Genomes and Genes
Experts and Doctors on escherichia coli proteins in Detroit, Michigan, United States
Locale: Detroit, Michigan, United States
Topic: escherichia coli proteins
- Roy T, Bhagwat A. Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation. Nucleic Acids Res. 2007;35:e147 pubmed..The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart. ..
- 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. ..
- 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
- Feng J, Atkinson M, McCleary W, Stock J, Wanner B, Ninfa A. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J Bacteriol. 1992;174:6061-70 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. ..
- Lee T, Feig A. The RNA binding protein Hfq interacts specifically with tRNAs. RNA. 2008;14:514-23 pubmed publisher..We infer that tRNA binding and reduced fidelity are linked by a role for Hfq in tRNA modification. ..
- Meng Y, Liu Z, Rosen B. As(III) and Sb(III) uptake by GlpF and efflux by ArsB in Escherichia coli. J Biol Chem. 2004;279:18334-41 pubmed..We propose that the actual substrate of ArsB is a polymer of (AsO)(n), (SbO)(n), or a co-polymer of the two metalloids. ..
- 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. ..
- 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. ..
- Bujnicki J, Radlinska M. Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases? A hypothesis. IUBMB Life. 1999;48:247-9 pubmed..We predict the structure and function of the putative catalytic domain of HemK proteins and speculate that the target-recognizing function may be conferred by the N-terminal variable region. ..
- Carlin A, Shi W, Dey S, Rosen B. The ars operon of Escherichia coli confers arsenical and antimonial resistance. J Bacteriol. 1995;177:981-6 pubmed..Expression of the ars genes was inducible by arsenite. By Southern hybridization, the operon was found in all strains of E. coli examined but not in Salmonella typhimurium, Pseudomonas aeruginosa, or Bacillus subtilis. ..
- Sun W, Nicholson A. Mechanism of action of Escherichia coli ribonuclease III. Stringent chemical requirement for the glutamic acid 117 side chain and Mn2+ rescue of the Glu117Asp mutant. Biochemistry. 2001;40:5102-10 pubmed..Glu117 is important for the function of both sites. The implications of these findings on the RNase III catalytic mechanism are discussed. ..
- Li H, Chelladurai B, Zhang K, Nicholson A. Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects. Nucleic Acids Res. 1993;21:1919-25 pubmed..Third, fluoride anion inhibits RNase III-catalyzed cleavage, by a mechanism which does not involve inhibition of substrate binding. ..
- Chen C, Wu H. LeuO protein delimits the transcriptionally active and repressive domains on the bacterial chromosome. J Biol Chem. 2005;280:15111-21 pubmed
- Li H, Nicholson A. Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants. EMBO J. 1996;15:1421-33 pubmed..1[WC-L] RNA, and dsRNA in general, while catalyzing only single cleavage of R1.1 RNA and related substrates in which the scissle bond is within an asymmetric internal loop. ..
- DeMel S, Shi J, Martin P, Rosen B, Edwards B. Arginine 60 in the ArsC arsenate reductase of E. coli plasmid R773 determines the chemical nature of the bound As(III) product. Protein Sci. 2004;13:2330-40 pubmed..We propose that this intermediate is more stable than the monohydroxyarsenite intermediate of the native enzyme, resulting in slow release of product and, consequently, loss of activity. ..
- Zhang K, Nicholson A. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc Natl Acad Sci U S A. 1997;94:13437-41 pubmed..Base pair antideterminants also may protect double-helical elements in other RNA molecules with essential functions. ..
- Chen C, Ghole M, Majumder A, Wang Z, Chandana S, Wu H. LeuO-mediated transcriptional derepression. J Biol Chem. 2003;278:38094-103 pubmed..The characterization provides clues for future elucidation of the molecular details whereby LeuO negates the gene-silencing activity. ..
- Calin Jageman I, Nicholson A. RNA structure-dependent uncoupling of substrate recognition and cleavage by Escherichia coli ribonuclease III. Nucleic Acids Res. 2003;31:2381-92 pubmed..1 asymmetric internal loop. The presence of both bulges is required for uncoupling. The bulge-helix-bulge motif acts as a 'catalytic' antideterminant, which is distinct from recognition antideterminants, which inhibit RNase III binding. ..
- 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
- 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. ..
- 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. ..
- 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...
- 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...
- Mekhovich O, Tang M, Romano L. Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. Biochemistry. 1998;37:571-9 pubmed..Most siginificantly, we find that the rate of UvrB and UvrBC-substrate complex formation correlates with the rate of UvrABC nuclease incision. ..
- Klapacz J, Bhagwat A. Transcription promotes guanine to thymine mutations in the non-transcribed strand of an Escherichia coli gene. DNA Repair (Amst). 2005;4:806-13 pubmed..These results suggest that the magnitudes of individual base substitutions and their relative numbers in other studies of mutational spectra may also be affected by transcription. ..
- Xu C, Shi W, Rosen B. The chromosomal arsR gene of Escherichia coli encodes a trans-acting metalloregulatory protein. J Biol Chem. 1996;271:2427-32 pubmed..In addition, the chromosomally-encoded repressor can regulate expression of the ars operon of plasmid R773, and the R773 repressor can cross-regulate expression from the chromosomal operon. ..
- 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. ..
- Chelladurai B, Li H, Nicholson A. A conserved sequence element in ribonuclease III processing signals is not required for accurate in vitro enzymatic cleavage. Nucleic Acids Res. 1991;19:1759-66 pubmed..These R1.1 variants are accurately cleaved at rates comparable to wild-type R1.1 RNA, indicating the nonessentiality of this conserved sequence element in establishing in vitro processing reactivity and selectivity. ..
- Ellis J, Carlin A, Steffes C, Wu J, Liu J, Rosen B. Topological analysis of the lysine-specific permease of Escherichia coli. Microbiology. 1995;141 ( Pt 8):1927-35 pubmed..From analysis of 30 gene fusions, a topological model of the LysP protein is proposed in which the protein has 12 membrane-spanning regions, with the N- and C-terminal in the cytosol. ..
- Monticello R, Angov E, Brusilow W. Effects of inducing expression of cloned genes for the F0 proton channel of the Escherichia coli F1F0 ATPase. J Bacteriol. 1992;174:3370-6 pubmed..Such induction did result in growth inhibition, but there was no correlation between growth inhibition and either increased membrane proton permeability or the presence of functional, reconstitutable F0. ..