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Escherichia coli Proteins

  • 1.
    Zhang D, Li S, King C, Wingreen N, Gitai Z, Li Z. Global and gene-specific translational regulation in Escherichia coli across different conditions. PLoS Comput Biol. 2022;18(10):e1010641. PMCID: PMC9624429
    Reference Link
  • 1.
    Doyle M, Jimah J, Dowdy T, Ohlemacher S, Larion M, Hinshaw J, Bernstein H. Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Cell. 2022;185(7):1143–1156.e13. PMCID: PMC8985213
    Reference Link
  • 1.
    Benn G, Mikheyeva I, Inns P, Forster J, Ojkic N, Bortolini C, Ryadnov M, Kleanthous C, Silhavy T, Hoogenboom B. Phase separation in the outer membrane of . Proc Natl Acad Sci U S A. 2021;118(44). PMCID: PMC8612244
    Reference Link
  • 1.
    Combs A, Silhavy T. The sacrificial adaptor protein Skp functions to remove stalled substrates from the β-barrel assembly machine. Proc Natl Acad Sci U S A. 2022;119(1). PMCID: PMC8740687
    Reference Link
  • 1.
    Wan X, Brynildsen M. Robustness of nitric oxide detoxification to nitrogen starvation in Escherichia coli requires RelA. Free Radic Biol Med. 2021;176:286–297. PMID: 34624482
    Reference Link
  • 1.
    Murawski A, Brynildsen M. Ploidy is an important determinant of fluoroquinolone persister survival. Curr Biol. 2021;31(10):2039–2050.e7. PMCID: PMC8183807
    Reference Link
  • 1.
    Seath C, Trowbridge A, Muir T, MacMillan D. Reactive intermediates for interactome mapping. Chem Soc Rev. 2021;50(5):2911–2926. PMID: 33458734
    Reference Link
  • 1.
    Guest R, Rutherford S, Silhavy T. Border Control: Regulating LPS Biogenesis. Trends Microbiol. 2021;29(4):334–345. PMCID: PMC7969359
    Reference Link
  • 1.
    Grimm J, Shi H, Wang W, Mitchell A, Wingreen N, Huang K, Silhavy T. The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in . Proc Natl Acad Sci U S A. 2020;117(43):26907–26914. PMCID: PMC7604412
    Reference Link
  • 1.
    Hart E, Silhavy T. Functions of the BamBCDE Lipoproteins Revealed by Bypass Mutations in BamA. J Bacteriol. 2020;202(21). PMCID: PMC7549358
    Reference Link
  • 1.
    Yao X, Fan X, Yan N. Cryo-EM analysis of a membrane protein embedded in the liposome. Proc Natl Acad Sci U S A. 2020;117(31):18497–18503. PMCID: PMC7414195
    Reference Link
  • 1.
    Hart E, Gupta M, Wühr M, Silhavy T. The gain-of-function allele bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. Proc Natl Acad Sci U S A. 2020;117(31):18737–18743. PMCID: PMC7414184
    Reference Link
  • 1.
    Werner J, Shi H, Hsin J, Huang K, Gitai Z, Klein E. AimB Is a Small Protein Regulator of Cell Size and MreB Assembly. Biophys J. 2020;119(3):593–604. PMCID: PMC7399478
    Reference Link
  • 1.
    Guest R, Guerra D, Wissler M, Grimm J, Silhavy T. YejM Modulates Activity of the YciM/FtsH Protease Complex To Prevent Lethal Accumulation of Lipopolysaccharide. mBio. 2020;11(2). PMCID: PMC7157816
    Reference Link
  • 1.
    Hart E, Mitchell A, Konovalova A, Grabowicz M, Sheng J, Han X, Rodriguez-Rivera F, Schwaid A, Malinverni J, Balibar C, Bodea S, Si Q, Wang H, Homsher M, Painter R, Ogawa A, Sutterlin H, Roemer T, Black T, Rothman D, Walker S, Silhavy T. A small-molecule inhibitor of BamA impervious to efflux and the outer membrane permeability barrier. Proc Natl Acad Sci U S A. 2019;116(43):21748–21757. PMCID: PMC6815139
    Reference Link
  • 1.
    Schober A, Mathis A, Ingle C, Park J, Chen L, Rabinowitz J, Junier I, Rivoire O, Reynolds K. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. Cell Rep. 2019;27(11):3359–3370.e7. PMCID: PMC6625508
    Reference Link
  • 1.
    Adolfsen K, Chou W, Brynildsen M. Transcriptional Regulation Contributes to Prioritized Detoxification of Hydrogen Peroxide over Nitric Oxide. J Bacteriol. 2019;201(14). PMCID: PMC6597392
    Reference Link
  • 1.
    Aedo S, Orman M, Brynildsen M. Stationary phase persister formation in Escherichia coli can be suppressed by piperacillin and PBP3 inhibition. BMC Microbiol. 2019;19(1):140. PMCID: PMC6591824
    Reference Link
  • 1.
    Hart E, Gupta M, Wühr M, Silhavy T. The Synthetic Phenotype of Δ Δ Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF. mBio. 2019;10(3). PMCID: PMC6529638
    Reference Link
  • 1.
    Silhavy T, Mitchell A. Genetic Analysis of Protein Translocation. Protein J. 2019;38(3):217–228. PMCID: PMC6589372
    Reference Link
  • 1.
    Stubbe J, Seyedsayamdost M. Discovery of a New Class I Ribonucleotide Reductase with an Essential DOPA Radical and NO Metal as an Initiator of Long-Range Radical Transfer. Biochemistry. 2019;58(6):435–437. PMID: 30586288
    Reference Link
  • 1.
    Ricci D, Silhavy T. Outer Membrane Protein Insertion by the β-barrel Assembly Machine. EcoSal Plus. 2019;8(2). PMCID: PMC6419762
    Reference Link
  • 1.
    Barrett T, Mok W, Murawski A, Brynildsen M. Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat Commun. 2019;10(1):1177. PMCID: PMC6414640
    Reference Link
  • 1.
    Hart E, O’Connell A, Tang K, Wzorek J, Grabowicz M, Kahne D, Silhavy T. Fine-Tuning of σ Activation Suppresses Multiple Assembly-Defective Mutations in Escherichia coli. J Bacteriol. 2019;201(11). PMCID: PMC6509652
    Reference Link
  • 1.
    Chou W, Brynildsen M. Loss of DksA leads to multi-faceted impairment of nitric oxide detoxification by Escherichia coli. Free Radic Biol Med. 2019;130:288–296. PMID: 30366060
    Reference Link
  • 1.
    Mitchell A, Srikumar T, Silhavy T. Cyclic Enterobacterial Common Antigen Maintains the Outer Membrane Permeability Barrier of Escherichia coli in a Manner Controlled by YhdP. mBio. 2018;9(4). PMCID: PMC6083912
    Reference Link
  • 1.
    Bratton B, Shaevitz J, Gitai Z, Morgenstein R. MreB polymers and curvature localization are enhanced by RodZ and predict E. coli’s cylindrical uniformity. Nat Commun. 2018;9(1):2797. PMCID: PMC6052060
    Reference Link
  • 1.
    Li S, Li Z, Park J, King C, Rabinowitz J, Wingreen N, Gitai Z. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nat Microbiol. 2018;3(8):939–947. PMCID: PMC6278830
    Reference Link
  • 1.
    Mok W, Brynildsen M. Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A. 2018;115(27):E6301-E6309. PMCID: PMC6142227
    Reference Link
  • 1.
    Konovalova A, Grabowicz M, Balibar C, Malinverni J, Painter R, Riley D, Mann P, Wang H, Garlisi C, Sherborne B, Rigel N, Ricci D, Black T, Roemer T, Silhavy T, Walker S. Inhibitor of intramembrane protease RseP blocks the σ response causing lethal accumulation of unfolded outer membrane proteins. Proc Natl Acad Sci U S A. 2018;115(28):E6614-E6621. PMCID: PMC6048503
    Reference Link
  • 1.
    Shi H, Bratton B, Gitai Z, Huang K. How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction. Cell. 2018;172(6):1294–1305. PMCID: PMC5846203
    Reference Link
  • 1.
    May K, Silhavy T. The Phospholipase PldA Regulates Outer Membrane Homeostasis via Lipid Signaling. mBio. 2018;9(2). PMCID: PMC5874903
    Reference Link
  • 1.
    Reece S, Seyedsayamdost M. Long-range proton-coupled electron transfer in the class Ia ribonucleotide reductase. Essays Biochem. 2017;61(2):281–292. PMID: 28487404
    Reference Link
  • 1.
    Szwajkajzer D, Dai L, Fukayama J, Abramczyk B, Fairman R, Carey J. Quantitative analysis of DNA binding by the Escherichia coli arginine repressor. J Mol Biol. 2001;312(5):949–62. PMID: 11580241
    Reference Link
  • 1.
    Degtjarik O, Brynda J, Ettrichova O, Kuty M, Sinha D, Smatanova I, Carey J, Ettrich R, Řeha D. Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA. J Phys Chem B. 2016;120(22):4867–77. PMID: 27183467
    Reference Link
  • 1.
    Lee J, Sutterlin H, Wzorek J, Mandler M, Hagan C, Grabowicz M, Tomasek D, May M, Hart E, Silhavy T, Kahne D. Substrate binding to BamD triggers a conformational change in BamA to control membrane insertion. Proc Natl Acad Sci U S A. 2018;115(10):2359–2364. PMCID: PMC5877925
    Reference Link
  • 1.
    Hoegler K, Hecht M. Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity. J Mol Evol. 2018;86(2):103–110. PMCID: PMC6116729
    Reference Link
  • 1.
    Hecht M, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that?. Curr Opin Struct Biol. 2018;48:124–132. PMID: 29306103
    Reference Link
  • 1.
    Donnelly A, Murphy G, Digianantonio K, Hecht M. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol. 2018;14(3):253–255. PMID: 29334382
    Reference Link
  • 1.
    Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu Y-N, Wang P, Yan N, Shi Y. Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature. 2009;462(7272):467–72. PMID: 19940917
    Reference Link
  • 1.
    Dang S, Sun L, Huang Y, Lu F, Liu Y, Gong H, Wang J, Yan N. Structure of a fucose transporter in an outward-open conformation. Nature. 2010;467(7316):734–8. PMID: 20877283
    Reference Link
  • 1.
    Lu F, Li S, Jiang Y, Jiang J, Fan H, Lu G, Deng D, Dang S, Zhang X, Wang J, Yan N. Structure and mechanism of the uracil transporter UraA. Nature. 2011;472(7342):243–6. PMID: 21423164
    Reference Link
  • 1.
    Sugihara J, Sun L, Yan N, Kaback R. Dynamics of the L-fucose/H+ symporter revealed by fluorescence spectroscopy. Proc Natl Acad Sci U S A. 2012;109(37):14847–51. PMCID: PMC3443143
    Reference Link
  • 1.
    Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, Yan N. Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature. 2012;490(7420):361–6. PMID: 23075985
    Reference Link
  • 1.
    Madej G, Dang S, Yan N, Kaback R. Evolutionary mix-and-match with MFS transporters. Proc Natl Acad Sci U S A. 2013;110(15):5870–4. PMCID: PMC3625355
    Reference Link
  • 1.
    Madej G, Sun L, Yan N, Kaback R. Functional architecture of MFS D-glucose transporters. Proc Natl Acad Sci U S A. 2014;111(7):E719–27. PMCID: PMC3932877
    Reference Link
  • 1.
    Deng D, Xu C, Sun P, Wu J, Yan C, Hu M, Yan N. Crystal structure of the human glucose transporter GLUT1. Nature. 2014;510(7503):121–5. PMID: 24847886
    Reference Link
  • 1.
    Yu X, Yang G, Yan C, Baylon J, Jiang J, Fan H, Lu G, Hasegawa K, Okumura H, Wang T, Tajkhorshid E, Li S, Yan N. Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters. Cell Res. 2017;27(8):1020–1033. PMCID: PMC5539350
    Reference Link
  • 1.
    Jiang X, Smirnova I, Kasho V, Wu J, Hirata K, Ke M, Pardon E, Steyaert J, Yan N, Kaback R. Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation. Proc Natl Acad Sci U S A. 2016;113(44):12420–12425. PMCID: PMC5098631
    Reference Link
  • 1.
    Ke M, Yuan Y, Jiang X, Yan N, Gong H. Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE. PLoS Comput Biol. 2017;13(6):e1005603. PMCID: PMC5491310
    Reference Link

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