Experts and Doctors on escherichia coli in Piscataway, New Jersey, United States


Locale: Piscataway, New Jersey, United States
Topic: escherichia coli

Top Publications

  1. Yu F, Jen Y, Takeuchi E, Inouye M, Nakayama H, Tagaya M, et al. Alpha-glucan phosphorylase from Escherichia coli. Cloning of the gene, and purification and characterization of the protein. J Biol Chem. 1988;263:13706-11 pubmed
    ..The amino acid sequence deduced was compared with those of alpha-glucan phosphorylases from other sources. ..
  2. Li C, Tao Y, Simon L. Expression of different-size transcripts from the clpP-clpX operon of Escherichia coli during carbon deprivation. J Bacteriol. 2000;182:6630-7 pubmed
    ..coli is in log phase. These and other data are consistent with the hypothesis that the shorter transcript results from premature transcription termination during production of the longer transcript. ..
  3. Kim D, Patel S. The kinetic pathway of RNA binding to the Escherichia coli transcription termination factor Rho. J Biol Chem. 2001;276:13902-10 pubmed
    ..These studies reveal common features used by hexameric helicases to bind nucleic acids in an efficient and specific manner. ..
  4. Forst S, Delgado J, Inouye M. Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli. Proc Natl Acad Sci U S A. 1989;86:6052-6 pubmed
    ..Based on these results we propose a model in which the phosphorylated state of OmpR modulates the expression of the ompF and ompC genes. ..
  5. Harlocker S, Bergstrom L, Inouye M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli. J Biol Chem. 1995;270:26849-56 pubmed
    ..Activation and repression of ompF expression are thus regulated by a total of eight OmpR molecules, including two molecules that bind to a distal site (-380 to -361). ..
  6. Nedea E, Markov D, Naryshkina T, Severinov K. Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature. J Bacteriol. 1999;181:2663-5 pubmed
    ..Thus, distinct, predominantly conserved beta' residues participate in interactions holding RNA polymerase together. ..
  7. Tzeng S, Kalodimos C. Allosteric inhibition through suppression of transient conformational states. Nat Chem Biol. 2013;9:462-5 pubmed publisher
    ..Structure information on such important intermediates can ultimately result in more efficient design of allosteric inhibitors. ..
  8. Ouimet M, Griffin J, Carbone Howell A, Wu W, Stebbins N, Di R, et al. Biodegradable ferulic acid-containing poly(anhydride-ester): degradation products with controlled release and sustained antioxidant activity. Biomacromolecules. 2013;14:854-61 pubmed publisher
    ..This renders the polymer a potential candidate for use as a controlled release system for skin care formulations. ..
  9. Gao R, Godfrey K, Sufian M, Stock A. Counterbalancing Regulation in Response Memory of a Positively Autoregulated Two-Component System. J Bacteriol. 2017;199: pubmed publisher
    ..Modeling allows prediction of response behavior in different scenarios and demonstrates both the robustness of the system output and its sensitivity to historical parameters such as timing and levels of exposure to stimuli. ..

More Information


  1. Yu Z, Visse R, Inouye M, Nagase H, Brodsky B. Defining requirements for collagenase cleavage in collagen type III using a bacterial collagen system. J Biol Chem. 2012;287:22988-97 pubmed publisher
    ..The recombinant bacterial-human collagen system characterized here is a good model to investigate the specificity and mechanism of action of collagenases. ..
  2. Crowther R, Georgiadis M. The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Proteins. 2005;61:680-4 pubmed
  3. Lara Gonzalez S, Birktoft J, Lawson C. Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain. Acta Crystallogr D Biol Crystallogr. 2010;66:806-12 pubmed publisher
    ..The new coordinates will facilitate the improved modeling of alphaCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction. ..
  4. Lin C, Shen B, Xu Z, K llner T, Degenhardt J, Dooner H. Characterization of the monoterpene synthase gene tps26, the ortholog of a gene induced by insect herbivory in maize. Plant Physiol. 2008;146:940-51 pubmed publisher
    ..A gene closely related to stc1/tps26 is found in the sorghum (Sorghum spp.) genome at a location that is not orthologous with stc1. The possible origin of stc1-like genes is discussed...
  5. Inostroza J, Mermelstein F, Ha I, Lane W, Reinberg D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell. 1992;70:477-89 pubmed
    ..Dr1 is phosphorylated in vivo and phosphorylation of Dr1 affected its interaction with TBP. Our results suggest a regulatory role for Dr1 in repression of transcription mediated via phosphorylation. ..
  6. Hwang J, Inouye M. Interaction of an essential Escherichia coli GTPase, Der, with the 50S ribosome via the KH-like domain. J Bacteriol. 2010;192:2277-83 pubmed publisher
    ..We also identified a region of Der that is critical for its specific interaction with 50S subunit. ..
  7. Dutta R, Inouye M. Reverse phosphotransfer from OmpR to EnvZ in a kinase-/phosphatase+ mutant of EnvZ (EnvZ.N347D), a bifunctional signal transducer of Escherichia coli. J Biol Chem. 1996;271:1424-9 pubmed
    ..N347D mutant involves a reversal of the phosphotransfer reaction from EnvZ to OmpR using the identical His243 residue. ..
  8. Lee J, Cook J, Yang Z, Mirochnitchenko O, Gunderson S, Felix A, et al. PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. J Biol Chem. 2005;280:3656-64 pubmed
    ..The data demonstrate that PRMT7 (like PRMT5) is a Type II methyltransferase capable of producing SDMA modifications in proteins. ..
  9. Bao X, Beatty W, Fan H. Exploration of chlamydial type III secretion system reconstitution in Escherichia coli. PLoS ONE. 2012;7:e50833 pubmed publisher
  10. Seol W, Shatkin A. Site-directed mutants of Escherichia coli alpha-ketoglutarate permease (KgtP). Biochemistry. 1992;31:3550-4 pubmed
    ..1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2969], a KgtP truncation mutant missing the last putative membrane-spanning region was relatively stable and also retained 10-50% of the wild-type level of alpha-ketoglutarate transport activity. ..
  11. Suzuki M, Mao L, Inouye M. Single protein production (SPP) system in Escherichia coli. Nat Protoc. 2007;2:1802-10 pubmed
    ..The procedure can be completed in 7 d after cloning of an ACA-less target gene into the expression system. ..
  12. Inouye M, Phadtare S. Cold shock response and adaptation at near-freezing temperature in microorganisms. Sci STKE. 2004;2004:pe26 pubmed
    ..This emphasizes the fact that different groups of microorganisms exhibit distinct types of cold shock responses. ..
  13. Zhang Y, Inouye M. RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation. Mol Microbiol. 2011;79:1418-29 pubmed publisher
    ..Here we demonstrate that RatA is a new E. coli toxin, which effectively blocks the translation initiation step. We propose that this toxin of previously unknown function be renamed as RatA (Ribosome association toxin A). ..
  14. Gennity J, Kim H, Inouye M. Structural determinants in addition to the amino-terminal sorting sequence influence membrane localization of Escherichia coli lipoproteins. J Bacteriol. 1992;174:2095-101 pubmed
    ..Therefore, structural determinants in addition to the amino-terminal sorting sequence influence the membrane localization of lipoproteins. ..
  15. Ishida Y, Park J, Mao L, Yamaguchi Y, Inouye M. Replacement of all arginine residues with canavanine in MazF-bs mRNA interferase changes its specificity. J Biol Chem. 2013;288:7564-71 pubmed publisher
    ..Mass spectrometry analysis confirmed that all Arg residues were replaced with Can. The present system offers a novel approach to create new functional proteins by replacing a specific amino acid in a protein with its analogues. ..
  16. Shimamoto T, Inouye M. Mutational analysis of Era, an essential GTP-binding protein of Escherichia coli. FEMS Microbiol Lett. 1996;136:57-62 pubmed
    ..However, the Km values for GTPase activity increased 5- and 12-fold for dE and T42A/T43A mutants, respectively. These results indicate that both the GTP-binding and GTPase activities are important for the Era function. ..
  17. Mart nez Hackert E, Stock A. The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor. Structure. 1997;5:109-24 pubmed
    ..The structure of OmpRc could be useful in helping to define the positioning of the alpha subunit of RNA polymerase in relation to transcriptional activators that are bound to DNA...
  18. Semenova E, Jore M, Datsenko K, Semenova A, Westra E, Wanner B, et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci U S A. 2011;108:10098-103 pubmed publisher
    ..The relaxed specificity of the CRISPR/Cas system limits escape possibilities and allows a single crRNA to effectively target numerous related viruses. ..
  19. Hu L, Yu C, Jiang Y, Han J, Li Z, Browne P, et al. Nitroaryl phosphoramides as novel prodrugs for E. coli nitroreductase activation in enzyme prodrug therapy. J Med Chem. 2003;46:4818-21 pubmed
    ..The superior activity was attributed to its better substrate activity (k(cat)/K(m) 19x better than 1) and/or excellent cytotoxicity of phosphoramide mustard released. ..
  20. Zhang Y, Yamaguchi Y, Inouye M. Characterization of YafO, an Escherichia coli toxin. J Biol Chem. 2009;284:25522-31 pubmed publisher
    ..These results demonstrate that YafO is a ribosome-dependent mRNA interferase inhibiting protein synthesis. ..
  21. Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione G. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci U S A. 2004;101:4041-6 pubmed
    ..Apart from the hairpin 35, parts of hairpins 33 and 34 also interact with the RlmA(I) dimer. ..
  22. Phadtare S, Severinov K. Extended -10 motif is critical for activity of the cspA promoter but does not contribute to low-temperature transcription. J Bacteriol. 2005;187:6584-9 pubmed
    ..In fact, transcription from the wild-type cspA promoter is cold sensitive in vitro and in vivo. Thus, transcription appears to play little or no role in low-temperature induction of cspA expression. ..
  23. Zhang Y, Zhang J, Hoeflich K, Ikura M, Qing G, Inouye M. MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell. 2003;12:913-23 pubmed
    ..The role of such endoribonucleases may have broad implication in cell physiology under various growth conditions...
  24. Inouye M. The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology. J Cell Physiol. 2006;209:670-6 pubmed
    ..The discovery of a novel way to interfere with mRNA function by mRNA interferases opens a wide variety of avenues in basic as well as applied and clinical sciences. ..
  25. Inoue K, Chen J, Tan Q, Inouye M. Era and RbfA have overlapping function in ribosome biogenesis in Escherichia coli. J Mol Microbiol Biotechnol. 2006;11:41-52 pubmed
    ..We propose that Era and RbfA have an overlapping function that is essential for ribosome biogenesis, and that RbfA becomes dispensable only at high temperatures because Era can complement its function only at higher temperatures. ..
  26. Lu Q, Inouye M. The gene for 16S rRNA methyltransferase (ksgA) functions as a multicopy suppressor for a cold-sensitive mutant of era, an essential RAS-like GTP-binding protein in Escherichia coli. J Bacteriol. 1998;180:5243-6 pubmed
    ..This is the first demonstration of suppression of impaired function of Era by overproduction of a functional enzyme. A possible mechanism of the suppression of the Era cold-sensitive phenotype by KsgA overproduction is discussed. ..
  27. Bae W, Jones P, Inouye M. CspA, the major cold shock protein of Escherichia coli, negatively regulates its own gene expression. J Bacteriol. 1997;179:7081-8 pubmed
    ..The mRNA stabilization in the deltacspA strain was observed for other mRNAs, supporting the notion that CspA functions as an mRNA chaperone to destabilize secondary structures in mRNAs. ..
  28. Eyre Walker A. The distance between Escherichia coli genes is related to gene expression levels. J Bacteriol. 1995;177:5368-9 pubmed
    ..It is suggested that this could be a strategy to avoid interference between ribosomes translating two different genes. ..
  29. Lee S, Xie A, Jiang W, Etchegaray J, Jones P, Inouye M. Family of the major cold-shock protein, CspA (CS7.4), of Escherichia coli, whose members show a high sequence similarity with the eukaryotic Y-box binding proteins. Mol Microbiol. 1994;11:833-9 pubmed
    ..A similar cold-shock induction to cspA was observed for cspB but not cspC and cspD. These results indicate that E. coli has a family of the cspA gene, some of which are induced by cold shock. ..
  30. Etchegaray J, Jones P, Inouye M. Differential thermoregulation of two highly homologous cold-shock genes, cspA and cspB, of Escherichia coli. Genes Cells. 1996;1:171-8 pubmed
    ..These features are considered to contribute to the nature of the thermostats for cspA and cspB. ..
  31. Mekler V, Minakhin L, Kuznedelov K, Mukhamedyarov D, Severinov K. RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes. Nucleic Acids Res. 2012;40:11352-62 pubmed publisher
    ..We suggest that the relative weakness of Taq RNAP interactions with DNA downstream of the transcription start point is the major reason of low stability and temperature sensitivity of promoter complexes formed by this enzyme. ..
  32. Lin Y, Sharer J, March P. GTPase-dependent signaling in bacteria: characterization of a membrane-binding site for era in Escherichia coli. J Bacteriol. 1994;176:44-9 pubmed
    ..These data provide evidence that Era may be involved in a GTPase-receptor-coupled membrane-signaling pathway that is essential for growth in E. coli. ..
  33. Damerau K, St John A. Role of Clp protease subunits in degradation of carbon starvation proteins in Escherichia coli. J Bacteriol. 1993;175:53-63 pubmed
    ..The clpP mutants had reduced rates of degradation of certain starvation proteins in the membrane fraction when a carbon source was resupplied to the starved cells. ..
  34. Stock A. Energy sensors for aerotaxis in Escherichia coli: something old, something new. Proc Natl Acad Sci U S A. 1997;94:10487-9 pubmed
  35. Kostyukova A, Hitchcock Degregori S. Effect of the structure of the N terminus of tropomyosin on tropomodulin function. J Biol Chem. 2004;279:5066-71 pubmed
    ..An even shorter fragment, Tmod1-(1-48), bound tropomyosin but did not influence actin filament elongation. Tropomyosin-Tmod may function to locally regulate cytoskeletal dynamics in cells by stabilizing actin filaments. ..
  36. Seol W, Shatkin A. Escherichia coli alpha-ketoglutarate permease is a constitutively expressed proton symporter. J Biol Chem. 1992;267:6409-13 pubmed
    ..These results indicate that KgtP is an alpha-ketoglutarate-proton symporter. ..
  37. Lerner C, Inouye M. Pleiotropic changes resulting from depletion of Era, an essential GTP-binding protein in Escherichia coli. Mol Microbiol. 1991;5:951-7 pubmed
    ..Thus, in addition to inhibition of cell growth and viability, loss of Era function results in pleiotropic changes including abnormal adaptation to thermal stress. ..
  38. Seol W, Shatkin A. Membrane topology model of Escherichia coli alpha-ketoglutarate permease by phoA fusion analysis. J Bacteriol. 1993;175:565-7 pubmed
    ..Comparisons of the phosphatase activity levels and the locations of the KgtP-PhoA junctions are consistent with the predicted membrane topology model of KgtP...
  39. Montelione G. Structural genomics: an approach to the protein folding problem. Proc Natl Acad Sci U S A. 2001;98:13488-9 pubmed
  40. Saxl R, Anand G, Stock A. Synthesis and biochemical characterization of a phosphorylated analogue of the response regulator CheB. Biochemistry. 2001;40:12896-903 pubmed
    ..Thus, D56C/C207S/C309S CheB-SPO(3) is a stable analogue that may be useful for characterization of the active form of CheB. ..
  41. Yamanaka K, Inouye M. Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli. J Bacteriol. 1997;179:5126-30 pubmed
    ..Moreover, the expression of cspD is inversely dependent on growth rates and induced upon glucose starvation. Using a (p)ppGpp-depleted strain, we found that (p)ppGpp is one of the positive factors for the regulation of cspD expression. ..
  42. Phadtare S, Zhu L, Uemori T, Mukai H, Kato I, Inouye M. Applications of nucleic acid chaperone activity of CspA and its homologues. J Mol Microbiol Biotechnol. 2009;17:110-7 pubmed publisher
    ..The low substrate specificity of Csps together with their compatibility with various enzymes and their stability and activity over a broad temperature range makes them ideal candidates to be used for a variety of processes. ..
  43. Minakhin L, Nechaev S, Campbell E, Severinov K. Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol. 2001;183:71-6 pubmed publisher
    ..Our results, together with the high-resolution structural information, should now allow a rational analysis of transcription mechanism by mutation...
  44. Phadtare S, Tadigotla V, Shin W, Sengupta A, Severinov K. Analysis of Escherichia coli global gene expression profiles in response to overexpression and deletion of CspC and CspE. J Bacteriol. 2006;188:2521-7 pubmed
    ..Bioinformatic analysis of the latter group reveals that many of those genes contain promoter-proximal sequences that can block transcript elongation and may be targeted by the nucleic acid melting function of CspE. ..
  45. Cruz J, Rothenbacher F, Maehigashi T, Lane W, Dunham C, Woychik N. Doc toxin is a kinase that inactivates elongation factor Tu. J Biol Chem. 2014;289:7788-98 pubmed publisher
    ..Moreover, we have established that all characterized Fic domain proteins, even those that phosphorylate, target pivotal GTPases for inactivation through a post-translational modification at a single functionally critical acceptor site. ..
  46. Chen G, Axley M, Hacia J, Inouye M. Overproduction of a selenocysteine-containing polypeptide in Escherichia coli: the fdhF gene product. Mol Microbiol. 1992;6:781-5 pubmed
    ..The product was specifically labelled with 75Se, proving that it consisted of a selenoprotein. The product was purified to homogeneity and shown to exhibit the catalytic properties characteristic of formate dehydrogenase H. ..
  47. Ryazanova L, Dorovkov M, Ansari A, Ryazanov A. Characterization of the protein kinase activity of TRPM7/ChaK1, a protein kinase fused to the transient receptor potential ion channel. J Biol Chem. 2004;279:3708-16 pubmed
    ..Considering intracellular ion concentrations, our results suggest that, among divalent metal ions, only Mg(2+) can directly modulate TRPM7/ChaK1 kinase activity in vivo. ..
  48. Gollop N, March P. A GTP-binding protein (Era) has an essential role in growth rate and cell cycle control in Escherichia coli. J Bacteriol. 1991;173:2265-70 pubmed
    ..Thus, the role of GTP-binding proteins as important regulators of cell growth and division may be ubiquitous in nature. ..
  49. Yamashiro S, Yamakita Y, Yoshida K, Takiguchi K, Matsumura F. Characterization of the COOH terminus of non-muscle caldesmon mutants lacking mitosis-specific phosphorylation sites. J Biol Chem. 1995;270:4023-30 pubmed
    ..This mutant should thus be useful to explore the functions of the mitosis-specific phosphorylation of caldesmon. ..
  50. Jiang W, Hou Y, Inouye M. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem. 1997;272:196-202 pubmed
    ..Such a function may be crucial for efficient translation of mRNAs at low temperatures and may also have an effect on transcription. ..
  51. Zakharova N, Bass I, Arsenieva E, Nikiforov V, Severinov K. Mutations in and monoclonal antibody binding to evolutionary hypervariable region of Escherichia coli RNA polymerase beta' subunit inhibit transcript cleavage and transcript elongation. J Biol Chem. 1998;273:24912-20 pubmed
    ..We propose that mutations in and antibody binding to the hypervariable, functionally dispensable region of beta' inhibit transcript cleavage and elongation by distorting the flanking conserved segment G in the active center. ..
  52. Schiltz J, Kesari K, Ashar H, Chada K. Hmgi-c-independent Activation of MuRantes in Vivo. Cell Growth Differ. 2002;13:39-45 pubmed
    ..Each of these systems clearly demonstrates that Hmgi-c is not required for the activation of MuRantes expression. ..
  53. Phadtare S, Tyagi S, Inouye M, Severinov K. Three amino acids in Escherichia coli CspE surface-exposed aromatic patch are critical for nucleic acid melting activity leading to transcription antitermination and cold acclimation of cells. J Biol Chem. 2002;277:46706-11 pubmed
  54. Xia B, Ke H, Shinde U, Inouye M. The role of RbfA in 16S rRNA processing and cell growth at low temperature in Escherichia coli. J Mol Biol. 2003;332:575-84 pubmed
  55. Minakhin L, Severinov K. On the role of the Escherichia coli RNA polymerase sigma 70 region 4.2 and alpha-subunit C-terminal domains in promoter complex formation on the extended -10 galP1 promoter. J Biol Chem. 2003;278:29710-8 pubmed
    ..2 but not alpha CTD was required for open promoter complex formation on galP1 derivatives with extended -10 motif. We propose a model involving sigma 70 region 4.2 interaction with the beta flap domain that explains these observations. ..
  56. Phadtare S, Inouye M, Severinov K. The nucleic acid melting activity of Escherichia coli CspE is critical for transcription antitermination and cold acclimation of cells. J Biol Chem. 2002;277:7239-45 pubmed
    ..Thus, the nucleic acid-melting activity of Csp is critical for its prototypical function of supporting low temperature survival of the cell. ..
  57. Chen L, Laskin J, Gordon M, Laskin D. Regulation of TREM expression in hepatic macrophages and endothelial cells during acute endotoxemia. Exp Mol Pathol. 2008;84:145-55 pubmed publisher
    ..These results suggest that TREM proteins are important in the inflammatory response of hepatic macrophages and endothelial cells to acute endotoxemia. ..
  58. Sood P, Lerner C, Shimamoto T, Lu Q, Inouye M. Characterization of the autophosphorylation of Era, an essential Escherichia coli GTPase. Mol Microbiol. 1994;12:201-8 pubmed
    ..Therefore, Era autophosphorylation is likely to play an important physiological role in the cell.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  59. Pillutla R, Ahnn J, Inouye M. Deletion of the putative effector region of Era, an essential GTP-binding protein in Escherichia coli, causes a dominant-negative phenotype. FEMS Microbiol Lett. 1996;143:47-55 pubmed
    ..Furthermore, it appears that some possible functions of Era include regulation of the TCA cycle and response to carbon starvation. ..
  60. Chen H, Tang H, Ebright R. Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription. Mol Cell. 2003;11:1621-33 pubmed
  61. Yamaguchi K, Inouye M. Lipoprotein 28, an inner membrane protein of Escherichia coli encoded by nlpA, is not essential for growth. J Bacteriol. 1988;170:3747-9 pubmed
    ..No discernible differences between the wild type and the deletion strain were observed in terms of cell morphology and sensitivity to various chemicals, except for kanamycin. ..
  62. Jiang W, Fang L, Inouye M. Complete growth inhibition of Escherichia coli by ribosome trapping with truncated cspA mRNA at low temperature. Genes Cells. 1996;1:965-76 pubmed
    ..LACE may provide a novel approach to the development of a new antibiotic. ..
  63. Qing G, Xia B, Inouye M. Enhancement of translation initiation by A/T-rich sequences downstream of the initiation codon in Escherichia coli. J Mol Microbiol Biotechnol. 2003;6:133-44 pubmed
    ..Collectively, the present data demonstrate that A/T richness of the region following the initiation codon plays a significant role in E. coli gene expression. ..
  64. Phadtare S, Kato I, Inouye M. DNA microarray analysis of the expression profile of Escherichia coli in response to treatment with 4,5-dihydroxy-2-cyclopenten-1-one. J Bacteriol. 2002;184:6725-9 pubmed
    ..Genes belonging to the regulon involved in synthesis of Cys are upregulated. In addition, rpoS and RpoS-regulated genes responding to various stresses and a number of genes responding to oxidative stress are upregulated. ..
  65. Phadtare S, Inouye M. Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. J Bacteriol. 2004;186:7007-14 pubmed
    ..Relevance of these findings with respect to the known RNA chaperone function of CspA homologues is discussed. ..
  66. Egger L, Inouye M. Purification and characterization of the periplasmic domain of EnvZ osmosensor in Escherichia coli. Biochem Biophys Res Commun. 1997;231:68-72 pubmed
    ..The periplasmic domain was released by factor Xa and purified to homogeneity. From circular dichroism analysis, the periplasmic domain was estimated to consist of 35% alpha-helices and 16% beta-sheets. ..
  67. Mitta M, Fang L, Inouye M. Deletion analysis of cspA of Escherichia coli: requirement of the AT-rich UP element for cspA transcription and the downstream box in the coding region for its cold shock induction. Mol Microbiol. 1997;26:321-35 pubmed
    ..It is proposed that DB in cold shock mRNAs allows the formation of a stable initiation complex at low temperature in the absence of the cold shock ribosomal factors. ..
  68. Hwang J, Inouye M. A bacterial GAP-like protein, YihI, regulating the GTPase of Der, an essential GTP-binding protein in Escherichia coli. J Mol Biol. 2010;399:759-72 pubmed publisher
    ..We propose that YihI is a GAP (GTPase-activating protein)-like protein that modulates Der function to negatively regulate cell growth at the beginning of exponential growth. ..
  69. Phadtare S, Inouye M. Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli. Mol Microbiol. 1999;33:1004-14 pubmed
    ..This motif is the putative CspE-mediated transcription pause recognition site in a 5'-untranslated region of the cspA mRNA. ..
  70. Kuo T, Pike D, Beizaeipour Z, Williams J. Sleep triggered by an immune response in Drosophila is regulated by the circadian clock and requires the NFkappaB Relish. BMC Neurosci. 2010;11:17 pubmed publisher
    ..Behavioral features of sleep as well as the innate immune response signaling pathways are well characterized in flies and are highly conserved in mammals...
  71. Phadtare S, Severinov K. Comparative analysis of changes in gene expression due to RNA melting activities of translation initiation factor IF1 and a cold shock protein of the CspA family. Genes Cells. 2009;14:1227-39 pubmed publisher
    ..Our results suggest that Csp proteins and IF1 have different sets of target genes as they may be suppressing the function of different types of transcription termination elements in specific genes. ..
  72. Bae W, Xia B, Inouye M, Severinov K. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc Natl Acad Sci U S A. 2000;97:7784-9 pubmed
    ..We propose that the cold-shock induction of nusA, infB, rbfA, and pnp occurs through transcription antitermination, which is mediated by CspA and other cold shock-induced Csp proteins. ..
  73. Zhang J, Inouye M. MazG, a nucleoside triphosphate pyrophosphohydrolase, interacts with Era, an essential GTPase in Escherichia coli. J Bacteriol. 2002;184:5323-9 pubmed
    ..Unlike mutT, a gene for another conserved nucleotide triphosphate pyrophosphohydrolase that functions as a mutator gene, the mazG deletion did not result in a mutator phenotype in E. coli...
  74. Jiang W, Jones P, Inouye M. Chloramphenicol induces the transcription of the major cold shock gene of Escherichia coli, cspA. J Bacteriol. 1993;175:5824-8 pubmed
    ..Measurement of the half-life revealed that the cspA mRNA induced by chloramphenicol was more stable than that induced by cold shock. ..
  75. Naryshkina T, Mustaev A, Darst S, Severinov K. The beta ' subunit of Escherichia coli RNA polymerase is not required for interaction with initiating nucleotide but is necessary for interaction with rifampicin. J Biol Chem. 2001;276:13308-13 pubmed
    ..However, the rifampicin binding center is formed only in the alpha(2)betabeta' core enzyme. We interpret our results in light of the high resolution structure of core RNA polymerase from Thermus aquaticus. ..