Experts and Doctors on escherichia coli proteins in Berkeley, California, United States

Summary

Locale: Berkeley, California, United States
Topic: escherichia coli proteins

Top Publications

  1. Dunkle J, Wang L, Feldman M, Pulk A, Chen V, Kapral G, et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science. 2011;332:981-4 pubmed publisher
    ..The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling. ..
  2. Goedken E, Levitus M, Johnson A, Bustamante C, O Donnell M, Kuriyan J. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol. 2004;336:1047-59 pubmed
  3. Sagawa S, Price M, Deutschbauer A, Arkin A. Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS ONE. 2017;12:e0178258 pubmed publisher
    ..Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions. ..
  4. Yu E, Aires J, Nikaido H. AcrB multidrug efflux pump of Escherichia coli: composite substrate-binding cavity of exceptional flexibility generates its extremely wide substrate specificity. J Bacteriol. 2003;185:5657-64 pubmed
  5. Fennell Fezzie R, Gradia S, Akey D, Berger J. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. EMBO J. 2005;24:1921-30 pubmed
    ..Our findings, together with sequence analyses, indicate that MukF is a kleisin subunit for E. coli condensin and suggest a means by which it may organize the MukBEF assembly. ..
  6. Kustu S, Inwood W. Biological gas channels for NH3 and CO2: evidence that Rh (Rhesus) proteins are CO2 channels. Transfus Clin Biol. 2006;13:103-10 pubmed
  7. Takatsuka Y, Nikaido H. Threonine-978 in the transmembrane segment of the multidrug efflux pump AcrB of Escherichia coli is crucial for drug transport as a probable component of the proton relay network. J Bacteriol. 2006;188:7284-9 pubmed
  8. Mejia Y, Mao H, Forde N, Bustamante C. Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J Mol Biol. 2008;382:628-37 pubmed publisher
    ..This observation suggests that arrest could play a regulatory role in vivo, possibly through interactions with specific elongation factors. ..
  9. Takatsuka Y, Nikaido H. Covalently linked trimer of the AcrB multidrug efflux pump provides support for the functional rotating mechanism. J Bacteriol. 2009;191:1729-37 pubmed publisher
    ..These observations provide strong biochemical evidence for the functionally rotating mechanism of AcrB pump action. The linked trimer will be useful for further biochemical studies of mechanisms of transport in the future. ..
  10. Hall J, Ganesan A, Chen J, Nikaido H. Two modes of ligand binding in maltose-binding protein of Escherichia coli. Functional significance in active transport. J Biol Chem. 1997;272:17615-22 pubmed

Detail Information

Publications62

  1. Dunkle J, Wang L, Feldman M, Pulk A, Chen V, Kapral G, et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science. 2011;332:981-4 pubmed publisher
    ..The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling. ..
  2. Goedken E, Levitus M, Johnson A, Bustamante C, O Donnell M, Kuriyan J. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol. 2004;336:1047-59 pubmed
  3. Sagawa S, Price M, Deutschbauer A, Arkin A. Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS ONE. 2017;12:e0178258 pubmed publisher
    ..Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions. ..
  4. Yu E, Aires J, Nikaido H. AcrB multidrug efflux pump of Escherichia coli: composite substrate-binding cavity of exceptional flexibility generates its extremely wide substrate specificity. J Bacteriol. 2003;185:5657-64 pubmed
  5. Fennell Fezzie R, Gradia S, Akey D, Berger J. The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. EMBO J. 2005;24:1921-30 pubmed
    ..Our findings, together with sequence analyses, indicate that MukF is a kleisin subunit for E. coli condensin and suggest a means by which it may organize the MukBEF assembly. ..
  6. Kustu S, Inwood W. Biological gas channels for NH3 and CO2: evidence that Rh (Rhesus) proteins are CO2 channels. Transfus Clin Biol. 2006;13:103-10 pubmed
  7. Takatsuka Y, Nikaido H. Threonine-978 in the transmembrane segment of the multidrug efflux pump AcrB of Escherichia coli is crucial for drug transport as a probable component of the proton relay network. J Bacteriol. 2006;188:7284-9 pubmed
  8. Mejia Y, Mao H, Forde N, Bustamante C. Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J Mol Biol. 2008;382:628-37 pubmed publisher
    ..This observation suggests that arrest could play a regulatory role in vivo, possibly through interactions with specific elongation factors. ..
  9. Takatsuka Y, Nikaido H. Covalently linked trimer of the AcrB multidrug efflux pump provides support for the functional rotating mechanism. J Bacteriol. 2009;191:1729-37 pubmed publisher
    ..These observations provide strong biochemical evidence for the functionally rotating mechanism of AcrB pump action. The linked trimer will be useful for further biochemical studies of mechanisms of transport in the future. ..
  10. Hall J, Ganesan A, Chen J, Nikaido H. Two modes of ligand binding in maltose-binding protein of Escherichia coli. Functional significance in active transport. J Biol Chem. 1997;272:17615-22 pubmed
  11. Raj S, Liu F. Engineering of RNase P ribozyme for gene-targeting applications. Gene. 2003;313:59-69 pubmed
    ..This review discusses the principle underlying M1GS-mediated gene inactivation and methodologies involved in effective M1GS construction, expression in vivo and emerging prospects of this technology for gene therapy. ..
  12. Ma D, Cook D, Alberti M, Pon N, Nikaido H, Hearst J. Molecular cloning and characterization of acrA and acrE genes of Escherichia coli. J Bacteriol. 1993;175:6299-313 pubmed
    ..coli polypeptides, EnvC and EnvD, respectively. Drug susceptibilities in one acrA mutant (N43) and one envCD mutant (PM61) have been determined and compared. Finally, the possible functions of these proteins are discussed. ..
  13. McCusker K, Klinman J. Modular behavior of tauD provides insight into the origin of specificity in alpha-ketoglutarate-dependent nonheme iron oxygenases. Proc Natl Acad Sci U S A. 2009;106:19791-5 pubmed publisher
  14. Woodgate R, Rajagopalan M, Lu C, Echols H. UmuC mutagenesis protein of Escherichia coli: purification and interaction with UmuD and UmuD'. Proc Natl Acad Sci U S A. 1989;86:7301-5 pubmed
    ..From these experiments and previous work, we infer that SOS mutagenesis depends on the action of the UmuC-UmuD' complex and probably RecA to rescue a stalled DNA polymerase III holoenzyme at the DNA lesion. ..
  15. Oyeyemi O, Sours K, Lee T, Kohen A, Resing K, Ahn N, et al. Comparative hydrogen-deuterium exchange for a mesophilic vs thermophilic dihydrofolate reductase at 25 °C: identification of a single active site region with enhanced flexibility in the mesophilic protein. Biochemistry. 2011;50:8251-60 pubmed publisher
    ..The region with increased flexibility in Ec-DHFR corresponds to one of two regions previously proposed to control the enthalpic barrier for hydride transfer in Bs-DHFR [Oyeyemi et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 10074]. ..
  16. Sandler S, Chackerian B, Li J, Clark A. Sequence and complementation analysis of recF genes from Escherichia coli, Salmonella typhimurium, Pseudomonas putida and Bacillus subtilis: evidence for an essential phosphate binding loop. Nucleic Acids Res. 1992;20:839-45 pubmed
    ..Lastly we made two chimeric recF genes by exchanging the amino terminal 48 amino acids of the S. typhimurium and E. coli recF genes. Both chimeras could complement E. coli chromosomal recF mutations. ..
  17. Nagano K, Nikaido H. Kinetic behavior of the major multidrug efflux pump AcrB of Escherichia coli. Proc Natl Acad Sci U S A. 2009;106:5854-8 pubmed publisher
    ..For the very hydrophilic cefazolin there was little sign of efflux. ..
  18. Greenfield D, McEvoy A, Shroff H, Crooks G, Wingreen N, Betzig E, et al. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol. 2009;7:e1000137 pubmed publisher
    ..coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport. ..
  19. Sandler S, Samra H, Clark A. Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC. Genetics. 1996;143:5-13 pubmed
    ..We conclude that priA's primosome-assembly activity is essential for DNA repair and recombination and that the dnaC suppressor mutations allow these processes to occur in the absence of priA. ..
  20. Khodursky A, Cozzarelli N. The mechanism of inhibition of topoisomerase IV by quinolone antibacterials. J Biol Chem. 1998;273:27668-77 pubmed
    ..We interpret our results in terms of distinct but complementary roles of Topo IV and gyrase in DNA replication. ..
  21. Rosenberg E, Ma D, Nikaido H. AcrD of Escherichia coli is an aminoglycoside efflux pump. J Bacteriol. 2000;182:1754-6 pubmed
  22. Zgurskaya H, Nikaido H. Cross-linked complex between oligomeric periplasmic lipoprotein AcrA and the inner-membrane-associated multidrug efflux pump AcrB from Escherichia coli. J Bacteriol. 2000;182:4264-7 pubmed
    ..We show that AcrA protein forms oligomers, most probably trimers. In this oligomeric form, AcrA interacts specifically with AcrB transporter independently of substrate and TolC. ..
  23. De Carlo S, Chen B, Hoover T, Kondrashkina E, Nogales E, Nixon B. The structural basis for regulated assembly and function of the transcriptional activator NtrC. Genes Dev. 2006;20:1485-95 pubmed
    ..Accompanying the hydrolysis cycle that is required for transcriptional activation, we observed major order-disorder changes in the GAFTGA loops involved in sigma(54) binding, as well as in the DNA-binding domains. ..
  24. Shin D, Brandsen J, Jancarik J, Yokota H, Kim R, Kim S. Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome. J Mol Biol. 2004;341:227-39 pubmed publisher
    ..The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome...
  25. Dean D, Hor L, Shuman H, Nikaido H. Interaction between maltose-binding protein and the membrane-associated maltose transporter complex in Escherichia coli. Mol Microbiol. 1992;6:2033-40 pubmed
    ..We found that the mutant FGK2 complex, containing MalG511, had a much higher apparent affinity towards the wild-type MBP than did the wild-type FGK2 complex.(ABSTRACT TRUNCATED AT 250 WORDS)..
  26. Yeh J, Biemann H, Pandit J, Koshland D, Kim S. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem. 1993;268:9787-92 pubmed
    ..4) The nature and magnitude of the aspartate-induced conformational changes in the non-cross-linked wild-type structures are very similar to those of the cross-linked structures. ..
  27. Christman M, Storz G, Ames B. OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. Proc Natl Acad Sci U S A. 1989;86:3484-8 pubmed
    ..G to T.A transition) that changes alanine to valine at amino acid position 234 of OxyR. ..
  28. Eliot A, Sandmark J, Schneider G, Kirsch J. The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation. Biochemistry. 2002;41:12582-9 pubmed
    ..These results indicate that the conserved arginine residue is not required for binding the alpha-amino acid SAM, but it is important for recognition of DAPA. ..
  29. Kim K, Pelton J, Inwood W, Andersen U, Kustu S, Wemmer D. The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J Bacteriol. 2010;192:4089-102 pubmed publisher
    ..The function of RutE appears to be the same as that of YdfG, which reduces malonic semialdehyde to 3-hydroxypropionic acid. RutG appears to be a uracil transporter...
  30. Soupene E, King N, Lee H, Kustu S. Aquaporin Z of Escherichia coli: reassessment of its regulation and physiological role. J Bacteriol. 2002;184:4304-7 pubmed
    ..Expression of the aqpZ-lac fusion was not affected by up- or downshifts in osmolality. Disruption of aqpZ had no detectable adverse effects. ..
  31. Hardy C, Cozzarelli N. A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol. 2005;57:1636-52 pubmed
    ..We suggest that at least H-NS, Fis and perhaps TktA assist directly in the supercoiling of domains by forming topological barriers on the E. coli chromosome. ..
  32. Thanassi D, Cheng L, Nikaido H. Active efflux of bile salts by Escherichia coli. J Bacteriol. 1997;179:2512-8 pubmed
    ..It followed saturation kinetics with Vmax and Km values in the neighborhood of 0.3 nmol min(-1) mg of protein(-1) and 50 microM, respectively. ..
  33. Deu E, Dhoot J, Kirsch J. The partially folded homodimeric intermediate of Escherichia coli aspartate aminotransferase contains a "molten interface" structure. Biochemistry. 2009;48:433-41 pubmed publisher
    ..Nuclei of tertiary structure, which are not involved in native intersubunit contacts, likely provide a scaffold for the unstructured interface of D*. Such a scaffold would account for the cooperative unfolding of the intermediate. ..
  34. Joo D, Ng N, Calendar R. A sigma32 mutant with a single amino acid change in the highly conserved region 2.2 exhibits reduced core RNA polymerase affinity. Proc Natl Acad Sci U S A. 1997;94:4907-12 pubmed
    ..Based on these results, we conclude that at least one specific amino acid in region 2.2 is involved in core RNAP interaction. ..
  35. Ratcliff K, Corn J, Marqusee S. Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic Chlorobium tepidum: comparison with thermophilic and mesophilic homologues. Biochemistry. 2009;48:5890-8 pubmed publisher
    ..It should now be possible to design RNases H that display the desired thermophilic or mesophilic properties, as defined by their DeltaC(p) values, and therefore fine-tune the energy landscape in a predictable fashion...
  36. Amarasinghe A, Calin Jageman I, Harmouch A, Sun W, Nicholson A. Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage. Methods Enzymol. 2001;342:143-58 pubmed
  37. Mahajan S, Chu C, Willis D, Templin A, Clark A. Physical analysis of spontaneous and mutagen-induced mutants of Escherichia coli K-12 expressing DNA exonuclease VIII activity. Genetics. 1990;125:261-73 pubmed
    ..These are presumed point mutations. Three seem to produce additional restriction nucleotide fragments complementary to lambda rev. The possible nature of these sbc mutations is discussed. ..
  38. Trinh C, Li J, Blanch H, Clark D. Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl Environ Microbiol. 2011;77:4894-904 pubmed publisher
    ..The glycolytic flux can be controlled to regulate the ratio of isobutanol to ethanol production...
  39. Yeung N, Gold B, Liu N, Prathapam R, Sterling H, Willams E, et al. The E. coli monothiol glutaredoxin GrxD forms homodimeric and heterodimeric FeS cluster containing complexes. Biochemistry. 2011;50:8957-69 pubmed publisher
  40. Vila Sanjurjo A, Schuwirth B, Hau C, Cate J. Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol. 2004;11:1054-9 pubmed
    ..The mechanism used by protein Y to reduce translation initiation during stress and quickly release ribosomes for renewed translation initiation may therefore occur widely in nature. ..
  41. Shin D, Yokota H, Kim R, Kim S. Crystal structure of a conserved hypothetical protein from Escherichia coli. J Struct Funct Genomics. 2002;2:53-66 pubmed
    ..There are several highly conserved residues including two possible functional cysteines in the putative active site. The possible molecular function of the protein is discussed. ..
  42. Chu C, Templin A, Clark A. Suppression of a frameshift mutation in the recE gene of Escherichia coli K-12 occurs by gene fusion. J Bacteriol. 1989;171:2101-9 pubmed
    ..These data indicate that about 70% of the N-terminal half of recE is not required to encode a hypothesized protein domain with exonuclease VIII activity. ..
  43. Rubin S, Lee S, Ruiz E, Pines A, Wemmer D. Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy. J Mol Biol. 2002;322:425-40 pubmed
    ..Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered...
  44. Imperial J, Hadi M, Amy N. Molybdate binding by ModA, the periplasmic component of the Escherichia coli mod molybdate transport system. Biochim Biophys Acta. 1998;1370:337-46 pubmed
    ..The affinity of ModA for molybdate was also determined in vivo and found to be similar to that determined in vitro...
  45. Rothman S, Voorhies M, Kirsch J. Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase. Protein Sci. 2004;13:763-72 pubmed
    ..Both residues are in close proximity to Arg292 and the mutations may function to modulate the arginine switch mechanism responsible for dual substrate recognition in TATases and HEX. ..
  46. Kim J, Linn S. The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites. Nucleic Acids Res. 1988;16:1135-41 pubmed
    ..Whereas these enzymes use a lyase-like rather than a hydrolytic mechanism, they nonetheless catalyze phosphodiester bond cleavage. We suggest that the term endonuclease can be properly applied to them. ..
  47. Voges D, Jap B. Recombinant expression, purification and characterization of Kch, a putative Escherichia coli potassium channel protein. FEBS Lett. 1998;429:104-8 pubmed
    ..CD spectroscopy of the purified protein indicates a significant alpha-helical content that is preserved upon addition of SDS. ..
  48. Aires J, Nikaido H. Aminoglycosides are captured from both periplasm and cytoplasm by the AcrD multidrug efflux transporter of Escherichia coli. J Bacteriol. 2005;187:1923-9 pubmed
    ..This result suggested that AcrD can also capture aminoglycosides from the periplasm to extrude them into the medium in intact cells, acting as a "periplasmic vacuum cleaner." ..
  49. Elkins C, Nikaido H. Substrate specificity of the RND-type multidrug efflux pumps AcrB and AcrD of Escherichia coli is determined predominantly by two large periplasmic loops. J Bacteriol. 2002;184:6490-8 pubmed
  50. Boyarskiy S, Davis López S, Kong N, Tullman Ercek D. Transcriptional feedback regulation of efflux protein expression for increased tolerance to and production of n-butanol. Metab Eng. 2016;33:130-137 pubmed publisher
    ..Furthermore, the system is responsive to stress from toxic overexpression of other membrane-associated proteins. Our results suggest a use for feedback regulation networks in membrane protein expression. ..
  51. Avila Sakar A, Misaghi S, Wilson Kubalek E, Downing K, Zgurskaya H, Nikaido H, et al. Lipid-layer crystallization and preliminary three-dimensional structural analysis of AcrA, the periplasmic component of a bacterial multidrug efflux pump. J Struct Biol. 2001;136:81-8 pubmed
    ..On one side the density has a tubular shape, with a thickness of about 25 A, while on the other side the densities of the upper and lower parts of the pseudo-helical path are fused into a shield. ..
  52. Juminaga D, Baidoo E, Redding Johanson A, Batth T, Burd H, Mukhopadhyay A, et al. Modular engineering of L-tyrosine production in Escherichia coli. Appl Environ Microbiol. 2012;78:89-98 pubmed publisher
    ..This work demonstrates the utility of targeted proteomics and metabolite profiling in pathway construction and optimization, which should be applicable to other metabolic pathways. ..
  53. Soupene E, van Heeswijk W, Plumbridge J, Stewart V, Bertenthal D, Lee H, et al. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol. 2003;185:5611-26 pubmed
    ..The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655. ..
  54. Yu E, Aires J, McDermott G, Nikaido H. A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study. J Bacteriol. 2005;187:6804-15 pubmed
    ..The MIC data were also confirmed by assays of ethidium influx rates in intact cells, and our results suggest that the periplasmic binding site plays a role in the physiological process of drug efflux. ..
  55. Janda J, Abbott S, Khashe S, Probert W. Phenotypic and genotypic properties of the genus Hafnia. J Med Microbiol. 2002;51:575-80 pubmed
    ..The results indicate that the genus Hafnia is heterogeneous and there do not appear to be any laboratory data available specifically linking these organisms to gastro-enteritis...
  56. Degnan P, Barry N, Mok K, Taga M, Goodman A. Human gut microbes use multiple transporters to distinguish vitamin B?? analogs and compete in the gut. Cell Host Microbe. 2014;15:47-57 pubmed publisher
  57. Wright A, Liu J, Knott G, Doxzen K, Nogales E, Doudna J. Structures of the CRISPR genome integration complex. Science. 2017;357:1113-1118 pubmed publisher
    ..These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity. ..
  58. Ha S, Pereira J, Jeong J, Huh J, Kim S. Purification of human transcription factors Nanog and Sox2, each in complex with Skp, an Escherichia coli periplasmic chaperone. Protein Expr Purif. 2009;67:164-8 pubmed publisher
    ..Purified Skp complexes of Nanog and Sox maintained DNA-binding activity toward its cognate DNA sequence. A similar approach may be applicable for some other mammalian proteins that are unstable or difficult to over-express in E. coli. ..
  59. Nikaido H, Takatsuka Y. Mechanisms of RND multidrug efflux pumps. Biochim Biophys Acta. 2009;1794:769-81 pubmed publisher
  60. Corn J, Pease P, Hura G, Berger J. Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol Cell. 2005;20:391-401 pubmed publisher
    ..Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis...
  61. Kim H, Nagore D, Nikaido H. Multidrug efflux pump MdtBC of Escherichia coli is active only as a B2C heterotrimer. J Bacteriol. 2010;192:1377-86 pubmed publisher
  62. Guliaev A, Singer B, Hang B. Chloroethylnitrosourea-derived ethano cytosine and adenine adducts are substrates for Escherichia coli glycosylases excising analogous etheno adducts. DNA Repair (Amst). 2004;3:1311-21 pubmed
    ..However, also as shown by MD, the stacking interaction between the EC base and Phe 30 in the Mug active site is reduced as compared to the epsilonC base, which could account for the lower EC activity observed in this study. ..