SEARCH

SEARCH BY CITATION

References

  • Aggarwal K, Choe LH & Lee KH (2005) Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements. Proteomics 5: 22972308.
  • Alami M, Dalal K, Lelj-Garolla B, Sligar SG & Duong F (2007) Nanodiscs unravel the interaction between the SecYEG channel and its cytosolic partner SecA. EMBO J 26: 19952004.
  • Alexander RP & Zhulin IB (2007) Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. P Natl Acad Sci USA 104: 28852890.
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 33893402.
  • Andrade MA, Brown NP, Leroy C et al. (1999) Automated genome sequence analysis and annotation. Bioinformatics 15: 391412.
  • Arai M, Mitsuke H, Ikeda M, Xia JX, Kikuchi T, Satake M & Shimizu T (2004) ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res 32: W390W393.
  • Archakov AI, Govorun VM, Dubanov AV, Ivanov YD, Veselovsky AV, Lewi P & Janssen P (2003) Protein–protein interactions as a target for drugs in proteomics. Proteomics 3: 380391.
  • Arifuzzaman M, Maeda M, Itoh A et al. (2006) Large-scale identification of protein–protein interaction of Escherichia coli K-12. Genome Res 16: 686691.
  • Ashburner M, Ball CA, Blake JA et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25: 2529.
  • Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL & Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
  • Babu MM, Priya ML, Selvan AT, Madera M, Gough J, Aravind L & Sankaran K (2006) A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol 188: 27612773.
  • Backert S & Meyer TF (2006) Type IV secretion systems and their effectors in bacterial pathogenesis. Curr Opin Microbiol 9: 207217.
  • Bader GD, Betel D & Hogue CW (2003) BIND: the biomolecular interaction network database. Nucleic Acids Res 31: 248250.
  • Bagos PG, Liakopoulos TD, Spyropoulos IC & Hamodrakas SJ (2004) PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res 32: W400W404.
  • Bagos PG, Liakopoulos TD & Hamodrakas SJ (2005) Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics 6: 7.
  • Bayan N, Guilvout I & Pugsley AP (2006) Secretins take shape. Mol Microbiol 60: 14.
  • Behrens S (2003) Periplasmic chaperones – preservers of subunit folding energy for organelle assembly. Cell 113: 556557.
  • Bendtsen JD, Nielsen H, Von Heijne G & Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783795.
  • Bendtsen JD, Nielsen H, Widdick D, Palmer T & Brunak S (2005) Prediction of twin-arginine signal peptides. BMC Bioinformatics 6: 167.
  • Berg HC (2003) The rotary motor of bacterial flagella. Annu Rev Biochem 72: 1954.
  • Bernsel A, Viklund H, Falk J, Lindahl E, Von Heijne G & Elofsson A (2008) Prediction of membrane-protein topology from first principles. P Natl Acad Sci USA 105: 71777181.
  • Berven FS, Flikka K, Jensen HB & Eidhammer I (2004) BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of gram-negative bacteria. Nucleic Acids Res 32: W394W399.
  • Bigelow HR, Petrey DS, Liu J, Przybylski D & Rost B (2004) Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res 32: 25662577.
  • Boeckmann B, Bairoch A, Apweiler R et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365370.
  • Bolhuis A, Bogsch EG & Robinson C (2000) Subunit interactions in the twin-arginine translocase complex of Escherichia coli. FEBS Lett 472: 8892.
  • Bos MP, Robert V & Tommassen J (2007) Biogenesis of the gram-negative bacterial outer membrane. Annu Rev Microbiol 61: 191214.
  • Braun M, Killmann H, Maier E, Benz R & Braun V (2002) Diffusion through channel derivatives of the Escherichia coli FhuA transport protein. Eur J Biochem 269: 49484959.
  • Braun RJ, Kinkl N, Beer M & Ueffing M (2007) Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem 389: 10331045.
  • Brutinel ED & Yahr TL (2008) Control of gene expression by type III secretory activity. Curr Opin Microbiol 11: 128133.
  • Butland G, Peregrin-Alvarez JM, Li J et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531537.
  • Butland G, Babu M, Diaz-Mejia JJ et al. (2008) eSGA: E. coli synthetic genetic array analysis. Nat Methods 5: 789795.
  • Cedano J, Aloy P, Perez-Pons JA & Querol E (1997) Relation between amino acid composition and cellular location of proteins. J Mol Biol 266: 594600.
  • Chapman E, Farr GW, Usaite R et al. (2006) Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL. P Natl Acad Sci USA 103: 1580015805.
  • Chou KC & Cai YD (2003) A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology. Biochem Bioph Res Co 311: 743747.
  • Chou KC & Shen HB (2006) Large-scale predictions of gram-negative bacterial protein subcellular locations. J Proteome Res 5: 34203428.
  • Cirulli C, Marino G & Amoresano A (2007) Membrane proteome in Escherichia coli probed by MS3 mass spectrometry: a preliminary report. Rapid Commun Mass Sp 21: 23892397.
  • Claros MG & Von Heijne G (1994) TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci 10: 685686.
  • Cluzel P, Surette M & Leibler S (2000) An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science 287: 16521655.
  • Cochran AG (2000) Antagonists of protein–protein interactions. Chem Biol 7: R85R94.
  • Cochran AG (2001) Protein–protein interfaces: mimics and inhibitors. Curr Opin Chem Biol 5: 654659.
  • Collin S, Guilvout I, Chami M & Pugsley AP (2007) YaeT-independent multimerization and outer membrane association of secretin PulD. Mol Microbiol 64: 13501357.
  • Daley DO, Rapp M, Granseth E, Melen K, Drew D & Von Heijne G (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 13211323.
  • Dobrovetsky E, Lu ML, Andorn-Broza R, Khutoreskaya G, Bray JE, Savchenko A, Arrowsmith CH, Edwards AM & Koth CM (2005) High-throughput production of prokaryotic membrane proteins. J Struct Funct Genom 6: 3350.
  • Doerrler WT (2006) Lipid trafficking to the outer membrane of gram-negative bacteria. Mol Microbiol 60: 542552.
  • Dong C, Beis K, Nesper J, Brunkan-Lamontagne AL, Clarke BR, Whitfield C & Naismith JH (2006) Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature 444: 226229.
  • Driessen AJ & Nouwen N (2008) Protein translocation across the bacterial cytoplasmic membrane. Annu Rev Biochem 77: 643667.
  • Emanuelsson O, Brunak S, Von Heijne G & Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953971.
  • Filloux A, Hachani A & Bleves S (2008) The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 154: 15701583.
  • Fountoulakis M & Gasser R (2003) Proteomic analysis of the cell envelope fraction of Escherichia coli. Amino Acids 24: 1941.
  • Fry DC (2006) Protein–protein interactions as targets for small molecule drug discovery. Biopolymers 84: 535552.
  • Galan JE & Wolf-Watz H (2006) Protein delivery into eukaryotic cells by type III secretion machines. Nature 444: 567573.
  • Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M et al. (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36: D120D124.
  • Garcia DL & Dillard JP (2008) Mutations in ampG or ampD affect peptidoglycan fragment release from Neisseria gonorrhoeae. J Bacteriol 190: 37993807.
  • Gardy JL & Brinkman FS (2006) Methods for predicting bacterial protein subcellular localization. Nat Rev Microbiol 4: 741751.
  • Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M & Brinkman FS (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21: 617623.
  • Garrow AG, Agnew A & Westhead DR (2005) TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics 6: 56.
  • Gerding MA, Ogata Y, Pecora ND, Niki H & De Boer PA (2007) The trans-envelope Tol-Pal complex is part of the cell division machinery and required for proper outer-membrane invagination during cell constriction in E. coli. Mol Microbiol 63: 10081025.
  • Girgis HS, Liu Y, Ryu WS & Tavazoie S (2007) A comprehensive genetic characterization of bacterial motility. PLoS Genet 3: 16441660.
  • Gromiha MM & Suwa M (2005) A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 21: 961968.
  • Gromiha MM, Ahmad S & Suwa M (2005) TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res 33: W164W167.
  • Gromiha MM, Yabuki Y, Kundu S, Suharnan S & Suwa M (2007a) TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res 35: D314D316.
  • Gromiha MM, Yabuki Y & Suwa M (2007b) TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences. J Chem Inf Model 47: 24562461.
  • Han MJ & Lee SY (2006) The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 70: 362439.
  • Haselbeck R, Wall D, Jiang B, Ketela T, Zyskind J, Bussey H, Foulkes JG & Roemer T (2002) Comprehensive essential gene identification as a platform for novel anti-infective drug discovery. Curr Pharm Design 8: 11551172.
  • Hedman M, Deloof H, Von Heijne G & Elofsson A (2002) Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci 11: 652658.
  • Hermjakob H, Montecchi-Palazzi L, Lewington C et al. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32: D452D455.
  • Hernandez-Montes G, Diaz-Mejia JJ, Perez-Rueda E & Segovia L (2008) The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. Genome Biol 9: R95.
  • Hirashima A, Wang S & Inouye M (1974) Cell-free synthesis of a specific lipoprotein of the Escherichia coli outer membrane directed by purified messenger RNA. P Natl Acad Sci USA 71: 41494153.
  • Holland IB, Schmitt L & Young J (2005) Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (review). Mol Membr Biol 22: 2939.
  • Holst O (2007) The structures of core regions from enterobacterial lipopolysaccharides – an update. FEMS Microbiol Lett 271: 311.
  • Hooker BS, Bigelow DJ & Lin CT (2007) Methods for mapping of interaction networks involving membrane proteins. Biochem Bioph Res Co 363: 457461.
  • Hritonenko V & Stathopoulos C (2007) Omptin proteins: an expanding family of outer membrane proteases in gram-negative Enterobacteriaceae. Mol Membr Biol 24: 395406.
  • Ivanov AS, Gnedenko OV, Molnar AA, Mezentsev YV, Lisitsa AV & Archakov AI (2007) Protein–protein interactions as new targets for drug design: virtual and experimental approaches. J Bioinform Comput Biol 5: 579592.
  • Jalili PR & Dass C (2004) Proteome analysis in the bovine adrenal medulla using liquid chromatography with tandem mass spectrometry. Rapid Commun Mass Sp 18: 18771884.
  • Janga SC, Collado-Vides J & Moreno-Hagelsieb G (2005) Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res 33: 25212530.
  • Jeong H, Mason SP, Barabasi AL & Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 4142.
  • Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23: 538544.
  • Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H & Krogh A (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12: 16521662.
  • Kall L, Krogh A & Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 10271036.
  • Karimova G, Dautin N & Ladant D (2005) Interaction network among Escherichia coli membrane proteins involved in cell division as revealed by bacterial two-hybrid analysis. J Bacteriol 187: 22332243.
  • Karp PD, Keseler IM, Shearer A et al. (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35: 75777590.
  • Kashino Y (2003) Separation methods in the analysis of protein membrane complexes. J Chromatogr B 797: 191216.
  • Kerrien S, Alam-Faruque Y, Aranda B et al. (2007) IntAct – open source resource for molecular interaction data. Nucleic Acids Res 35: D561D565.
  • Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M & Karp PD (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33: D334D337.
  • Kim S, Malinverni JC, Sliz P, Silhavy TJ, Harrison SC & Kahne D (2007) Structure and function of an essential component of the outer membrane protein assembly machine. Science 317: 961964.
  • Kleinschmidt JH (2003) Membrane protein folding on the example of outer membrane protein A of Escherichia coli. Cell Mol Life Sci 60: 15471558.
  • Krause F (2006) Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (membrane) protein complexes and supercomplexes. Electrophoresis 27: 27592781.
  • Krogh A, Larsson B, Von Heijne G & Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567580.
  • Krojer T, Sawa J, Schafer E, Saibil HR, Ehrmann M & Clausen T (2008) Structural basis for the regulated protease and chaperone function of DegP. Nature 453: 885890.
  • Kuhn M, Campillos M, Gonzalez P, Jensen LJ & Bork P (2008a) Large-scale prediction of drug-target relationships. FEBS Lett 582: 12831290.
  • Kuhn M, Von Mering C, Campillos M, Jensen LJ & Bork P (2008b) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36: D684D688.
  • Kustos I, Kocsis B & Kilar F (2007) Bacterial outer membrane protein analysis by electrophoresis and microchip technology. Expert Rev Proteomics 4: 91106.
  • Kyte J & Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105132.
  • Lao DM, Arai M, Ikeda M & Shimizu T (2002) The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics 18: 15621566.
  • Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S & Bonneu M (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27: 33063321.
  • Lee PA, Tullman-Ercek D & Georgiou G (2006) The bacterial twin-arginine translocation pathway. Annu Rev Microbiol 60: 373395.
  • Link AJ, Jeong KJ & Georgiou G (2007) Beyond toothpicks: new methods for isolating mutant bacteria. Nat Rev Microbiol 5: 680688.
  • Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH & Ellison MJ (2005) Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 4: 12051209.
  • Lu P, Szafron D, Greiner R, Wishart DS, Fyshe A, Pearcy B, Poulin B, Eisner R, Ngo D & Lamb N (2005) PA-GOSUB: a searchable database of model organism protein sequences with their predicted gene ontology molecular function and subcellular localization. Nucleic Acids Res 33: D147D153.
  • Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C & Eisner R (2004) Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics 20: 547556.
  • Madan Babu M & Sankaran K (2002) DOLOP – database of bacterial lipoproteins. Bioinformatics 18: 641643.
  • Maslov S & Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910913.
  • Meacci G, Ries J, Fischer-Friedrich E, Kahya N, Schwille P & Kruse K (2006) Mobility of Min-proteins in Escherichia coli measured by fluorescence correlation spectroscopy. Phys Biol 3: 255263.
  • Michnick SW (2000) Chemical biology beyond binary codes. Chem Biol 7: R217R221.
  • Molloy MP, Herbert BR, Williams KL & Gooley AA (1999) Extraction of Escherichia coli proteins with organic solvents prior to two-dimensional electrophoresis. Electrophoresis 20: 701704.
  • Molloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL & Gooley AA (2000) Proteomic analysis of the Escherichia coli outer membrane. Eur J Biochem 267: 28712881.
  • Mosyak L, Zhang Y, Glasfeld E, Haney S, Stahl M, Seehra J & Somers WS (2000) The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography. EMBO J 19: 31793191.
  • Muller T, Rahmann S & Rehmsmeier M (2001) Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 17 (suppl 1): S182S189.
  • Nair R & Rost B (2002a) Inferring sub-cellular localization through automated lexical analysis. Bioinformatics 18 (Suppl 1): S78S86.
  • Nair R & Rost B (2002b) Sequence conserved for subcellular localization. Protein Sci 11: 28362847.
  • Najafabadi HS & Salavati R (2008) Sequence-based prediction of protein–protein interactions by means of codon usage. Genome Biol 9: R87.
  • Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67: 593656.
  • Ou YY, Gromiha MM, Chen SA & Suwa M (2008) TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem 32: 227231.
  • Pirovano W, Feenstra KA & Heringa J (2008) PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 24: 492497.
  • Poetsch A & Wolters D (2008) Bacterial membrane proteomics. Proteomics 8: 41004122.
  • Pratt LA & Kolter R (1998) Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 30: 285293.
  • Pruitt KD, Tatusova T & Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501D504.
  • Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J & Rost B (2007) Membrane protein prediction methods. Methods 41: 460474.
  • Rajagopala SV, Titz B, Goll J, Parrish JR, Wohlbold K, McKevitt MT, Palzkill T, Mori H, Finley Jr RL & Uetz P (2007) The protein network of bacterial motility. Mol Syst Biol 3: 128.
  • Rangachari K, Davis CT, Eccleston JF, Hirst EM, Saldanha JW, Strath M & Wilson RJ (2002) SufC hydrolyzes ATP and interacts with SufB from Thermotoga maritima. FEBS Lett 514: 225228.
  • Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G & Li H (2008) Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Cell 133: 640652.
  • Rey S, Acab M, Gardy JL, Laird MR, DeFays K, Lambert C & Brinkman FS (2005a) PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Res 33: D164D168.
  • Rey S, Gardy JL & Brinkman FS (2005b) Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. BMC Genomics 6: 162.
  • Rick PD, Barr K, Sankaran K, Kajimura J, Rush JS & Waechter CJ (2003) Evidence that the wzxE gene of Escherichia coli K-12 encodes a protein involved in the transbilayer movement of a trisaccharide-lipid intermediate in the assembly of enterobacterial common antigen. J Biol Chem 278: 1653416542.
  • Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M & Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotech 17: 10301032.
  • Riley M, Abe T, Arnaud MB et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot – 2005. Nucleic Acids Res 34: 19.
  • Rizzitello AE, Harper JR & Silhavy TJ (2001) Genetic evidence for parallel pathways of chaperone activity in the periplasm of Escherichia coli. J Bacteriol 183: 67946800.
  • Ruiz N, Gronenberg LS, Kahne D & Silhavy TJ (2008) Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. P Natl Acad Sci USA 105: 55375542.
  • Saier Jr MH (2006) Protein secretion and membrane insertion systems in gram-negative bacteria. J Membr Biol 214: 7590.
  • Saier Jr MH, Tran CV & Barabote RD (2006) TCDB: the transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res 34: D181D186.
  • Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU & Eisenberg D (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32: D449D451.
  • Sansom MS (1999) Membrane proteins: a tale of barrels and corks. Curr Biol 9: R254R257.
  • Santoni V, Molloy M & Rabilloud T (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21: 10541070.
  • Sasarman A, Echelard Y, Letowski J, Tardif D & Drolet M (1988) Nucleotide sequence of the hemX gene, the third member of the Uro operon of Escherichia coli K12. Nucleic Acids Res 16: 11835.
  • Scheurwater EM & Clarke AJ (2008) The C-terminal domain of Escherichia coli YfhD functions as a lytic transglycosylase. J Biol Chem 283: 83638373.
  • Schleiff E & Soll J (2005) Membrane protein insertion: mixing eukaryotic and prokaryotic concepts. EMBO Rep 6: 10231027.
  • Schuster SC, Swanson RV, Alex LA, Bourret RB & Simon MI (1993) Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance. Nature 365: 343347.
  • Schwartz CJ, Djaman O, Imlay JA & Kiley PJ (2000) The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. P Natl Acad Sci USA 97: 90099014.
  • Schwille P, Bieschke J & Oehlenschlager F (1997) Kinetic investigations by fluorescence correlation spectroscopy: the analytical and diagnostic potential of diffusion studies. Biophys Chem 66: 211228.
  • Serres MH, Goswami S & Riley M (2004) GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res 32: D300D302.
  • Shafrir Y & Guy HR (2004) STAM: simple transmembrane alignment method. Bioinformatics 20: 758769.
  • Sharan R, Ulitsky I & Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3: 88.
  • Shih YL & Rothfield L (2006) The bacterial cytoskeleton. Microbiol Mol Biol Rev 70: 729754.
  • Shoemaker BA & Panchenko AR (2007a) Deciphering protein–protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3: e42.
  • Shoemaker BA & Panchenko AR (2007b) Deciphering protein–protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3: e43.
  • Sklar JG, Wu T, Kahne D & Silhavy TJ (2007) Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev 21: 24732484.
  • Spears KJ, Roe AJ & Gally DL (2006) A comparison of enteropathogenic and enterohaemorrhagic Escherichia coli pathogenesis. FEMS Microbiol Lett 255: 187202.
  • Spelbrink RE, Kolkman A, Slijper M, Killian JA & De Kruijff B (2005) Detection and identification of stable oligomeric protein complexes in Escherichia coli inner membranes: a proteomics approach. J Biol Chem 280: 2874228748.
  • Spory A, Bosserhoff A, Von Rhein C, Goebel W & Ludwig A (2002) Differential regulation of multiple proteins of Escherichia coli and Salmonella enterica serovar Typhimurium by the transcriptional regulator SlyA. J Bacteriol 184: 35493559.
  • Stenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, Von Heijne G & Daley DO (2005) Protein complexes of the Escherichia coli cell envelope. J Biol Chem 280: 3440934419.
  • Strauch EM & Georgiou G (2007) A bacterial two-hybrid system based on the twin-arginine transporter pathway of E. coli. Protein Sci 16: 10011008.
  • Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M & Wishart DS (2004) The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 32: D293D295.
  • Tamae C, Liu A, Kim K et al. (2008) Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli. J Bacteriol 190: 59815988.
  • Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N & Isobe T (2004) Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins. Mol Cell Proteomics 3: 780787.
  • Tatusov RL, Galperin MY, Natale DA & Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 3336.
  • Thanassi DG, Stathopoulos C, Karkal A & Li H (2005) Protein secretion in the absence of ATP: the autotransporter, two-partner secretion and chaperone/usher pathways of gram-negative bacteria (review). Mol Membr Biol 22: 6372.
  • Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK & Hamon C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75: 18951904.
  • Tikhonova EB & Zgurskaya HI (2004) AcrA, AcrB, and TolC of Escherichia coli form a stable intermembrane multidrug efflux complex. J Biol Chem 279: 3211632124.
  • Tokuda H & Matsuyama S (2004) Sorting of lipoproteins to the outer membrane in E. coli. Biochim Biophys Acta 1694: IN1-9.
  • Tusnady GE & Simon I (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283: 489506.
  • Tusnády GE, Kalmár L & Simon I (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res: D234D239.
  • Typas A, Nichols RJ, Siegele DA et al. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 5: 781787.
  • Vaknin A & Berg HC (2004) Single-cell FRET imaging of phosphatase activity in the Escherichia coli chemotaxis system. P Natl Acad Sci USA 101: 1707217077.
  • Van Der Laan M, Houben EN, Nouwen N, Luirink J & Driessen AJ (2001) Reconstitution of Sec-dependent membrane protein insertion: nascent FtsQ interacts with YidC in a SecYEG-dependent manner. EMBO Rep 2: 519523.
  • Veldhuis G, Hink M, Krasnikov V, Van Den Bogaart G, Hoeboer J, Visser AJ, Broos J & Poolman B (2006) The oligomeric state and stability of the mannitol transporter, EnzymeII(mtl), from Escherichia coli: a fluorescence correlation spectroscopy study. Protein Sci 15: 19771986.
  • Visudtiphole V, Chalton DA, Hong Q & Lakey JH (2006) Determining OMP topology by computation, surface plasmon resonance and cysteine labelling: the test case of OMPG. Biochem Biophys Res Commun 351: 113117.
  • Volker U & Hecker M (2005) From genomics via proteomics to cellular physiology of the gram-positive model organism Bacillus subtilis. Cell Microbiol 7: 10771085.
  • Von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B & Bork P (2007) STRING 7 – recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358D362.
  • Wagner K, Racaityte K, Unger KK, Miliotis T, Edholm LE, Bischoff R & Marko-Varga G (2000) Protein mapping by two-dimensional high performance liquid chromatography. J Chromatogr A 893: 293305.
  • Wallin E & Von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 10291038.
  • Wang J, Sung WK, Krishnan A & Li KB (2005) Protein subcellular localization prediction for gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines. BMC Bioinformatics 6: 174.
  • Weiner JH & Li L (2008) Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. Biochim Biophys Acta 1778: 16981713.
  • Werner J & Misra R (2005) YaeT (Omp85) affects the assembly of lipid-dependent and lipid-independent outer membrane proteins of Escherichia coli. Mol Microbiol 57: 14501459.
  • Wimley WC (2003) The versatile beta-barrel membrane protein. Curr Opin Struct Biol 13: 404411.
  • Wu CC, MacCoss MJ, Howell KE & Yates JR III (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21: 532538.
  • Wu T, Malinverni J, Ruiz N, Kim S, Silhavy TJ & Kahne D (2005) Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121: 235245.
  • Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM & Eisenberg D (2000) DIP: the database of interacting proteins. Nucleic Acids Res 28: 289291.
  • Yan A, Guan Z & Raetz CR (2007) An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli. J Biol Chem 282: 3607736089.
  • Yan JX, Devenish AT, Wait R, Stone T, Lewis S & Fowler S (2002) Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2: 16821698.
  • Yang J, Chen L, Sun L, Yu J & Jin Q (2008) VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res 36: D539D542.
  • Yellaboina S, Goyal K & Mande SC (2007) Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data. Genome Res 17: 527535.
  • Yokota N, Kuroda T, Matsuyama S & Tokuda H (1999) Characterization of the LolA–LolB system as the general lipoprotein localization mechanism of Escherichia coli. J Biol Chem 274: 3099530999.
  • Yu CS, Lin CJ & Hwang JK (2004) Predicting subcellular localization of proteins for gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 13: 14021406.
  • Yu CS, Chen YC, Lu CH & Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64: 643651.
  • Zeghouf M, Li J, Butland G, Borskowska A, Canadien V, Richards D, Beattie B, Emili A & Greenblatt JF (2004) Sequential peptide affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res 3: 463468.
  • Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH & Li L (2007) Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics 7: 484493.
  • Zhang Z & Henzel WJ (2004) Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Sci 13: 28192824.
  • Zhou M, Boekhorst J, Francke C & Siezen RJ (2008) LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 9: 173.