J. E. Galán, M. Lara-tejero, T. C. Marlovits, and S. Wagner, Bacterial type III secretion systems: specialized nanomachines for protein delivery into target cells, Annu Rev Microbiol, vol.68, pp.415-438, 2014.

S. Ehsani, C. D. Rodrigues, and J. Enninga, Turning on the spotlight-using light to monitor and characterize bacterial effector secretion and translocation, Curr Opin Microbiol, vol.12, pp.24-30, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-01899508

F. X. Campbell-valois and P. J. Sansonetti, Tracking bacterial pathogens with genetically-encoded reporters, FEBS Lett, vol.588, pp.2428-2436, 2014.

M. P. Sory, A. Boland, I. Lambermont, and G. R. Cornelis, Identification of the YopE and YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach, Proc Natl Acad Sci USA, vol.92, pp.11998-12002, 1995.

X. Charpentier and E. Oswald, Identification of the secretion and translocation domain of the enteropathogenic and enterohemorrhagic Escherichia coli effector Cif, using TEM-1 beta-lactamase as a new fluorescence-based reporter, J Bacteriol, vol.186, pp.5486-5495, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02683194

A. Subtil, C. Parsot, and A. Dautry-varsat, Secretion of predicted Inc proteins of Chlamydia pneumoniae by a heterologous type III machinery, Mol Microbiol, vol.39, pp.792-800, 2001.

D. Burstein, S. Satanower, M. Simovitch, Y. Belnik, M. Zehavi et al., Novel type III effectors in Pseudomonas aeruginosa, mBio, vol.6, p.161, 2015.

S. Ong, B. Blagoev, I. Kratchmarova, D. B. Kristensen, H. Steen et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol Cell Proteomics, vol.1, pp.376-386, 2002.

S. Wiese, K. A. Reidegeld, H. E. Meyer, and B. Warscheid, Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research, Proteomics, vol.7, p.17177251, 2007.

W. Deng, C. L. De-hoog, H. B. Yu, Y. Li, M. A. Croxen et al., A comprehensive proteomic analysis of the type III secretome of Citrobacter rodentium, J Biol Chem, vol.285, pp.6790-6800, 2010.

W. Deng, H. B. Yu, C. L. De-hoog, N. Stoynov, Y. Li et al., Quantitative proteomic analysis of type III secretome of enteropathogenic Escherichia coli reveals an expanded effector repertoire for attaching/effacing bacterial pathogens, Mol Cell Proteomics, vol.11, pp.692-709, 2012.

C. W. Vander-broek, K. J. Chalmers, M. P. Stevens, and J. M. Stevens, Quantitative proteomic analysis of Burkholderia pseudomallei Bsa type III secretion system effectors using hypersecreting mutants, Mol Cell Proteomics, vol.14, pp.905-916, 2015.

E. Altindis, T. Dong, C. Catalano, and J. Mekalanos, Secretome analysis of Vibrio cholerae type VI secretion system reveals a new effector-immunity pair, mBio, vol.6, pp.75-90, 2015.

N. Kapitein and A. Mogk, Deadly syringes: type VI secretion system activities in pathogenicity and interbacterial competition, Curr Opin Microbiol, vol.16, pp.52-58, 2013.

A. Hachani, T. E. Wood, and A. Filloux, Type VI secretion and anti-host effectors, Curr Opin Microbiol, vol.29, pp.81-93, 2016.

X. Liu, L. Lu, X. Liu, X. Liu, C. Pan et al., Proteomic analysis of Shigella virulence effectors secreted under different conditions, J Microbiol Biotechnol, 2016.

C. Buchrieser, P. Glaser, C. Rusniok, H. Nedjari, D. 'hauteville et al., The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri, Mol Microbiol, vol.38, pp.760-771, 2000.

M. M. Venkatesan, M. B. Goldberg, D. J. Rose, E. J. Grotbeck, V. Burland et al., Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri, Infect Immun, vol.69, pp.3271-3285, 2001.

T. Sanada, M. Kim, H. Mimuro, M. Suzuki, M. Ogawa et al., The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response, Nature, vol.483, pp.623-626, 2012.

N. Burnaevskiy, T. G. Fox, D. A. Plymire, J. M. Ertelt, B. A. Weigele et al., Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ, Nature, vol.496, pp.106-109, 2013.

H. Ashida, T. Toyotome, T. Nagai, and C. Sasakawa, Shigella chromosomal IpaH proteins are secreted via the type III secretion system and act as effectors, Mol Microbiol, vol.63, p.17214743, 2007.

L. Liu, H. L. Johnson, S. Cousens, J. Perin, S. Scott et al., Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since, Lancet, vol.379, pp.2151-2161, 2000.

F. X. Campbell-valois and S. M. Pontier, Implications of Spatiotemporal Regulation of Shigella flexneri Type Three Secretion Activity on Effector Functions: Think Globally, Act Locally. Front Cell Infect Microbiol, vol.6, p.28, 2016.

A. Phalipon and P. J. Sansonetti, Shigella's ways of manipulating the host intestinal innate and adaptive immune system: a tool box for survival?, Immunol Cell Biol, vol.85, pp.119-129, 2007.

R. Ménard, P. Sansonetti, and C. Parsot, The secretion of the Shigella flexneri Ipa invasins is activated by epithelial cells and controlled by IpaB and IpaD, EMBO J, vol.13, pp.5293-5302, 1994.

A. Allaoui, P. J. Sansonetti, and C. Parsot, MxiD, an outer membrane protein necessary for the secretion of the Shigella flexneri lpa invasins, Mol Microbiol, vol.7, pp.59-68, 1993.

P. J. Sansonetti, D. J. Kopecko, and S. B. Formal, Involvement of a plasmid in the invasive ability of Shigella flexneri, Infect Immun, vol.35, pp.852-860, 1982.

R. Ménard, P. J. Sansonetti, and C. Parsot, Nonpolar mutagenesis of the ipa genes defines IpaB, IpaC, and IpaD as effectors of Shigella flexneri entry into epithelial cells, J Bacteriol, vol.175, pp.5899-5906, 1993.

F. Campbell-valois, P. Schnupf, G. Nigro, M. Sachse, P. J. Sansonetti et al., A fluorescent reporter reveals on/off regulation of the Shigella type III secretion apparatus during entry and cell-to-cell spread, Cell Host Microbe, vol.15, pp.177-189, 2014.

M. Sörensen, C. Lippuner, T. Kaiser, A. Misslitz, T. Aebischer et al., Rapidly maturing red fluorescent protein variants with strongly enhanced brightness in bacteria, FEBS Lett, vol.552, pp.110-114, 2003.

L. Käll, J. D. Canterbury, J. Weston, W. S. Noble, and M. J. Maccoss, Semi-supervised learning for peptide identification from shotgun proteomics datasets, Nat Methods, vol.4, pp.923-925, 2007.

J. C. Silva, M. V. Gorenstein, G. Li, J. Vissers, and S. J. Geromanos, Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition, Mol Cell Proteomics, vol.5, pp.144-156, 2006.

J. Grossmann, B. Roschitzki, C. Panse, C. Fortes, S. Barkow-oesterreicher et al., Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods, J Proteomics, vol.73, pp.1740-1746, 2010.

J. Reinhardt and M. Kolbe, Secretion assay in Shigella flexneri, Bio-protocol, vol.4, p.1302, 2014.

K. Dohlich, A. B. Zumsteg, C. Goosmann, and M. Kolbe, A substrate-fusion protein is trapped inside the Type III Secretion System channel in Shigella flexneri, PLoS Pathog, vol.10, p.1003881, 2014.

C. S. Faherty and A. T. Maurelli, Spa15 of Shigella flexneri is secreted through the type III secretion system and prevents staurosporine-induced apoptosis, Infect Immun, vol.77, pp.5281-5290, 2009.

M. Mavris, A. Page, R. Tournebize, B. Demers, P. Sansonetti et al., Regulation of transcription by the activity of the Shigella flexneri type III secretion apparatus, Mol Microbiol, vol.43, pp.1543-1553, 2002.

C. Penno, P. Sansonetti, and C. Parsot, Frameshifting by transcriptional slippage is involved in production of MxiE, the transcription activator regulated by the activity of the type III secretion apparatus in Shigella flexneri, Mol Microbiol, vol.56, pp.204-214, 2005.

A. Page, P. Sansonetti, and C. Parsot, Spa15 of Shigella flexneri, a third type of chaperone in the type III secretion pathway, Mol Microbiol, vol.43, pp.1533-1542, 2002.

C. Parsot, E. Ageron, C. Penno, M. Mavris, K. Jamoussi et al., A secreted anti-activator, OspD1, and its chaperone, Spa15, are involved in the control of transcription by the type III secretion apparatus activity in Shigella flexneri, Mol Microbiol, vol.56, p.15916611, 2005.

J. Schindelin, I. Arganda-carreras, E. Frise, V. Kaynig, M. Longair et al., Fiji: an open-source platform for biological-image analysis, Nat Methods, vol.9, pp.676-682, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02616466

M. L. Bernardini, J. Mounier, D. 'hauteville, H. Coquis-rondon, M. Sansonetti et al., Identification of icsA, a plasmid locus of Shigella flexneri that governs bacterial intra-and intercellular spread through interaction with F-actin, Proc Natl Acad Sci, vol.86, pp.3867-3871, 1989.

S. Sidik, H. Kottwitz, J. Benjamin, J. Ryu, A. Jarrar et al., A Shigella flexneri virulence plasmid encoded factor controls production of outer membrane vesicles. G3 (Bethesda), vol.4, pp.2493-2503, 2014.

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci USA, vol.97, pp.6640-6645, 2000.

E. V. Oaks, M. E. Wingfield, and S. B. Formal, Plaque formation by virulent Shigella flexneri, Infect Immun, vol.48, pp.124-129, 1985.

J. A. Vizcaíno, E. W. Deutsch, R. Wang, A. Csordas, F. Reisinger et al., ProteomeXchange provides globally coordinated proteomics data submission and dissemination, Nat Biotechnol, vol.32, pp.223-226, 2014.

D. V. Zurawski, K. L. Mumy, L. Badea, J. A. Prentice, E. L. Hartland et al., The NleE/OspZ family of effector proteins is required for polymorphonuclear transepithelial migration, a characteristic shared by enteropathogenic Escherichia coli and Shigella flexneri infections, Infect Immun, vol.76, p.17984206, 2008.

L. Gall, T. Mavris, M. Martino, M. C. Bernardini, M. Denamur et al., Analysis of virulence plasmid gene expression defines three classes of effectors in the type III secretion system of Shigella flexneri, Microbiology, vol.151, pp.951-962, 2005.

M. B. Goldberg, O. Bârzu, C. Parsot, and P. J. Sansonetti, Unipolar localization and ATPase activity of IcsA, a Shigella flexneri protein involved in intracellular movement, J Bacteriol, vol.175, pp.2189-2196, 1993.

Z. Benjelloun-touimi, P. J. Sansonetti, and C. Parsot, SepA, the major extracellular protein of Shigella flexneri: autonomous secretion and involvement in tissue invasion, Mol Microbiol, vol.17, pp.123-135, 1995.

D. Santapaola, D. Chierico, F. Petrucca, A. Uzzau, S. Casalino et al., Apyrase, the product of the virulence plasmid-encoded phoN2 (apy) gene of Shigella flexneri, is necessary for proper unipolar IcsA localization and for efficient intercellular spread, J Bacteriol, vol.188, pp.1620-1627, 2006.

J. Lee, R. Page, R. García-contreras, J. Palermino, X. Zhang et al., Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance, J Mol Biol, vol.373, pp.11-26, 2007.

G. Mcvicker and C. M. Tang, Deletion of toxin-antitoxin systems in the evolution of Shigella sonnei as a hostadapted pathogen, Nat Microbiol, vol.2, p.16204, 2016.

Y. Yamaguchi, J. Park, and M. Inouye, Toxin-antitoxin systems in bacteria and archaea, Annu Rev Genet, vol.45, pp.61-79, 2011.

E. Mills, K. Baruch, X. Charpentier, S. Kobi, and I. Rosenshine, Real-time analysis of effector translocation by the type III secretion system of enteropathogenic Escherichia coli, Cell Host Microbe, vol.3, pp.104-113, 2008.

L. Pinaud, F. Samassa, Z. Porat, M. L. Ferrari, I. Belotserkovsky et al., Injection of T3SS effectors not resulting in invasion is the main targeting mechanism of Shigella toward human lymphocytes, Proc Natl Acad Sci, vol.114, pp.9954-9959, 2017.

C. Parsot, R. Ménard, P. Gounon, and P. J. Sansonetti, Enhanced secretion through the Shigella flexneri Mxi-Spa translocon leads to assembly of extracellular proteins into macromolecular structures, Mol Microbiol, vol.16, pp.291-300, 1995.

G. Zlokarnik, P. A. Negulescu, T. E. Knapp, L. Mere, N. Burres et al., Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter, Science, vol.279, pp.84-88, 1998.

C. Konradt, E. Frigimelica, K. Nothelfer, A. Puhar, W. Salgado-pabon et al., The Shigella flexneri type three secretion system effector IpgD inhibits T cell migration by manipulating host phosphoinositide metabolism, Cell Host Microbe, vol.9, pp.263-272, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00594631

M. Ogawa, T. Suzuki, I. Tatsuno, H. Abe, and C. Sasakawa, IcsB, secreted via the type III secretion system, is chaperoned by IpgA and required at the post-invasion stage of Shigella pathogenicity, Mol Microbiol, vol.48, pp.913-931, 2003.

P. Bernard and M. Couturier, Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes, J Mol Biol, vol.226, pp.735-745, 1992.

S. Sayeed, L. Reaves, L. Radnedge, and S. Austin, The stability region of the large virulence plasmid of Shigella flexneri encodes an efficient postsegregational killing system, J Bacteriol, vol.182, pp.2416-2421, 2000.

H. Yen, Q. Xu, D. M. Chou, Z. Zhao, and S. J. Elledge, Global protein stability profiling in mammalian cells, Science, vol.322, pp.918-923, 2008.

J. E. Galán and H. Wolf-watz, Protein delivery into eukaryotic cells by type III secretion machines, Nature, vol.444, pp.567-573, 2006.

A. Santiago, J. S. Mendes, S. Dos, C. A. De-toledo, M. Beloti et al., The Antitoxin Protein of a Toxin-Antitoxin System from Xylella fastidiosa Is Secreted via Outer Membrane Vesicles, Front Microbiol, vol.7, p.2030, 2016.

M. Ogawa, T. Yoshimori, T. Suzuki, H. Sagara, N. Mizushima et al., Escape of intracellular Shigella from autophagy, Science, vol.307, pp.727-731, 2005.

F. Campbell-valois, M. Sachse, P. J. Sansonetti, and C. Parsot, Escape of Actively Secreting Shigella flexneri from ATG8/LC3-Positive Vacuoles Formed during Cell-To-Cell Spread Is Facilitated by IcsB and VirA, mBio, vol.6, pp.2567-2581, 2015.

A. M. Cheverton, B. Gollan, M. Przydacz, C. T. Wong, A. Mylona et al., A Salmonella Toxin Promotes Persister Formation through Acetylation of tRNA, Mol Cell, vol.63, pp.86-96, 2016.