Genomes and Genes
Experts and Doctors on escherichia coli in Canberra, Australian Capital Territory, Australia
Locale: Canberra, Australian Capital Territory, Australia
Topic: escherichia coli
- Edwards K, Ollis D, Dixon N. Crystal structure of cytoplasmic Escherichia coli peptidyl-prolyl isomerase: evidence for decreased mobility of loops upon complexation. J Mol Biol. 1997;271:258-65 pubmed..There is evidence to suggest that two surface loops have significantly reduced mobility in the complexed structure. ..
- Vasudevan S, Shaw D, Armarego W. Dihydropteridine reductase from Escherichia coli. Biochem J. 1988;255:581-8 pubmed..The pure reductase has a yellow colour and contains bound FAD. The enzyme also has pterin-independent NADH and NADPH oxidoreductase activities when potassium ferricyanide is the electron acceptor. ..
- Wilson K, Sessitsch A, Corbo J, Giller K, Akkermans A, Jefferson R. beta-Glucuronidase (GUS) transposons for ecological and genetic studies of rhizobia and other gram-negative bacteria. Microbiology. 1995;141 ( Pt 7):1691-705 pubmed..The variety of assays available for GUS enable both quantitative assays and spatial localization of marked bacteria to be carried out. ..
- Keniry M, Park A, Owen E, Hamdan S, Pintacuda G, Otting G, et al. Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit. J Bacteriol. 2006;188:4464-73 pubmed..The pseudocontact shifts indicated that the helices of theta are located about 15 A or farther from the lanthanide ion in the active site of epsilon186, in agreement with the extensive biochemical data for the theta-epsilon system. ..
- Gilchrist C, Baker R. Characterization of the ubiquitin-specific protease activity of the mouse/human Unp/Unph oncoprotein. Biochim Biophys Acta. 2000;1481:297-309 pubmed..These data suggest that Unp is not a general modulator of ubiquitin-dependent proteolysis. However, Unp may have a role in the regulation of the degradation of a specific, as yet undescribed, substrate(s). ..
- Schaeffer P, Headlam M, Dixon N. Protein--protein interactions in the eubacterial replisome. IUBMB Life. 2005;57:5-12 pubmed..coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7. ..
- Holloway A, Occhiodoro F, Mittler G, Meisterernst M, Shannon M. Functional interaction between the HIV transactivator Tat and the transcriptional coactivator PC4 in T cells. J Biol Chem. 2000;275:21668-77 pubmed..We propose that PC4 may be involved in linking Tat to the basal transcription machinery. ..
- Keniry M, Berthon H, Yang J, Miles C, Dixon N. NMR solution structure of the theta subunit of DNA polymerase III from Escherichia coli. Protein Sci. 2000;9:721-33 pubmed..Preliminary chemical shift mapping experiments with a domain of the epsilon subunit have identified a loop region (Ala20-Glu29) in theta as the site of association with epsilon. ..
- Blackburn A, Tzeng H, Anders M, Board P. Discovery of a functional polymorphism in human glutathione transferase zeta by expressed sequence tag database analysis. Pharmacogenetics. 2000;10:49-57 pubmed..6-fold higher activity towards dichloroacetate. This report demonstrates the discovery of a functional polymorphism by analysis of the EST database. ..
- El Adhami W, Kyd J, Bastin D, Cripps A. Characterization of the gene encoding a 26-kilodalton protein (OMP26) from nontypeable Haemophilus influenzae and immune responses to the recombinant protein. Infect Immun. 1999;67:1935-42 pubmed..This study has characterized a 26-kDa protein from NTHI that shows significant potential as a vaccine candidate...
- Mulcair M, Schaeffer P, Oakley A, Cross H, Neylon C, Hill T, et al. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell. 2006;125:1309-19 pubmed..Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus. ..
- Kim H, Liu J, Carr P, Ollis D. Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase. Acta Crystallogr D Biol Crystallogr. 2005;61:920-31 pubmed..This rotation of the inhibitor caused the displacement of a large section of a loop on one side of the active site. Residues that could stabilize the transition state for the reaction were identified. ..
- Hanzlik T, Dorrian S, Johnson K, Brooks E, Gordon K. Sequence of RNA2 of the Helicoverpa armigera stunt virus (Tetraviridae) and bacterial expression of its genes. J Gen Virol. 1995;76 ( Pt 4):799-811 pubmed publisher..Bacterial expression of p71 did not produce virus-like particles while expression of p17 produced large arrays of mostly hollow, hexagonal tube-like structures...
- Liu J, Hadler K, Schenk G, Ollis D. Using directed evolution to improve the solubility of the C-terminal domain of Escherichia coli aminopeptidase P. Implications for metal binding and protein stability. FEBS J. 2007;274:4742-51 pubmed..In this case, directed evolution has identified active site residues that destabilize the domain structure. ..
- Ozawa K, Headlam M, Schaeffer P, Henderson B, Dixon N, Otting G. Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy. Eur J Biochem. 2004;271:4084-93 pubmed..In addition, the activity of peptide deformylase appeared to be generally reduced in the cell-free expression system. ..
- Lunn J. Sucrose-phosphatase gene families in plants. Gene. 2003;303:187-96 pubmed..An SPP-like sequence from the bryophyte (moss) Physcomitrella patens also contains this C-terminal domain, indicating that its acquisition was an early event in the evolution of higher plants...
- Vasudevan S, Gedye C, Dixon N, Cheah E, Carr P, Suffolk P, et al. Escherichia coli PII protein: purification, crystallization and oligomeric structure. FEBS Lett. 1994;337:255-8 pubmed..A sedimentation equilibrium experiment of the meniscus depletion type was used to estimate a molecular weight of 35,000 +/- 1,000 for PII in solution. This result is consistent with the native protein being a homotrimer. ..
- John M, Schmitz C, Park A, Dixon N, Huber T, Otting G. Sequence-specific and stereospecific assignment of methyl groups using paramagnetic lanthanides. J Am Chem Soc. 2007;129:13749-57 pubmed..The approaches are demonstrated with the complex between the N-terminal domain of the subunit epsilon and the subunit theta of the Escherichia coli DNA polymerase III...
- Li Z, Chu X, Mouille G, Yan L, Kosar Hashemi B, Hey S, et al. The localization and expression of the class II starch synthases of wheat. Plant Physiol. 1999;120:1147-56 pubmed..We discuss the roles of the SGP-1 proteins in starch biosynthesis in wheat. ..
- Dulhunty A, Pouliquin P, Coggan M, Gage P, Board P. A recently identified member of the glutathione transferase structural family modifies cardiac RyR2 substate activity, coupled gating and activation by Ca2+ and ATP. Biochem J. 2005;390:333-43 pubmed..CLIC-2 provides a unique probe for substate activity, coupled gating and ligand-induced activation of cardiac RyR channels. ..
- Lunn J, Ashton A, Hatch M, Heldt H. Purification, molecular cloning, and sequence analysis of sucrose-6F-phosphate phosphohydrolase from plants. Proc Natl Acad Sci U S A. 2000;97:12914-9 pubmed..A PSI-BLAST search of the GenBank database indicated that the maize SPP is a member of the haloacid dehalogenase hydrolase/phosphatase superfamily. ..
- Mueller Cajar O, Morell M, Whitney S. Directed evolution of rubisco in Escherichia coli reveals a specificity-determining hydrogen bond in the form II enzyme. Biochemistry. 2007;46:14067-74 pubmed..coli for identifying catalytically relevant residues (in particular nonobvious residues disconnected from active site residues) and their potential molecular interactions that influence Rubisco's catalytic chemistry. ..
- Apponyi M, Ozawa K, Dixon N, Otting G. Cell-free protein synthesis for analysis by NMR spectroscopy. Methods Mol Biol. 2008;426:257-68 pubmed publisher..This chapter describes in detail the protocol used in the authors' laboratory...
- Lilley P, Stamford N, Vasudevan S, Dixon N. The 92-min region of the Escherichia coli chromosome: location and cloning of the ubiA and alr genes. Gene. 1993;129:9-16 pubmed..Subcloning of alr downstream from tandem bacteriophage lambda promoters produced a plasmid that directed high-level overproduction of a soluble approx. 40-kDa protein with ARase activity. ..
- Watson M, Liu J, Ollis D. Directed evolution of trimethoprim resistance in Escherichia coli. FEBS J. 2007;274:2661-71 pubmed..Several mutations were found to grant resistance to trimethoprim, both by reducing the binding affinity of the enzyme for the drug, and by increasing the activity of the enzyme. ..
- Williams N, Liepinsh E, Watt S, Prosselkov P, Matthews J, Attard P, et al. Stabilization of native protein fold by intein-mediated covalent cyclization. J Mol Biol. 2005;346:1095-108 pubmed..Global unfolding of the N-terminal domain of E.coli DnaB is thus promoted strongly by spatial separation of the N and C termini, whereas their proximity is much less important for folding. ..
- Li F, Feterl M, Mulyana Y, Warner J, Collins J, Keene F. In vitro susceptibility and cellular uptake for a new class of antimicrobial agents: dinuclear ruthenium(II) complexes. J Antimicrob Chemother. 2012;67:2686-95 pubmed publisher..aureus, Escherichia coli and Pseudomonas aeruginosa...
- Barnes B, Sidhu H, Gordon D. Host gastro-intestinal dynamics and the frequency of colicin production by Escherichia coli. Microbiology. 2007;153:2823-7 pubmed..The model predicted that a colicin producer was more likely to dominate in the gut of a host with lower gut turnover rates, and a non-producer to dominate in hosts with rapid gut turnover rates. ..
- Hardy C, Holland M. Cloning and expression of recombinant rabbit fertilin. Mol Reprod Dev. 1996;45:107-16 pubmed..These antibodies detect components of the native fertilin complex from rabbit sperm. ..
- Stamford N, Lilley P, Dixon N. Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein. Biochim Biophys Acta. 1992;1132:17-25 pubmed..Potential zinc-binding amino-acid residues near the N-terminus of the protein were identified. Although a mutant primase lacking 27 amino acid residues from the N-terminus was partly soluble, it was completely inactive. ..
- Board P, Mannervik B. The contribution of the C-terminal sequence to the catalytic activity of GST2, a human alpha-class glutathione transferase. Biochem J. 1991;275 ( Pt 1):171-4 pubmed..In contrast, this region appears not to be directly involved in GSH binding and is not absolutely essential for catalytic activity. ..
- Baker R, Williamson N, Wettenhall R. The yeast homolog of mammalian ribosomal protein S30 is expressed from a duplicated gene without a ubiquitin-like protein fusion sequence. Evolutionary implications. J Biol Chem. 1996;271:13549-55 pubmed..Analysis of available DNA sequence data bases reveals that rpS30 is synthesized as a fusion to a ubiquitin-like protein in nematodes and mammals but unfused in yeast, plants, and protazoa. ..
- Walker J, Verma N. Cloning and characterisation of the aroA and aroD genes of Shigella dysenteriae type 1. Microbiol Immunol. 1997;41:809-13 pubmed..The use of the cloned aroA and aroD genes in the development of a vaccine strain against S. dysenteriae is discussed...
- Hardy C, Mobbs K. Expression of recombinant mouse sperm protein sp56 and assessment of its potential for use as an antigen in an immunocontraceptive vaccine. Mol Reprod Dev. 1999;52:216-24 pubmed..Litter sizes of sp56FLAG-treated mice were significantly smaller than control-treated animals after five boosts. ..
- Neylon C, Brown S, Kralicek A, Miles C, Love C, Dixon N. Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance. Biochemistry. 2000;39:11989-99 pubmed..The kinetic and thermodynamic data suggest a model for Tus binding to TerB which involves an ordered series of events that include structural changes in the protein. ..
- Park H, Kreunen S, Cuttriss A, DellaPenna D, Pogson B. Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis. Plant Cell. 2002;14:321-32 pubmed..The absence of PLBs in crtISO mutants demonstrates a function for this unique structure and carotenoids in facilitating chloroplast development during the first critical days of seedling germination and photomorphogenesis. ..
- Hamdan S, Carr P, Brown S, Ollis D, Dixon N. Structural basis for proofreading during replication of the Escherichia coli chromosome. Structure. 2002;10:535-46 pubmed..These data are used to develop a mechanism for epsilon and to produce a plausible model of the complex of epsilon186 with DNA. ..
- Clarke B, Phongkham T, Gianibelli M, Beasley H, Bekes F. The characterisation and mapping of a family of LMW-gliadin genes: effects on dough properties and bread volume. Theor Appl Genet. 2003;106:629-35 pubmed publisher..Rheological analysis showed that the protein effected dough strength and resistance break down during mixing of the dough, and provided a 20% increase in loaf height after baking...
- Davy D, Campbell H, Fountain S, De Jong D, Crouch M. The flightless I protein colocalizes with actin- and microtubule-based structures in motile Swiss 3T3 fibroblasts: evidence for the involvement of PI 3-kinase and Ras-related small GTPases. J Cell Sci. 2001;114:549-62 pubmed..Functionally, we suggest that flightless I may act to prepare actin filaments or provide factors required for cytoskeletal rearrangements necessary for cell migration and/or adhesion. ..
- Adhikari P, Allison G, Whittle B, Verma N. Serotype 1a O-antigen modification: molecular characterization of the genes involved and their novel organization in the Shigella flexneri chromosome. J Bacteriol. 1999;181:4711-8 pubmed..6-kb region of the Y53 chromosome is unique and suggests that the serotype conversion genes were originally brought into the host by a bacteriophage. Several features of this region are also characteristic of pathogenicity islands...
- Adams M, Allison G, Verma N. Type IV O antigen modification genes in the genome of Shigella flexneri NCTC 8296. Microbiology. 2001;147:851-60 pubmed publisher..Comparison of the GtrIV(Sf) and GtrIV(Ec) (o443) proteins revealed that they are 41% identical and 63% similar, which is the highest degree of similarity reported among the S. flexneri O antigen glucosyltransferases...
- Upadhyaya N, Zinkowsky E, Kositratana W, Waterhouse P. The M(r) 43K major capsid protein of rice ragged stunt oryzavirus is a post-translationally processed product of a M(r) 67,348 polypeptide encoded by genome segment 8. Arch Virol. 1996;141:1689-701 pubmed..The data also suggest that the 26K protein is the self cleaving protease and that the 46K product is further processed or undergoes stable conformational changes to a approximately 43K major capsid protein...
- Edwards K, Thorn J, Daniher J, Dixon N, Ollis D. Crystallization and preliminary X-ray diffraction studies on a soluble Escherichia coli quinone oxidoreductase. J Mol Biol. 1994;240:501-3 pubmed..0 A. The space group was determined to be P2(1)2(1)2(1) with unit cell dimensions of a = 107.44 A, b = 104.06 A, c = 77.45 A. There is one dimer in the asymmetric unit. ..
- Young Park A, Elvin C, Hamdan S, Wood R, Liyou N, Hamwood T, et al. Hydrolysis of the 5'-p-nitrophenyl ester of TMP by oligoribonucleases (ORN) from Escherichia coli, Mycobacterium smegmatis, and human. Protein Expr Purif. 2008;57:180-7 pubmed..2-0.6 mM. The availability of large amounts of the purified enzymes and a simple spectrophotometric assay for ORN activity should facilitate large-scale screening for new inhibitors of bacterial oligoribonucleases. ..
- Alonso H, Blayney M, Beck J, Whitney S. Substrate-induced assembly of Methanococcoides burtonii D-ribulose-1,5-bisphosphate carboxylase/oxygenase dimers into decamers. J Biol Chem. 2009;284:33876-82 pubmed publisher..5 microM). The catalytic and structural similarities of MbR to other archaeal Rubiscos contrast with its closer sequence homology to bacterial L(2) Rubisco, complicating its classification within the Rubisco superfamily...
- Vasudevan S, Armarego W, Shaw D, Lilley P, Dixon N, Poole R. Isolation and nucleotide sequence of the hmp gene that encodes a haemoglobin-like protein in Escherichia coli K-12. Mol Gen Genet. 1991;226:49-58 pubmed..We conclude that E. coli produces a soluble haemoglobin-like protein, the product of the hmp gene (for haemoprotein). Although the protein has DHPR activity, it is distinct from the previously purified E. coli DHPR. ..
- Hudson G, Rellos P, Davidson B. Two promoters control the aroH gene of Escherichia coli. Gene. 1991;102:87-91 pubmed..The second promoter is active under conditions of growth in rich medium, and may be involved in ensuring sufficient levels of precursors for the biosynthesis of aromatic vitamins under these growth conditions. ..
- Loscha K, Oakley A, Bancia B, Schaeffer P, Prosselkov P, Otting G, et al. Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase. Protein Expr Purif. 2004;33:304-10 pubmed..2A, c=192.1A, and diffracted beyond 2.7A resolution with synchrotron radiation. ..
- Cheah E, Carr P, Suffolk P, Vasudevan S, Dixon N, Ollis D. Structure of the Escherichia coli signal transducing protein PII. Structure. 1994;2:981-90 pubmed..These are surrounded by six alpha-helices. The structure of PII suggests potential regions of interaction with other proteins and serves as an initial step in understanding its signal transducing role in nitrogen regulation...
- Thorn J, Barton J, Dixon N, Ollis D, Edwards K. Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH. J Mol Biol. 1995;249:785-99 pubmed..The overall structure of quinone oxidoreductase shows strong structural homology to that of horse liver alcohol dehydrogenase. ..
- Walker J, Verma N. Identification of a putative pathogenicity island in Shigella flexneri using subtractive hybridisation of the S. flexneri and Escherichia coli genomes. FEMS Microbiol Lett. 2002;213:257-64 pubmed..These findings indicate that this region may form a new PAI in the S. flexneri genome. ..