G. N. Schroeder and H. Hilbi, Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion, Clin Microbiol Rev, vol.21, issue.1, pp.134-56, 2008.

G. R. Cornelis, The type III secretion injectisome, Nat Rev Microbiol, vol.4, issue.11, pp.811-836, 2006.

S. E. Girardin, R. Tournebize, M. Mavris, A. L. Page, X. Li et al., CARD4/Nod1 mediates NF-kappaB and JNK activation by invasive Shigella flexneri, EMBO Rep, vol.2, issue.8, pp.736-778, 2001.

S. E. Girardin, I. G. Boneca, L. A. Carneiro, A. Antignac, M. Jehanno et al., Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan, Science, vol.300, issue.5625, 2003.

M. Hasegawa, Y. Fujimoto, P. C. Lucas, H. Nakano, K. Fukase et al., A critical role of RICK/RIP2 polyubiquitination in Nod-induced NF-kappaB activation, EMBO J, vol.27, issue.2, pp.373-83, 2008.

C. Wang, L. Deng, M. Hong, G. R. Akkaraju, J. Inoue et al., TAK1 is a ubiquitin-dependent kinase of MKK and IKK, Nature, vol.412, issue.6844, 2001.

N. Dupont, S. Lacas-gervais, J. Bertout, I. Paz, B. Freche et al., Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy, Cell Host Microbe, vol.6, issue.2, pp.137-186, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02109149

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, issue.7391, pp.623-629, 2012.

D. W. Kim, G. Lenzen, A. L. Page, P. Legrain, P. J. Sansonetti et al., The Shigella flexneri effector OspG interferes with innate immune responses by targeting ubiquitin-conjugating enzymes, Proc Natl Acad Sci, vol.102, issue.39, 2005.

, PtdIns5P. Immunity, vol.39, issue.6, pp.1121-1152, 2013.

C. A. Kasper, I. Sorg, C. Schmutz, T. Tschon, H. Wischnewski et al., Cell-cell propagation of NFkappaB transcription factor and MAP kinase activation amplifies innate immunity against bacterial infection, Epub 2010/11/26, vol.33, p.21093316, 2010.

T. Dolowschiak, C. Chassin, B. Mkaddem, S. Fuchs, T. M. Weiss et al., Potentiation of epithelial innate host responses by intercellular communication, PLoS Pathog, vol.6, issue.11, p.21124989, 2010.

S. J. Patel, K. R. King, M. Casali, and M. L. Yarmush, DNA-triggered innate immune responses are propagated by gap junction communication, Proc Natl Acad Sci, vol.106, issue.31, pp.12867-72, 2009.

A. Ablasser, J. L. Schmid-burgk, I. Hemmerling, G. L. Horvath, T. Schmidt et al., Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP, Nature, vol.503, issue.7477, pp.530-534, 2013.

B. Kneidinger, C. Marolda, M. Graninger, A. Zamyatina, F. Mcarthur et al., Caspase-11 protects against bacteria that escape the vacuole, Science, vol.339, p.975, 2013.

D. W. Abbott, Y. Yang, J. E. Hutti, S. Madhavarapu, M. A. Kelliher et al., , 2007.

, Coordinated Regulation of Toll-Like Receptor and NOD2 Signaling by K63-Linked Polyubiquitin Chains, Mol. Cell. Biol, vol.27, p.6012

A. Ablasser, J. L. Schmid-burgk, I. Hemmerling, G. L. Horvath, T. Schmidt et al., Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP, Nature, vol.503, pp.530-534, 2013.

C. Abraham and R. Medzhitov, Interactions Between the Host Innate Immune System and Microbes in Inflammatory Bowel Disease, Gastroenterology, vol.140, p.1729, 2011.

M. T. Abreu, Toll-like receptor signalling in the intestinal epithelium: how bacterial recognition shapes intestinal function, Nat. Rev. Immunol, vol.10, pp.131-144, 2010.

M. T. Abreu, P. Vora, E. Faure, L. S. Thomas, E. T. Arnold et al., Decreased expression of Toll-like receptor-4 and MD-2 correlates with intestinal epithelial cell protection against dysregulated proinflammatory gene expression in response to bacterial lipopolysaccharide, J. Immunol. Baltim. Md, vol.167, pp.1609-1616, 1950.

M. T. Abreu, E. T. Arnold, L. S. Thomas, R. Gonsky, Y. Zhou et al., TLR4 and MD-2 expression is regulated by immune-mediated signals in human intestinal epithelial cells, J. Biol. Chem, vol.277, pp.20431-20437, 2002.

A. Aderem and R. J. Ulevitch, Toll-like receptors in the induction of the innate immune response, Nature, vol.406, pp.782-787, 2000.

Y. Akeda and J. E. Galán, Chaperone release and unfolding of substrates in type III secretion, Nature, vol.437, pp.911-915, 2005.

S. Akira, S. Uematsu, and O. Takeuchi, Pathogen Recognition and Innate Immunity, Cell, vol.124, pp.783-801, 2006.

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.

I. C. Allen, J. E. Wilson, M. Schneider, J. D. Lich, R. A. Roberts et al., NLRP12 Suppresses Colon Inflammation and Tumorigenesis through the Negative Regulation of Noncanonical NF-?B Signaling, Immunity, vol.36, pp.742-754, 2012.

L. Arbibe, D. W. Kim, E. Batsche, T. Pedron, B. Mateescu et al., An injected bacterial effector targets chromatin access for transcription factor NF-?B to alter transcription of host genes involved in immune responses, Nat. Immunol, vol.8, pp.47-56, 2007.

J. Arondel, M. Singer, A. Matsukawa, A. Zychlinsky, and P. J. Sansonetti, Increased Interleukin-1 (IL-1) and Imbalance between IL-1 and IL-1 Receptor Antagonist during Acute Inflammation in Experimental Shigellosis, Infect. Immun, vol.67, pp.6056-6066, 1999.

J. S. Arthur, MSK activation and physiological roles, Front. Biosci. J. Virtual Libr, vol.13, pp.5866-5879, 2008.

H. Ashida and C. Sasakawa, Shigella IpaH Family Effectors as a Versatile Model for Studying Pathogenic Bacteria, Front. Cell. Infect. Microbiol, vol.5, 2016.

H. Ashida, M. Kim, M. Schmidt-supprian, A. Ma, M. Ogawa et al., A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKK to dampen the host NF-?B-mediated inflammatory response, Nat. Cell Biol, vol.12, pp.66-69, 2010.

H. Ashida, M. Ogawa, H. Mimuro, T. Kobayashi, T. Sanada et al., , 2011.

, Shigella are versatile mucosal pathogens that circumvent the host innate immune system, Curr. Opin. Immunol, vol.23, pp.448-455

H. Ashida, H. Nakano, and C. Sasakawa, Shigella IpaH0722 E3 Ubiquitin Ligase Effector Targets TRAF2 to Inhibit PKC-NF-?B Activity in Invaded Epithelial Cells. PLOS Pathog. 9, 2013.

P. Ataie-kachoie, M. H. Pourgholami, D. R. Richardson, and D. L. Morris, Gene of the month: Interleukin 6 (IL-6), J. Clin. Pathol, vol.67, pp.932-937, 2014.

T. Ayabe, D. P. Satchell, C. L. Wilson, W. C. Parks, M. E. Selsted et al., Secretion of microbicidal alpha-defensins by intestinal Paneth cells in response to bacteria, Nat. Immunol, vol.1, pp.113-118, 2000.

S. Barman, D. R. Saha, T. Ramamurthy, and H. Koley, Development of a new guineapig model of shigellosis, FEMS Immunol. Med. Microbiol, vol.62, pp.304-314, 2011.

F. Bauernfeind, G. Horvath, A. Stutz, E. S. Alnemri, K. Macdonald et al., NF-kB activating pattern recognition and cytokine receptors license NLRP3 inflammasome activation by regulating NLRP3 expression, J. Immunol. Baltim. Md, p.787, 1950.

B. Beck-schimmer, R. C. Schimmer, R. L. Warner, H. Schmal, G. Nordblom et al., Expression of Lung Vascular and Airway ICAM-1 after Exposure to Bacterial Lipopolysaccharide, Am. J. Respir. Cell Mol. Biol, vol.17, pp.344-352, 1997.

S. Beinke, M. J. Robinson, M. Hugunin, and S. C. Ley, Lipopolysaccharide activation of the TPL-2/MEK/extracellular signal-regulated kinase mitogen-activated protein kinase cascade is regulated by IkappaB kinase-induced proteolysis of NF-kappaB1 p105, Mol. Cell. Biol, vol.24, pp.9658-9667, 2004.

M. Bennett, Gap junctions, New Encyclopedia of Neuroscience, L. Squire, 2007.

T. Bergsbaken, S. L. Fink, and B. T. Cookson, Pyroptosis: host cell death and inflammation, Nat. Rev. Microbiol, vol.7, pp.99-109, 2009.

M. L. Bernardini, J. Mounier, H. Hauteville, M. Coquis-rondon, and P. J. Sansonetti, 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. U. S. A, vol.86, pp.3867-3871, 1989.

J. Bertin, W. Nir, C. M. Fischer, O. V. Tayber, P. R. Errada et al., Human CARD4 Protein Is a Novel CED, 1999.

, Apaf-1 Cell Death Family Member That Activates NF-?B, J. Biol. Chem, vol.274, pp.12955-12958

A. Blocker, P. Gounon, E. Larquet, K. Niebuhr, V. Cabiaux et al.,

, The Tripartite Type III Secreton of Shigella flexneri Inserts Ipab and Ipac into Host Membranes, J. Cell Biol, vol.147, p.683

A. Blocker, N. Jouihri, E. Larquet, P. Gounon, F. Ebel et al., Structure and composition of the Shigella flexneri "needle complex", a part of its type III secreton, Mol. Microbiol, vol.39, pp.652-663

A. Blocker, K. Komoriya, and S. Aizawa, Type III secretion systems and bacterial flagella: Insights into their function from structural similarities, Proc. Natl. Acad. Sci, vol.100, pp.3027-3030, 2003.

A. Bowen, Chapter 3 -shigellosis, Health Information for International Travel, G. Brunette, ed, 2017.

J. Branger, S. Knapp, S. Weijer, J. C. Leemans, J. M. Pater et al., Role of Toll-like receptor 4 in gram-positive and gram-negative pneumonia in mice, Infect. Immun, vol.72, pp.788-794, 2004.

C. Buchrieser, P. Glaser, C. Rusniok, H. Nedjari, H. 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.

Z. Cao, J. Xiong, M. Takeuchi, T. Kurama, and D. V. Goeddel, TRAF6 is a signal transducer for interleukin-1, Nature, vol.383, pp.443-446, 1996.

N. Carayol, T. Van-nhieu, and G. , Tips and tricks about Shigella invasion of epithelial cells, Curr. Opin. Microbiol, vol.16, pp.32-37, 2013.

E. Cario and D. K. Podolsky, Differential Alteration in Intestinal Epithelial Cell Expression of Toll-Like Receptor 3 (TLR3) and TLR4 in Inflammatory Bowel Disease, Infect. Immun, vol.68, p.7010, 2000.

R. Caruso, N. Warner, N. Inohara, and G. Núñez, NOD1 and NOD2: Signaling, Host Defense, and Inflammatory Disease, vol.41, pp.898-908, 2014.

M. Chamaillard, M. Hashimoto, Y. Horie, J. Masumoto, S. Qiu et al., An essential role for NOD1 in host recognition of bacterial peptidoglycan containing diaminopimelic acid, Nat. Immunol, vol.4, pp.702-707, 2003.

C. Chassin, M. Picardeau, J. Goujon, P. Bourhy, N. Quellard et al., TLR4-and TLR2-mediated B cell responses control the clearance of the bacterial pathogen, Leptospira interrogans, J. Immunol. Baltim. Md, vol.183, pp.2669-2677, 1950.

G. Y. Chen, Role of Nlrp6 and Nlrp12 in the maintenance of intestinal homeostasis, Eur. J. Immunol, vol.44, pp.321-327, 2014.

Z. Chen, J. Hagler, V. J. Palombella, F. Melandri, D. Scherer et al., Signal-induced site-specific phosphorylation targets I kappa B alpha to the ubiquitinproteasome pathway, Genes Dev, vol.9, pp.1586-1597, 1995.

T. Chiba, H. Matsuo, M. Sakiyama, A. Nakayama, S. Shimizu et al., Common variant of ALPK1 is not associated with gout: a replication study, Hum. Cell, vol.28, pp.1-4, 2015.

M. Chmiela, E. Miszczyk, and K. Rudnicka, Structural modifications of Helicobacter pylori lipopolysaccharide: an idea for how to live in peace, World J. Gastroenterol, vol.20, pp.9882-9897, 2014.

F. Ciacci-woolwine, I. C. Blomfield, S. H. Richardson, and S. B. Mizel, Salmonella flagellin induces tumor necrosis factor alpha in a human promonocytic cell line, Infect. Immun, vol.66, pp.1127-1134, 1998.

K. Clark, J. Middelbeek, M. V. Dorovkov, C. G. Figdor, A. G. Ryazanov et al., The alpha-kinases TRPM6 and TRPM7, but not eEF-2 kinase, phosphorylate the assembly domain of myosin IIA, IIB and IIC, FEBS Lett, vol.582, pp.2993-2997, 2008.

D. B. Conze, C. Wu, J. A. Thomas, A. Landstrom, and J. D. Ashwell, Lys63-linked polyubiquitination of IRAK-1 is required for interleukin-1 receptor-and toll-like receptor-mediated NF-kappaB activation, Mol. Cell. Biol, vol.28, pp.3538-3547, 2008.

F. S. Cordes, K. Komoriya, E. Larquet, S. Yang, E. H. Egelman et al., Helical structure of the needle of the type III secretion system of Shigella flexneri, J. Biol. Chem, vol.278, pp.17103-17107, 2003.

G. R. Cornelis, The type III secretion injectisome, Nat. Rev. Microbiol, vol.4, pp.811-825, 2006.

P. Cossart, Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes, Proc. Natl. Acad. Sci. U. S. A, vol.108, pp.19484-19491, 2011.

I. M. Dambuza and G. D. Brown, C-type lectins in immunity: recent developments, Curr. Opin. Immunol, vol.32, pp.21-27, 2015.

L. Deng, C. Wang, E. Spencer, L. Yang, A. Braun et al., Activation of the IkappaB kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chain, Cell, vol.103, pp.351-361, 2000.

N. Desroy, F. Moreau, S. Briet, G. L. Fralliec, S. Floquet et al., Towards Gram-negative antivirulence drugs: New inhibitors of HldE kinase, Bioorg. Med. Chem, vol.17, pp.1276-1289, 2009.

N. Desroy, A. Denis, C. Oliveira, D. Atamanyuk, S. Briet et al., Novel HldE-K Inhibitors Leading to Attenuated Gram Negative Bacterial Virulence, J. Med. Chem, vol.56, pp.1418-1430, 2013.

J. A. Didonato, M. Hayakawa, D. M. Rothwarf, E. Zandi, K. et al., A cytokineresponsive IkappaB kinase that activates the transcription factor NF-kappaB, Nature, vol.388, pp.548-554, 1997.

A. Diepold and J. P. Armitage, Type III secretion systems: the bacterial flagellum and the injectisome, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.370, 2015.

C. A. Dinarello, Interleukin-1 and interleukin-1 antagonism, Blood, vol.77, pp.1627-1652, 1991.

C. A. Dinarello, Immunological and Inflammatory Functions of the Interleukin-1 Family, Annu. Rev. Immunol, vol.27, pp.519-550, 2009.

T. Dolowschiak, C. Chassin, S. B. Mkaddem, T. M. Fuchs, S. Weiss et al., Potentiation of Epithelial Innate Host Responses by Intercellular Communication, PLOS Pathog, vol.6, 2010.

Y. Dorsett and T. Tuschl, siRNAs: applications in functional genomics and potential as therapeutics, Nat. Rev. Drug Discov, vol.3, pp.318-329, 2004.

H. L. Dupont, M. M. Levine, R. B. Hornick, and S. B. Formal, Inoculum size in shigellosis and implications for expected mode of transmission, J. Infect. Dis, vol.159, pp.1126-1128, 1989.

N. Dupont, S. Lacas-gervais, J. Bertout, I. Paz, B. Freche et al., Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy, Cell Host Microbe, vol.6, pp.137-149, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02109149

R. Dziarski, Recognition of bacterial peptidoglycan by the innate immune system, Cell. Mol. Life Sci. CMLS, vol.60, pp.1793-1804, 2003.

C. Ea, L. Sun, J. Inoue, C. , and Z. J. , TIFA activates IkappaB kinase (IKK) by promoting oligomerization and ubiquitination of TRAF6, Proc. Natl. Acad. Sci. U. S. A, vol.101, pp.15318-15323, 2004.

L. Eckmann, M. F. Kagnoff, and J. Fierer, Epithelial cells secrete the chemokine interleukin-8 in response to bacterial entry, Infect. Immun, vol.61, p.4569, 1993.

R. Eferl and E. F. Wagner, AP-1: a double-edged sword in tumorigenesis, Nat. Rev. Cancer, vol.3, pp.859-868, 2003.

C. Egile, T. P. Loisel, V. Laurent, R. Li, D. Pantaloni et al., Activation of the CDC42 effector N-WASP by the Shigella flexneri IcsA protein promotes actin nucleation by Arp2/3 complex and bacterial actin-based motility, J. Cell Biol, vol.146, pp.1319-1332, 1999.

E. Elinav, T. Strowig, A. L. Kau, J. Henao-mejia, C. A. Thaiss et al., NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis, vol.145, pp.745-757, 2011.

C. R. Epler, N. E. Dickenson, A. J. Olive, W. L. Picking, and W. D. Picking, Liposomes recruit IpaC to the Shigella flexneri type III secretion apparatus needle as a final step in secretion induction, Infect. Immun, vol.77, pp.2754-2761, 2009.

M. Espina, A. J. Olive, R. Kenjale, D. S. Moore, S. F. Ausar et al., IpaD localizes to the tip of the type III secretion system needle of Shigella flexneri, Infect. Immun, vol.74, pp.4391-4400, 2006.

M. I. Fernandez, A. Thuizat, T. Pedron, M. Neutra, A. Phalipon et al., A newborn mouse model for the study of intestinal pathogenesis of shigellosis, Cell. Microbiol, vol.5, pp.481-491, 2003.

C. A. Fielding, R. M. Mcloughlin, L. Mcleod, C. S. Colmont, M. Najdovska et al., IL-6 Regulates Neutrophil Trafficking during Acute Inflammation via STAT3, J. Immunol, vol.181, pp.2189-2195, 2008.

L. Franchi, N. Kamada, Y. Nakamura, A. Burberry, P. Kuffa et al., NLRC4-driven production of IL-1 discriminates between pathogenic and commensal bacteria and promotes host intestinal defense, Nat. Immunol, vol.13, pp.449-456, 2012.

H. Frey, N. Schroeder, T. Manon-jensen, R. V. Iozzo, and L. Schaefer, Biological interplay between proteoglycans and their innate immune receptors in inflammation, FEBS J, vol.280, p.2165, 2013.

T. Fujimaki, H. Horibe, M. Oguri, K. Kato, and Y. Yamada, Association of genetic variants of the ?-kinase 1 gene with myocardial infarction in community-dwelling individuals, Biomed. Rep, vol.2, pp.127-131, 2014.

A. Fukazawa, C. Alonso, K. Kurachi, S. Gupta, C. F. Lesser et al., GEF-H1 Mediated Control of NOD1 Dependent NF-?B Activation by Shigella Effectors, PLOS Pathog, vol.4, 2008.

M. Fukumatsu, M. Ogawa, S. Arakawa, M. Suzuki, K. Nakayama et al., Shigella targets epithelial tricellular junctions and uses a noncanonical clathrin-dependent endocytic pathway to spread between cells, Cell Host Microbe, vol.11, pp.325-336, 2012.

R. D. Fusunyan, N. N. Nanthakumar, M. E. Baldeon, and W. A. Walker, Evidence for an innate immune response in the immature human intestine: toll-like receptors on fetal enterocytes, Pediatr. Res, vol.49, pp.589-593, 2001.

A. Gall, R. G. Gaudet, S. D. Gray-owen, and N. R. Salama, TIFA Signaling in Gastric Epithelial Cells Initiates the cag Type 4 Secretion System-Dependent Innate Immune Response to Helicobacter pylori Infection, MBio, vol.8, 2017.

R. G. Gaudet, A. Sintsova, C. M. Buckwalter, N. Leung, A. Cochrane et al., INNATE IMMUNITY. Cytosolic detection of the bacterial metabolite HBP activates TIFA-dependent innate immunity, Science, vol.348, pp.1251-1255, 2015.

R. G. Gaudet, C. X. Guo, R. Molinaro, H. Kottwitz, J. R. Rohde et al., Innate Recognition of Intracellular Bacterial Growth Is Driven by the TIFA-Dependent Cytosolic Surveillance Pathway, Cell Rep, vol.19, pp.1418-1430, 2017.

N. J. Gay, M. F. Symmons, M. Gangloff, and C. E. Bryant, Assembly and localization of Toll-like receptor signalling complexes, Nat. Rev. Immunol, vol.14, pp.546-558, 2014.

A. T. Gewirtz, T. A. Navas, S. Lyons, P. J. Godowski, and J. L. Madara, Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression, J. Immunol. Baltim. Md, vol.167, pp.1882-1885, 1950.

S. Ghosh, M. J. May, and E. B. Kopp, NF-kappa B and Rel proteins: evolutionarily conserved mediators of immune responses, Annu. Rev. Immunol, vol.16, pp.225-260, 1998.

S. E. Girardin, R. Tournebize, M. Mavris, A. Page, X. Li et al., CARD4/Nod1 mediates NF-?B and JNK activation by invasive Shigella flexneri, EMBO Rep, vol.2, pp.736-742, 2001.

S. E. Girardin, L. H. Travassos, M. Hervé, D. Blanot, I. G. Boneca et al., Peptidoglycan Molecular Requirements Allowing Detection by Nod1 and Nod2, J. Biol. Chem, vol.278, pp.41702-41708, 2003.

S. E. Girardin, I. G. Boneca, L. A. Carneiro, A. Antignac, M. Jéhanno et al., Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan, Science, vol.300, pp.1584-1587, 2003.

C. L. Grimes, L. D. Ariyananda, J. E. Melnyk, and E. K. Shea, The Innate Immune Protein Nod2 Binds Directly to MDP, a Bacterial Cell Wall Fragment, J. Am. Chem. Soc, vol.134, pp.13535-13537

A. M. Grishin, T. E. Condos, K. R. Barber, F. Campbell-valois, C. Parsot et al., Structural basis for the inhibition of host protein ubiquitination by Shigella effector kinase OspG, Struct. Lond. Engl, vol.22, pp.878-888, 1993.

G. Häcker, V. Redecke, and H. Häcker, Activation of the immune system by bacterial CpG-DNA, Immunology, vol.105, pp.245-251, 2002.

J. A. Hagar, D. A. Powell, Y. Aachoui, R. K. Ernst, and E. A. Miao, Cytoplasmic LPS activates caspase-11: implications in TLR4-independent endotoxic shock, Science, vol.341, pp.1250-1253, 2013.

L. Hao, A. Sakurai, T. Watanabe, E. Sorensen, C. A. Nidom et al., Drosophila RNAi screen identifies host genes important for influenza virus replication, Nature, vol.454, pp.890-893, 2008.

H. Harouz, C. Rachez, B. M. Meijer, B. Marteyn, F. Donnadieu et al., Shigella flexneri targets the HP1 subcode through the phosphothreonine lyase OspF, EMBO J, vol.33, pp.2606-2622
URL : https://hal.archives-ouvertes.fr/hal-02168073

M. Hasegawa, Y. Fujimoto, P. C. Lucas, H. Nakano, K. Fukase et al., A critical role of RICK/RIP2 polyubiquitination in Nod-induced NF-?B activation, EMBO J, vol.27, p.373, 2008.

F. Hayashi, K. D. Smith, A. Ozinsky, T. R. Hawn, E. C. Yi et al., The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5, Nature, vol.410, pp.1099-1103, 2001.

M. Heine, C. I. Cramm-behrens, A. Ansari, H. Chu, A. G. Ryazanov et al., Alpha-kinase 1, a new component in apical protein transport, J. Biol. Chem, vol.280, pp.25637-25643, 2005.

T. Henkel, T. Machleidt, I. Alkalay, M. Krönke, Y. Ben-neriah et al., , 1993.

, Rapid proteolysis of I kappa B-alpha is necessary for activation of transcription factor NF-kappa B, Nature, vol.365, pp.182-185

S. Herget, P. V. Toukach, R. Ranzinger, W. E. Hull, Y. A. Knirel et al., Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans, BMC Struct. Biol, vol.8, p.35, 2008.

N. High, J. Mounier, M. C. Prévost, and P. J. Sansonetti, IpaB of Shigella flexneri causes entry into epithelial cells and escape from the phagocytic vacuole, EMBO J, vol.11, 1991.

H. Hilbi, J. E. Moss, D. Hersh, Y. Chen, J. Arondel et al., Shigella-induced apoptosis is dependent on caspase-1 which binds to IpaB, J. Biol. Chem, vol.273, pp.32895-32900, 1998.

L. W. Hillier, T. A. Graves, R. S. Fulton, L. A. Fulton, K. H. Pepin et al., Generation and annotation of the DNA sequences of human chromosomes 2 and 4, Nature, vol.434, pp.724-731, 2005.

K. Hoebe, P. Georgel, S. Rutschmann, X. Du, S. Mudd et al., CD36 is a sensor of diacylglycerides, Nature, vol.433, pp.523-527, 2005.

K. Hofmann and P. Bucher, The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors, Trends Biochem. Sci, vol.20, pp.347-349, 1995.

A. M. Holmgren, C. A. Mcconkey, and S. Shin, Outrunning the Red Queen: bystander activation as a means of outpacing innate immune subversion by intracellular pathogens, Cell. Mol. Immunol, vol.14, pp.14-21, 2017.

M. W. Hornef, B. H. Normark, A. Vandewalle, and S. Normark, Intracellular Recognition of Lipopolysaccharide by Toll-like Receptor 4 in Intestinal Epithelial Cells, J. Exp. Med, vol.198, p.1225, 2003.

K. Hoshino, O. Takeuchi, T. Kawai, H. Sanjo, T. Ogawa et al., Cutting Edge: Toll-Like Receptor 4 (TLR4)-Deficient Mice Are Hyporesponsive to Lipopolysaccharide: Evidence for TLR4 as the Lps Gene Product, J. Immunol, vol.162, pp.3749-3752, 1999.

M. Hosoyamada, Y. Takiue, T. Shibasaki, and H. Saito, The effect of testosterone upon the urate reabsorptive transport system in mouse kidney, Nucleosides Nucleotides Nucleic Acids, vol.29, pp.574-579, 2010.

H. Hu and S. Sun, Ubiquitin signaling in immune responses, Cell Res, vol.26, pp.457-483, 2016.

C. F. Huang, J. Weng, T. W. Wei, P. G. Wu, P. Hsu et al., Intermolecular binding between TIFA-FHA and TIFA-pT mediates tumor necrosis factor alpha stimulation and NF-?B activation, Mol. Cell. Biol, vol.32, pp.2664-2673, 2012.

J. Huang, Y. Xie, X. Sun, H. J. Zeh, . Iii et al., DAMPs, Ageing, and Cancer: The 'DAMP Hypothesis, Ageing Res. Rev, vol.24, p.3, 2015.

K. Husnjak and I. Dikic, Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions, Annu. Rev. Biochem, vol.81, pp.291-322, 2012.

N. Inohara, T. Koseki, L. Del-peso, Y. Hu, C. Yee et al., Nod1, an Apaf-1-like activator of caspase-9 and nuclear factor-kappaB, J. Biol. Chem, vol.274, pp.14560-14567, 1999.

N. Inohara, Y. Ogura, F. F. Chen, A. Muto, and G. Nuñez, Human Nod1 Confers Responsiveness to Bacterial Lipopolysaccharides, J. Biol. Chem, vol.276, pp.2551-2554, 2001.

C. A. Janeway, Approaching the asymptote? Evolution and revolution in immunology, Cold Spring Harb. Symp. Quant. Biol. 54 Pt, vol.1, pp.1-13, 1989.

L. Janot, T. Secher, D. Torres, I. Maillet, J. Pfeilschifter et al., CD14 Works with Toll-Like Receptor 2 to Contribute to Recognition and Control of Listeria monocytogenes Infection, J. Infect. Dis, vol.198, pp.115-124, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00318570

K. Jeong, Q. Zhang, J. Nunnari, and S. Tzipori, A piglet model of acute gastroenteritis induced by Shigella dysenteriae Type 1, J. Infect. Dis, vol.201, pp.903-911, 2010.

M. J. Jimenez-dalmaroni, N. Xiao, A. L. Corper, P. Verdino, G. D. Ainge et al., Soluble CD36 Ectodomain Binds Negatively Charged Diacylglycerol Ligands and Acts as a Co-Receptor for TLR2, PLOS ONE, vol.4, p.7411, 2009.

M. S. Jin, S. E. Kim, J. Y. Heo, M. E. Lee, H. M. Kim et al., , 2007.

, Crystal Structure of the TLR1-TLR2 Heterodimer Induced by Binding of a Tri-Acylated Lipopeptide, Cell, vol.130, pp.1071-1082

S. Johnson, P. Roversi, M. Espina, A. Olive, J. E. Deane et al., Self-Chaperoning of the Type III Secretion System needle tip proteins IpaD and BipD, J. Biol. Chem, vol.282, pp.4035-4044, 2007.

A. C. Johnston, A. Piro, B. Clough, M. Siew, S. Virreira-winter et al., Human GBP1 does not localize to pathogen vacuoles but restricts Toxoplasma gondii, Cell. Microbiol, vol.18, pp.1056-1064, 2016.

C. Jolly, S. Winfree, B. Hansen, and O. Steele-mortimer, The Annexin A2/p11 complex is required for efficient invasion of Salmonella Typhimurium in epithelial cells, Cell. Microbiol, vol.16, pp.64-77, 2014.

R. Jørgensen, P. A. Ortiz, A. Carr-schmid, P. Nissen, T. G. Kinzy et al., Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase, Nat. Struct. Biol, vol.10, pp.379-385, 2003.

N. Jouihri, M. Sory, A. Page, P. Gounon, C. Parsot et al., MxiK and MxiN interact with the Spa47 ATPase and are required for transit of the needle components MxiH and MxiI, but not of Ipa proteins, through the type III secretion apparatus of Shigella flexneri, Mol. Microbiol, vol.49, pp.755-767, 2003.

C. Juliana, T. Fernandes-alnemri, S. Kang, A. Farias, F. Qin et al., Nontranscriptional Priming and Deubiquitination Regulate NLRP3 Inflammasome Activation, J. Biol. Chem, vol.287, p.36617, 2012.

M. Kanamori, H. Suzuki, R. Saito, M. Muramatsu, and Y. Hayashizaki, T2BP, a Novel TRAF2 Binding Protein, Can Activate NF-?B and AP-1 without TNF Stimulation, Biochem. Biophys. Res. Commun, vol.290, pp.1108-1113, 2002.

A. Kanayama, R. B. Seth, L. Sun, C. Ea, M. Hong et al., TAB2 and TAB3 activate the NF-kappaB pathway through binding to polyubiquitin chains, Mol. Cell, vol.15, pp.535-548, 2004.

J. Y. Kang, X. Nan, M. S. Jin, S. Youn, Y. H. Ryu et al., Recognition of Lipopeptide Patterns by Toll-like Receptor 2-Toll-like Receptor 6 Heterodimer, Immunity, vol.31, pp.873-884, 2009.

M. I. Kanipes, L. C. Holder, A. T. Corcoran, A. P. Moran, and P. Guerry, A deep-rough mutant of Campylobacter jejuni 81-176 is noninvasive for intestinal epithelial cells, Infect. Immun, vol.72, pp.2452-2455, 2004.

M. Kaparakis, L. Turnbull, L. Carneiro, S. Firth, H. A. Coleman et al., Bacterial membrane vesicles deliver peptidoglycan to NOD1 in epithelial cells, Cell. Microbiol, vol.12, pp.372-385, 2010.

C. A. Kasper, I. Sorg, C. Schmutz, T. Tschon, H. Wischnewski et al., Cell-cell propagation of NF-?B transcription factor and MAP kinase activation amplifies innate immunity against bacterial infection, Immunity, vol.33, pp.804-816, 2010.

S. H. Kaufmann, The contribution of immunology to the rational design of novel antibacterial vaccines, Nat. Rev. Microbiol, vol.5, pp.491-504, 2007.

T. Kawai, A. , and S. , The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors, Nat. Immunol, vol.11, pp.373-384, 2010.

N. Kayagaki, M. T. Wong, I. B. Stowe, S. R. Ramani, L. C. Gonzalez et al., Noncanonical Inflammasome Activation by Intracellular LPS Independent of TLR4, Science, vol.341, pp.1246-1249

S. A. Killackey, M. T. Sorbara, and S. E. Girardin, Cellular Aspects of Shigella Pathogenesis: Focus on the Manipulation of Host Cell Processes, Front. Cell. Infect. Microbiol, 2016.

Y. S. Kim and S. B. Ho, Intestinal Goblet Cells and Mucins in Health and Disease: Recent Insights and Progress, Curr. Gastroenterol. Rep, vol.12, pp.319-330, 2010.

D. W. Kim, G. Lenzen, A. Page, P. Legrain, P. J. Sansonetti et al., The Shigella flexneri effector OspG interferes with innate immune responses by targeting ubiquitinconjugating enzymes, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.14046-14051, 2005.

J. G. Kim, S. J. Lee, and M. F. Kagnoff, Nod1 is an essential signal transducer in intestinal epithelial cells infected with bacteria that avoid recognition by toll-like receptors, Infect. Immun, vol.72, pp.1487-1495, 2004.

B. Kneidinger, C. Marolda, M. Graninger, A. Zamyatina, F. Mcarthur et al., Biosynthesis Pathway of ADP-l-glycero--d-manno-Heptose in Escherichia coli, J. Bacteriol, vol.184, p.363, 2002.

L. A. Knodler, S. M. Crowley, H. P. Sham, H. Yang, M. Wrande et al., Noncanonical Inflammasome Activation of Caspase-4/Caspase-11 Mediates Epithelial Defenses against Enteric Bacterial Pathogens, Cell Host Microbe, vol.16, pp.249-256, 2014.

L. A. Knodler, V. Nair, and O. Steele-mortimer, Quantitative Assessment of Cytosolic Salmonella in Epithelial Cells, PLOS ONE, vol.9, p.84681, 2014.

T. Kobayashi, M. Ogawa, T. Sanada, H. Mimuro, M. Kim et al., The Shigella OspC3 Effector Inhibits Caspase-4, Antagonizes Inflammatory Cell Death, and Promotes Epithelial Infection, Cell Host Microbe, vol.13, pp.570-583, 2013.

G. Kolios, D. A. Robertson, N. J. Jordan, A. Minty, D. Caput et al., Interleukin-8 production by the human colon epithelial cell line HT-29: modulation by interleukin-13, Br. J. Pharmacol, vol.119, pp.351-359, 1996.

H. Kono, C. Chen, F. Ontiveros, and K. L. Rock, Uric acid promotes an acute inflammatory response to sterile cell death in mice, J. Clin. Invest, vol.120, pp.1939-1949, 2010.

J. Kortmann, S. W. Brubaker, and D. M. Monack, Cutting Edge: Inflammasome Activation in Primary Human Macrophages Is Dependent on Flagellin, J. Immunol, vol.195, pp.815-819, 2015.

J. P. Kraehenbuhl and M. R. Neutra, Epithelial M cells: differentiation and function, Annu. Rev. Cell Dev. Biol, vol.16, pp.301-332, 2000.

S. Kreibich, M. Emmenlauer, J. Fredlund, P. Rämö, C. Münz et al., Autophagy Proteins Promote Repair of Endosomal Membranes Damaged by the Salmonella Type Three Secretion System 1, Cell Host Microbe, vol.18, pp.527-537, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01899446

T. Kubori, Y. Matsushima, D. Nakamura, J. Uralil, M. Lara-tejero et al., Supramolecular Structure of the Salmonella typhimurium Type III Protein Secretion System, Science, vol.280, pp.602-605, 1998.

T. A. Kufer, E. Kremmer, A. C. Adam, D. J. Philpott, and P. J. Sansonetti, The patternrecognition molecule Nod1 is localized at the plasma membrane at sites of bacterial interaction, Cell. Microbiol, vol.10, pp.477-486, 2008.

C. Kung, S. Hsiao, T. Tsai, C. Su, W. Chang et al., Plasma nuclear and mitochondrial DNA levels as predictors of outcome in severe sepsis patients in the emergency room, J. Transl. Med, vol.10, p.130, 2012.

T. Kuo, C. Huang, H. Tu, M. Ko, A. Wang et al., URAT1 inhibition by ALPK1 is associated with uric acid homeostasis, Rheumatol. Oxf. Engl, vol.56, pp.654-659, 2017.

B. Lamothe, A. Besse, A. D. Campos, W. K. Webster, H. Wu et al., Sitespecific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of I kappa B kinase activation, J. Biol. Chem, vol.282, pp.4102-4112, 2007.

D. L. Larock, A. Chaudhary, and S. I. Miller, Salmonellae interactions with host processes, Nat. Rev. Microbiol, vol.13, pp.191-205, 2015.

H. Laroui, Y. Yan, Y. Narui, S. A. Ingersoll, S. Ayyadurai et al., L-Ala--D-Glu-meso-diaminopimelic acid (DAP) interacts directly with leucine-rich region domain of nucleotide-binding oligomerization domain 1, increasing phosphorylation activity of receptor, 2011.

, its interaction with nucleotide-binding oligomerization domain 1, J. Biol. Chem, vol.286, pp.31003-31013

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

K. Le-barillec, J. G. Magalhaes, E. Corcuff, A. Thuizat, P. J. Sansonetti et al., Roles for T and NK cells in the innate immune response to Shigella flexneri, J. Immunol. Baltim. Md, vol.175, pp.1735-1740, 1950.

C. Lee, S. Chiang, A. M. Ko, .. Liu, Y. Ma et al., ALPK1 phosphorylates myosin IIA modulating TNF-? trafficking in gout flares, Sci. Rep, vol.6, p.25740, 2016.

J. Lee, D. Rachmilewitz, and E. Raz, Homeostatic effects of TLR9 signaling in experimental colitis, Ann. N. Y. Acad. Sci, vol.1072, pp.351-355, 2006.

J. Lee, I. Tattoli, K. A. Wojtal, S. R. Vavricka, D. J. Philpott et al., pHdependent Internalization of Muramyl Peptides from Early Endosomes Enables Nod1 and Nod2 Signaling, J. Biol. Chem, vol.284, pp.23818-23829, 2009.

B. Lemaitre, E. Nicolas, L. Michaut, J. M. Reichhart, and J. A. Hoffmann, The dorsoventral regulatory gene cassette spätzle/Toll/cactus controls the potent antifungal response in Drosophila adults, Cell, vol.86, pp.973-983, 1996.

M. A. Lemmon and J. Schlessinger, Cell signaling by receptor-tyrosine kinases, Cell, vol.141, pp.1117-1134, 2010.

H. Li, H. Xu, Y. Zhou, J. Zhang, C. Long et al., The phosphothreonine lyase activity of a bacterial type III effector family, Science, vol.315, pp.1000-1003, 2007.

H. Liao, H. Lee, Y. Chang, C. Lin, T. Liu et al., Down-regulated and Commonly mutated ALPK1 in Lung and Colorectal Cancers, Sci. Rep, vol.6, p.27350, 2016.

G. J. Lieschke and P. D. Currie, Animal models of human disease: zebrafish swim into view, Nat. Rev. Genet, vol.8, pp.353-367, 2007.

F. Y. Liew, D. Xu, E. K. Brint, and L. A. Neill, Negative regulation of Toll-like receptor-mediated immune responses, Nat. Rev. Immunol, vol.5, pp.446-458

S. Lin, Y. Lo, and H. Wu, Helical assembly in the MyD88:IRAK4:IRAK2 complex in TLR/IL-1R signaling, vol.465, p.885, 2010.

T. Lin, T. W. Wei, S. Li, S. Wang, M. He et al., TIFA as a crucial mediator for NLRP3 inflammasome, Proc. Natl. Acad. Sci. U. S. A, vol.113, pp.15078-15083, 2016.

A. A. Lindberg, A. Kärnell, and A. Weintraub, The Lipopolysaccharide of Shigella Bacteria as a Virulence Factor, Rev. Infect. Dis, vol.13, pp.279-284, 1991.

H. Lindgren, H. Shen, C. Zingmark, I. Golovliov, W. Conlan et al., , 2007.

, Resistance of Francisella tularensis strains against reactive nitrogen and oxygen species with special reference to the role of KatG, Infect. Immun, vol.75, pp.1303-1309

J. Magdalena, A. Hachani, M. Chamekh, N. Jouihri, P. Gounon et al., Spa32 Regulates a Switch in Substrate Specificity of the Type III Secreton of Shigella flexneri from Needle Components to Ipa Proteins, J. Bacteriol, vol.184, pp.3433-3441, 2002.

A. Mahajan, C. Yuan, H. Lee, E. S. Chen, .. Wu et al., Structure and function of the phosphothreonine-specific FHA domain, Sci. Signal, vol.1, p.12, 2008.

J. K. Maier, S. Balabanian, C. R. Coffill, A. Stewart, L. Pelletier et al., Distribution of neuronal apoptosis inhibitory protein in human tissues, J. Histochem. Cytochem. Off. J. Histochem. Soc, vol.55, pp.911-923, 2007.

R. J. Malott, B. O. Keller, R. G. Gaudet, S. E. Mccaw, C. C. Lai et al., Neisseria gonorrhoeae-derived heptose elicits an innate immune response and drives HIV-1 expression, Proc. Natl. Acad. Sci. U. S. A, vol.110, pp.10234-10239, 2013.

S. M. Man, R. Karki, R. K. Malireddi, G. Neale, P. Vogel et al., The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection, Nat. Immunol, vol.16, pp.467-475, 2015.

S. Mani, T. Wierzba, and R. I. Walker, Status of vaccine research and development for Shigella, Vaccine, vol.34, pp.2887-2894, 2016.

N. Marina-garcía, L. Franchi, Y. Kim, Y. Hu, D. E. Smith et al., Clathrin-and Dynamin-Dependent Endocytic Pathway Regulates Muramyl Dipeptide Internalization and NOD2 Activation, J. Immunol, vol.182, pp.4321-4327, 2009.

F. Martinon, K. Burns, and J. Tschopp, The Inflammasome. Mol. Cell, vol.10, pp.417-426, 2002.

E. Mattock and A. J. Blocker, How Do the Virulence Factors of Shigella Work Together to Cause Disease? Front, Cell. Infect. Microbiol, vol.7, 2017.

P. Matzinger, Tolerance, danger, and the extended family, Annu. Rev. Immunol, vol.12, pp.991-1045, 1994.

P. Matzinger, The danger model: a renewed sense of self, Science, vol.296, pp.301-305, 2002.

A. T. Maurelli, B. Baudry, H. Hauteville, T. L. Hale, and P. J. Sansonetti, Cloning of plasmid DNA sequences involved in invasion of HeLa cells by Shigella flexneri, Infect. Immun, vol.49, pp.164-171, 1985.

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.

B. Mcdonald, K. Pittman, G. B. Menezes, S. A. Hirota, I. Slaba et al., Intravascular Danger Signals Guide Neutrophils to Sites of Sterile Inflammation, Science, vol.330, pp.362-366, 2010.

R. Medzhitov and C. A. Janeway, Innate Immunity: The Virtues of a Nonclonal System of Recognition, Cell, vol.91, pp.295-298, 1997.

R. Medzhitov, P. Preston-hurlburt, and C. A. Janeway, A human homologue of the Drosophila Toll protein signals activation of adaptive immunity, Nature, vol.388, pp.394-397, 1997.

N. Mellouk, A. Weiner, N. Aulner, C. Schmitt, M. Elbaum et al., Shigella Subverts the Host Recycling Compartment to Rupture Its Vacuole, Cell Host Microbe, vol.16, pp.517-530, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01113365

R. Mempin, H. Tran, C. Chen, H. Gong, K. Kim-ho et al., Release of extracellular ATP by bacteria during growth, BMC Microbiol, vol.13, p.301, 2013.

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.

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.

P. Menu and J. E. Vince, The NLRP3 inflammasome in health and disease: the good, the bad and the ugly, Clin. Exp. Immunol, vol.166, pp.1-15, 2011.

F. Mercurio, H. Zhu, B. W. Murray, A. Shevchenko, B. L. Bennett et al., IKK-1 and IKK-2: cytokine-activated IkappaB kinases essential for NF-kappaB activation, Science, vol.278, pp.860-866, 1997.

E. Meunier, M. S. Dick, R. F. Dreier, N. Schürmann, D. K. Broz et al., Caspase-11 activation requires lysis of pathogen-containing vacuoles by IFN-induced GTPases, Nature, vol.509, pp.366-370, 2014.

E. Meunier, P. Wallet, R. F. Dreier, S. Costanzo, L. Anton et al., Guanylate-binding proteins promote activation of the AIM2 inflammasome during infection with Francisella novicida, Nat. Immunol, vol.16, pp.476-484, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01924091

E. A. Miao, C. M. Alpuche-aranda, M. Dors, A. E. Clark, M. W. Bader et al., Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1 via Ipaf, Nat. Immunol, vol.7, pp.569-575, 2006.

E. A. Miao, D. P. Mao, N. Yudkovsky, R. Bonneau, C. G. Lorang et al., Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome, Proc. Natl. Acad. Sci. U. S. A, vol.107, p.3076, 2010.

J. Middelbeek, K. Clark, H. Venselaar, M. A. Huynen, and F. N. Van-leeuwen, The alpha-kinase family: an exceptional branch on the protein kinase tree, Cell. Mol. Life Sci, vol.67, pp.875-890, 2010.

M. Milivojevic, A. Dangeard, C. A. Kasper, T. Tschon, M. Emmenlauer et al., ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria, PLoS Pathog, vol.13, 2017.

S. E. Mohr, J. A. Smith, C. E. Shamu, R. A. Neumüller, and N. Perrimon, RNAi screening comes of age: improved techniques and complementary approaches, Nat. Rev. Mol. Cell Biol, vol.15, pp.591-600, 2014.

D. M. Monack and J. A. Theriot, Actin-based motility is sufficient for bacterial membrane protrusion formation and host cell uptake, Cell. Microbiol, vol.3, pp.633-647, 2001.

T. Morita-ishihara, M. Ogawa, H. Sagara, M. Yoshida, E. Katayama et al.,

, Shigella Spa33 Is an Essential C-ring Component of Type III Secretion Machinery, J. Biol. Chem, vol.281, pp.599-607

S. Mostowy, L. Boucontet, M. J. Moya, A. Sirianni, P. Boudinot et al., The Zebrafish as a New Model for the In Vivo Study of Shigella flexneri Interaction with Phagocytes and Bacterial Autophagy, PLoS Pathog, vol.9, 2013.

P. G. Motshwene, M. C. Moncrieffe, J. G. Grossmann, C. Kao, M. Ayaluru et al., An Oligomeric Signaling Platform Formed by the Toll-like Receptor Signal Transducers MyD88 and IRAK-4, J. Biol. Chem, vol.284, p.25404, 2009.

V. Motta, F. Soares, T. Sun, and D. J. Philpott, NOD-like receptors: versatile cytosolic sentinels, Physiol. Rev, vol.95, pp.149-178, 2015.

J. Mounier, T. Vasselon, R. Hellio, M. Lesourd, and P. J. Sansonetti, Shigella flexneri enters human colonic Caco-2 epithelial cells through the basolateral pole, Infect. Immun, vol.60, pp.237-248, 1992.

A. A. Müller, T. Dolowschiak, M. E. Sellin, B. Felmy, C. Verbree et al., An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection, PLOS Pathog, vol.12, p.1005723, 2016.

R. Muñoz-planillo, P. Kuffa, G. Martínez-colón, B. L. Smith, T. M. Rajendiran et al., K+ efflux is the Common Trigger of NLRP3 inflammasome Activation by Bacterial Toxins and Particulate Matter, Immunity, vol.38, pp.1142-1153, 2013.

Y. Nagai, S. Akashi, M. Nagafuku, M. Ogata, Y. Iwakura et al., Essential role of MD-2 in LPS responsiveness and TLR4 distribution, Nat. Immunol, vol.3, pp.667-672, 2002.

H. J. Newton, J. S. Pearson, L. Badea, M. Kelly, M. Lucas et al., The type III effectors NleE and NleB from enteropathogenic E. coli and OspZ from Shigella block nuclear translocation of NF-kappaB p65, PLoS Pathog, vol.6, 2010.

K. Niebuhr, S. Giuriato, T. Pedron, D. J. Philpott, F. Gaits et al., Conversion of PtdIns(4,5)P(2) into PtdIns(5)P by the S.flexneri effector IpgD reorganizes host cell morphology, EMBO J, vol.21, pp.5069-5078, 2002.

S. Nordlander, J. Pott, and K. J. Maloy, NLRC4 expression in intestinal epithelial cells mediates protection against an enteric pathogen, Mucosal Immunol, vol.7, pp.775-785, 2014.

Y. Ogura, N. Inohara, A. Benito, F. F. Chen, S. Yamaoka et al., Nod2, a Nod1/Apaf-1 Family Member That Is Restricted to Monocytes and Activates NF-?B, J. Biol. Chem, vol.276, pp.4812-4818, 2001.

A. J. Olive, R. Kenjale, M. Espina, D. S. Moore, W. L. Picking et al., Bile salts stimulate recruitment of IpaB to the Shigella flexneri surface, where it colocalizes with IpaD at the tip of the type III secretion needle, Infect. Immun, vol.75, pp.2626-2629, 2007.

L. Oliveira-nascimento, P. Massari, and L. M. Wetzler, The Role of TLR2 in, Infection and Immunity. Front. Immunol, vol.3, 2012.

L. A. O'neill and A. G. Bowie, The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling, Nat. Rev. Immunol, vol.7, pp.353-364

B. Opitz, A. Püschel, W. Beermann, A. C. Hocke, S. Förster et al., Listeria monocytogenes activated p38 MAPK and induced IL-8 secretion in a nucleotide-binding oligomerization domain 1-dependent manner in endothelial cells, J. Immunol. Baltim. Md, vol.176, pp.484-490, 1950.

K. Papenfort and B. L. Bassler, Quorum sensing signal-response systems in Gramnegative bacteria, Nat. Rev. Microbiol, vol.14, pp.576-588, 2016.

B. S. Park, D. H. Song, H. M. Kim, B. Choi, H. Lee et al., The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex, Nature, vol.458, pp.1191-1195, 2009.

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.

L. Pastorelli, C. De-salvo, M. A. Cominelli, M. Vecchi, and T. T. Pizarro, Novel cytokine signaling pathways in inflammatory bowel disease: insight into the dichotomous functions of IL-33 during chronic intestinal inflammation, Ther. Adv. Gastroenterol, vol.4, pp.311-323, 2011.

S. J. Patel, K. R. King, M. Casali, and M. L. Yarmush, DNA-triggered innate immune responses are propagated by gap junction communication, Proc. Natl. Acad. Sci. U. S. A, vol.106, pp.12867-12872, 2009.

I. Paz, M. Sachse, N. Dupont, J. Mounier, C. Cederfur et al., Galectin-3, a marker for vacuole lysis by invasive pathogens, Cell. Microbiol, vol.12, pp.530-544, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00486248

S. Pennell, S. Westcott, M. Ortiz-lombardía, D. Patel, J. Li et al., Structural and functional analysis of phosphothreonine-dependent FHA domain interactions, Struct. Lond. Engl, vol.18, pp.1587-1595, 1993.

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

R. Philip and L. B. Epstein, Tumour necrosis factor as immunomodulator and mediator of monocyte cytotoxicity induced by itself, gamma-interferon and interleukin-1, Nature, vol.323, pp.86-89, 1986.

D. J. Philpott and S. E. Girardin, The role of Toll-like receptors and Nod proteins in bacterial infection, Mol. Immunol, vol.41, pp.1099-1108, 2004.

D. J. Philpott, S. Yamaoka, A. Israël, and P. J. Sansonetti, Invasive Shigella flexneri activates NF-kappa B through a lipopolysaccharide-dependent innate intracellular response and leads to IL-8 expression in epithelial cells, J. Immunol. Baltim. Md, vol.165, pp.903-914, 1950.

D. J. Philpott, M. T. Sorbara, S. J. Robertson, K. Croitoru, and S. E. Girardin, NOD proteins: regulators of inflammation in health and disease, Nat. Rev. Immunol, vol.14, pp.9-23, 2014.

W. L. Picking, H. Nishioka, P. D. Hearn, M. A. Baxter, A. T. Harrington et al., IpaD of Shigella flexneri is independently required for regulation of Ipa protein secretion and efficient insertion of IpaB and IpaC into host membranes, Infect. Immun, vol.73, pp.1432-1440, 2005.

A. Poltorak, X. He, I. Smirnova, M. Y. Liu, C. Van-huffel et al., Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene, Science, vol.282, pp.2085-2088, 1998.

J. Pott and M. Hornef, Innate immune signalling at the intestinal epithelium in homeostasis and disease, EMBO Rep, vol.13, pp.684-698, 2012.

J. N. Pruneda, F. D. Smith, A. Daurie, D. L. Swaney, J. Villén et al., E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis, EMBO J, vol.33, pp.437-449, 2014.

A. Puhar, H. Tronchère, B. Payrastre, G. Tran-van-nhieu, and P. J. Sansonetti, A Shigella Effector Dampens Inflammation by Regulating Epithelial Release of Danger Signal ATP through Production of the Lipid Mediator PtdIns5P, Immunity, vol.39, pp.1121-1131, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-01012066

S. T. Qureshi, L. Larivière, G. Leveque, S. Clermont, K. J. Moore et al.,

, Endotoxin-tolerant Mice Have Mutations in Toll-like Receptor 4 (Tlr4), J. Exp. Med, vol.189, pp.615-625

C. R. Raetz and C. Whitfield, Lipopolysaccharide Endotoxins, Annu. Rev. Biochem, vol.71, pp.635-700, 2002.

P. Rämö, A. Drewek, C. Arrieumerlou, N. Beerenwinkel, H. Ben-tekaya et al., Simultaneous analysis of large-scale RNAi screens for pathogen entry, BMC Genomics, vol.15, 2014.

K. Ray, A. Bobard, A. Danckaert, I. Paz-haftel, C. Clair et al., Tracking the dynamic interplay between bacterial and host factors during pathogen-induced vacuole rupture in real time, Cell. Microbiol, vol.12, pp.545-556, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01899489

V. Reiterer, L. Grossniklaus, T. Tschon, C. A. Kasper, I. Sorg et al., , 2011.

, Shigella flexneri type III secreted effector OspF reveals new crosstalks of proinflammatory signaling pathways during bacterial infection, Cell. Signal, vol.23, pp.1188-1196

K. A. Roebuck, Regulation of interleukin-8 gene expression, J. Interferon Cytokine Res. Off. J. Int. Soc. Interferon Cytokine Res, vol.19, pp.429-438, 1999.

A. D. Roehrich, E. Guillossou, A. J. Blocker, and I. Martinez-argudo, Shigella IpaD has a dual role: signal transduction from the type III secretion system needle tip and intracellular secretion regulation, Mol. Microbiol, vol.87, pp.690-706, 2013.

T. Roger, C. Froidevaux, D. L. Roy, M. K. Reymond, A. Chanson et al., Protection from lethal Gram-negative bacterial sepsis by targeting Toll-like receptor 4, Proc. Natl. Acad. Sci, vol.106, pp.2348-2352, 2009.

J. R. Rohde, A. Breitkreutz, A. Chenal, P. J. Sansonetti, and C. Parsot, Type III secretion effectors of the IpaH family are E3 ubiquitin ligases, Cell Host Microbe, vol.1, pp.77-83, 2007.
URL : https://hal.archives-ouvertes.fr/pasteur-01540876

S. Romero, G. Grompone, N. Carayol, J. Mounier, S. Guadagnini et al., ATP-mediated Erk1/2 activation stimulates bacterial capture by filopodia, which precedes Shigella invasion of epithelial cells, Cell Host Microbe, vol.9, pp.508-519, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00685251

D. M. Rothwarf, E. Zandi, G. Natoli, K. , and M. , IKK-gamma is an essential regulatory subunit of the IkappaB kinase complex, Nature, vol.395, pp.297-300, 1998.

A. G. Ryazanov, K. S. Pavur, and M. V. Dorovkov, Alpha-kinases: a new class of protein kinases with a novel catalytic domain, Curr. Biol, vol.9, pp.43-45, 1999.

T. Sakaguchi, H. Köhler, X. Gu, B. A. Mccormick, and H. Reinecker, Shigella flexneri regulates tight junction-associated proteins in human intestinal epithelial cells, Cell. Microbiol, vol.4, pp.367-381, 2002.

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.

M. Sani, A. Allaoui, F. Fusetti, G. T. Oostergetel, W. Keegstra et al., Structural organization of the needle complex of the type III secretion apparatus of Shigella flexneri, Micron, vol.38, pp.291-301, 2007.

P. J. Sansonetti, War and peace at mucosal surfaces, Nat. Rev. Immunol, vol.4, pp.953-964, 2004.

P. J. Sansonetti, A. Ryter, P. Clerc, A. T. Maurelli, and J. Mounier, Multiplication of Shigella flexneri within HeLa cells: lysis of the phagocytic vacuole and plasmid-mediated contact hemolysis, Infect. Immun, vol.51, pp.461-469, 1986.

P. J. Sansonetti, J. Arondel, M. Huerre, A. Harada, and K. Matsushima, , 1999.

, Controls Bacterial Transepithelial Translocation at the Cost of Epithelial Destruction in Experimental Shigellosis, Infect. Immun, vol.67, pp.1471-1480

P. J. Sansonetti, A. Phalipon, J. Arondel, K. Thirumalai, S. Banerjee et al., Caspase-1 activation of IL-1beta and IL-18 are essential for Shigella flexneri-induced inflammation, Immunity, vol.12, pp.581-590, 2000.

C. Sasakawa, B. Adler, T. Tobe, N. Okada, S. Nagai et al., Functional organization and nucleotide sequence of virulence Region-2 on the large virulence plasmid in Shigella flexneri 2a, Mol. Microbiol, vol.3, pp.1191-1201, 1989.

L. Schaefer, Complexity of Danger: The Diverse Nature of Damage-associated Molecular Patterns, J. Biol. Chem, vol.289, pp.35237-35245, 2014.

G. N. Schroeder and H. Hilbi, Molecular Pathogenesis of Shigella spp.: Controlling Host Cell Signaling, Invasion, and Death by Type III Secretion, Clin. Microbiol. Rev, vol.21, pp.134-156, 2008.

G. N. Schroeder, N. J. Jann, and H. Hilbi, Intracellular type III secretion by cytoplasmic Shigella flexneri promotes caspase-1-dependent macrophage cell death, Microbiol. Read. Engl, vol.153, pp.2862-2876, 2007.

R. Schuch and A. T. Maurelli, MxiM and MxiJ, base elements of the Mxi-Spa type III secretion system of Shigella, interact with and stabilize the MxiD secretin in the cell envelope, J. Bacteriol, vol.183, pp.6991-6998, 2001.

S. A. Seibert, P. Mex, A. Köhler, S. H. Kaufmann, and H. Mittrücker, TLR2-, TLR4-and Myd88-independent acquired humoral and cellular immunity against Salmonella enterica serovar Typhimurium, Immunol. Lett, vol.127, pp.126-134, 2010.

M. E. Sellin, A. A. Müller, and W. Hardt, Consequences of Epithelial Inflammasome Activation by Bacterial Pathogens, J. Mol. Biol, 2014.

M. E. Sellin, K. M. Maslowski, K. J. Maloy, and W. Hardt, Inflammasomes of the intestinal epithelium, Trends Immunol, vol.36, pp.442-450, 2015.

R. Sen and D. Baltimore, Inducibility of kappa immunoglobulin enhancer-binding protein Nf-kappa B by a posttranslational mechanism, Cell, vol.47, pp.921-928, 1986.

L. Senerovic, S. P. Tsunoda, C. Goosmann, V. Brinkmann, A. Zychlinsky et al., Spontaneous formation of IpaB ion channels in host cell membranes reveals how Shigella induces pyroptosis in macrophages, 2012.

M. R. Shalaby, A. Waage, L. Aarden, and T. Espevik, Endotoxin, tumor necrosis factor-? and interleukin 1 induce interleukin 6 production in vivo, Clin. Immunol. Immunopathol, vol.53, pp.488-498, 1989.

W. Shen, A. Chang, J. Wang, W. Zhou, R. Gao et al., TIFA, an inflammatory signaling adaptor, is tumor suppressive for liver cancer, vol.4, p.173, 2015.

J. Shi, Y. Zhao, Y. Wang, W. Gao, J. Ding et al., Inflammatory caspases are innate immune receptors for intracellular LPS, Nature, vol.514, pp.187-192, 2014.

H. Shibuya, K. Yamaguchi, K. Shirakabe, A. Tonegawa, Y. Gotoh et al., TAB1: an activator of the TAK1 MAPKKK in TGF-beta signal transduction, Science, vol.272, pp.1179-1182, 1996.

D. Shim, T. Suzuki, S. Chang, S. Park, P. J. Sansonetti et al., New animal model of shigellosis in the Guinea pig: its usefulness for protective efficacy studies, J. Immunol. Baltim. Md, vol.178, pp.2476-2482, 1950.

R. Shimazu, S. Akashi, H. Ogata, Y. Nagai, K. Fukudome et al., , 1999.

, MD-2, a Molecule that Confers Lipopolysaccharide Responsiveness on Toll-like Receptor 4, J. Exp. Med, vol.189, p.1777

S. Shimokata, M. Oguri, T. Fujimaki, H. Horibe, K. Kato et al., Association between polymorphisms of the ?-kinase 1 gene and type 2 diabetes mellitus in communitydwelling individuals, Biomed. Rep, vol.1, pp.940-944, 2013.

F. Sisti, J. Fernández, M. E. Rodríguez, A. Lagares, N. Guiso et al., In vitro and in vivo characterization of a Bordetella bronchiseptica mutant strain with a deep rough lipopolysaccharide structure, Infect. Immun, vol.70, pp.1791-1798, 2002.

A. Skoudy, J. Mounier, A. Aruffo, H. Ohayon, P. Gounon et al., CD44 binds to the Shigella IpaB protein and participates in bacterial invasion of epithelial cells, Cell. Microbiol, vol.2, pp.19-33, 2000.

C. W. Smith, R. Rothlein, B. J. Hughes, M. M. Mariscalco, H. E. Rudloff et al., Recognition of an endothelial determinant for CD 18-dependent human neutrophil adherence and transendothelial migration, J. Clin. Invest, vol.82, pp.1746-1756, 1988.

N. Song, Z. Liu, W. Xue, Z. Bai, Q. Wang et al., NLRP3 Phosphorylation Is an Essential Priming Event for Inflammasome Activation, Mol. Cell, 2017.

G. X. Song-zhao, N. Srinivasan, J. Pott, D. Baban, G. Frankel et al., Nlrp3 activation in the intestinal epithelium protects against a mucosal pathogen, Mucosal Immunol, vol.7, pp.763-774, 2014.

S. Spiller, S. Dreher, G. Meng, A. Grabiec, W. Thomas et al., Cellular recognition of trimyristoylated peptide or enterobacterial lipopolysaccharide via both TLR2 and TLR4, J. Biol. Chem, vol.282, pp.13190-13198, 2007.

S. Spiller, G. Elson, R. Ferstl, S. Dreher, T. Mueller et al., TLR4-induced IFN-production increases TLR? sensitivity and drives Gram-negative sepsis in mice, J. Exp. Med, vol.205, p.1747, 2008.

G. V. Sridharan, K. Choi, C. Klemashevich, C. Wu, D. Prabakaran et al., Prediction and quantification of bioactive microbiota metabolites in the mouse gut, Nat. Commun, vol.5, p.6492, 2014.

S. C. Stein, E. Faber, S. H. Bats, T. Murillo, Y. Speidel et al.,

, Helicobacter pylori modulates host cell responses by CagT4SS-dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis, PLoS Pathog, vol.13, 1006514.

I. Stojiljkovic, V. Hwa, J. Larson, L. Lin, M. So et al., Cloning and characterization of the Neisseria meningitidis rfaC gene encoding ?-1,5 heptosyltransferase I, FEMS Microbiol. Lett, vol.151, pp.41-49, 1997.

J. Strietz, S. S. Stepputtis, B. Preca, C. Vannier, M. M. Kim et al., ERN1 and ALPK1 inhibit differentiation of bi-potential tumor-initiating cells in human breast cancer, Oncotarget, vol.7, pp.83278-83293, 2016.

M. Suzuki, T. Hisamatsu, and D. K. Podolsky, Gamma interferon augments the intracellular pathway for lipopolysaccharide (LPS) recognition in human intestinal epithelial cells through coordinated up-regulation of LPS uptake and expression of the intracellular Toll-like receptor 4-MD-2 complex, Infect. Immun, vol.71, pp.3503-3511, 2003.

S. Suzuki, H. Mimuro, M. Kim, M. Ogawa, H. Ashida et al., Shigella IpaH7.8 E3 ubiquitin ligase targets glomulin and activates inflammasomes to demolish macrophages, Proc. Natl. Acad. Sci. U. S. A, vol.111, pp.4254-4263, 2014.

T. Suzuki, L. Franchi, C. Toma, H. Ashida, M. Ogawa et al., Differential regulation of caspase-1 activation, pyroptosis, and autophagy via Ipaf and ASC in Shigella-infected macrophages, PLoS Pathog, vol.3, p.111, 2007.

G. Takaesu, S. Kishida, A. Hiyama, K. Yamaguchi, H. Shibuya et al., TAB2, a novel adaptor protein, mediates activation of TAK1 MAPKKK by linking TAK1 to TRAF6 in the IL-1 signal transduction pathway, Mol. Cell, vol.5, pp.649-658, 2000.

H. Takatsuna, H. Kato, J. Gohda, T. Akiyama, A. Moriya et al., Identification of TIFA as an adapter protein that links tumor necrosis factor receptor-associated factor 6 (TRAF6) to interleukin-1 (IL-1) receptor-associated kinase-1 (IRAK-1) in IL-1 receptor signaling, J. Biol. Chem, vol.278, pp.12144-12150, 2003.

O. Takeuchi, K. Hoshino, A. , and S. , Cutting edge: TLR2-deficient and MyD88-deficient mice are highly susceptible to Staphylococcus aureus infection, J. Immunol. Baltim. Md, vol.165, pp.5392-5396, 1950.

O. Takeuchi, T. Kawai, P. F. Mühlradt, M. Morr, J. D. Radolf et al., Discrimination of bacterial lipoproteins by Toll-like receptor 6, Int. Immunol, vol.13, pp.933-940, 2001.

O. Takeuchi, S. Sato, T. Horiuchi, K. Hoshino, K. Takeda et al., Cutting edge: role of Toll-like receptor 1 in mediating immune response to microbial lipoproteins, J. Immunol. Baltim. Md, vol.169, pp.10-14, 1950.

K. Tamano, S. Aizawa, E. Katayama, T. Nonaka, S. Imajoh-ohmi et al., Supramolecular structure of the Shigella type III secretion machinery: the needle part is changeable in length and essential for delivery of effectors, EMBO J, vol.19, pp.3876-3887, 2000.

I. Tattoli, L. Lembo-fazio, G. Nigro, L. A. Carneiro, E. Ferraro et al., Intracellular bacteriolysis triggers a massive apoptotic cell death in Shigella-infected epithelial cells, Microbes Infect, vol.10, pp.1114-1123, 2008.

J. P. Ting, .. Lovering, R. C. Alnemri, E. S. Bertin, J. Boss et al., The NLR gene family: a standard nomenclature, Immunity, vol.28, pp.285-287, 2008.

T. Tobe, S. Nagai, N. Okada, B. Adler, M. Yoshikawa et al., , 1991.

, Temperature-regulated expression of invasion genes in Shigella flexneri is controlled through the transcriptional activation of the virB gene on the large plasmid, Mol. Microbiol, vol.5, pp.887-893

T. Tobe, M. Yoshikawa, T. Mizuno, and C. Sasakawa, Transcriptional control of the invasion regulatory gene virB of Shigella flexneri: activation by virF and repression by H-NS, J. Bacteriol, vol.175, pp.6142-6149, 1993.

K. Tominaga, T. Yoshimoto, K. Torigoe, M. Kurimoto, K. Matsui et al., IL-12 synergizes with IL-18 or IL-1beta for IFN-gamma production from human T cells, Int. Immunol, vol.12, pp.151-160, 2000.

D. Torres, M. Barrier, F. Bihl, V. J. Quesniaux, I. Maillet et al., Toll-like receptor 2 is required for optimal control of Listeria monocytogenes infection, Infect. Immun, vol.72, pp.2131-2139, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00095013

M. Uhlén, L. Fagerberg, B. M. Hallström, C. Lindskog, P. Oksvold et al., Proteomics. Tissue-based map of the human proteome. Science, vol.347, p.1260419, 2015.

R. J. Ulevitch and P. S. Tobias, Receptor-dependent mechanisms of cell stimulation by bacterial endotoxin, Annu. Rev. Immunol, vol.13, pp.437-457, 1995.

V. Urbonaviciute, B. G. Fürnrohr, S. Meister, L. Munoz, P. Heyder et al., Induction of inflammatory and immune responses by HMGB1-nucleosome complexes: implications for the pathogenesis of SLE, J. Exp. Med, vol.205, pp.3007-3018, 2008.

S. Vallabhapurapu, K. , and M. , Regulation and function of NF-kappaB transcription factors in the immune system, Annu. Rev. Immunol, vol.27, pp.693-733, 2009.

A. S. Vamadevan, M. Fukata, E. T. Arnold, L. S. Thomas, D. Hsu et al., Regulation of TLR4-associated MD-2 in intestinal epithelial cells: a comprehensive analysis, Innate Immun, vol.16, p.93, 2010.

G. T. Van-nhieu, C. Clair, R. Bruzzone, M. Mesnil, P. Sansonetti et al., , 2003.

, Connexin-dependent inter-cellular communication increases invasion and dissemination of Shigella in epithelial cells, Nat. Cell Biol, vol.5, pp.720-726

M. G. Varga, C. L. Shaffer, J. C. Sierra, G. Suarez, M. B. Piazuelo et al., Pathogenic Helicobacter pylori Strains Translocate DNA and Activate TLR9 via the Cancer-Associated cag Type IV Secretion System, Oncogene, vol.35, pp.6262-6269, 2016.

A. K. Veenendaal, J. L. Hodgkinson, L. Schwarzer, D. Stabat, S. F. Zenk et al., The type III secretion system needle tip complex mediates host cell sensing and translocon insertion, Mol. Microbiol, vol.63, pp.1719-1730, 2007.

L. L. Van-de-verg, C. P. Mallett, H. H. Collins, T. Larsen, C. Hammack et al., , 1995.

, Antibody and cytokine responses in a mouse pulmonary model of Shigella flexneri serotype 2a infection, Infect. Immun, vol.63, pp.1947-1954

I. M. Verma, J. K. Stevenson, E. M. Schwarz, D. Van-antwerp, and S. Miyamoto, , 1995.

, Rel/NF-kappa B/I kappa B family: intimate tales of association and dissociation, Genes Dev, vol.9, pp.2723-2735

J. Viala, P. Sansonetti, and D. J. Philpott, Nods and "intracellular" innate immunity, C. R. Biol, vol.327, pp.551-555

I. I. Vlasov, A. A. Shiryaev, T. Rendler, S. Steinert, S. Lee et al., Molecular-sized fluorescent nanodiamonds, Nat. Nanotechnol, vol.9, pp.54-58, 2014.

H. Wajant, F. Henkler, and P. Scheurich, The TNF-receptor-associated factor family, Cell. Signal, vol.13, pp.389-400, 2001.

M. C. Walsh, J. Lee, and Y. Choi, Tumor necrosis factor receptor-associated factor 6 (TRAF6) regulation of development, function, and homeostasis of the immune system, Immunol. Rev, vol.266, pp.72-92, 2015.

X. Wang and P. J. Quinn, Lipopolysaccharide: Biosynthetic pathway and structure modification, Prog. Lipid Res, vol.49, pp.97-107, 2010.

C. Wang, L. Deng, M. Hong, G. R. Akkaraju, J. Inoue et al., TAK1 is a ubiquitin-dependent kinase of MKK and IKK, Nature, vol.412, pp.346-351, 2001.

F. Wang, Z. Jiang, Y. Li, X. He, J. Zhao et al.,

, Shigella flexneriT3SS effector IpaH4.5 modulates the host inflammatory response via interaction with NF-?B p65 protein, Cell. Microbiol, vol.15, pp.474-485

S. Wang, H. Tu, A. M. Ko, .. Chiang, S. Chiou et al., Lymphocyte ?-kinase is a gout-susceptible gene involved in monosodium urate monohydrate-induced inflammatory responses, J. Mol. Med. Berl. Ger, vol.89, issue.?011, pp.1241-1251

X. Wang, C. Moser, J. Louboutin, E. S. Lysenko, D. J. Weiner et al., Toll-like receptor 4 mediates innate immune responses to Haemophilus influenzae infection in mouse lung, J. Immunol. Baltim. Md, vol.168, pp.810-815, 1950.

J. S. Wassef, D. F. Keren, and J. L. Mailloux, Role of M cells in initial antigen uptake and in ulcer formation in the rabbit intestinal loop model of shigellosis, Infect. Immun, vol.57, pp.858-863, 1989.

M. Watarai, S. Funato, and C. Sasakawa, Interaction of Ipa proteins of Shigella flexneri with alpha5beta1 integrin promotes entry of the bacteria into mammalian cells, J. Exp. Med, vol.183, pp.991-999, 1996.

S. S. Way, A. C. Borczuk, R. Dominitz, and M. B. Goldberg, An essential role for gamma interferon in innate resistance to Shigella flexneri infection, Infect. Immun, vol.66, pp.1342-1348, 1998.

S. J. Webster, S. Brode, L. Ellis, T. J. Fitzmaurice, M. J. Elder et al., Detection of a microbial metabolite by STING regulates inflammasome activation in response to Chlamydia trachomatis infection, PLOS Pathog, vol.13, p.1006383, 2017.

T. W. Wei, P. Wu, T. Wu, H. Hou, W. Chou et al., Aurora A and NF-?B Survival Pathway Drive Chemoresistance in Acute Myeloid Leukemia via the TRAF-Interacting Protein TIFA, Cancer Res, vol.77, pp.494-508, 2017.

A. Weiner, N. Mellouk, N. Lopez-montero, Y. Chang, C. Souque et al., Macropinosomes are Key Players in Early Shigella Invasion and Vacuolar Escape in Epithelial Cells, PLOS Pathog, vol.12, p.1005602, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01899441

D. A. Wesener, K. Wangkanont, R. Mcbride, X. Song, M. B. Kraft et al., Recognition of microbial glycans by human intelectin-1, Nat. Struct. Mol. Biol, vol.22, pp.603-610, 2015.

D. S. Wheeler, M. A. Chase, A. P. Senft, S. E. Poynter, H. R. Wong et al., , 2009.

, Extracellular Hsp72, an endogenous DAMP, is released by virally infected airway epithelial cells and activates neutrophils via Toll-like receptor (TLR)-4, Respir. Res, vol.10, p.31

J. R. White, J. A. Winter, R. , and K. , Differential inflammatory response to Helicobacter pylori infection: etiology and clinical outcomes, J. Inflamm. Res, vol.8, pp.137-147, 2015.

A. J. Whitmarsh, Regulation of gene transcription by mitogen-activated protein kinase signaling pathways, Biochim. Biophys. Acta BBA -Mol. Cell Res, vol.1773, pp.1285-1298, 2007.

T. M. Williams, R. A. Leeth, D. E. Rothschild, S. L. Coutermarsh-ott, D. K. Mcdaniel et al., The NLRP1 inflammasome attenuates colitis and colitis-associated tumorigenesis, J. Immunol. Baltim. Md, pp.3369-3380, 2015.

M. Wlodarska, C. A. Thaiss, R. Nowarski, J. Henao-mejia, J. Zhang et al., NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion, Cell, vol.156, 1045.

A. J. Wolf, C. N. Reyes, W. Liang, C. Becker, K. Shimada et al., Hexokinase Is an Innate Immune Receptor for the Detection of Bacterial Peptidoglycan, Cell, vol.166, pp.624-636, 2016.

J. J. Worthington, F. Reimann, and F. M. Gribble, Enteroendocrine cells-sensory sentinels of the intestinal environment and orchestrators of mucosal immunity, Mucosal Immunol, 2017.

C. Wu, D. B. Conze, T. Li, S. M. Srinivasula, and J. D. Ashwell, Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation, 2006.

, Nat. Cell Biol, vol.8, pp.398-406

X. Wu, Z. Li, X. Chen, S. Fossey, J. et al., Selective sensing of saccharides using simple boronic acids and their aggregates, Chem. Soc. Rev, vol.42, pp.8032-8048, 2013.

Z. Xia, L. Sun, X. Chen, G. Pineda, X. Jiang et al., Direct activation of protein kinases by unanchored polyubiquitin chains, Nature, vol.461, pp.114-119, 2009.

P. Xie, TRAF molecules in cell signaling and in human diseases, J. Mol. Signal, vol.8, p.7, 2013.

H. Xue, L. Ji, A. Gao, P. Liu, J. He et al., CRISPR-Cas9 for medical genetic screens: applications and future perspectives, J. Med. Genet, vol.53, pp.91-97, 2016.

Y. Yamada, T. Nishida, S. Ichihara, K. Kato, T. Fujimaki et al., Identification of chromosome 3q28 and ALPK1 as susceptibility loci for chronic kidney disease in Japanese individuals by a genome-wide association study, J. Med. Genet, vol.50, pp.410-418, 2013.

Y. Yamada, K. Matsui, I. Takeuchi, and T. Fujimaki, Association of genetic variants with coronary artery disease and ischemic stroke in a longitudinal population-based genetic epidemiological study, Biomed. Rep, vol.3, pp.413-419, 2015.

Y. Yamada, K. Matsui, I. Takeuchi, M. Oguri, and T. Fujimaki, , 2015.

Y. Yamada, K. Matsui, I. Takeuchi, and T. Fujimaki, Association of genetic variants with dyslipidemia and chronic kidney disease in a longitudinal population-based genetic epidemiological study, Int. J. Mol. Med, vol.35, pp.1290-1300, 2015.

K. Yamamoto, Intracellular lectins are involved in quality control of glycoproteins, Proc. Jpn. Acad. Ser. B Phys. Biol. Sci, vol.90, pp.67-82, 2014.

S. Yamaoka, G. Courtois, C. Bessia, S. T. Whiteside, R. Weil et al., Complementation cloning of NEMO, a component of the IkappaB kinase complex essential for NF-kappaB activation, Cell, vol.93, pp.1231-1240, 1998.

J. Yang, Y. Zhao, J. Shi, and F. Shao, Human NAIP and mouse NAIP1 recognize bacterial type III secretion needle protein for inflammasome activation, Proc. Natl. Acad. Sci. U. S. A, vol.110, pp.14408-14413, 2013.

S. Yang, A. D. Sharrocks, and A. J. Whitmarsh, Transcriptional regulation by the MAP kinase signaling cascades, Gene, vol.320, pp.3-21, 2003.

H. Ye, J. R. Arron, B. Lamothe, M. Cirilli, T. Kobayashi et al., Distinct molecular mechanism for initiating TRAF6 signalling, Nature, vol.418, pp.443-447, 2002.

M. Yeager and B. J. Nicholson, Structure of gap junction intercellular channels, Curr. Opin. Struct. Biol, vol.6, pp.183-192, 1996.

Q. Zhang, M. Raoof, Y. Chen, Y. Sumi, T. Sursal et al., Circulating Mitochondrial DAMPs Cause Inflammatory Responses to Injury, Nature, vol.464, pp.104-107, 2010.

Y. Zhao, J. Yang, J. Shi, Y. Gong, Q. Lu et al., The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus, Nature, vol.477, pp.596-600, 2011.

R. Zhou, A. S. Yazdi, P. Menu, and J. Tschopp, A role for mitochondria in NLRP3 inflammasome activation, Nature, vol.469, pp.221-225, 2011.

Y. Zhou, N. Dong, L. Hu, and F. Shao, The Shigella type three secretion system effector OspG directly and specifically binds to host ubiquitin for activation, PloS One, vol.8, p.57558, 2013.

S. Zimmermann, C. Wagner, W. Müller, G. Brenner-weiss, F. Hug et al., Induction of Neutrophil Chemotaxis by the Quorum-Sensing Molecule N-(3-Oxododecanoyl)-l-Homoserine Lactone, Infect. Immun, vol.74, p.5687, 2006.

S. Zimmermann, L. Pfannkuch, M. A. Al-zeer, S. Bartfeld, M. Koch et al., ALPK1-and TIFA-Dependent Innate Immune Response Triggered by the Helicobacter pylori Type IV Secretion System, Cell Rep, vol.20, pp.2384-2395, 2017.

A. Zychlinsky, M. C. Prevost, and P. J. Sansonetti, Shigella flexneri induces apoptosis in infected macrophages, Nature, vol.358, pp.167-169, 1992.