M. E. Salazar and M. T. Laub, Temporal and evolutionary dynamics of two-component signaling pathways, Curr Opin Microbiol, vol.24, p.25589045, 2015.
DOI : 10.1016/j.mib.2014.12.003
URL : http://dspace.mit.edu/bitstream/1721.1/105366/1/Lander_Temporal%20and.pdf

T. Tian and A. Harding, How MAP kinase modules function as robust, yet adaptable, circuits, Cell Cycle, vol.13, p.25483189, 2014.
DOI : 10.4161/cc.29349
URL : http://www.tandfonline.com/doi/pdf/10.4161/cc.29349?needAccess=true

E. J. Capra, B. S. Perchuk, J. M. Skerker, and M. T. Laub, Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families, Cell, vol.150, pp.222-232, 2012.
DOI : 10.1016/j.cell.2012.05.033
URL : https://doi.org/10.1016/j.cell.2012.05.033

K. Jonas, Y. E. Chen, and M. T. Laub, Modularity of the bacterial cell cycle enables independent spatial and temporal control of DNA replication, Curr Biol, vol.21, p.21683595, 2011.

S. M. Murray, G. Panis, C. Fumeaux, P. H. Viollier, and M. Howard, Computational and genetic reduction of a cell cycle to its simplest, primordial components, PLoS Biol, vol.11, p.24415923, 2013.
DOI : 10.1371/journal.pbio.1001749
URL : https://doi.org/10.1371/journal.pbio.1001749

A. M. Stock, V. L. Robinson, and P. N. Goudreau, Two-Component Signal Transduction, Annual Review of Biochemistry, vol.69, p.10966457, 2000.

J. M. Skerker, B. S. Perchuk, A. Siryaporn, E. A. Lubin, O. Ashenberg et al., Rewiring the specificity of two-component signal transduction systems, Cell, vol.133, pp.1043-1054, 2008.
DOI : 10.1016/j.cell.2008.04.040
URL : https://doi.org/10.1016/j.cell.2008.04.040

J. R. Kirby, Chemotaxis-like regulatory systems: unique roles in diverse bacteria, Annu Rev Microbiol, vol.63, pp.45-59, 2009.
DOI : 10.1146/annurev.micro.091208.073221

G. H. Wadhams and J. P. Armitage, Making sense of it all: bacterial chemotaxis, Nat Rev Mol Cell Biol, vol.5, p.15573139, 2004.
DOI : 10.1038/nrm1524

K. He and C. E. Bauer, Chemosensory signaling systems that control bacterial survival, Trends Microbiol, vol.22, pp.389-398, 2014.
DOI : 10.1016/j.tim.2014.04.004
URL : http://europepmc.org/articles/pmc4273944?pdf=render

K. Wuichet and I. B. Zhulin, Origins and diversification of a complex signal transduction system in prokaryotes, Sci Signal, vol.3, p.20587806, 2010.

Y. Zhang, A. Ducret, J. Shaevitz, and T. Mignot, From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus, FEMS Microbiol Rev, vol.36, p.22091711, 2012.
DOI : 10.1111/j.1574-6976.2011.00307.x
URL : https://academic.oup.com/femsre/article-pdf/36/1/149/18129206/36-1-149.pdf

H. Sun, D. R. Zusman, and W. Y. Shi, Type IV pilus of Myxococcus xanthus is a motility apparatus controlled by the frz chemosensory system, Current Biology, vol.10, p.10996798, 2000.

Y. Li, H. Sun, X. Ma, A. Lu, R. Lux et al., Extracellular polysaccharides mediate pilus retraction during social motility of Myxococcus xanthus, Proc Natl Acad Sci U S A, vol.100, p.12704238, 2003.
DOI : 10.1073/pnas.0836639100
URL : http://www.pnas.org/content/100/9/5443.full.pdf

R. Agrebi, M. Wartel, C. Brochier-armanet, and T. Mignot, An evolutionary link between capsular biogenesis and surface motility in bacteria, Nat Rev Microbiol, vol.13, pp.318-326, 2015.
DOI : 10.1038/nrmicro3431
URL : https://hal.archives-ouvertes.fr/hal-01452071

J. Luciano, R. Agrebi, L. Gall, A. V. Wartel, M. Fiegna et al., Emergence and modular evolution of a novel motility machinery in bacteria, PLoS Genet, vol.7, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00698033

B. Nan, M. J. Mcbride, J. Chen, D. R. Zusman, and G. Oster, Bacteria that glide with helical tracks, Curr Biol, vol.24, p.24556443, 2014.
DOI : 10.1016/j.cub.2013.12.034
URL : https://doi.org/10.1016/j.cub.2013.12.034

I. Bulyha, C. Schmidt, P. Lenz, V. Jakovljevic, A. Hone et al., Regulation of the type IV pili molecular machine by dynamic localization of two motor proteins, Mol Microbiol, vol.74, pp.691-706, 2009.

T. Mignot, J. P. Merlie, and D. R. Zusman, Regulated pole-to-pole oscillations of a bacterial gliding motility protein, Science, vol.310, p.16272122, 2005.
DOI : 10.1126/science.1119052

T. Mignot, J. W. Shaevitz, P. L. Hartzell, and D. R. Zusman, Evidence that focal adhesion complexes power bacterial gliding motility, Science, vol.315, p.17289998, 2007.
DOI : 10.1126/science.1137223
URL : http://europepmc.org/articles/pmc4095873?pdf=render

B. D. Blackhart and D. R. Zusman, Frizzy" genes of Myxococcus xanthus are involved in control of frequency of reversal of gliding motility, Proc Natl Acad Sci U S A, vol.82, p.3936045, 1985.

D. R. Zusman, Frizzy" mutants: a new class of aggregation-defective developmental mutants of Myxococcus xanthus, J Bacteriol, vol.150, p.6281244, 1982.

S. Leonardy, M. Miertzschke, I. Bulyha, E. Sperling, A. Wittinghofer et al., Regulation of dynamic polarity switching in bacteria by a Ras-like G-protein and its cognate GAP, Embo J, vol.29, p.20543819, 2010.

Y. Zhang, M. Franco, A. Ducret, and T. Mignot, A bacterial Ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility, PLoS Biol, vol.8, p.20652021, 2010.
DOI : 10.1371/journal.pbio.1000430
URL : https://doi.org/10.1371/journal.pbio.1000430

E. Mauriello, F. Mouhamar, B. Nan, A. Ducret, D. Dai et al., Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA. EMBO J, vol.29, pp.315-326, 2010.
DOI : 10.1038/emboj.2009.356
URL : http://emboj.embopress.org/content/embojnl/29/2/315.full.pdf

D. Keilberg, K. Wuichet, F. Drescher, and L. Søgaard-andersen, A response regulator interfaces between the Frz chemosensory system and the MglA/MglB GTPase/GAP module to regulate polarity in Myxococcus xanthus, PLoS Genet, vol.8, p.1002951, 2012.

Y. Zhang, M. Guzzo, A. Ducret, Y. Li, and T. Mignot, A dynamic response regulator protein modulates G-protein-dependent polarity in the bacterium Myxococcus xanthus, PLoS Genet, vol.8, p.22916026, 2012.

M. Miertzschke, C. Koerner, I. R. Vetter, D. Keilberg, E. Hot et al., Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity, EMBO J, vol.30, pp.4185-4197, 2011.

E. Eckhert, P. Rangamani, A. E. Davis, G. Oster, and J. E. Berleman, Dual Biochemical Oscillators May Control Cellular Reversals in Myxococcus xanthus, Biophys J, vol.107, p.25468349, 2014.
DOI : 10.1016/j.bpj.2014.09.046
URL : https://doi.org/10.1016/j.bpj.2014.09.046

Y. F. Inclan, H. C. Vlamakis, and D. R. Zusman, FrzZ, a dual CheY-like response regulator, functions as an output for the Frz chemosensory pathway of Myxococcus xanthus, Mol Microbiol, vol.65, p.17581122, 2007.

V. H. Bustamante, I. Martinez-flores, H. C. Vlamakis, and D. R. Zusman, Analysis of the Frz signal transduction system of Myxococcus xanthus shows the importance of the conserved C-terminal region of the cytoplasmic chemoreceptor FrzCD in sensing signals, Mol Microbiol, vol.53, p.15387825, 2004.

Y. F. Inclan, S. Laurent, and D. R. Zusman, The receiver domain of FrzE, a CheA-CheY fusion protein, regulates the CheA histidine kinase activity and downstream signalling to the A-and S-motility systems of Myxococcus xanthus, Mol Microbiol, vol.68, pp.1328-1367, 2008.

C. Kaimer and D. R. Zusman, Phosphorylation-dependent localization of the response regulator FrzZ signals cell reversals in Myxococcus xanthus, Mol Microbiol, vol.88, p.23551551, 2013.

S. Leonardy, G. Freymark, S. Hebener, E. Ellehauge, and L. Sogaard-andersen, Coupling of protein localization and cell movements by a dynamically localized response regulator in Myxococcus xanthus, Embo J, vol.26, p.17932488, 2007.

S. Karlin, L. Brocchieri, J. Mrázek, and D. Kaiser, Distinguishing features of delta-proteobacterial genomes, Proc Natl Acad Sci USA, vol.103, p.16844781, 2006.
DOI : 10.1073/pnas.0604311103
URL : http://www.pnas.org/content/103/30/11352.full.pdf

M. Wartel, A. Ducret, S. Thutupalli, F. Czerwinski, L. Gall et al., A Versatile Class of Cell Surface Directional Motors Gives Rise to Gliding Motility and Sporulation in Myxococcus xanthus, PLoS Biol, vol.11, 2013.

K. Wuichet and L. Søgaard-andersen, Evolution and diversity of the ras superfamily of small GTPases in prokaryotes, Genome Biol Evol, vol.7, pp.57-70, 2014.

D. S. Milner, R. Till, I. Cadby, A. L. Lovering, S. M. Basford et al., Ras GTPase-like protein MglA, a controller of bacterial social-motility in Myxobacteria, has evolved to control bacterial predation by Bdellovibrio, PLoS Genet, vol.10, p.24721965, 2014.

R. F. Yang, S. Bartle, R. Otto, A. Stassinopoulos, M. Rogers et al., AglZ is a filament-forming coiled-coil protein required for adventurous gliding motility of Myxococcus xanthus, Journal of Bacteriology, vol.186, p.15342587, 2004.

T. Mignot, J. P. Merlie, and D. R. Zusman, Two localization motifs mediate polar residence of FrzS during cell movement and reversals of Myxococcus xanthus, Mol Microbiol, vol.65, p.17590236, 2007.

J. S. Fraser, J. P. Merlie, N. Echols, S. R. Weisfield, T. Mignot et al., An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS, Mol Microbiol, vol.65, p.17573816, 2007.

M. L. Gibiansky, W. Hu, K. A. Dahmen, W. Shi, and G. Wong, Earthquake-like dynamics in Myxococcus xanthus social motility, Proc Natl Acad Sci USA, vol.110, pp.2330-2335, 2013.
DOI : 10.1073/pnas.1215089110
URL : http://www.pnas.org/content/110/6/2330.full.pdf

M. J. Mcbride, T. Kohler, and D. R. Zusman, Methylation of FrzCD, a methyl-accepting taxis protein of Myxococcus xanthus, is correlated with factors affecting cell behavior, J Bacteriol, vol.174, p.1624419, 1992.

M. J. Mcbride, R. A. Weinberg, and D. R. Zusman, Frizzy" aggregation genes of the gliding bacterium Myxococcus xanthus show sequence similarities to the chemotaxis genes of enteric bacteria, Proc Natl Acad Sci U S A, vol.86, p.2492105, 1989.

D. L. Englert, M. D. Manson, and A. Jayaraman, Investigation of bacterial chemotaxis in flow-based microfluidic devices, Nat Protoc, vol.5, pp.864-872, 2010.
DOI : 10.1038/nprot.2010.18

A. C. Lamanna, G. W. Ordal, and L. L. Kiessling, Large increases in attractant concentration disrupt the polar localization of bacterial chemoreceptors, Mol Microbiol, vol.57, p.16045621, 2005.

I. Bulyha, S. Lindow, L. Lin, K. Bolte, K. Wuichet et al., Two small GTPases act in concert with the bactofilin cytoskeleton to regulate dynamic bacterial cell polarity, Dev Cell, vol.25, p.23583757, 2013.

M. Sun, M. Wartel, E. Cascales, J. W. Shaevitz, and T. Mignot, Motor-driven intracellular transport powers bacterial gliding motility, Proc Natl Acad Sci USA, vol.108, p.21482768, 2011.
DOI : 10.1073/pnas.1101101108
URL : https://hal.archives-ouvertes.fr/hal-01458263

E. J. Capra, B. S. Perchuk, O. Ashenberg, C. A. Seid, H. R. Snow et al., Spatial tethering of kinases to their substrates relaxes evolutionary constraints on specificity, Molecular Microbiology, vol.86, p.23078131, 2012.
DOI : 10.1111/mmi.12064
URL : http://onlinelibrary.wiley.com/doi/10.1111/mmi.12064/pdf

V. Sourjik and R. Schmitt, Phosphotransfer between CheA, CheY1, and CheY2 in the chemotaxis signal transduction chain of Rhizobium meliloti, Biochemistry, vol.37, p.9485379, 1998.

K. He, J. N. Marden, E. M. Quardokus, and C. E. Bauer, Phosphate flow between hybrid histidine kinases CheA? and CheS? controls Rhodospirillum centenum cyst formation, PLoS Genet, vol.9, p.24367276, 2013.
DOI : 10.1371/journal.pgen.1004002
URL : https://doi.org/10.1371/journal.pgen.1004002

M. Goulian, Two-component signaling circuit structure and properties, Curr Opin Microbiol, vol.13, pp.184-189, 2010.
DOI : 10.1016/j.mib.2010.01.009
URL : http://europepmc.org/articles/pmc2847654?pdf=render

A. Y. Mitrophanov and E. A. Groisman, Signal integration in bacterial two-component regulatory systems, Genes Dev, vol.22, pp.2601-2611, 2008.
DOI : 10.1101/gad.1700308
URL : http://genesdev.cshlp.org/content/22/19/2601.full.pdf

L. E. Ulrich and I. B. Zhulin, MiST: a microbial signal transduction database, Nucleic Acids Res, vol.35, p.17135192, 2007.
DOI : 10.1093/nar/gkl932
URL : https://academic.oup.com/nar/article-pdf/35/suppl_1/D386/3876657/gkl932.pdf

P. G. Charest and R. A. Firtel, Big roles for small GTPases in the control of directed cell movement, Biochem J, vol.401, p.17173542, 2007.

M. L. Gibiansky, J. C. Conrad, J. F. Gordon, V. D. Motto, D. A. Mathewson et al., Bacteria use type IV pili to walk upright and detach from surfaces, Science, vol.330, p.20929769, 2010.
DOI : 10.1126/science.1194238
URL : https://repositories.lib.utexas.edu/bitstream/2152/39116/2/2010_Gibiansky.pdf

F. Jin, J. C. Conrad, M. L. Gibiansky, and G. Wong, Bacteria use type-IV pili to slingshot on surfaces, Proc Natl Acad Sci USA, vol.108, pp.12617-12622, 2011.
DOI : 10.1073/pnas.1105073108
URL : http://www.pnas.org/content/108/31/12617.full.pdf

A. Ducret, O. Théodoly, and T. Mignot, Single cell microfluidic studies of bacterial motility, Methods Mol Biol, vol.966, pp.97-107, 2013.
DOI : 10.1007/978-1-62703-245-2_6

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.
DOI : 10.1038/nmeth.2019
URL : http://europepmc.org/articles/pmc3855844?pdf=render

A. Komeili, Z. Li, D. K. Newman, and G. J. Jensen, Magnetosomes are cell membrane invaginations organized by the actin-like protein MamK, Science, vol.311, p.16373532, 2006.
DOI : 10.1126/science.1123231
URL : https://authors.library.caltech.edu/24658/2/KOMs06supp.pdf

S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSIBLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, p.9254694, 1997.
DOI : 10.1093/nar/25.17.3389
URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, 2013.
DOI : 10.1093/molbev/mst010
URL : https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf

A. Criscuolo, S. Gribaldo, and . Bmge, Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol Biol, vol.10, p.210, 2010.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximum-likelihood trees for large alignments, PLoS ONE, vol.5, p.20224823, 2010.
DOI : 10.1371/journal.pone.0009490
URL : http://doi.org/10.1371/journal.pone.0009490

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

F. Ronquist, M. Teslenko, P. Van-der-mark, D. L. Ayres, A. Darling et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst Biol, vol.61, pp.539-542, 2012.

C. Brochier, E. Bapteste, D. Moreira, and H. Philippe, Eubacterial phylogeny based on translational apparatus proteins, Trends Genet, vol.18, p.11750686, 2002.
DOI : 10.1016/s0168-9525(01)02522-7

J. R. Brown, C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope, Universal trees based on large combined protein sequence data sets, Nat Genet, vol.28, p.11431701, 2001.
DOI : 10.1038/90129

F. D. Ciccarelli, T. Doerks, C. Von-mering, C. J. Creevey, B. Snel et al., Toward automatic reconstruction of a highly resolved tree of life, Science, vol.311, p.16513982, 2006.

F. Delsuc, H. Brinkmann, and H. Philippe, Phylogenomics and the reconstruction of the tree of life, Nat Rev Genet, vol.6, p.15861208, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00193293

R. Liu and H. Ochman, Stepwise formation of the bacterial flagellar system, Proc Natl Acad Sci USA, vol.104, p.17438286, 2007.
DOI : 10.1073/pnas.0700266104
URL : http://www.pnas.org/content/104/17/7116.full.pdf

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, p.116, 2011.
DOI : 10.1186/1471-2105-12-116
URL : https://hal.archives-ouvertes.fr/hal-00698365