Crystal structure of YfiR, an unusual TetR/CamR-type putative transcriptional regulator from Bacillus subtilis.
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Bacillus subtilis↗
Biomedical subjects
Xiaojing Yang
Publications and source records attributed to Xiaojing Yang.
Urea coordinated titanium trichloride Ti(III)[OC(NH)2]6Cl3: a single molecular precursor yielding highly visible light responsive TiO2 nanocrystallites.
A coordination complex, Ti(III)[OC(NH2)2]6Cl3, was first synthesized via reacting hot alcoholic solutions of TiCl3 and urea, which was subsequently employed as a molecular precursor for nanocrystalline TiO2 via thermal decomposition. Fourier transform IR spectroscopy confirmed C=O-->Ti coordination bond formation, while Rietveld refinement revealed a hexagonal crystal structure (space group: Pc1) for the complex with a = b = 16.438(4) A, c = 15.423(3) A, alpha = beta = 90 degrees , gamma = 120 degrees , and V = 3608.9(13) A3. Thermal decomposition and phase evolution processes of the complex were investigated in air by combined means of elemental analysis, Fourier transform IR, differential thermal analysis/thermogravimetry, X-ray diffraction, and Raman spectroscopy. Characterizations of the resultant TiO2 powders were achieved by scanning electron microscopy, high-resolution transmission electron microscopy, the Brunauer-Emmett-Teller analysis, thermal desorption spectroscopy, and UV-vis spectroscopy. Simultaneous doping of C, N, and Cl was realized upon pyrolyzing the molecular precursor in air, leading to significantly lowered direct and indirect interband transition energies of the resultant TiO2. As a consequence, the anatase nanopowders obtained at 450 and 500 degrees C, with specific surface areas of 97.8 and 64.1 m2/g, respectively, exhibit significantly higher efficiency than Degussa P25 in the bleaching of methyl orange solution under visible light (mainly consisting two wavelengths of 405 and 436 nm at 81:100 intensity ratio) irradiation, either at a fixed weight of TiO2 loading or at a fixed surface area of the loaded TiO2 powder.
Journal Article↗
Picoliter-volume aqueous droplets in oil: electrochemical detection and yeast cell electroporation.
An electrochemical detection method was introduced for aqueous droplet analysis in oil phase of microfluidic devices. This method is based on the electrochemical signal difference between aqueous and oil. Applying a low alternating current (AC) voltage to a couple of Au microelectrodes, this method can offer size information and ion concentration range from 0.02 mmol/L to 1 mol/L of tens of picoliter to nanoliter aqueous droplets. Alternatively, applying a relative high AC voltage (18 Vpp) at a frequency of 1 kHz leads to electroporation of yeast cells encapsulated into picoliter droplets. We believe that this simple technique is useful for a number of aqueous droplet-based chemical and biological analyses as well as cell electroporation.
Electrochemistry↗
Analysis of the glycodynamics of primary osteoblasts and bone cancer cells.
Bone cells produce a variety of glycoproteins that contribute to bone health, and function in cell adhesion, stabilizing the extracellular matrix, promoting growth and differentiation, and the induction of apoptosis. Some of these processes appear to be disturbed in arthritis. In this chapter, in vitro studies aimed at an understanding of the biological effects of inflammatory stimuli in the bone of arthritis patients are described. The glycodynamics of cells can be studied using primary cultures of osteoblasts or bone cancer cell cultures, to examine the relationship between the biosynthesis of cell-surface glycoproteins and inflammatory stimuli affecting cell growth and cell death. Cell-surface carbohydrates are assessed by lectin staining of cells, and the potential of cells to synthesize glycoproteins is determined by glycosyltransferase assays. These parameters are then related to [3H]thymidine incorporation as a measure of cell proliferation, and to flow cytometry of terminal deoxynucleotidyl transferase dUTP-mediated nick end labeling (TUNEL) and annexin V-stained cells as a measure of apoptosis. These in vitro studies are aimed at an understanding of the role of glycosylation in the bone of arthritis patients, but they can also be applied to other diseases.
Apoptosis↗
N-Acyl derivatives of glucosamine as acceptor substrates for galactosyltransferase from bone and cartilage cells.
Glucosamine is commonly used as a nutraceutical by arthritis patients. However, its mode of action is still unknown, and there is controversy about its clinical efficacy. Synthetic N-acyl glucosamines (acyl group>2 carbons) comprise a new class of drugs. We examined these derivatives for their effect in bone and cartilage cells, and for their ability to serve as acceptor substrates for galactosyltransferase. With the exception of N-benzoylglucosamine, compounds of the series were good substrates for galactosyltransferases from bone and cartilage cells, and for purified enzyme from bovine milk. When N-butyrylglucosamine (GlcNBu) was added to the cell medium of primary bovine chondrocytes and human osteoblasts, small amounts were found to enter the cells and a radiolabeled metabolite appeared in the medium. However, GlcNBu did not appear to be incorporated directly into oligosaccharides. GlcNBu at 1 and 5mM concentrations in the glucose-free cell medium of primary human osteoblasts from osteoarthritis patients did not significantly alter cell proliferation or cell differentiation.
Animals↗
Structural basis for an unexpected mode of SERM-mediated ER antagonism.
Tamoxifen is effective for the prevention and treatment of estrogen-dependent breast cancers, but is associated with an increased incidence of endometrial tumors. We report the crystal structure of the estrogen receptor alpha (ERalpha) ligand binding domain (LBD) bound to the structurally similar compound GW5638, which has therapeutic potential and does not stimulate the uterus. Like tamoxifen, GW5638 relocates the carboxy-terminal helix (H12) to the known coactivator-docking site in the ERalpha LBD. However, GW5638 repositions residues in H12 through specific contacts with the N terminus of this helix. In contrast to tamoxifen, the resulting increase in exposed hydrophobic surface of ERalpha LBD correlates with a significant destabilization of ERalpha in MCF-7 cells. Thus, the GW5638-ERalpha LBD structure reveals an unexpected mode of SERM-mediated ER antagonism, in which the stability of ERalpha is decreased through an altered position of H12. This dual mechanism of antagonism may explain why GW5638 can inhibit tamoxifen-resistant breast tumors.
Amino Acid Sequence↗
NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-beta-D-glucosides.
The import of disaccharides by many bacteria is achieved through their simultaneous translocation and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). The imported phospho-disaccharides are, in some cases, subsequently hydrolyzed by members of the unusual glycoside hydrolase family GH4. The GH4 enzymes, occasionally found also in bacteria such as Thermotoga maritima that do not utilise a PEP-PTS system, require both NAD(+) and Mn(2+) for catalysis. A further curiosity of this family is that closely related enzymes may show specificity for either alpha-d- or beta-d-glycosides. Here, we present, for the first time, the three-dimensional structure (using single-wavelength anomalous dispersion methods, harnessing extensive non-crystallographic symmetry) of the 6-phospho-beta-glycosidase, BglT, from T.maritima in native and complexed (NAD(+) and Glc6P) forms. Comparison of the active-center structure with that of the 6-phospho-alpha-glucosidase GlvA from Bacillus subtilis reveals a striking degree of structural similarity that, in light of previous kinetic isotope effect data, allows the postulation of a common reaction mechanism for both alpha and beta-glycosidases. Given that the "chemistry" occurs primarily on the glycone sugar and features no nucleophilic attack on the intact disaccharide substrate, modulation of anomeric specificity for alpha and beta-linkages is accommodated through comparatively minor structural changes.
Bacterial Proteins↗
YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology.
YfiT, a 19-kDa polypeptide from Bacillus subtilis, belongs to a small sequence family with members predominantly from Gram positive bacteria. We have determined the crystal structure of YfiT in complex with Ni(2+) to a resolution of 1.7 A. YfiT exists as a dimer and binds Ni(2+) in a 1:1 stoichiometry. The protein has an unusual four-helix bundle topology and coordinates Ni(2+) in an octahedral geometry with three conserved histidines and three waters. Although there is no similarity in their overall structures, the coordination geometry of the metal and the residues that constitute the putative active site in YfiT are similar to those of metalloproteases such as thermolysin. Our structural analyses suggest that YfiT might function as a metal-dependent hydrolase.
Bacillus subtilis↗
An unusual mechanism of glycoside hydrolysis involving redox and elimination steps by a family 4 beta-glycosidase from Thermotoga maritima.
Among the numerous well-characterized families of glycosidases, family 4 appears to be the anomaly, requiring both catalytic NAD+ and a divalent metal for activity. The unusual cofactor requirement prompted the proposal of a mechanism involving key NAD+-mediated redox steps as well as elimination of the glycosidic oxygen. Primary kinetic isotope effects for the 2- and 3-deutero substrate analogues, isotopic exchange with solvent, and structural analysis of a 6-phospho-beta-glucosidase, BglT (E.C. 3.2.1.6), provided evidence in support of the proposed mechanism, which has striking resemblances to that of the sugar dehydratases. Furthermore, analysis of the stereochemical outcome indicated that family 4 enzymes are retaining glycosidases.
Glucosidases↗
Isochromosome 22 in trisomy 22 mosaic with five cell lines.
This report describes a full-term male infant with trisomy 22 due to an isochromosome 22. Prenatal diagnosis with amniotic fluid showed two cell lines, one with an isochromosome 22 and the other with a deleted isochromosome 22. Subsequent cytogenetic analyses of cord blood, umbilical cord tissue, and placenta revealed additional cell lines. A normal cell line was found in umbilical cord tissue and two of three placental sites. The newborn had numerous dysmorphic features and died within 48 hrs of birth.
Abnormalities, Multiple↗
Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis.
GlvA, a 6-phospho-alpha-glucosidase from Bacillus subtilis, catalyzes the hydrolysis of maltose-6'-phosphate and belongs to glycoside hydrolase family GH4. GH4 enzymes are unique in their requirement for NAD(H) and a divalent metal for activity. We have determined the crystal structure of GlvA in complex with its ligands to 2.05 A resolution. Analyses of the active site architecture, in conjunction with mechanistic studies and precedent from the nucleotide diphosphate hexose dehydratases and other systems, suggest a novel mechanism of glycoside hydrolysis by GlvA that involves both the NAD(H) and the metal.
Amino Acid Sequence↗
The effect of TNF-alpha on glycosylation pathways in bovine synoviocytes.
Synoviocytes are fibroblastic cells that line joint cavities. These cells synthesize numerous cell-surface and extracellular-matrix glycoproteins that are required for maintenance of the joint. Joint inflammation, such as occurs in arthritis, has been shown to have major effects on synoviocyte proliferation and on the biosynthesis of glycoproteins. The structures of the carbohydrate moieties of glycoproteins, however, and the enzymes involved in their synthesis have not yet been described for synoviocytes. Therefore, to characterize the cell-surface glycoconjugates, synoviocytes were isolated from bovine ankles, and the cells were grown in primary cultures. Lectin-binding assays were used to identify exposed N- and O-glycan carbohydrate determinants on synoviocytes, and specific enzyme assays were used to identify some of the glycosyltransferases involved in the synthesis of the glycan chains. A number of the enzymes that synthesize N- and O-linked oligosaccharides were found to be active in cell-free extracts of synoviocytes, including those that synthesize core-1-based O-glycans and the more complex bi-antennary N-glycans. To understand the molecular events underlying the inflammatory response in the synovium of arthritis patients, we examined the effect of the inflammatory cytokine tumour necrosis factor alpha (TNF-alpha) on synoviocytes and on glycosylation profiles. TNF-alpha treatment, which induces apoptosis in synoviocytes, was accompanied by changes in lectin-binding patterns, indicating alterations in the expression of cell-surface oligosaccharides. Concurrently, changes in specific enzyme activities were observed in treated cells. Two enzymes potentially important to the inflammatory process, core 2 beta6-GlcNAc-transferase and beta4-Gal-transferase, increased after TNF-alpha treatment. This is the first study of glycoprotein biosynthesis in synoviocytes, and it shows that synoviocytes have a characteristic glycosylation phenotype that is altered in the presence of inflammatory cytokines.
Animals↗
Pyk2 activation is integral to acid stimulation of sodium/hydrogen exchanger 3.
The present study examines the role of Pyk2 in acid regulation of sodium/hydrogen exchanger 3 (NHE3) activity in OKP cells, a kidney proximal tubule epithelial cell line. Incubation of OKP cells in acid media caused a transient increase in Pyk2 phosphorylation that peaked at 30 seconds and increased Pyk2/c-Src binding at 90 seconds. Pyk2 isolated by immunoprecipitation and studied in a cell-free system was activated and phosphorylated at acidic pH. Acid activation of Pyk2 (a) was specific for Pyk2 in that acid did not activate focal adhesion kinase, (b) required calcium, and (c) was associated with increased affinity for ATP. Transfection of OKP cells with dominant-negative pyk2(K457A) or small interfering pyk2 duplex RNA blocked acid activation of NHE3, while neither had an effect on glucocorticoid activation of NHE3. In addition, pyk2(K457A) blocked acid activation of c-Src kinase, which is also required for acid regulation of NHE3. The present results demonstrate that Pyk2 is directly activated by acidic pH and that Pyk2 activation is required for acid activation of c-Src kinase and NHE3. Given that partially purified Pyk2 can be activated by acid in a cell-free system, Pyk2 may serve as the pH sensor that initiates the acid-regulated signaling cascade involved in NHE3 regulation.
ADP-Ribosylation Factors↗
Intercalation of cobaltammine complex ions into layered manganese oxide.
The intercalation of Co(2+), [Co(NH(3))(6)](3+), and [Co(NH(3))(5)Cl](2+) ions into layered manganese oxide (birnessite) was studied by chemical, XRD, SEM, IR, and DTA-TG analyses. The intercalation reaction progressed by a 2:1 or 3:1 ion-exchange mechanism depending on the valence of the starting ions. The oxidation state of cobalt did not change with the intercalation reaction. The intercalation of [Co(NH(3))(6)](3+) ions resulted in an increase of basal spacing from 0.716 to 0.956 nm, giving a layered structure material consisting mainly of platelike particles. The chemical analysis results showed that the structure of [Co(NH(3))(6)](3+) ions was maintained in the interlayer. On the other hand, an H(2)O/NH(3) ligand exchange reaction progressed for the intercalation of [Co(NH(3))(5)Cl](2+) ions, resulting in an increase in the basal spacing from 0.716 to 0.956 nm.
Journal Article↗
Automated crystallographic system for high-throughput protein structure determination.
High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.
Automation↗
Soluble human core 2 beta6-N-acetylglucosaminyltransferase C2GnT1 requires its conserved cysteine residues for full activity.
Human UDP-GlcNAc: Galbeta1-3GalNAc- (GlcNAc to GalNAc) beta1,6-GlcNAc-transferase (C2GnT1) is a member of a group of beta6-GlcNAc-transferases that belongs to CAZy family 14. One of the striking features of these beta6-GlcNAc-transferases is the occurrence of nine completely conserved cysteine residues that are located throughout the catalytic domain. We have expressed the soluble catalytic domain of human C2GnT1 in insect cells, and isolated active enzyme as a secreted protein. beta-Mercaptoethanol (beta-ME) and dithiothreitol (DTT) were found to stimulate the enzyme activity up to 20-fold, indicating a requirement for a reduced sulfhydryl for activity. When the enzyme was subjected to nonreducing PAGE, the migration of the protein was identical to the migration in reducing gels, demonstrating the absence of intermolecular disulfide bonds. This suggested that the monomer is the active form of the enzyme. Sulfhydryl reagents such as 5,5'-dithiobis-2-nitrobenzoic acid (DTNB) and N-ethylmaleimide (NEM) inactivated the enzyme, and the inactivation was partially prevented by prior addition of donor or acceptor substrate and by sulfhydryl reducing agents. We therefore investigated the role of all nine conserved cysteine residues in enzyme stability and activity by site-directed mutagenesis where individual cysteine residues were changed to serine. All of the mutants were expressed as soluble proteins. Seven of the Cys mutants were found to be inactive, while C100S and C217S mutants had 10% and 41% activity, respectively, when compared to the wild-type enzyme. Wild-type and C217S enzymes had similar K(M) and V(max) values for acceptor substrate Galbeta1-3GalNAcalpha-p-nitrophenyl (GGApnp), but the K(M) value for UDP-GlcNAc was higher for C217S than for the wild-type enzyme. In contrast to wild-type enzyme, C217S was not stimulated by reducing agents and was not inhibited by sulfhydryl specific reagents. These results suggest that Cys-217 is a free sulfhydryl in active wild-type enzyme and that Cys-217, although not required for activity, is in or near the active site of the protein. Since seven of the mutations were totally inactive, it is likely that these seven Cys residues play a role in maintaining an active conformation of soluble C2GnT1 by forming disulfide bonds. These bonds are only broken at high concentrations of disulfide reducing agents.
Amino Acid Sequence↗
Submicroscopic terminal deletion of 1p36.3 and Xp23 hidden in complex chromosome rearrangements: independent mechanism of telomere restitution on the two chromatids.
In this study, we report two cases each with a complex chromosome rearrangement concealing a submicroscopic terminal deletion. The first case had a mos 46,XX,der(1)t(1;9)(p36.3;p13). ish der(1)(wcp9 +, 1ptel-, 9ptel +, pan tel +)[88]/46,XX. ish del(1)(1ptel -, 9ptel -, pan tel +)[12] karyotype. Scrutiny by FISH using wcp 9, 1ptel, 9ptel, and pan telomeric probes found a subtelomeric 1ptel deletion on the der(1) in the abnormal cell line and on a chromosome 1 in the apparently normal cell line. The telomere (TTAGGG)n, however, was present on the terminal ends of both copies of chromosome 1 in the apparently normal and abnormal cell lines. The second case had a de novo mos 46,X,der(X)t(X;22)(p22.3;q11.2),inv dup(22)(q11.2).ish der(X)(wcpX +,wcp22 +,KAL +, STS -,Xptel -,BCR +),inv dup(22)(wcp22 +,TUPLE ++,BCR -)[85]/45,X,der(X)t(X;22)(p22.3;q11.2),- 22[15].ish der(X)(wcpX +,wcp22 +, KAL +,STS -,Xptel -,BCR +) karyotype. FISH probes identified a terminal Xpter deletion, distal to the KAL gene. The two rearrangements are hypothesized to have been initiated by a terminal deletion. We propose a model for the formation of the rearrangement in Case 1, which invokes independent telomere stabilization of the sister chromatids. A terminal deletion 1pter in meiosis, was followed by acquiring or regenerating a telomere (TTAGGG)n cap on one chromatid and the other chromatid was involved in a translocation with a chromosome 9 chromatid. Following segregation of this chromosome the viable cell line survives to form the mosaic karyotype. Our findings suggest that subtelomeric deletions should be ruled out in cases with complex and simple rearrangements involving the terminal regions.
Chromatids↗
Crystal structure of the specificity domain of ribonuclease P.
RNase P is the only endonuclease responsible for processing the 5' end of transfer RNA by cleaving a precursor and leading to tRNA maturation. It contains an RNA component and a protein component and has been identified in all organisms. It was one of the first catalytic RNAs identified and the first that acts as a multiple-turnover enzyme in vivo. RNase P and the ribosome are so far the only two ribozymes known to be conserved in all kingdoms of life. The RNA component of bacterial RNase P can catalyse pre-tRNA cleavage in the absence of the RNase P protein in vitro and consists of two domains: a specificity domain and a catalytic domain. Here we report a 3.15-A resolution crystal structure of the 154-nucleotide specificity domain of Bacillus subtilis RNase P. The structure reveals the architecture of this domain, the interactions that maintain the overall fold of the molecule, a large non-helical but well-structured module that is conserved in all RNase P RNA, and the regions that are involved in interactions with the substrate.
Bacillus subtilis↗