Genomes and Genes
Experts and Doctors on escherichia coli in Detroit, Michigan, United States
Locale: Detroit, Michigan, United States
Topic: escherichia coli
- Radaev S, Dastidar P, Patel M, Woodard R, Gatti D. Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase. J Biol Chem. 2000;275:9476-84 pubmed..This observation suggests that KDO8P synthase and DAH7P synthase evolved from a common ancestor and that they adopt the same catalytic strategy...
- Atkinson M, Ninfa A. Characterization of Escherichia coli glnL mutations affecting nitrogen regulation. J Bacteriol. 1992;174:4538-48 pubmed..We hypothesize that mutants of the latter type result in a subtle perturbation of the NRII-PII interaction and suggest two possible mechanisms for their effects. ..
- Scully J, Evans D. Comparative modeling of mammalian aspartate transcarbamylase. Proteins. 1991;9:191-206 pubmed publisher..While the CAD ATCase domain can undergo the local conformational changes that accompany catalysis in the E. coli enzyme, the high activity, closed conformation is probably more stable in the mammalian enzyme...
- Mukhopadhyay R, Rosen B, Phung L, Silver S. Microbial arsenic: from geocycles to genes and enzymes. FEMS Microbiol Rev. 2002;26:311-25 pubmed..Proposed reaction mechanisms in each case involve three cysteine thiols and S-As bond intermediates, so convergent evolution to similar mechanisms has taken place. ..
- Brown P, Freeman A, Foxman B. Prevalence and predictors of trimethoprim-sulfamethoxazole resistance among uropathogenic Escherichia coli isolates in Michigan. Clin Infect Dis. 2002;34:1061-6 pubmed..Recent antibiotic use is a risk factor for infection with a TMP-SMX-resistant isolate; patients who are infected with a TMP-SMX-resistant isolate and who are treated with this agent are at a higher risk for clinical failure. ..
- Wu J, Tisa L, Rosen B. Membrane topology of the ArsB protein, the membrane subunit of an anion-translocating ATPase. J Biol Chem. 1992;267:12570-6 pubmed..The location of a periplasmic loop was determined from V8 protease digestion of an ArsA-ArsB chimera. From analysis of data from 26 fusions, a topological model of the ArsB protein with 12 membrane-spanning regions is proposed. ..
- Robertson E, Aggison L, Nicholson A. Phosphorylation of elongation factor G and ribosomal protein S6 in bacteriophage T7-infected Escherichia coli. Mol Microbiol. 1994;11:1045-57 pubmed..Finally, several experimental variables are analysed which influence the production and pattern of phosphorylated proteins in both uninfected and T7-infected cells. ..
- Sharma R, Rensing C, Rosen B, Mitra B. The ATP hydrolytic activity of purified ZntA, a Pb(II)/Cd(II)/Zn(II)-translocating ATPase from Escherichia coli. J Biol Chem. 2000;275:3873-8 pubmed..Our results confirm that ZntA is the first Pb(II)-dependent ATPase discovered to date. ..
- Sheng J, Ye J, Rosen B. Crystallization and preliminary X-ray crystallographic analysis of Escherichia coliglutaredoxin 2 in complex with glutathione and of a cysteine-less variant without glutathione. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:280-2 pubmed..The crystals diffracted to 2.40 A and belong to space group P2(1)2(1)2(1), with one molecule in the asymmetric unit. The unit-cell parameters are a = 28.16, b = 78.65, c = 89.16 A. ..
- Yamazaki R, Chau V. Bacterial expression of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Ubc7. Protein Expr Purif. 1996;7:122-7 pubmed
- Hanna I, Roberts E, Hollenberg P. Molecular basis for the differences in lidocaine binding and regioselectivity of oxidation by cytochromes P450 2B1 and 2B2. Biochemistry. 1998;37:311-8 pubmed..The altered regioselectivity was accompanied with approximately 10-fold increases in the measured Ks, Km, and kcat values for LIDO. ..
- Sun W, Jun E, Nicholson A. Intrinsic double-stranded-RNA processing activity of Escherichia coli ribonuclease III lacking the dsRNA-binding domain. Biochemistry. 2001;40:14976-84 pubmed..These findings support an RNase III mechanism of action in which the catalytic domain (i) can function independently of the dsRBD, (ii) is dsRNA-specific, and (iii) participates in cleavage site selection. ..
- Schemidt R, Hsu D, Deckers Hebestreit G, Altendorf K, Brusilow W. The effects of an atpE ribosome-binding site mutation on the stoichiometry of the c subunit in the F1F0 ATPase of Escherichia coli. Arch Biochem Biophys. 1995;323:423-8 pubmed..Therefore, the stoichiometry of the c subunit assembled into the F1F0 complex appears to be variable, depending on the expression of atpE. ..
- Pati S, DiSilvestre D, Brusilow W. Regulation of the Escherichia coli uncH gene by mRNA secondary structure and translational coupling. Mol Microbiol. 1992;6:3559-66 pubmed
- Calin Jageman I, Amarasinghe A, Nicholson A. Ethidium-dependent uncoupling of substrate binding and cleavage by Escherichia coli ribonuclease III. Nucleic Acids Res. 2001;29:1915-25 pubmed
- Mitra B, Sharma R. The cysteine-rich amino-terminal domain of ZntA, a Pb(II)/Zn(II)/Cd(II)-translocating ATPase from Escherichia coli, is not essential for its function. Biochemistry. 2001;40:7694-9 pubmed..Residues involved in the ATP-dependent soft metal ion-translocating mechanism as well as those responsible for recognition of specific metal ions must be part of the core structure of the P1-type ATPases. ..
- Liu Z, Lu Y, Zhang J, Pardee K, Wang P. P1 Trisaccharide (Galalpha1,4Galbeta1,4GlcNAc) synthesis by enzyme glycosylation reactions using recombinant Escherichia coli. Appl Environ Microbiol. 2003;69:2110-5 pubmed..4 g in a 200-ml reaction volume), with a 67% yield based on the consumption of N-acetylglucosamine. This study provides an efficient approach for the preparative-scale synthesis of P1 trisaccharide with recombinant bacteria. ..
- Chen C, Chou M, Huang C, Majumder A, Wu H. A cis-spreading nucleoprotein filament is responsible for the gene silencing activity found in the promoter relay mechanism. J Biol Chem. 2005;280:5101-12 pubmed..The geometric requirement, which was revealed for this silencing activity, explains the decisive role of transcription-generated DNA supercoiling found in the promoter relay mechanism. ..
- Gill J, Romano L. Mechanism for N-acetyl-2-aminofluorene-induced frameshift mutagenesis by Escherichia coli DNA polymerase I (Klenow fragment). Biochemistry. 2005;44:15387-95 pubmed
- Qin J, Fu H, Ye J, Bencze K, Stemmler T, Rawlings D, et al. Convergent evolution of a new arsenic binding site in the ArsR/SmtB family of metalloregulators. J Biol Chem. 2007;282:34346-55 pubmed..These results suggest that the As(III)-S(3) binding sites in AfArsR and R773 ArsR arose independently at spatially distinct locations in their three-dimensional structures. ..
- San Francisco M, Tisa L, Rosen B. Identification of the membrane component of the anion pump encoded by the arsenical resistance operon of R-factor R773. Mol Microbiol. 1989;3:15-21 pubmed..In addition to the previously identified ArsA and ArsC proteins, the cells synthesized an inner membrane protein with an apparent mass of 36 kD identified as the ArsB protein. ..
- Hou Z, Mitra B. The metal specificity and selectivity of ZntA from Escherichia coli using the acylphosphate intermediate. J Biol Chem. 2003;278:28455-61 pubmed..Thus, metal ion selectivity in ZntA and possibly other P1-type ATPases is based on the charge and the ligand preference of particular metal ions but not on their size. ..
- Bondarenko V, Liu Y, Ninfa A, Studitsky V. Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit. Nucleic Acids Res. 2002;30:636-42 pubmed..These studies exclude the hypothesis that enhancer action during multiple-round transcription involves the memory of the initial activation event...
- Chopra T, Marchaim D, Veltman J, Johnson P, Zhao J, Tansek R, et al. Impact of cefepime therapy on mortality among patients with bloodstream infections caused by extended-spectrum-?-lactamase-producing Klebsiella pneumoniae and Escherichia coli. Antimicrob Agents Chemother. 2012;56:3936-42 pubmed publisher
- Steffes C, Ellis J, Wu J, Rosen B. The lysP gene encodes the lysine-specific permease. J Bacteriol. 1992;174:3242-9 pubmed..Cells carrying a plasmid with the lysP gene exhibited a 10- to 20-fold increase in the rate of lysine uptake above wild-type levels. These results demonstrate that the lysP gene encodes the lysine-specific permease. ..
- Fang M, Majumder A, Tsai K, Wu H. ppGpp-dependent leuO expression in bacteria under stress. Biochem Biophys Res Commun. 2000;276:64-70 pubmed publisher..The stationary phase-associated leuO expression is ppGpp dependent and rpoS (sigma(s) factor) independent...
- Simmer J, Kelly R, Rinker A, Zimmermann B, Scully J, Kim H, et al. Mammalian dihydroorotase: nucleotide sequence, peptide sequences, and evolution of the dihydroorotase domain of the multifunctional protein CAD. Proc Natl Acad Sci U S A. 1990;87:174-8 pubmed..Although these families may have arisen by convergent evolution, we favor a model involving DHOase gene duplication and insertion into an ancestral bifunctional locus...
- Shelef L, Firstenberg Eden R. Novel selective and non-selective optical detection of microorganisms. Lett Appl Microbiol. 1997;25:202-6 pubmed
- Fu H, Meng Y, Ord ez E, Villadangos A, Bhattacharjee H, Gil J, et al. Properties of arsenite efflux permeases (Acr3) from Alkaliphilus metalliredigens and Corynebacterium glutamicum. J Biol Chem. 2009;284:19887-95 pubmed publisher..A scanning cysteine accessibility method was used to show that Acr3 has 10 transmembrane segments, and the conserved cysteine would be predicted to be in the fourth transmembrane segment...
- Fan B, Rosen B. Biochemical characterization of CopA, the Escherichia coli Cu(I)-translocating P-type ATPase. J Biol Chem. 2002;277:46987-92 pubmed..These results imply that the cysteine residues of the Cys-Pro-Cys motif (but not the N-terminal cysteine residues) are required for CopA function. ..
- Dutta S, Liu J, Stemmler A, Mitra B. Conservative and nonconservative mutations of the transmembrane CPC motif in ZntA: effect on metal selectivity and activity. Biochemistry. 2007;46:3692-703 pubmed..Therefore, conserved residues contribute to metal selectivity by supplying ligands that bind metal ions not only with high affinity, as for Pb2+, but also with the most favorable binding geometry that results in efficient catalysis. ..
- Liu Z, Styblo M, Rosen B. Methylarsonous acid transport by aquaglyceroporins. Environ Health Perspect. 2006;114:527-31 pubmed..Identification of MAs(III) as an AQP9 substrate is an important step in understanding physiologic responses to arsenic in mammals, including humans. ..
- Cao T, Wang A, Liang X, Tang H, Auner G, Salley S, et al. Patterned immobilization of antibodies in mechanically induced cracks. J Phys Chem B. 2008;112:2727-33 pubmed publisher..This technique shows a great potential for applications in the fields of sensing and tissue engineering. ..
- Ahuja A, Purcarea C, Ebert R, Sadecki S, Guy H, Evans D. Aquifex aeolicus dihydroorotase: association with aspartate transcarbamoylase switches on catalytic activity. J Biol Chem. 2004;279:53136-44 pubmed publisher..At pH 7.4, the equilibrium ratio of carbamoyl aspartate to dihydroorotate is 17 and complex formation may drive the reaction in the biosynthetic direction...
- Malkowski M, Wu J, Lazar J, Johnson P, Edwards B. The crystal structure of recombinant human neutrophil-activating peptide-2 (M6L) at 1.9-A resolution. J Biol Chem. 1995;270:7077-87 pubmed..The Glu-Leu-Arg sequence that is critical for receptor binding is fully defined by electron density and exhibits multiple conformations. ..
- Yao R, Palchaudhuri S. Nucleotide sequence of the ipaBCD structural genes of Shigella dysenteriae. Mol Microbiol. 1991;5:2217-21 pubmed..dysenteriae and S. flexneri. The nucleotide composition of ipa genes revealed an unusually large number of codons that are rarely used in Escherichia coli chromosomal genes, indicating a different origin. ..
- Rensing C, Fan B, Sharma R, Mitra B, Rosen B. CopA: An Escherichia coli Cu(I)-translocating P-type ATPase. Proc Natl Acad Sci U S A. 2000;97:652-6 pubmed..The results indicate that CopA is a Cu(I)-translocating efflux pump that is similar to the copper pumps related to Menkes and Wilson diseases and provides a useful prokaryotic model for these human diseases. ..
- Hou Z, Narindrasorasak S, Bhushan B, Sarkar B, Mitra B. Functional analysis of chimeric proteins of the Wilson Cu(I)-ATPase (ATP7B) and ZntA, a Pb(II)/Zn(II)/Cd(II)-ATPase from Escherichia coli. J Biol Chem. 2001;276:40858-63 pubmed..Also, these results suggest that this domain interacts with the rest of the transporter in a metal ion-specific manner; the amino-terminal domain of ATP7B cannot replace that of ZntA in restoring full catalytic activity. ..
- Beletskii A, Bhagwat A. Transcription-induced cytosine-to-thymine mutations are not dependent on sequence context of the target cytosine. J Bacteriol. 2001;183:6491-3 pubmed
- Mokkapati S, Fernandez de Henestrosa A, Bhagwat A. Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells. Mol Microbiol. 2001;41:1101-11 pubmed..Thus, Mug joins a very small coterie of DNA repair enzymes whose principal function is to avoid mutations in stationary-phase cells. ..
- Bhagwat A, Lieb M. Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli. Mol Microbiol. 2002;44:1421-8 pubmed..We review here recent information about the biochemistry of both repair processes and describe the balancing act performed by cells to optimize the competing processes during different phases of the bacterial life cycle. ..
- Ninfa E, Atkinson M, Kamberov E, Ninfa A. Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): trans-phosphorylation between subunits. J Bacteriol. 1993;175:7024-32 pubmed..These results indicate that the autophosphorylation reaction occurs within the dimer by a trans, intersubunit mechanism in which one subunit binds ATP and phosphorylates the other subunit. ..
- Shi W, Dong J, Scott R, Ksenzenko M, Rosen B. The role of arsenic-thiol interactions in metalloregulation of the ars operon. J Biol Chem. 1996;271:9291-7 pubmed
- Sumita M, Jiang J, SantaLucia J, Chow C. Comparison of solution conformations and stabilities of modified helix 69 rRNA analogs from bacteria and human. Biopolymers. 2012;97:94-106 pubmed publisher..These findings may be significant with respect to H69 as a potential drug target site. ..
- Bhattacharjee H, Rosen B. Structure-function analysis of the ArsA ATPase: contribution of histidine residues. J Bioenerg Biomembr. 2001;33:459-68 pubmed..The results indicate that no single histidine residue plays a direct role in catalysis, and the inhibition by DEPC may be caused by steric hindrance from the carbethoxy group. ..
- Monticello R, Brusilow W. Role of the delta subunit in enhancing proton conduction through the F0 of the Escherichia coli F1F0 ATPase. J Bacteriol. 1994;176:1383-9 pubmed..These results demonstrate that an interaction between the delta subunit and the F0 during synthesis and assembly produces a significant change in the proton permeability of the F0 proton channel. ..
- Kamberov E, Atkinson M, Chandran P, Ninfa A. Effect of mutations in Escherichia coli glnL (ntrB), encoding nitrogen regulator II (NRII or NtrB), on the phosphatase activity involved in bacterial nitrogen regulation. J Biol Chem. 1994;269:28294-9 pubmed..Thus, while the kinase and phosphatase activities of NRII could be genetically separated, some of the highly conserved residues in the C-terminal domain of NRII (Asp-287, Gly-289, Gly-291) are apparently important for both activities. ..
- Nicholson A, Niebling K, McOsker P, Robertson H. Accurate in vitro cleavage by RNase III of phosphorothioate-substituted RNA processing signals in bacteriophage T7 early mRNA. Nucleic Acids Res. 1988;16:1577-91 pubmed..Thus, RNase III cleavage specificity is not altered by phosphorothioate internucleotide linkages...
- Fang D, Lord R, Cisneros G. Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. J Phys Chem B. 2013;117:6410-20 pubmed publisher..These conserved residues are proposed as targets for experimental mutagenesis studies. ..
- Ruan X, Bhattacharjee H, Rosen B. Cys-113 and Cys-422 form a high affinity metalloid binding site in the ArsA ATPase. J Biol Chem. 2006;281:9925-34 pubmed
- Xu C, Rosen B. Dimerization is essential for DNA binding and repression by the ArsR metalloregulatory protein of Escherichia coli. J Biol Chem. 1997;272:15734-8 pubmed..These results suggest that a core sequence of about 80 residues has all of the information necessary for dimerization, repression, and metal recognition. ..
- Chow C, Cunningham P, Lee K, Meroueh M, SantaLucia J, Varma S. Photoinduced cleavage by a rhodium complex at G.U mismatches and exposed guanines in large and small RNAs. Biochimie. 2002;84:859-68 pubmed..In general, RNA backbone scission by the metal complex was induced at G.U mismatches and at exposed G residues. The cleavage activity was observed on the three small RNA hairpins as well as on the isolated 1542-nucleotide ribosomal RNA. ..
- Mukhopadhyay R, Shi J, Rosen B. Purification and characterization of ACR2p, the Saccharomyces cerevisiae arsenate reductase. J Biol Chem. 2000;275:21149-57 pubmed..This suggests that during the catalytic cycle, Acr2p forms a mixed disulfide with GSH before being reduced by glutaredoxin to regenerate the active Acr2p reductase. ..
- Wu R, Wang X, Womble D, Rownd R. Suppression of replication-deficient mutants of IncFII plasmid NR1 can occur by two different mechanisms that increase expression of the repA1 gene. J Bacteriol. 1993;175:3161-73 pubmed..Plasmids that lacked either circuit were less stable than wild-type plasmids. ..
- Chau V, Tobias J, Bachmair A, Marriott D, Ecker D, Gonda D, et al. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. Science. 1989;243:1576-83 pubmed..The experiments with ubiquitin mutated at its Lys48 residue indicate that the multiubiquitin chain in a targeted protein is essential for the degradation of the protein. ..
- Yang J, Rawat S, Stemmler T, Rosen B. Arsenic binding and transfer by the ArsD As(III) metallochaperone. Biochemistry. 2010;49:3658-66 pubmed publisher..Neither MgADP nor MgATP-gamma-S could replace MgATP. These results suggest that transfer occurs with a conformation of ArsA that transiently forms during the catalytic cycle. ..
- Radaev S, Dastidar P, Patel M, Woodard R, Gatti D. Preliminary X-ray analysis of a new crystal form of the Escherichia coli KDO8P synthase. Acta Crystallogr D Biol Crystallogr. 2000;56:516-9 pubmed..The observation that the same quaternary structure of KDO8P synthase is observed in two different crystal forms belonging to distinct crystal systems (monoclinic and cubic) suggests that a tetramer is the native form of the enzyme. ..
- Hayakawa K, Gattu S, Marchaim D, Bhargava A, Palla M, Alshabani K, et al. Epidemiology and risk factors for isolation of Escherichia coli producing CTX-M-type extended-spectrum ?-lactamase in a large U.S. Medical Center. Antimicrob Agents Chemother. 2013;57:4010-8 pubmed publisher..Septic patients with risk factors for isolation of CTX-M E. coli should be empirically treated with appropriate agents. Regional infection control efforts and judicious antibiotic use are needed to control the spread of these organisms. ..
- Majumder A, Fang M, Tsai K, Ueguchi C, Mizuno T, Wu H. LeuO expression in response to starvation for branched-chain amino acids. J Biol Chem. 2001;276:19046-51 pubmed..coli K-12 relA1 strain. This result supports a functional role for LeuO in the bacterial stringent response. ..
- Franklin M, Brusilow W, Woodbury D. Determination of proton flux and conductance at pH 6.8 through single FO sectors from Escherichia coli. Biophys J. 2004;87:3594-9 pubmed..We find that wild-type FO has a proton flux of 3100 +/- 500 H+/s/FO at a transmembrane potential of 106 mV (25 degrees C and pH 6.8). This corresponds to a proton conductance of 4.4 fS. ..
- Walter W, Kireeva M, Studitsky V, Kashlev M. Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes. J Biol Chem. 2003;278:36148-56 pubmed..Furthermore, the data argue that the general elongation properties of polymerases may determine the mechanism used for transcription through the nucleosome. ..
- Liu J, Rosen B. Ligand interactions of the ArsC arsenate reductase. J Biol Chem. 1997;272:21084-9 pubmed..Cys-12 thiolate was also required. Thus the intrinsic fluorescence of Trp-11 provides a useful probe to investigate the mechanism of this novel reductase. ..
- Bhagwat A, McClelland M. DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res. 1992;20:1663-8 pubmed..Further, they provide an explanation for the known scarcity of CTAG containing restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a force in shaping the sequence composition of bacterial genomes. ..