTGAT-3' tandemly repeated DNA sequence in the cholera toxin promoter region. ToxR is a membrane protein having distinct periplasmic and cytoplasmic domains. The two domains have been cloned, over-expressed and purified for structural studies. The cytoplasmic domain is more compact than the periplasmic domain. The periplasmic domain exists as dimer due to the presence of an interchain disulfide linkage, while the cytoplasmic domain is monomeric in solution implying the importance of the disulfide bond to homodimerize the native ToxR. By replacing one of the cysteines C293 with alanine, using site-directed mutagenesis, a C293A mutant was created at the periplasmic domain to elucidate the role of cysteine in dimerization of ToxR.

Galactose-specific fimbrial adhesin of enteroaggregative Escherichia coli: a possible aggregative factor

A galactose-specific adhesin was isolated from the fimbriae of an enteroaggregative Escherichia coli (EAEC) strain. The adhesin was found to be a high molecular weight aggregate of the 18-kDa monomer. The dimeric (36 kDa) and tetrameric (76 kDa) forms appeared in sodium dodecyl sulphate polyacrylamide gel electrophoresis when a higher concentration of the adhesin was used. The IgGAD (IgG against adhesin) obtained from the immune sera raised in rabbits against purified adhesin could detect all three forms of the adhesin even from the crude fimbrial preparation. The IgGAD failed to recognize the adhesin in the presence of galactose, thereby suggesting the antibody-binding site and the sugar-binding site on the adhesin might be same or overlapping. Furthermore, the IgGAD could localize the adhesin exclusively on the fimbriae as observed in immunogold electron microscopy. The aggregative adherence of the bacteria to HEp-2 cells was reduced to 70% in the presence of the IgGAD. A glycoprotein (34 kDa) present in the membrane fraction of HEp-2 cells interacted with the purified adhesin in a galactose-specific manner. The IgGAD could recognize the adhesin from the crude fimbrial preparation of 9 out of 10 clinical isolates of EAEC strains but failed to identify any protein from the crude fimbrial preparation of Salmonella typhimurium (fim +ve as well as fim -ve strain), Vibrio cholerae (WO7) or Escherichia coli DH5alpha.

Directed evolution of aryl carrier proteins in the enterobactin synthetase

The recognition of carrier proteins by multiple catalytic partners occurs in every cycle of chain elongation in the biosynthesis of fatty acids and of the pharmacologically important polyketide and nonribosomal peptide natural products. To dissect the features of carrier proteins that determine specific recognition at distinct points in assembly lines, we have used the two-module Escherichia coli enterobactin synthetase as a model system. Using an entB knockout strain, we developed a selection for growth on iron-limiting medium to evolve aryl carrier protein domains. The aryl carrier proteins from VibB of Vibrio cholerae vibriobactin and HMWP2 of Yersinia pestis yersiniabactin assembly lines were evolved by random mutagenesis to support growth under selection conditions, yielding a convergent set of mutations. Subsequent in vitro biochemical characterizations with partner enzymes EntE, EntF, and Sfp on the evolved VibB aryl carrier protein revealed a approximately 500-fold improvement in reconstituted enterobactin production activity. Mechanistic characterization identified three distinct specific recognition surfaces of VibBArCP for three catalytic partners in enterobactin biosynthesis. Our results suggest that heterologous carrier protein interactions can be engineered with a small number of mutations given a suitable selection scheme and provide insights for reprogramming nonribosomal peptide biosynthesis.

[Vibrio cholerae hemolytic activity]

Mechanisms of realization of Vibrio cholerae hemolytic activitywere analyzed using summarized own results and data from the literature. It has been shown that lectin receptor, which coded by hlyA gene, participates in lysis of sheep erythrocytes, but not of rabbit erythrocytes, as well as interact with D-galactose with selectivity to 3 anomers. Lectin nature of HlyA can determine formation of its complexes with lypopolysaccharides (LPS) and enzymes, which promote realization of hemolysis (by lipase, lecitinase, neuraminidase). It has been determined that lipase activity correlates with hemolytic activity of nonepidemic variants of V. cholerae. Lipase is considered as the enzyme marker of sheep erythrocytes hemolysis. It is assumed that LPS and lipase play shaperon-like role during interaction of HlyA with lipids, which promote denaturation of hemolytic active monomer in hemagglutinating oligomer.

Crystal structure of the Vibrio cholerae quorum-sensing regulatory protein HapR

Quorum sensing in Vibrio cholerae involves signaling between two-component sensor protein kinases and the response regulator LuxO to control the expression of the master regulator HapR. HapR, in turn, plays a central role in regulating a number of important processes, such as virulence gene expression and biofilm formation. We have determined the crystal structure of HapR to 2.2-A resolution. Its structure reveals a dimeric, two-domain molecule with an all-helical structure that is strongly conserved with members of the TetR family of transcriptional regulators. The N-terminal DNA-binding domain contains a helix-turn-helix DNA-binding motif and alteration of certain residues in this domain completely abolishes the ability of HapR to bind to DNA, alleviating repression of both virulence gene expression and biofilm formation. The C-terminal dimerization domain contains a unique solvent accessible tunnel connected to an amphipathic cavity, which by analogy with other TetR regulators, may serve as a binding pocket for an as-yet-unidentified ligand.

Autoprocessing of the Vibrio cholerae RTX toxin by the cysteine protease domain

Vibrio cholerae RTX is a large multifunctional bacterial toxin that causes actin crosslinking. Due to its size, it was predicted to undergo proteolytic cleavage during translocation into host cells to deliver activity domains to the cytosol. In this study, we identified a domain within the RTX toxin that is conserved in large clostridial glucosylating toxins TcdB, TcdA, TcnA, and TcsL; putative toxins from V. vulnificus, Yersinia sp., Photorhabdus sp., and Xenorhabdus sp.; and a filamentous/hemagglutinin-like protein FhaL from Bordetella sp. In vivo transfection studies and in vitro characterization of purified recombinant protein revealed that this domain from the V. cholerae RTX toxin is an autoprocessing cysteine protease whose activity is stimulated by the intracellular environment. A cysteine point mutation within the RTX holotoxin attenuated actin crosslinking activity suggesting that processing of the toxin is an important step in toxin translocation. Overall, we have uncovered a new mechanism by which large bacterial toxins and proteins deliver catalytic activities to the eukaryotic cell cytosol by autoprocessing after translocation.

Membrane association and multimerization of TcpT, the cognate ATPase ortholog of the Vibrio cholerae toxin-coregulated-pilus biogenesis apparatus

The toxin-coregulated pilus (TCP) is one of the major virulence factors of Vibrio cholerae. Biogenesis of this type 4 pilus (Tfp) requires a number of structural components encoded by the tcp operon. TcpT, the cognate putative ATPase, is required for TCP biogenesis and all TCP-mediated functions. We studied the stability and localization of TcpT in cells containing in-frame deletions in each of the tcp genes. TcpT was detectable in each of the biogenesis mutants except the DeltatcpT strain. TcpT was localized to the inner membrane (IM) in a TcpR-dependent manner. TcpR is a predicted bitopic inner membrane protein of the TCP biogenesis apparatus. Using metal affinity pull-down experiments, we demonstrated interaction between TcpT and TcpR. Using Escherichia coli as a heterologous system, we investigated direct interaction between TcpR and TcpT. We report that TcpR is sufficient for TcpT IM localization per se; however, stable IM localization of TcpT requires an additional V. cholerae-specific factor(s). A LexA-based two-hybrid system was utilized to define interaction domains of the two proteins. We demonstrate a strong interaction between the cytoplasmic domain of TcpR and the N-terminal 100 amino acid residues of TcpT. We also demonstrated the ability of the C-terminal domain of TcpT to multimerize.

NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein

PA4608 is a 125 residue protein from Pseudomonas aeruginosa with a recent identification as a PilZ domain and putative bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) adaptor protein that plays a role in bacterial second-messenger regulated processes. The nuclear magnetic resonance (NMR) structure of PA4608 has been determined and c-di-GMP binding has been confirmed by NMR titration studies. The monomeric core structure of PA4608 contains a six-stranded anti-parallel beta barrel flanked by three helices. Conserved surface residues among PA4608 homologs suggest the c-di-GMP binding site is at one end of the barrel and includes residues in the helices as well as in the unstructured N-terminus. Chemical shift changes in PA4608 resonances upon titration with c-di-GMP confirm binding. This evidence supports the hypothesis that proteins containing PilZ domains are the long-sought c-di-GMP adaptor proteins.

Resonance Raman spectroscopic investigation of the light-harvesting chromophore in escherichia coli photolyase and Vibrio cholerae cryptochrome-1

Photolyases and cryptochromes are flavoproteins that belong to the class of blue-light photoreceptors. They usually bind two chromophores: flavin adenine dinucleotide (FAD), which forms the active site, and a light-harvesting pigment, which is a 5,10-methenyltetrahydrofolate polyglutamate (MTHF) in most cases. In Escherichia coli photolyase (EcPhr), the MTHF cofactor is present in substoichiometric amounts after purification, while in Vibrio cholerae cryptochrome-1 (VcCry1) the MTHF cofactor is bound more strongly and is present at stoichiometric levels after purification. In this paper, we have used resonance Raman spectroscopy to monitor the effect of loss of MTHF on the protein-FAD interactions in EcPhr and to probe the protein-MTHF interactions in both EcPhr and VcCry1. We find that removal of MTHF does not perturb protein-FAD interactions, suggesting that it may not affect the physicochemical properties of FAD in EcPhr. Our data demonstrate that the pteridine ring of MTHF in EcPhr has different interactions with the protein matrix than that of MTHF in VcCry1. Comparison to solution resonance Raman spectra of MTHF suggests that the carbonyl of its pteridine ring in EcPhr experiences stronger hydrogen bonding and a more polar environment than in VcCry1, but that hydrogen bonding to the pteridine ring amine hydrogens is stronger in VcCry-1. These differences in hydrogen bonding may account for the higher binding affinity of MTHF in VcCry1 compared to EcPhr.

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae

Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem aptamer as a function of Mg(2+) and glycine concentration. We fit a simple three-state thermodynamic model that describes the energetic coupling between magnesium-induced folding and glycine binding. Furthermore, we characterize the structural conformations of each of the three states: In low salt with no magnesium present, the VCI-II construct has an extended overall conformation, presumably representing unfolded structures. Addition of millimolar concentrations of Mg(2+) in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg(2+) concentrations, the tandem aptamer binds glycine cooperatively. The glycine binding transition involves a further compaction, additional tertiary packing interactions and further uptake of magnesium ions relative to the state in high Mg(2+) but no glycine. Employing density reconstruction algorithms, we obtain low resolution 3-D structures for all three states from the SAXS measurements. These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies.

Theoretical model of the three-dimensional structure of a disease resistance gene homolog encoding resistance protein in Vigna mungo

Plant disease resistance (R) genes, the key players of innate immunity system in plants encode 'R' proteins. 'R' protein recognizes product of avirulance gene from the pathogen and activate downstream signaling responses leading to disease resistance. No three dimensional (3D) structural information of any 'R' proteins is available as yet. We have reported a 'R' gene homolog, the 'VMYR1', encoding 'R' protein in Vigna mungo. Here, we describe the homology modeling of the 'VMYR1' protein. The model was created by using the 3D structure of an ATP-binding cassette transporter protein from Vibrio cholerae as a template. The strategy for homology modeling was based on the high structural conservation in the superfamily of P-loop containing nucleoside triphosphate hydrolase in which target and template proteins belong. This is the first report of theoretical model structure of any 'R' proteins.

Bacterial capsular antigens. Structural patterns of capsular antigens

Structural patterns of bacterial capsular antigens including capsular polysaccharides and exoglycans are given in this review. In addition, the immunological activity of capsular antigens and their role in type specificity of bacteria are discussed.

Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU

Background

The SmtB/ArsR family of prokaryotic metal-regulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of heavy metal ions, while derepression results from direct binding of metal ions by these 'metal-sensor' proteins. The HlyU protein from Vibrio cholerae is the positive regulator of haemolysin gene, it also plays important role in the regulation of expression of the virulence genes. Despite the understanding of biochemical properties, its structure and relationship to other protein families remain unknown.

Results

We find that HlyU exhibits structural features common to the SmtB/ArsR family of transcriptional repressors. Analysis of the modeled structure of HlyU reveals that it does not have the key metal-sensing residues which are unique to the SmtB/ArsR family of repressors, yet the tertiary structure is very similar to the family members. HlyU is the only member that has a positive control on transcription, while all the other members in the family are repressors. An evolutionary analysis with other SmtB/ArsR family members suggests that during evolution HlyU probably occurred by gene duplication and mutational events that led to the emergence of this protein from ancestral transcriptional repressor by the loss of the metal-binding sites.

Conclusion

The study indicates that the same protein family can contain both the positive regulator of transcription and repressors – the exact function being controlled by the absence or the presence of metal-binding sites.