Team:Paris/Papers

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Revision as of 01:55, 22 October 2009

iGEM > Paris > Papers

Contents

OMV Overview

N° Date Authors Article Pubmed
[] 1999 Terry J. Beveridge Structures of gram-negative cell walls and their derived membrane vesicles. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]
[] 2003 Miller SI & Guina T. Bacterial vesicle formation as a mechanism of protein transfer to animals. [http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]
[] 2005 Kuehn MJ & Kesty NC. Bacterial outer membrane vesicles and the host-pathogen interaction. [http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]
[] 2006 McBroom AJ & Kuehn MJ. Outer membrane vesicle production by Escherichia coli is independent of membrane instability. [http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]
[1] 2007 McBroom AJ & Kuehn MJ. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. [http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]
[2] 2009 Deatherage BL & Cookson BT. Biogenesis of bacterial membrane vesicles [http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]
[] 2009 Purnick PE & Weiss R. The second wave of synthetic biology: from modules to systems. [http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]

OMV Production

N° Date Authors Article Pubmed
[] 2008 Mashburn-Warren L & Whiteley M. Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation. [http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]
OmpA
[] 2001 Arora A. & Tamm LK. Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. [http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]
[] 2007 Brown EA & Hardwidge PR. Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein. [http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]
[] 2008 Burgess NK & Fleming KG. Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro. [http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]
Tol/Pal
[] 1986 Robert CHEN & Ulf HENNING. Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12 [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]
[1] 1995 Lazzaroni & Geli - Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]
[] 1999 Derouiche & Loret Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains. [http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]
[2] 2001 Lloubès & RJournet L. The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity? [http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]
[] 2002 Dubuisson JF & Lazzaroni JC. Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]
[] 2003 Llamas M & ARamos JL. Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]
[3] 2004 Henry T & Lloubès R. Improved methods for producing outer membrane vesicles in Gram-negative bacteria. [http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]

OMV Adressing

N° Date Authors Article Pubmed
[] 1997 Kadurugamuwa JL & Beveridge TJ. Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release. [http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]
[] 1998 Santini CL & Wu LF. A novel sec-independent periplasmic protein translocation pathway in Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]
[] 2000 Berks BC & Palmer T. The Tat protein export pathway. [http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]
[] 2001 Mishima Y & Murata K. Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter. [http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]
[] 2001 Sargent F & Berks BC. Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure. [http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]
[] 2001 Yahr TL & Wickner WT. Functional reconstitution of bacterial Tat translocation in vitro. [http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]
[] 2004 Robinson C & Bolhuis A. Tat-dependent protein targeting in prokaryotes and chloroplasts. [http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]
[] 2006 Sargent F & Palmer T. Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins. [http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]
[] 2006 Lee PA & Georgiou G. The bacterial twin-arginine translocation pathway. [http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]
[] 2007 Maillard J & Sargent F. Structural diversity in twin-arginine signal peptide-binding proteins. [http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]
[] 2007 Sargent F. The twin-arginine transport system: moving folded proteins across membranes. [http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]
[] 2008 Ferrandez Y & Condemine G. Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria. [http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]
[] 2008 Thie H & Hust M. SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. [http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]
[] 2009 Pradel N & Bonnet R Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane. [http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]
[] 2009 de Marco A. Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]
ClyA
[5] 2008 Kim JY & DeLisa MP. Engineered bacterial outer membrane vesicles with enhanced functionality. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]
[1] 2009 Mueller M & Ban N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]
OmpA
[] 2002 Wang Y. The function of OmpA in Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]
[] 2008 Dramsi S & Arthur M. Covalent attachment of proteins to peptidoglycan. [http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]

OMV Reception

N° Date Authors Article Pubmed
Adhesin
[] 1989 Smeal T & Karin M. Different requirements for formation of Jun:Jun and Jun:Fos complexes. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]
[] 1994 Heffernan EJ & Guiney DG. Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica. [http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]
[] 2003 Veiga E & Fernández LA. Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains. [http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]
[6] 2004 Kesty NC & Kuehn MJ. Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles. [http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]
G3P
[] 1982 JEF D. BOEKE & PETER MODEL A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. [http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]
[] 1999 Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. [http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]
[] 1999 Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. [http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]
[] 2002 Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. [http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]
[] 2003 Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. [http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]
Snare
[] 2000 Waters MG & Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. [http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]
[] 2000 Woodbury DJ & Rognlien K. The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes. [http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]
[] 2002 Bowen ME,Brunger AT. Mutational analysis of synaptobrevin transmembrane domain oligomerization. [http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]
[] 2003 Hu C & Rothman JE. Fusion of cells by flipped SNAREs. [http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]
[] 2003 Weninger K & Brunger AT. Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations. [http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]
[] 2006 Giraudo CG & Rothman JE. A clamping mechanism involved in SNARE-dependent exocytosis. [http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]
[] 2006 Low HH & Löwe J. A bacterial dynamin-like protein. [http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]
[] 2007 Weninger K & Brunger AT. Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex. [http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]
[] 2008 Delevoye C & Subtil A. SNARE protein mimicry by an intracellular bacterium. [http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]
[] 2009 Giraudo CG & Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. [http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]

OMV Signal transduction

N° Date Authors Article Pubmed
[] 1984 Lopilato JE & Beckwith JR. D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. [http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]
[] 1995 Härle C & Braun V. Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface. [http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]
[] 1998 Tomii K & Kanehisa M. A comparative analysis of ABC transporters in complete microbial genomes. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]
[] 1999 De Wulf P & Lin EC. The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons. [http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]
[] 2000 Stock AM & Goudreau PN. Two-component signal transduction. [http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]
[] 2000 Yaron S & Matthews KR. Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. [http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]
[] 2004 Dwyer MA & Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. [http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]
[] 2006 Braun V & Sauter A. Gene regulation by transmembrane signaling. [http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]
[] 2007 Baker MD & Stock JB Signal transduction: networks and integrated circuits in bacterial cognition. [http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]
[] 2007 Baker MD & Stock JB. Systems biology of bacterial chemotaxis. [http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]
[] 2007 Ibrahim M & Monnet V. Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system? [http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]
[] 2008 Thie H & Hust M. SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. [http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]
[] 2009 Kyriakidis DA & Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. [http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]
[] 2009 Tomii & Kanehisa comparative analysis of ABC transporter [http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]

Modelling

N° Date Authors Article Pubmed
Genetic Regulatory Network
[1] 1977 Gillespie Daniel T. Exact Stochastic Simlation of Coupled Chemical Equations [http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]
[3] 1997 J.B. Andersen & S.Molin New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria [http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]
[6] 1999 M.Ellowitz & S.Leibler A Synthetic oscillatory network of transcriptionnal regulators [http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]
[2] 1997 D.T.Gillespie The Chemical Langevin Equation [http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]
[5] 2002 N.Rosenfold & U.Alon Negative Autoregulation Speeds The Response TImes of Transcription Network [http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]
[] 2002 M.B.Ellowitz & P.S.Swain Stochastic Gene Expression In A Single Cell [http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]
[7] 2003 S.Mangan & U.Alon Structure and function ot the feed-forward Loop Network Motif [http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]
[4] 2003 S.Basu & R.Weiss Spatiotemporal control of gene expression with pulse-generating networks [http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]
[1] 2005 S.Hooshangi & R.Weiss Ultrasensitivity and noise propagation in a synthetic transcriptional cascade [http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]
[3] 2006 H.Li & L.Petzold Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems [http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]
[2] 2007 U.Alon Network motifs : theory and experimental approaches [http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]
[] 2006 J.Stricker & J.Hasty A Fast Robust and Tunable synthetic gene oscillator [http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]
Vesicle biophysics model
[6] 1977 Harbich et al Optical observation of rotationally symmetric lecithin vesicle shapes J. Physique, 38:727–729
[4] 1987 Ou-Yang & Helfrich Instability and deformation of a spherical vesicle by pressure Phys. Rev. Lett., 59:2486-2488
[1] 1991 Lipowsky The conformation of membranes Nature, 349(6309):475-481
[5] 1995 Fattal et al The vesicle-micelle transition in mixed lipid-surfactant Langmuir, 11:1154-1161
[3] 1998 Zhou et al On the origin of membrane vesicles in gram-negative bacteria FEMS microbiology letters, 163(2):223-228
[8] 2005 Kuehn & Kesty Bacterial outer membrane vesicles and the host pathogen interaction Genes & Dev, 19:2645-2655
[2] 2008 Park & Uehara How bacteria consume their own exoskeletons Microbiol Mol Biol Rev, 72(2):211-227
[7] 2009 Deatherage et al Biogenesis of bacterial membrane vesicles, Mol Microbiol, 72(6):1395-1407
[9] 2009 Kumaran & Losick Negative membrane curvature as a cue for subcellular localization of a bacterial protein. PNAS USA, 106(32):13541-13545

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