Genomes and Genes
Experts and Doctors on escherichia coli in Ithaca, New York, United States
Locale: Ithaca, New York, United States
Topic: escherichia coli
Publications136 found, 100 shown here
- Jarvis G, Fields M, Adamovich D, Arthurs C, Russell J. The mechanism of carbonate killing of Escherichia coli. Lett Appl Microbiol. 2001;33:196-200 pubmed..Previous methods of eradicating E. coli were either expensive or environmentally unsound. However, cattle manure can be treated with carbonate to eliminate E. coli, and the cost of this treatment is less than $0.03 per cow per day. ..
- Fisher A, Kim W, DeLisa M. Genetic selection for protein solubility enabled by the folding quality control feature of the twin-arginine translocation pathway. Protein Sci. 2006;15:449-58 pubmed
- Borbat P, Surendhran K, Bortolus M, Zou P, Freed J, McHaourab H. Conformational motion of the ABC transporter MsbA induced by ATP hydrolysis. PLoS Biol. 2007;5:e271 pubmed..Our results suggest that ATP-powered transport entails LPS sequestering into the open cytoplasmic chamber prior to its translocation by alternating access of the chamber, made possible by 10-20-A conformational changes...
- Joshi C, Panda D, Martell D, Andoy N, Chen T, Gaballa A, et al. Direct substitution and assisted dissociation pathways for turning off transcription by a MerR-family metalloregulator. Proc Natl Acad Sci U S A. 2012;109:15121-6 pubmed
- Brooks Y, Collins S, Mbullo P, Boateng G, Young S, Richardson R. Evaluating Human Sensory Perceptions and the Compartment Bag Test Assays as Proxies for the Presence and Concentration of Escherichia coli in Drinking Water in Western Kenya. Am J Trop Med Hyg. 2017;97:1005-1008 pubmed publisher..640). In low-resource settings, CBT provides comparable assessments of E. coli concentrations to Colilert. ..
- Vander Horn P, Zahler S. Cloning and nucleotide sequence of the leucyl-tRNA synthetase gene of Bacillus subtilis. J Bacteriol. 1992;174:3928-35 pubmed..subtilis ilv-leu operon. The DNA of the B. subtilis leuS open reading frame is 48% identical to the leuS gene of Escherichia coli and is predicted to encode a polypeptide with 46% identity to the leucyl-tRNA synthetase of E. coli. ..
- Reddick J, Saha S, Lee J, Melnick J, Perkins J, Begley T. The mechanism of action of bacimethrin, a naturally occurring thiamin antimetabolite. Bioorg Med Chem Lett. 2001;11:2245-8 pubmed..Bacimethrin does not cause repression of the genes coding for the thiamin biosynthetic enzymes. ..
- Helmann J. Purification of Bacillus subtilis RNA polymerase and associated factors. Methods Enzymol. 2003;370:10-24 pubmed
- Settembre E, Chittuluru J, Mill C, Kappock T, Ealick S. Acidophilic adaptations in the structure of Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase (PurE). Acta Crystallogr D Biol Crystallogr. 2004;60:1753-60 pubmed..A chain of histidines linking two active sites is discussed in the context of the proton transfers catalyzed by the enzyme...
- Parks A, Peters J. Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. J Bacteriol. 2007;189:2170-3 pubmed..These elements form functionally diverse genomic islands at the specific site of Tn7 insertion adjacent to glmS. This work presents the first example of genomic island formation by a DDE type transposon. ..
- Pagano A, Yasuda K, Roneker K, Crenshaw T, Lei X. Supplemental Escherichia coli phytase and strontium enhance bone strength of young pigs fed a phosphorus-adequate diet. J Nutr. 2007;137:1795-801 pubmed..The similar benefit of supplemental Sr was mainly due to an effect on bone chemical properties. ..
- Celik E, Fisher A, Guarino C, Mansell T, DeLisa M. A filamentous phage display system for N-linked glycoproteins. Protein Sci. 2010;19:2006-13 pubmed publisher..coli cells. ..
- Paul D, Chatterjee A, Begley T, Ealick S. Domain organization in Candida glabrata THI6, a bifunctional enzyme required for thiamin biosynthesis in eukaryotes. Biochemistry. 2010;49:9922-34 pubmed publisher..This suggests that an unidentified enzyme is necessary to produce the substrate for THI6 from the THI4 product. ..
- Bicalho R, Machado V, Bicalho M, Gilbert R, Teixeira A, Caixeta L, et al. Molecular and epidemiological characterization of bovine intrauterine Escherichia coli. J Dairy Sci. 2010;93:5818-30 pubmed publisher..coli carrying fimH and at least 1 of the other 5 identified virulence factors were pathogenic, and phylogenetic analysis based on the nucleotide sequence of DNA gyrase from 41 such IUEC revealed 2 clades. ..
- Watts A, Nixon A, Papich M, Sparks H, Schwark W. In vitro elution of amikacin and ticarcillin from a resorbable, self-setting, fiber reinforced calcium phosphate cement. Vet Surg. 2011;40:563-70 pubmed publisher..The results of this study underscore the importance of testing drug combinations, despite success of the combination systemically, before their use in local applications. ..
- Pereira R, Santos T, Bicalho M, Caixeta L, Machado V, Bicalho R. Antimicrobial resistance and prevalence of virulence factor genes in fecal Escherichia coli of Holstein calves fed milk with and without antimicrobials. J Dairy Sci. 2011;94:4556-65 pubmed publisher..Phylogenetic analysis based on the nucleotide sequence of the DNA gyrase gene (gyrB) from 31 fecal E. coli isolates revealed 3 main clades. ..
- Schukken Y, Gunther J, Fitzpatrick J, Fontaine M, Goetze L, Holst O, et al. Host-response patterns of intramammary infections in dairy cows. Vet Immunol Immunopathol. 2011;144:270-89 pubmed publisher..The relevance of fully understanding the bovine host response to intramammary infection is discussed, some major gaps in our knowledge are highlighted and directions for future research are indicated. ..
- Clark S, Egan R, Frazier P, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics. 2013;29:435-43 pubmed publisher..ALE is released as open source software under the UoI/NCSA license at http://www.alescore.org. It is implemented in C and Python. ..
- Baeumner A, Jones C, Wong C, Price A. A generic sandwich-type biosensor with nanomolar detection limits. Anal Bioanal Chem. 2004;378:1587-93 pubmed
- Baek S, Hartsock A, Shapleigh J. Agrobacterium tumefaciens C58 uses ActR and FnrN to control nirK and nor expression. J Bacteriol. 2008;190:78-86 pubmed publisher..Inactivation of paz reduced Nir activity by 55%. These results help explain why Nir activity is very low in the actR mutant even though a nirK promoter with mutations in the ActR binding site showed significant expression...
- Mukherjee T, Hanes J, Tews I, Ealick S, Begley T. Pyridoxal phosphate: biosynthesis and catabolism. Biochim Biophys Acta. 2011;1814:1585-96 pubmed publisher..This review provides a concise overview of the mechanistic enzymology of vitamin B(6) biosynthesis and catabolism. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology. ..
- Nassar N, Hoffman G, Manor D, Clardy J, Cerione R. Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP. Nat Struct Biol. 1998;5:1047-52 pubmed..Comparison of the structures for the wild type and mutant Cdc42GAP complexes provides important insights into the GAP-catalyzed GTP hydrolytic reaction. ..
- Waldron M, Kulick A, Bell A, Overton T. Acute experimental mastitis is not causal toward the development of energy-related metabolic disorders in early postpartum dairy cows. J Dairy Sci. 2006;89:596-610 pubmed
- Echtenkamp P, Wilson D, Shuler M. Cell cycle progression in Escherichia coli B/r affects transcription of certain genes: Implications for synthetic genome design. Biotechnol Bioeng. 2009;102:902-9 pubmed publisher..In conclusion, gene position, with regard to the C period, and gene function are important factors to incorporate into design criteria for synthetic bacterial genomes. ..
- McCulloch K, Mukherjee T, Begley T, Ealick S. Structure of the PLP degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. Biochemistry. 2009;48:4139-49 pubmed publisher..1 A using SAD phasing with and without the substrate MHPC bound. These crystal structures provide insight into the reaction mechanism and suggest roles for active site residues in the catalysis of a novel oxidative ring-opening reaction. ..
- Zhang S, Kongsaeree P, Clardy J, Wilson D, Ganem B. Site-directed mutagenesis of monofunctional chorismate mutase engineered from the E. coli P-protein. Bioorg Med Chem. 1996;4:1015-20 pubmed..8. However, activity of the Gln88Glu mutant at pH 4.5 exceeded wild-type EcCM. Implications for the mechanism of mutase catalysis are discussed. ..
- Fredrick K, Helmann J. RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates. Proc Natl Acad Sci U S A. 1997;94:4982-7 pubmed..Thus, sigmaA appears to recognize the -10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, sigma also localizes the transcription start site. ..
- Feltham J, Dotsch V, Raza S, Manor D, Cerione R, Sutcliffe M, et al. Definition of the switch surface in the solution structure of Cdc42Hs. Biochemistry. 1997;36:8755-66 pubmed..These studies indicate the insert region forms a stable invariant "footrest" for docking of regulatory and effector proteins. ..
- Wang W, Kappock T, Stubbe J, Ealick S. X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Biochemistry. 1998;37:15647-62 pubmed..The N and C domains appear to be largely responsible for substrate specificity. The structure of GAR-syn allows modeling studies of possible channeling complexes with PPRP amidotransferase. ..
- Begley T, Downs D, Ealick S, McLafferty F, van Loon A, Taylor S, et al. Thiamin biosynthesis in prokaryotes. Arch Microbiol. 1999;171:293-300 pubmed..The specific reactions catalyzed by ThiC (pyrimidine formation), and ThiGH and ThiI (thiazole formation) have not yet been identified. ..
- Dhawan M, Wise F, Baeumner A. Development of a laser-induced cell lysis system. Anal Bioanal Chem. 2002;374:421-6 pubmed..Miniaturized lasers and miniaturized cell-lysis chambers will create a simple, field-usable cell lysis system and allow the application of laser-induced cell lysis in micro Total Analysis Systems...
- Helmann J. Sensing nickel. NikRs with two pockets. Chem Biol. 2002;9:1055-7 pubmed..Recent results suggest that repression is elicited by binding of nickel to a high-affinity site, but a low-affinity binding pocket may also play a role...
- Manoj N, Ealick S. Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase. Acta Crystallogr D Biol Crystallogr. 2003;59:1762-6 pubmed..Thus, the true space group is R3 with four monomers per asymmetric unit. ..
- Roberts J, Park J. Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr Opin Microbiol. 2004;7:120-5 pubmed..The mechanism of RNA release has been illuminated by the discovery that Mfd causes forward translocation of RNA polymerase, using an ATP-dependent motor that is highly homologous to that of the Holliday branch migration protein RecG. ..
- Zhang Y, Cottet S, Ealick S. Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases. Structure. 2004;12:1383-94 pubmed..The structure of the regulatory domain consists of a long helix and a four-stranded sheet and has a novel topology. ..
- Cavatorta D, Erb H, Flaminio M. Ex vivo generation of mature equine monocyte-derived dendritic cells. Vet Immunol Immunopathol. 2009;131:259-67 pubmed publisher..0001) and upregulation of pro-inflammatory cytokine mRNA, particularly IL-12/IL-23p40 (p<0.05) and IL-23p19 (p<0.05). The ability to measure DC activation state will facilitate future investigations of equine DC function. ..
- Galvao K, Felippe M, Brittin S, Sper R, Fraga M, Galvão J, et al. Evaluation of cytokine expression by blood monocytes of lactating Holstein cows with or without postpartum uterine disease. Theriogenology. 2012;77:356-72 pubmed publisher..We concluded that altered levels of expression and production of pro-inflammatory cytokines postpartum could contribute to impaired inflammatory response and predispose cows to development of metritis. ..
- Volkova V, Lanzas C, Lu Z, Gröhn Y. Mathematical model of plasmid-mediated resistance to ceftiofur in commensal enteric Escherichia coli of cattle. PLoS ONE. 2012;7:e36738 pubmed publisher..coli, such as the frequency of transfer of plasmids carrying resistance-genes, the rate of replacement of enteric E. coli by ingested E. coli, and the frequency of ceftiofur resistance in the latter. ..
- Waraho Zhmayev D, Gkogka L, Yu T, DeLisa M. A microbial sensor for discovering structural probes of protein misfolding and aggregation. Prion. 2013;7:151-6 pubmed publisher..g., ?-synuclein, amyloid-? protein). Taken together, these studies highlight the utility of engineered bacteria for rapidly and inexpensively uncovering potent anti-aggregation factors. ..
- Yasui T, McCarthy M, Ryan C, Gilbert R, Felippe M, Mechor G, et al. Effects of monensin and starch level in early lactation diets on indices of immune function in dairy cows. J Dairy Sci. 2016;99:1351-1363 pubmed publisher..Overall, results suggest that feeding higher starch diets postpartum and peripartal supplementation with monensin may have some beneficial effects on immune function, although uterine cytology was not affected by treatment. ..
- Berg B, Li J, Heider J, Stewart V. Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine. J Biol Chem. 1991;266:22380-5 pubmed..Evidence from sequence and spectral analyses suggest that FdnI encodes cytochrome bFdn556. Implications for the membrane topology of formate dehydrogenase-N and its mechanism of proton translocation are discussed. ..
- Chen S, Hao Z, Bieniek E, Calvo J. Modulation of Lrp action in Escherichia coli by leucine: effects on non-specific binding of Lrp to DNA. J Mol Biol. 2001;314:1067-75 pubmed..We propose that the net effect of these processes is to regulate the relative concentrations of free Lrp hexadecamer and leucine-bound octamer, leading to promoter selection in response to environmental conditions. ..
- Platko J, Willins D, Calvo J. The ilvIH operon of Escherichia coli is positively regulated. J Bacteriol. 1990;172:4563-70 pubmed..We propose that the designation lrp be used in the future instead of oppI or ihb and that Lrp (leucine-responsive regulatory protein) be used in place of IHB. ..
- Shi Q, Parks A, Potter B, Safir I, Luo Y, Forster B, et al. DNA damage differentially activates regional chromosomal loci for Tn7 transposition in Escherichia coli. Genetics. 2008;179:1237-50 pubmed publisher..Our results are consistent with the idea that Tn7 recognizes DNA replication involved in DNA repair and reveals discrete regions of the chromosome that are differentially activated as transposition targets. ..
- Mann S, Siler J, Jordan D, Warnick L. Antimicrobial susceptibility of fecal Escherichia coli isolates in dairy cows following systemic treatment with ceftiofur or penicillin. Foodborne Pathog Dis. 2011;8:861-7 pubmed publisher..Although we found the potential for selection pressure by documenting the change in E. coli concentration after ceftiofur treatment, an increase in ceftiofur resistance was not found. ..
- Machado V, Bicalho M, Pereira R, Caixeta L, Bittar J, Oikonomou G, et al. The effect of intrauterine administration of mannose or bacteriophage on uterine health and fertility of dairy cows with special focus on Escherichia coli and Arcanobacterium pyogenes. J Dairy Sci. 2012;95:3100-9 pubmed publisher..8 and 2.66 higher odds of being diagnosed with clinical endometritis, respectively. Additionally, cows negative for E. coli at 2 ± 1 DIM were 1.39 times more likely to conceive than cows positive cows for E. coli. ..
- O Brien S, DeLisa M. Functional reconstitution of a tunable E3-dependent sumoylation pathway in Escherichia coli. PLoS ONE. 2012;7:e38671 pubmed publisher..Overall, this system provides a rapid and controllable platform for studying the enzymology of the entire sumoylation cascade directly in living cells. ..
- Rabin R, Stewart V. Either of two functionally redundant sensor proteins, NarX and NarQ, is sufficient for nitrate regulation in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1992;89:8419-23 pubmed..Analysis of narX* and narL missense alleles in narQ+ versus narQ::Tn10 backgrounds suggests that NarQ and NarX may have subtle functional differences. ..
- Mathews I, Kappock T, Stubbe J, Ealick S. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure. 1999;7:1395-406 pubmed..The environment of the active site and the analysis of conserved residues between the two classes of PurEs suggests a model for the differences in their substrate specificities and the relationship between their mechanisms. ..
- Appleby T, Mathews I, Porcelli M, Cacciapuoti G, Ealick S. Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. J Biol Chem. 2001;276:39232-42 pubmed publisher..Examination of the three-dimensional structure of SsMTAP suggests that unlike most thermophilic enzymes, disulfide linkages play a key in role in its thermal stability...
- Zhang Y, Parker W, Sorscher E, Ealick S. PNP anticancer gene therapy. Curr Top Med Chem. 2005;5:1259-74 pubmed..coli PNP anticancer gene therapy. We also review the structural basis for activity of nucleoside phosphorylases and suggest future directions for the development of activating enzymes for suicide gene therapy. ..
- Kornreich B, Niu L, Roberson M, Oswald R. Identification of C-terminal domain residues involved in protein kinase A-mediated potentiation of kainate receptor subtype 6. Neuroscience. 2007;146:1158-68 pubmed
- Stewart V, Berg B. Influence of nar (nitrate reductase) genes on nitrate inhibition of formate-hydrogen lyase and fumarate reductase gene expression in Escherichia coli K-12. J Bacteriol. 1988;170:4437-44 pubmed..Insertions in narL had a lesser effect, and insertions in narX had no effect. We conclude that nitrate affects formate-hydrogen lyase synthesis by a pathway distinct from that for nitrate reductase and fumarate reductase. ..
- Zhang S, Wilson D, Ganem B. Probing the catalytic mechanism of prephenate dehydratase by site-directed mutagenesis of the Escherichia coli P-protein dehydratase domain. Biochemistry. 2000;39:4722-8 pubmed..2- and 3.5-fold, respectively), which was due to enhanced substrate binding. For the double mutant enzyme (E159A-E232A), k(cat)/K(m) was ca. 7-fold higher than for the WT enzyme, while its K(m) was 4.6-fold lower. ..
- Vincent S, Chen S, Wilson D, Ganem B. Probing the overlap of chorismate mutase and prephenate dehydrogenase sites in the escherichia coli T-protein: a dehydrogenase-selective inhibitor. Bioorg Med Chem Lett. 2002;12:929-31 pubmed..An inhibitor of prephenate dehydrogenase has been identified that has no effect on the chorismate mutase activity in the Escherichia coli T-protein, thus supporting the idea of two separate active sites. ..
- Chao X, Muff T, Park S, Zhang S, Pollard A, Ordal G, et al. A receptor-modifying deamidase in complex with a signaling phosphatase reveals reciprocal regulation. Cell. 2006;124:561-71 pubmed publisher..A point mutation that dissociates CheC from CheD impairs chemotaxis in vivo. Thus, CheC incorporates an element of an upstream receptor to influence both its own effect on receptor output and that of its binding partner, CheD...
- Mukherjee T, Kinsland C, Begley T. PLP catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in Mesorhizobium loti MAFF303099. Bioorg Chem. 2007;35:458-64 pubmed..The k cat for NADH production is 0.01s(-1). The KM values for 4-pyridoxic acid and NAD are 5.8 and 6.6microM, respectively. ..
- Aggarwal K, Lee K. Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli. J Bacteriol. 2011;193:4869-80 pubmed publisher..Based on these observations, we suspect a translation product of ext-a1 affects different regulatory mechanisms that control rRNA synthesis. ..
- Mao C, Cook W, Zhou M, Koszalka G, Krenitsky T, Ealick S. The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology. Structure. 1997;5:1373-83 pubmed..This structural data may be useful in designing prodrugs that can be activated by E. coli PNP but not the human enzyme. ..
- Gilbert R, Santos N. Dynamics of postpartum endometrial cytology and bacteriology and their relationship to fertility in dairy cows. Theriogenology. 2016;85:1367-74 pubmed publisher..These findings suggest that rapid mobilization of neutrophils to the postpartum uterus is a beneficial response for uterine health in dairy cows. ..
- Batt C, Jamieson A, Vandeyar M. Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase. Proc Natl Acad Sci U S A. 1990;87:618-22 pubmed..Replacement of His-271 may render the enzyme thermolabile, since this residue appears to be a ligand for one of the metal ions in the active site of the enzyme. ..
- Wang Q, Wu J, Friedberg D, Plakto J, Calvo J. Regulation of the Escherichia coli lrp gene. J Bacteriol. 1994;176:1831-9 pubmed..These results demonstrate that autogenous regulation of lrp involves Lrp acting directly to cause repression of lrp transcription. ..
- Wang Q, Calvo J. Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvIH. J Mol Biol. 1993;229:306-18 pubmed..We propose a model in which multiple binding sites contribute to the formation of a nucleoprotein complex, but only a particular proximal site positions Lrp properly so that it interacts with RNA polymerase. ..
- Williams S, Stewart V. Nitrate- and nitrite-sensing protein NarX of Escherichia coli K-12: mutational analysis of the amino-terminal tail and first transmembrane segment. J Bacteriol. 1997;179:721-9 pubmed..We conclude that the amino terminus of the NarX protein is important for the differential response to nitrate and nitrite. ..
- Hatoum A, Roberts J. Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol Microbiol. 2008;68:17-28 pubmed publisher..In addition to promoter-proximal RNAP trapping, we observed transcription-dependent DNA modifications spanning the tnaA and cspA leader regions up to 100 bp downstream of the transcription start site. ..
- ..These results provide a quantitative framework for understanding how dynamic modification of DNA supercoiling regulates transcription. ..
- Willins D, Ryan C, Platko J, Calvo J. Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine. J Biol Chem. 1991;266:10768-74 pubmed..Lrp has some amino acid sequence similarity to AsnC, a protein that regulates asnA expression (Kolling, R., and Lother, H. (1985) J. Bacteriol. 164, 310-315). ..
- Darwin A, Stewart V. Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site. J Mol Biol. 1995;251:15-29 pubmed..5 binding site to regulate aeg-46.5 operon expression in response to nitrate and nitrite. Apparently, only the NarP protein is competent to activate transcription of the aeg-46.5 operon when bound to the -44.5 region...
- Yarnell W, Roberts J. Mechanism of intrinsic transcription termination and antitermination. Science. 1999;284:611-5 pubmed..These effects illuminate the structure of the complex and the mechanism of transcription termination. ..
- Marr M, Roberts J. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol Cell. 2000;6:1275-85 pubmed..Furthermore, GreA and GreB are required to mediate efficient function of the lambda gene Q antiterminator at this site. Thus, cleavage factors are necessary for the natural progression of RNA polymerase in vivo. ..
- Lin Q, Lo C, Cerione R, Yang W. The Cdc42 target ACK2 interacts with sorting nexin 9 (SH3PX1) to regulate epidermal growth factor receptor degradation. J Biol Chem. 2002;277:10134-8 pubmed..EGF receptor levels were significantly decreased following EGF stimulation of cells co-expressing ACK2 and SH3PX1, thus highlighting a novel role for ACK2, working together with SH3PX1 to promote the degradation of the EGF receptor. ..
- Abbi S, Ueda H, Zheng C, Cooper L, Zhao J, Christopher R, et al. Regulation of focal adhesion kinase by a novel protein inhibitor FIP200. Mol Biol Cell. 2002;13:3178-91 pubmed..Together, these results identify FIP200 as a novel protein inhibitor for FAK. ..
- Lawhorn B, Gerdes S, Begley T. A genetic screen for the identification of thiamin metabolic genes. J Biol Chem. 2004;279:43555-9 pubmed..The gene products YmfB and Cof catalyze the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate. YmfB also converts thiamin pyrophosphate into thiamin phosphate. ..
- Choe L, Aggarwal K, Franck Z, Lee K. A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells. Electrophoresis. 2005;26:2437-49 pubmed..81 using 2-DE and less than 0.53 using isobaric tags. The selective removal of outlier data points from the shotgun method using Grubb's and Rosner's statistical outlier tests improves the consistency of the quantitation data obtained. ..
- Paul D, O Leary S, Rajashankar K, Bu W, Toms A, Settembre E, et al. Glycal formation in crystals of uridine phosphorylase. Biochemistry. 2010;49:3499-509 pubmed publisher..These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds. ..
- Jamieson A, Batt C. Fluorescent properties of the Escherichia coli D-xylose isomerase active site. Protein Eng. 1992;5:235-40 pubmed..In the case of H101S, a mutant protein with measurable isomerizing activity, substrate binding with novel fluorescent properties was observed, possibly the bound pyranose form of xylose under steady-state conditions. ..
- Egan S, Stewart V. Mutational analysis of nitrate regulatory gene narL in Escherichia coli K-12. J Bacteriol. 1991;173:4424-32 pubmed..This finding suggests that narL505(V88A) did not confer molybdate-independent expression of fdnGHI. ..
- Elsinghorst E, Mortlock R. Molecular cloning of the Escherichia coli B L-fucose-D-arabinose gene cluster. J Bacteriol. 1994;176:7223-32 pubmed..D-Arabinose metabolism by E. coli B appears to be the result of acquisitive evolution, but the source of the darK gene has not been determined. ..
- Folley L, Fox T. Reduced dosage of genes encoding ribosomal protein S18 suppresses a mitochondrial initiation codon mutation in Saccharomyces cerevisiae. Genetics. 1994;137:369-79 pubmed
- van Der Hoeven R, Monforte A, Breeden D, Tanksley S, Steffens J. Genetic control and evolution of sesquiterpene biosynthesis in Lycopersicon esculentum and L. hirsutum. Plant Cell. 2000;12:2283-94 pubmed
- Williams E, Perez Martinez X, Fox T. MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria. Genetics. 2004;167:65-75 pubmed..We propose that MrpL36p represents a highly diverged L31 homolog with derived domains functioning in mRNA selection in yeast mitochondria. ..
- Kim M, Lei X. Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR. Appl Microbiol Biotechnol. 2008;79:69-75 pubmed publisher..5, respectively. Thus, the catalytic efficiency of these enzymes was not inversely related to their thermostability. ..
- Liao P, Gupta P, Petrov A, Dinman J, Lee K. A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting. Nucleic Acids Res. 2008;36:2619-29 pubmed publisher..These analyses suggest that P-site tRNA slippage is the driving force for +1 ribosomal frameshifting while the presence of a 'hungry codon' in the A-site and destabilization in the E-site further enhance +1 PRF in E. coli. ..
- Li J, Stewart V. Localization of upstream sequence elements required for nitrate and anaerobic induction of fdn (formate dehydrogenase-N) operon expression in Escherichia coli K-12. J Bacteriol. 1992;174:4935-42 pubmed..The other putative FNR protein binding site, centered at -97.5, was not involved in anaerobic induction. It might play a negative role in fdn operon expression during anaerobic growth in the absence of nitrate. ..
- Friedberg D, Platko J, Tyler B, Calvo J. The amino acid sequence of Lrp is highly conserved in four enteric microorganisms. J Bacteriol. 1995;177:1624-6 pubmed..This analysis suggests that the Lrp amino acid sequence is highly adapted for function and that almost all amino acid changes lead to a protein that functions less well than the wild-type protein. ..
- Ring H, Lis J. The SR protein B52/SRp55 is essential for Drosophila development. Mol Cell Biol. 1994;14:7499-506 pubmed..Therefore, B52 is not required for all splicing in vivo. This is the first in vivo deficiency analysis of a member of the SR protein family. ..