Team:Paris/Papers

From 2009.igem.org

(Difference between revisions)
(OMV Signal transduction)
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|1999
|1999
|Terry J. Beveridge
|Terry J. Beveridge
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|2003
|2003
|Miller SI & Guina T.
|Miller SI & Guina T.
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|2005
|2005
|Kuehn MJ & Kesty NC.
|Kuehn MJ & Kesty NC.
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|2006
|2006
|McBroom AJ & Kuehn MJ.
|McBroom AJ & Kuehn MJ.
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|2009
|2009
|Purnick PE & Weiss R.
|Purnick PE & Weiss R.
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|2008
|2008
|Mashburn-Warren L & Whiteley M.
|Mashburn-Warren L & Whiteley M.
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|2007
|2007
|Brown EA & Hardwidge PR.
|Brown EA & Hardwidge PR.
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|2008
|2008
|Burgess NK & Fleming KG.
|Burgess NK & Fleming KG.
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! colspan="5" style="background: #ccccff;" | Tol/Pal
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|- style="background: #d8d8d8; text-align: center;"   
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|1986
|1986
|Robert CHEN & Ulf HENNING.
|Robert CHEN & Ulf HENNING.
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|1999
|1999
|Derouiche & Loret
|Derouiche & Loret
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|2002
|2002
|Dubuisson JF & Lazzaroni JC.
|Dubuisson JF & Lazzaroni JC.
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|2003
|2003
|Llamas M & ARamos JL.
|Llamas M & ARamos JL.
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|1997
|1997
|Kadurugamuwa JL & Beveridge TJ.
|Kadurugamuwa JL & Beveridge TJ.
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|1998
|1998
|Santini CL & Wu LF.
|Santini CL & Wu LF.
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|2000
|2000
|Berks BC & Palmer T.
|Berks BC & Palmer T.
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|2001
|2001
|Mishima Y & Murata K.
|Mishima Y & Murata K.
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|2001
|2001
|Sargent F & Berks BC.
|Sargent F & Berks BC.
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|2001
|2001
|Yahr TL & Wickner WT.
|Yahr TL & Wickner WT.
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|2004
|2004
|Robinson C & Bolhuis A.
|Robinson C & Bolhuis A.
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|2006
|2006
|Sargent F & Palmer T.
|Sargent F & Palmer T.
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|2006
|2006
|Lee PA & Georgiou G.
|Lee PA & Georgiou G.
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|2007
|2007
|Maillard J & Sargent F.
|Maillard J & Sargent F.
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|2007
|2007
|Sargent F.
|Sargent F.
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|2008
|2008
|Ferrandez Y & Condemine G.
|Ferrandez Y & Condemine G.
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|2008
|2008
|Thie H & Hust M.
|Thie H & Hust M.
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|2009
|2009
|Pradel N & Bonnet R
|Pradel N & Bonnet R
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|2009
|2009
|de Marco A.
|de Marco A.
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|2008
|2008
|Dramsi S & Arthur M.
|Dramsi S & Arthur M.
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|1989
|1989
|Smeal T & Karin M.
|Smeal T & Karin M.
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|1994
|1994
|Heffernan EJ & Guiney DG.
|Heffernan EJ & Guiney DG.
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|2003
|2003
|Veiga E & Fernández LA.
|Veiga E & Fernández LA.
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|1982
|1982
|JEF D. BOEKE & PETER MODEL
|JEF D. BOEKE & PETER MODEL
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|1984
|1984
|Lopilato JE & Beckwith JR.
|Lopilato JE & Beckwith JR.
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|1995
|1995
|Härle C & Braun V.
|Härle C & Braun V.
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|1999
|1999
|De Wulf P & Lin EC.
|De Wulf P & Lin EC.
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|2000
|2000
|Yaron S & Matthews KR.
|Yaron S & Matthews KR.
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|2004
|2004
|Dwyer MA & Hellinga HW.
|Dwyer MA & Hellinga HW.
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|2006
|2006
|Braun V & Sauter A.
|Braun V & Sauter A.
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|2007
|2007
|Baker MD & Stock JB
|Baker MD & Stock JB
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|Baker MD & Stock JB.
|Baker MD & Stock JB.
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|2007
|2007
|Ibrahim M & Monnet V.
|Ibrahim M & Monnet V.
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|Thie H & Hust M.
|Thie H & Hust M.
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|2009
|2009
|Tomii & Kanehisa
|Tomii & Kanehisa
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|2002
|2002
|M.B.Ellowitz & P.S.Swain
|M.B.Ellowitz & P.S.Swain
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|2006
|2006
|J.Stricker & J.Hasty
|J.Stricker & J.Hasty

Revision as of 03:26, 22 October 2009

iGEM > Paris > Papers

Contents

OMV Overview

Date Authors Article Pubmed
[X] 1999 Terry J. Beveridge Structures of gram-negative cell walls and their derived membrane vesicles. 10438737
[X] 2003 Miller SI & Guina T. Bacterial vesicle formation as a mechanism of protein transfer to animals. 14531993
[X] 2005 Kuehn MJ & Kesty NC. Bacterial outer membrane vesicles and the host-pathogen interaction. 16291643
[X] 2006 McBroom AJ & Kuehn MJ. Outer membrane vesicle production by Escherichia coli is independent of membrane instability. 16855227
[1] 2007 McBroom AJ & Kuehn MJ. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. 17163978
[2] 2009 Deatherage BL & Cookson BT. Biogenesis of bacterial membrane vesicles 19432795
[X] 2009 Purnick PE & Weiss R. The second wave of synthetic biology: from modules to systems. 19461664

OMV Production

Date Authors Article Pubmed
[X] 2008 Mashburn-Warren L & Whiteley M. Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation. 18630345
OmpA
[2] 2001 Arora A. & Tamm LK. Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. 11276254
[X] 2007 Brown EA & Hardwidge PR. Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein. 17975086
[X] 2008 Burgess NK & Fleming KG. Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro. 18641391
Tol/Pal
[X] 1986 Robert CHEN & Ulf HENNING. Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12 210680
[3] 1995 Lazzaroni & Geli - Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex. 179564
[X] 1999 Derouiche & Loret Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains. 10380085
[4] 2001 Lloubès & RJournet L. The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity? 11501670
[X] 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. 12142433
[X] 2003 Llamas M & ARamos JL. Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane. 12896989
[5] 2004 Henry T & Lloubès R. Improved methods for producing outer membrane vesicles in Gram-negative bacteria. 15249060

OMV Adressing

Date Authors Article Pubmed
[X] 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. 9421308
[X] 1998 Santini CL & Wu LF. A novel sec-independent periplasmic protein translocation pathway in Escherichia coli. 9427745
[X] 2000 Berks BC & Palmer T. The Tat protein export pathway. 10652088
[X] 2001 Mishima Y & Murata K. Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter. 11731126
[X] 2001 Sargent F & Berks BC. Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure. 11422364
[X] 2001 Yahr TL & Wickner WT. Functional reconstitution of bacterial Tat translocation in vitro. 11350936
[X] 2004 Robinson C & Bolhuis A. Tat-dependent protein targeting in prokaryotes and chloroplasts. 15546663
[X] 2006 Sargent F & Palmer T. Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins. 16445746
[X] 2006 Lee PA & Georgiou G. The bacterial twin-arginine translocation pathway. 16756481
[X] 2007 Maillard J & Sargent F. Structural diversity in twin-arginine signal peptide-binding proteins. 17901208
[X] 2007 Sargent F. The twin-arginine transport system: moving folded proteins across membranes. 17956229
[X] 2008 Ferrandez Y & Condemine G. Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria. 18643934
[X] 2008 Thie H & Hust M. SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. 18504019
[X] 2009 Pradel N & Bonnet R Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane. 18643934
[X] 2009 de Marco A. Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. 19442264
ClyA
[5] [1] 2008 Kim JY & DeLisa MP. Engineered bacterial outer membrane vesicles with enhanced functionality. 18511069
[1] [2] 2009 Mueller M & Ban N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. 19421192
OmpA
[1] 2002 Wang Y. The function of OmpA in Escherichia coli. 11906175
[X] 2008 Dramsi S & Arthur M. Covalent attachment of proteins to peptidoglycan. 18266854

OMV Reception

Date Authors Article Pubmed
Adhesin
[X] 1989 Smeal T & Karin M. Different requirements for formation of Jun:Jun and Jun:Fos complexes. 2516828
[X] 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. 7927803
[X] 2003 Veiga E & Fernández LA. Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains. 12949111
[6] 2004 Kesty NC & Kuehn MJ. Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles. 14578354
G3P
[X] 1982 JEF D. BOEKE & PETER MODEL A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 6291030
[8] 1999 Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 10606756
[9] 1999 Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 10404600
[10] 2002 Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 11861923
[11] 2003 Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 12670988
Snare
[17] 2000 Waters MG & Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. 11208146
[X] 2000 Woodbury DJ & Rognlien K. The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes. 11067766
[X] 2002 Bowen ME,Brunger AT. Mutational analysis of synaptobrevin transmembrane domain oligomerization. 12501216
[X] 2003 Hu C & Rothman JE. Fusion of cells by flipped SNAREs. 12805548
[X] 2003 Weninger K & Brunger AT. Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations. 14657376
[X] 2006 Giraudo CG & Rothman JE. A clamping mechanism involved in SNARE-dependent exocytosis. 16794037
[X] 2006 Low HH & Löwe J. A bacterial dynamin-like protein. 17122778
[X] 2007 Weninger K & Brunger AT. Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex. 18275821
[X] 2008 Delevoye C & Subtil A. SNARE protein mimicry by an intracellular bacterium. 18369472
[18] 2009 Giraudo CG & Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. 19164750

OMV Signal transduction

Date Authors Article Pubmed
[X] 1984 Lopilato JE & Beckwith JR. D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. 6327616
[X] 1995 Härle C & Braun V. Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface. 7729419
[1] 1998 Tomii K & Kanehisa M. A comparative analysis of ABC transporters in complete microbial genomes. 9799792
[X] 1999 De Wulf P & Lin EC. The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons. 10542180
[6] 2000 Stock AM & Goudreau PN. Two-component signal transduction. 10966457
[X] 2000 Yaron S & Matthews KR. Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. 11010892
[X] 2004 Dwyer MA & Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. 15313245
[X] 2006 Braun V & Sauter A. Gene regulation by transmembrane signaling. 16718597
[X] 2007 Baker MD & Stock JB Signal transduction: networks and integrated circuits in bacterial cognition. 18054766
[X] 2007 Baker MD & Stock JB. Systems biology of bacterial chemotaxis. 16529985
[X] 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? 17921293
[X] 2008 Thie H & Hust M. SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. 18504019
[9] 2009 Kyriakidis DA & Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. 19198978
[X] 2009 Tomii & Kanehisa comparative analysis of ABC transporter pdf-link

Modelling

Date Authors Article Pubmed
Genetic Regulatory Network
[1] 1977 Gillespie Daniel T. Exact Stochastic Simlation of Coupled Chemical Equations Gillespie1
[3] 1997 J.B. Andersen & S.Molin New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria LVA tag
[6] 1999 M.Ellowitz & S.Leibler A Synthetic oscillatory network of transcriptionnal regulators 10659856
[2] 1997 D.T.Gillespie The Chemical Langevin Equation Gillespie2
[5] 2002 N.Rosenfold & U.Alon Negative Autoregulation Speeds The Response TImes of Transcription Network 2417193
[X] 2002 M.B.Ellowitz & P.S.Swain Stochastic Gene Expression In A Single Cell 12183631
[7] 2003 S.Mangan & U.Alon Structure and function ot the feed-forward Loop Network Motif 14530388
[4] 2003 S.Basu & R.Weiss Spatiotemporal control of gene expression with pulse-generating networks 15096621
[1] 2005 S.Hooshangi & R.Weiss Ultrasensitivity and noise propagation in a synthetic transcriptional cascade 15738412
[3] 2006 H.Li & L.Petzold Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems Sto.Sim
[2] 2007 U.Alon Network motifs : theory and experimental approaches 117510665
[X] 2006 J.Stricker & J.Hasty A Fast Robust and Tunable synthetic gene oscillator 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