Team:Paris/Papers

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Contents

Bibliography

In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part.


For the references of the Ethical part go to the Material or References.


OMV Overview

N° Date Authors Article Pubmed
[X] 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]
[X] 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$=citationsensor 14531993]
[X] 2005 Kuehn MJ & Kesty NC. Bacterial outer membrane vesicles and the host-pathogen interaction. [http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]
[X] 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$=citationsensor 16855227]
[1] 2007 McBroom AJ & Kuehn MJ. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. [http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]
[2] 2009 Deatherage BL & Cookson BT. Biogenesis of bacterial membrane vesicles [http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]
[X] 2009 Purnick PE & Weiss R. The second wave of synthetic biology: from modules to systems. [http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]

OMV Production

N° Date Authors Article Pubmed
[X] 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
[2] 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]
[X] 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]
[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. [http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]
Tol/Pal
[X] 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]
[3] 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]
[X] 1999 Derouiche & Loret Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains. [http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]
[4] 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]
[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. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]
[X] 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]
[5] 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
[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. [http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]
[X] 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]
[X] 2000 Berks BC & Palmer T. The Tat protein export pathway. [http://www.ncbi.nlm.nih.gov/pubmed/10652088 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. [http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]
[X] 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]
[X] 2001 Yahr TL & Wickner WT. Functional reconstitution of bacterial Tat translocation in vitro. [http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]
[X] 2004 Robinson C & Bolhuis A. Tat-dependent protein targeting in prokaryotes and chloroplasts. [http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]
[X] 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]
[X] 2006 Lee PA & Georgiou G. The bacterial twin-arginine translocation pathway. [http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]
[X] 2007 Maillard J & Sargent F. Structural diversity in twin-arginine signal peptide-binding proteins. [http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]
[X] 2007 Sargent F. The twin-arginine transport system: moving folded proteins across membranes. [http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]
[X] 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]
[X] 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]
[X] 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]
[X] 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] [1] 2008 Kim JY & DeLisa MP. Engineered bacterial outer membrane vesicles with enhanced functionality. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]
[1] [2] 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
[1] 2002 Wang Y. The function of OmpA in Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]
[X] 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
[X] 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]
[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. [http://www.ncbi.nlm.nih.gov/pubmed/7927803 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. [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
[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. [http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]
[8] 1999 Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. [http://www.ncbi.nlm.nih.gov/pubmed/10606756 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. [http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]
[10] 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]
[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. [http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]
Snare
[17] 2000 Waters MG & Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. [http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]
[X] 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]
[X] 2002 Bowen ME,Brunger AT. Mutational analysis of synaptobrevin transmembrane domain oligomerization. [http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]
[X] 2003 Hu C & Rothman JE. Fusion of cells by flipped SNAREs. [http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]
[X] 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]
[X] 2006 Giraudo CG & Rothman JE. A clamping mechanism involved in SNARE-dependent exocytosis. [http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]
[X] 2006 Low HH & Löwe J. A bacterial dynamin-like protein. [http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]
[X] 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]
[X] 2008 Delevoye C & Subtil A. SNARE protein mimicry by an intracellular bacterium. [http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]
[18] 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
[X] 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]
[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. [http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]
[1] 1998 Tomii K & Kanehisa M. A comparative analysis of ABC transporters in complete microbial genomes. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 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. [http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]
[6] 2000 Stock AM & Goudreau PN. Two-component signal transduction. [http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]
[X] 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]
[X] 2004 Dwyer MA & Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. [http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]
[X] 2006 Braun V & Sauter A. Gene regulation by transmembrane signaling. [http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]
[X] 2007 Baker MD & Stock JB Signal transduction: networks and integrated circuits in bacterial cognition. [http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]
[X] 2007 Baker MD & Stock JB. Systems biology of bacterial chemotaxis. [http://www.ncbi.nlm.nih.gov/pubmed/16529985 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? [http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]
[X] 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]
[9] 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]
[X] 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]
[X] 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]
[X] 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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