P. V. Afonine, B. K. Poon, R. J. Read, O. V. Sobolev, T. C. Terwilliger et al., Real-817 space refinement in PHENIX for cryo-EM and crystallography, Acta Crystallogr. Sect. D Struct, 2018.

, Biol, vol.74, pp.531-544

D. Asarnow, Pyem. GitHub Available, 2016.

M. Aschtgen, C. S. Bernard, D. Bentzmann, S. Lloubes, R. Cascales et al., SciN Is an Outer, vol.821, 2008.

, Membrane Lipoprotein Required for Type VI Secretion in Enteroaggregative Escherichia coli

, Bacteriol, vol.190, pp.7523-7531

M. Aschtgen, C. S. Bernard, D. Bentzmann, S. Lloubes, R. Cascales et al., SciN Is an Outer, vol.824, 2008.

, Membrane Lipoprotein Required for Type VI Secretion in Enteroaggregative Escherichia coli

, Bacteriol, vol.190, pp.7523-7531

M. S. Aschtgen, A. Zoued, R. Lloubès, L. Journet, and E. Cascales, The C-tail anchored TssL subunit, an 827 essential protein of the enteroaggregative Escherichia coli Sci-1 Type VI secretion system, 2012.

M. Basler, M. Pilhofer, G. P. Henderson, G. J. Jensen, and J. J. Mekalanos, Type VI secretion requires a 830 dynamic contractile phage tail-like structure, Nature, vol.483, pp.182-186, 2012.

F. Boyer, G. Fichant, J. Berthod, Y. Vandenbrouck, and I. Attree, Dissecting the bacterial type VI 832 secretion system by a genome wide in silico analysis: what can be learned from available 833 microbial genomic resources?, BMC Genomics, vol.10, p.104, 2009.

Y. R. Brunet, C. S. Bernard, M. Gavioli, R. Lloubès, and E. Cascales, An Epigenetic Switch Involving, vol.835, 2011.

, Overlapping Fur and DNA Methylation Optimizes Expression of a Type VI Secretion Gene 836 Cluster, PLoS Genet, vol.7, p.1002205

Y. R. Brunet, L. Espinosa, S. Harchouni, T. Mignot, and E. Cascales, Imaging Type VI Secretion-838, 2013.

, Mediated Bacterial Killing. Cell Rep, vol.3, pp.36-41

Y. R. Brunet, J. Henin, H. Celia, and E. Cascales, Type VI secretion and bacteriophage tail tubes share a 840 common assembly pathway, EMBO Rep, vol.15, pp.315-321, 2014.

Y. R. Brunet, A. Zoued, F. Boyer, B. Douzi, and E. Cascales, The Type VI Secretion TssEFGK-VgrG, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01778563

, Like Baseplate Is Recruited to the TssJLM Membrane Complex via Multiple Contacts and Serves 843

, As Assembly Platform for Tail Tube/Sheath Polymerization, PLOS Genet, vol.11, p.1005545

G. Celniker, G. Nimrod, H. Ashkenazy, F. Glaser, E. Martz et al., , p.845, 2013.

. Consurf, Using Evolutionary Data to Raise Testable Hypotheses about Protein Function, Isr. J, vol.846

, Chem, vol.53, pp.199-206

J. Chang and Y. Kim, Crystal structure of the bacterial type VI secretion system component system revealed by electron cryotomography, EMBO Rep, vol.18, pp.1090-1099, 2015.

M. K. Chaveroche, J. M. Ghigo, and C. &-d'enfert, A rapid method for efficient gene replacement in the 852 filamentous fungus Aspergillus nidulans, Nucleic Acids Res, vol.28, p.97, 2000.

V. B. Chen, W. B. Arendall, J. J. Headd, D. A. Keedy, R. M. Immormino et al., , vol.854

D. C. Richardson, MolProbity : all-atom structure validation for macromolecular 855 crystallography, Acta Crystallogr. Sect. D Biol. Crystallogr, vol.66, pp.12-21, 2010.

Y. Cherrak, C. Rapisarda, R. Pellarin, G. Bouvier, B. Bardiaux et al., , p.857

E. Cascales, R. Fronzes, and E. Durand, Biogenesis and structure of a type VI secretion 858 baseplate, Nat. Microbiol, vol.3, pp.1404-1416, 2018.

D. L. Clemens, P. Ge, B. Lee, M. A. Horwitz, and Z. H. Zhou, Atomic Structure of T6SS Reveals Interlaced, vol.860, 2015.

, Array Essential to Function. Cell, vol.160, pp.940-951

R. Danev and W. Baumeister, Cryo-EM single particle analysis with the Volta phase plate, Elife, vol.5, p.862, 2016.

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-863 12 using PCR products, Proc. Natl. Acad. Sci, vol.97, pp.6640-6645, 2000.

A. Ducret, E. M. Quardokus, and Y. V. Brun, MicrobeJ, a tool for high throughput bacterial cell 865 detection and quantitative analysis, Nat. Microbiol, vol.1, p.16077, 2016.

E. Durand, V. S. Nguyen, A. Zoued, L. Logger, G. Péhau-arnaudet et al., , vol.867

B. Bardiaux, A. Dujeancourt, A. Roussel, C. Cambillau, E. Cascales et al., Biogenesis 868 and structure of a type VI secretion membrane core complex, Nature, vol.523, pp.555-560, 2015.

E. Durand, A. Zoued, S. Spinelli, P. Watson, M. Aschtgen et al., , p.870, 2012.

, Structural characterization and oligomerization of the TssL protein, a component shared by 871 bacterial type VI and type IVb secretion systems, J. Biol. Chem, vol.287, pp.14157-68

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Crystallogr. Sect. D Biol. Crystallogr, vol.873, pp.486-501, 2010.

C. Felisberto-rodrigues, D. E. Aschtgen, M. Blangy, S. Ortiz-lombardia, M. Douzi et al., , vol.875

E. Cascales, Towards a structural comprehension of bacterial type VI secretion systems: 876 characterization of the TssJ-TssM complex of an Escherichia coli pathovar, PLoS Pathog, vol.7, p.877, 2011.

N. Flaugnatti, T. Le, S. Canaan, M. Aschtgen, V. S. Nguyen et al., , vol.879

C. Cambillau, E. Cascales, and L. Journet, A phospholipase A 1 antibacterial Type VI secretion 880 effector interacts directly with the C-terminal domain of the VgrG spike protein for delivery, 2016.

, Mol. Microbiol, vol.99, pp.1099-1118

X. Fu, B. A. Himes, D. Ke, W. J. Rice, J. Ning et al., Controlled bacterial lysis for electron 883 tomography of native cell membranes, Structure, vol.22, pp.1875-1882, 2014.

P. Goyal, P. Krasteva, N. Van-gerven, and F. Gubellini, Van den Broeck I, Troupiotis-Tsaïlaki A, Jonckheere 889 CTS1 Type VI Secretion System in Interbacterial Competition, Appl. Environ. Microbiol, vol.79, p.38

A. Hachani, T. E. Wood, and A. Filloux, Type VI secretion and anti-host effectors, Curr. Opin, 2016.

. Microbiol, , vol.29, pp.81-93

M. F. Hayles, D. J. Stokes, D. Phifer, and K. C. Findlay, A technique for improved focused ion beam 894 milling of cryo-prepared life science specimens, J. Microsc, vol.226, pp.263-272, 2007.

B. Hu, M. Lara-tejero, Q. Kong, J. E. Galán, and J. Liu, Situ Molecular Architecture of the Salmonella 896, 2017.

, Type III Secretion Machine. Cell, vol.168, pp.1065-1074

S. Jo, T. Kim, and W. Im, Automated builder and database of protein/membrane complexes for 898 molecular dynamics simulations, PLoS One, vol.2, 2007.

M. Källberg, H. Wang, S. Wang, J. Peng, Z. Wang et al., Template-based protein structure 900 modeling using the RaptorX web server, Nat. Protoc, vol.7, pp.1511-1522, 2012.

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. Sternberg, The Phyre2 web portal for protein 902 modeling, prediction and analysis, Nat. Protoc, vol.10, pp.845-858, 2015.

J. R. Kremer, D. N. Mastronarde, and J. R. Mcintosh, Computer Visualization of Three-Dimensional 904, 1996.

, Image Data Using IMOD, J. Struct. Biol, vol.116, pp.71-76

J. R. Kremer, D. N. Mastronarde, and J. R. Mcintosh, Computer Visualization of Three-Dimensional 906, 1996.

, Image Data Using IMOD, J. Struct. Biol, vol.116, pp.71-76

E. Krissinel and K. Henrick, Inference of Macromolecular Assemblies from Crystalline State, J. Mol, 2007.

, Biol, vol.372, pp.774-797

M. Kudryashev, R. Wang, M. Brackmann, S. Scherer, T. Maier et al.,

E. H. Egelman and M. Basler, Structure of the Type VI Secretion System Contractile Sheath. 911 Cell, vol.160, pp.952-962, 2015.

A. J. Link, D. Phillips, and G. M. Church, Methods for generating precise deletions and insertions in the 913 genome of wild-type Escherichia coli: application to open reading frame characterization, 1997.

, Bacteriol, vol.179, pp.6228-6237

L. Logger, M. Aschtgen, M. Guérin, E. Cascales, and E. Durand, Molecular Dissection of the 916 Interface between the Type VI Secretion TssM Cytoplasmic Domain and the TssG Baseplate 917 Component, J. Mol. Biol, vol.428, pp.4424-4437, 2016.

L. Ma, J. Lin, and E. Lai, An IcmF Family Protein, ImpLM, Is an Integral Inner Membrane 919, 2009.

, Protein Interacting with ImpKL, and Its Walker A Motif Is Required for Type VI Secretion System-920

, Mediated Hcp Secretion in Agrobacterium tumefaciens, J. Bacteriol, vol.191, pp.4316-4329

M. Marko, C. Hsieh, R. Schalek, J. Frank, and C. Mannella, Focused-ion-beam thinning of frozen-922 hydrated biological specimens for cryo-electron microscopy, Nat. Methods, vol.4, pp.215-217, 2007.

T. G. Martin, A. Boland, A. Fitzpatrick, and S. Scheres, , 2016.

D. N. Mastronarde, Automated electron microscope tomography using robust prediction of 925 specimen movements, J. Struct. Biol, vol.152, pp.36-51, 2005.

J. M. Medeiros, D. Böck, and M. Pilhofer, Imaging bacteria inside their host by cryo-focused ion 927 beam milling and electron cryotomography, Curr. Opin. Microbiol, vol.43, pp.62-68, 2018.

J. M. Medeiros, D. Böck, G. L. Weiss, R. Kooger, R. A. Wepf et al., Robust workflow and 929 instrumentation for cryo-focused ion beam milling of samples for electron cryotomography, 930 Ultramicroscopy, vol.190, pp.1-11, 2018.

J. D. Mougous, M. E. Cuff, S. Raunser, A. Shen, M. Zhou et al., A virulence locus of Pseudomonas 933 aeruginosa encodes a protein secretion apparatus, Science, vol.312, pp.1526-1556, 2006.

G. N. Murshudov, P. Skubák, A. A. Lebedev, N. S. Pannu, and R. A. Steiner, , p.935

, AA (2011) REFMAC 5 for the refinement of macromolecular crystal structures, Acta Crystallogr

, Sect. D Biol. Crystallogr, vol.67, pp.355-367

S. Nazarov, J. P. Schneider, M. Brackmann, K. N. Goldie, H. Stahlberg et al., Cryo-EM 938 reconstruction of Type VI secretion system baseplate and sheath distal end, EMBO J, vol.37, p.97103, 2018.

D. Nicastro, The Molecular Architecture of Axonemes Revealed by Cryoelectron Tomography, 2006.

S. Ovchinnikov, H. Park, N. Varghese, P. Huang, G. A. Pavlopoulos et al.,

D. Baker, Protein structure determination using metagenome sequence data. Science (80-. 944 ), vol.355, pp.294-298, 2017.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, and D. M. Greenblatt, Meng EC & Ferrin TE, 2004.

, Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.947-1605

A. Punjani, J. L. Rubinstein, D. J. Fleet, and M. A. Brubaker, cryoSPARC: algorithms for rapid 949 unsupervised cryo-EM structure determination, Nat. Methods, vol.14, pp.290-296, 2017.

D. Quentin, S. Ahmad, P. Shanthamoorthy, J. D. Mougous, J. C. Whitney et al., Mechanism of 951 loading and translocation of type VI secretion system effector Tse6, Nat. Microbiol, vol.3, p.1152, 2018.

E. Ramírez-aportela, J. L. Vilas, R. Melero, and P. Conesa, Automatic local resolution-based 954 sharpening of cryo-EM maps, pp.1-21, 2018.

C. S. Robb, M. Assmus, F. E. Nano, and A. B. Boraston, Structure of the T6SS lipoprotein TssJ1 from 962, 2013.

, Pseudomonas aeruginosa, Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun, vol.69, pp.607-617

C. S. Robb, F. E. Nano, and A. B. Boraston, The structure of the conserved type six secretion protein 964, 2012.

, TssL (DotU) from Francisella novicida, J. Mol. Biol

P. Rosenthal and R. Henderson, Optimal Determination of Particle Orientation, Absolute Hand, 966 and Contrast Loss in Single-particle Electron Cryomicroscopy, J. Mol. Biol, vol.333, pp.721-745, 2003.

A. B. Russell, R. D. Hood, N. K. Bui, M. Leroux, W. Vollmer et al., Type VI secretion delivers 968 bacteriolytic effectors to target cells, Nature, vol.475, pp.343-347, 2011.

A. B. Russell, S. B. Peterson, and J. D. Mougous, Type VI secretion system effectors: Poisons with a 970 purpose, Nat. Rev. Microbiol, vol.12, pp.137-148, 2014.

S. Scheres, RELION: implementation of a Bayesian approach to cryo-EM structure 972 determination, J. Struct. Biol, vol.180, pp.519-549, 2012.

C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, NIH Image to ImageJ: 25 years of image analysis, Nat. 974 Methods, vol.9, pp.671-676, 2012.

M. M. Shneider, S. A. Buth, B. T. Ho, M. Basler, J. J. Mekalanos et al., PAAR-repeat proteins 976 sharpen and diversify the type VI secretion system spike, Nature, vol.500, pp.350-353, 2013.

J. M. Silverman, D. M. Agnello, H. Zheng, B. T. Andrews, M. Li et al., , p.978, 2013.

, Haemolysin Coregulated Protein Is an Exported Receptor and Chaperone of Type VI Secretion 979

. Substrates, Mol. Cell

O. S. Smart, J. G. Neduvelil, X. Wang, B. A. Wallace, and M. Sansom, HOLE: A program for the analysis 981 of the pore dimensions of ion channel structural models, J. Mol. Graph, vol.14, pp.354-360, 1996.

J. Spagnuolo, N. Opalka, W. X. Wen, D. Gagic, E. Chabaud et al., , p.983

M. Russel and J. Rakonjac, Identification of the gate regions in the primary structure of the 984 secretin pIV, Mol. Microbiol, vol.76, pp.133-150, 2010.

T. C. Terwilliger, O. V. Sobolev, P. Afonine, and P. D. Adams, Automated map sharpening by 986 maximization of detail and connectivity, Acta Crystallogr. Sect. D Struct. Biol, vol.74, pp.545-559, 2018.

D. Unterweger, B. Kostiuk, and S. Pukatzki, Adaptor Proteins of Type VI Secretion System Effectors, 2017.

, Trends Microbiol, vol.25, pp.8-10

J. Wang, M. Brackmann, D. Castaño-díez, M. Kudryashev, K. N. Goldie et al., Cryo-EM structure of the extended type VI secretion system sheath-tube complex, 2017.

. Microbiol, , vol.2, pp.1507-1512

R. Wang, Y. Song, B. A. Barad, Y. Cheng, J. S. Fraser et al., Automated structure refinement 993 of macromolecular assemblies from cryo-EM maps using Rosetta, Elife, vol.5, 2016.

X. Wang, B. Sun, M. Xu, S. Qiu, D. Xu et al., Crystal structure of the periplasmic 995 domain of TssL, a key membrane component of Type VI secretion system, Int. J. Biol. Macromol, vol.996, issue.120, pp.1474-1479, 2018.

G. L. Weiss, J. M. Medeiros, and M. Pilhofer, In situ imaging of bacterial secretion systems by electron 998 cryotomography, Methods in Molecular Biology pp, pp.353-375, 2017.

Z. Yan, M. Yin, D. Xu, Y. Zhu, and X. Li, Structural insights into the secretin translocation channel in 1000 the type II secretion system, Nat. Struct. Mol. Biol, vol.24, pp.177-183, 2017.

A. Zaslaver, A. Bren, M. Ronen, S. Itzkovitz, I. Kikoin et al., Surette MG & Alon U 1002 (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli, Nat. 1003 Methods, vol.3, pp.623-628

K. Zhang, Gctf: Real-time CTF determination and correction, J. Struct. Biol, vol.193, pp.1-12, 2016.

W. Zhao, F. Caro, W. Robins, and J. J. Mekalanos, Antagonism toward the intestinal microbiota and 1006 its effect on Vibrio cholerae virulence. Science (80-. ), vol.359, pp.210-213, 2018.

S. Q. Zheng, B. Keszthelyi, E. Branlund, J. M. Lyle, M. B. Braunfeld et al., UCSF 1008 tomography: An integrated software suite for real-time electron microscopic tomographic data 1009 collection, alignment, and reconstruction, J. Struct. Biol, vol.157, pp.138-147, 2007.

S. Q. Zheng, E. Palovcak, J. Armache, K. A. Verba, Y. Cheng et al., MotionCor2: anisotropic 1011 correction of beam-induced motion for improved cryo-electron microscopy, Nat. Methods, vol.14, pp.1012-331, 2017.

A. Zoued, C. J. Cassaro, E. Durand, B. Douzi, A. P. España et al., , p.1014, 2016.

, Structure-Function Analysis of the TssL Cytoplasmic Domain Reveals a New Interaction 1015 between the Type VI Secretion Baseplate and Membrane Complexes, J. Mol. Biol, vol.428, p.4423

A. Zoued, J. P. Duneau, E. Durand, A. P. España, L. Journet et al., Tryptophan-1018 mediated Dimerization of the TssL Transmembrane Anchor Is Required for Type VI Secretion 1019 System Activity, J. Mol. Biol, 2018.

A. Zoued, E. Durand, C. Bebeacua, Y. R. Brunet, B. Douzi et al., TssK 1021 is a trimeric cytoplasmic protein interacting with components of both phage-like and 1022 membrane anchoring complexes of the type VI secretion system, J. Biol. Chem, vol.288, p.27041, 2013.