S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-169, 2015.

S. Asuthkar, S. Velineni, J. Stadlmann, F. Altmann, and M. Sritharan, Expression and characterization of an iron-regulated hemin-binding protein, HbpA, from Leptospira interrogans serovar Lai, Infect. Immun, vol.75, pp.4582-4591, 2007.

A. R. Bharti, J. E. Nally, J. N. Ricaldi, M. A. Matthias, M. M. Diaz et al., Leptospirosis: a zoonotic disease of global importance, Lancet Infect. Dis, vol.3, pp.757-771, 2003.

P. Bourhy, H. Louvel, I. Saint-girons, and M. Picardeau, Random insertional mutagenesis of Leptospira interrogans, the agent of leptospirosis, using a mariner transposon, J. Bacteriol, vol.187, pp.3255-3258, 2005.

A. Busch, J. Lacal, A. Martos, J. L. Ramos, and T. Krell, Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.13774-13779, 2007.

M. J. Caimano, S. K. Sivasankaran, A. Allard, D. Hurley, K. Hokamp et al., A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni, PLoS Pathog, vol.10, p.1004004, 2014.

L. Cerveny, A. Straskova, V. Dankova, A. Hartlova, M. Ceckova et al., Tetratricopeptide repeat motifs in the world of bacterial pathogens: role in virulence mechanisms, Infect. Immun, vol.81, pp.629-635, 2013.

J. Cheung and W. A. Hendrickson, Sensor domains of twocomponent regulatory systems, Curr. Opin. Microbiol, vol.13, pp.116-123, 2010.

F. Costa, J. E. Hagan, J. Calcagno, M. Kane, P. Torgerson et al., Global morbidity and mortality of leptospirosis: a systematic review, PLoS Negl. Trop. Dis, vol.9, p.3898, 2015.

F. Costa, E. A. Wunder, D. De-oliveira, V. Bisht, G. Rodrigues et al., Patterns in Leptospira shedding in norway rats (Rattus norvegicus) from brazilian slum communities at high risk of disease transmission, PLoS Negl. Trop. Dis, vol.9, p.3819, 2015.

A. Eshghi, J. Becam, A. Lambert, O. Sismeiro, M. A. Dillies et al., A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans, Infect. Immun, vol.82, pp.2542-2552, 2014.

J. Espinosa, F. Rodríguez-mateos, P. Salinas, V. F. Lanza, R. Dixon et al., PipX, the coactivator of NtcA, is a global regulator in cyanobacteria, Proc. Natl. Acad. Sci. U.S.A, vol.111, 2014.

D. E. Fouts, M. A. Matthias, H. Adhikarla, B. Adler, L. Amorim-santos et al., What makes a bacterial species pathogenic?: comparative genomic analysis of the genus Leptospira, PLoS Negl. Trop. Dis, vol.10, p.4403, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01436457

R. Gao, T. R. Mack, and A. M. Stock, Bacterial response regulators: versatile regulatory strategies from common domains, Trends Biochem. Sci, vol.32, pp.225-234, 2007.

R. Gao and A. M. Stock, Biological insights from structures of two-component proteins, Annu. Rev. Microbiol, vol.63, pp.133-154, 2009.

A. Garzon and J. S. Parkinson, Chemotactic signaling by the P1 phosphorylation domain liberated from the CheA histidine kinase of Escherichia coli, J. Bacteriol, vol.178, pp.6752-6758, 1996.

M. Goulian, Two-component signaling circuit structure and properties, Curr. Opin. Microbiol, vol.13, pp.184-189, 2010.

M. R. Graham, L. M. Smoot, C. A. Migliaccio, K. Virtaneva, D. E. Sturdevant et al., Virulence control in group a Streptococcus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.13855-13860, 2002.

S. Guindon, J. F. 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.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

J. T. Henry and S. Crosson, Ligand-binding PAS domains in a genomic, cellular, and structural context, Annu. Rev. Microbiol, vol.65, pp.261-286, 2011.

R. C. Johnson and V. G. Harris, Differentiation of pathogenic and saprophytic leptospires. I. Growth at low temperatures, J. Bacteriol, vol.94, pp.27-31, 1967.

A. Kaczmarczyk, R. Hochstrasser, J. A. Vorholt, and A. Francez-charlot, Two-tiered histidine kinase pathway involved in heat shock and salt sensing in the general stress response of Sphingomonas melonis Fr1, J. Bacteriol, vol.197, pp.1466-1477, 2015.

K. Kassegne, W. Hu, D. M. Ojcius, D. Sun, Y. Ge et al., Identification of collagenase as a critical virulence factor for invasiveness and transmission of pathogenic Leptospira species, J. Infect. Dis, vol.209, pp.1105-1115, 2014.

A. I. Ko, M. Galvao-reis, C. M. Ribeiro-dourado, W. D. Johnson, and L. W. Riley, Urban epidemic of severe leptospirosis in Brazil. Salvador Leptospirosis Study Group, Lancet, vol.354, pp.820-825, 1999.

A. I. Ko, C. Goarant, and M. Picardeau, Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen, Nat. Rev. Microbiol, vol.7, pp.736-747, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-00450871

A. Kumar, J. C. Toledo, R. P. Patel, J. R. Lancaster, and A. J. Steyn, Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.11568-11573, 2007.

A. Lambert, J. Wong-ng, and M. Picardeau, Gene inactivation of a chemotaxis operon in the pathogen Leptospira interrogans, FEMS Microbiol. Lett, vol.362, pp.1-8, 2015.

O. Lenz, F. , and B. , A novel multicomponent regulatory system mediates H 2 sensing in Alcaligenes eutrophus, Proc. Natl. Acad. Sci. U.S.A, vol.95, pp.12474-12479, 1998.

K. Liu, T. J. Warnow, M. T. Holder, S. M. Nelesen, J. Yu et al., SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees, Syst. Biol, vol.61, pp.90-106, 2012.

T. Liu, A. Ramesh, Z. Ma, S. K. Ward, L. Zhang et al., CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator, Nat. Chem. Biol, vol.3, pp.60-68, 2007.

H. Louvel, J. M. Betton, and M. Picardeau, Heme rescues a two-component system Leptospira biflexa mutant, BMC Microbiol, vol.8, p.25, 2008.

M. I. Love, W. Huber, A. , and S. , Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

J. Malmström, M. Beck, A. Schmidt, V. Lange, E. W. Deutsch et al., Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans, Nature, vol.460, pp.762-765, 2009.

T. Mascher, J. D. Helmann, and G. Unden, Stimulus perception in bacterial signal-transducing histidine kinases. Microbiol, Mol. Biol. Rev, vol.70, pp.910-938, 2006.

I. Miras, F. Saul, M. Nowakowski, P. Weber, A. Haouz et al., Structural characterization of a novel subfamily of leucinerich repeat proteins from the human pathogen Leptospira interrogans, Acta Crystallogr. D Biol. Crystallogr, vol.71, pp.1351-1359, 2015.

N. R. Morero, H. Botti, K. R. Nitta, F. Carrión, G. Obal et al., HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes, Mol. Microbiol, vol.94, pp.340-352, 2014.

A. L. Nascimento, A. I. Ko, E. A. Martins, C. B. Monteiro-vitorello, P. L. Ho et al., Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis, J. Bacteriol, vol.186, pp.2164-2172, 2004.

W. S. Noble, How does multiple testing correction work?, Nat. Biotechnol, vol.27, pp.1135-1137, 2009.

Z. E. Phillips and M. A. Strauch, Bacillus subtilis sporulation and stationary phase gene expression, Cell. Mol. Life Sci, vol.59, pp.392-402, 2002.

M. Pinne, J. Matsunaga, and D. A. Haake, Leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins, J. Bacteriol, vol.194, pp.6074-6087, 2012.

A. J. Powell, G. C. Conant, D. E. Brown, I. Carbone, and R. A. Dean, Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens, BMC Genomics, vol.9, p.147, 2008.

R. B. Reis, G. S. Ribeiro, R. D. Felzemburgh, F. S. Santana, S. Mohr et al., Impact of environment and social gradient on Leptospira infection in urban slums, PLoS Negl. Trop. Dis, vol.2, 2008.

L. J. Reitzer and D. , Ammonia assimilation and the biosynthesis of glutamine, Escherichia coli and Salmonella: Cellular and Molecular Biology, pp.391-407, 1996.

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.

T. D. Schmittgen and K. J. Livak, Analyzing real-time PCR data by the comparative C(T) method, Nat. Protoc, vol.3, pp.1101-1108, 2008.

C. Trapnell, L. Pachter, and S. L. Salzberg, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, vol.25, pp.1105-1111, 2009.

M. A. Uhl and J. F. Miller, Central role of the BvgS receiver as a phosphorylated intermediate in a complex two-component phosphorelay, J. Biol. Chem, vol.271, pp.33176-33180, 1996.

F. Van-den-ent and J. Löwe, RF cloning: a restriction-free method for inserting target genes into plasmids, J. Biochem. Biophys. Methods, vol.67, pp.67-74, 2006.

M. L. Vieira, L. G. Fernandes, R. F. Domingos, R. Oliveira, G. H. Siqueira et al., Leptospiral extracellular matrix adhesins as mediators of pathogen-host interactions, FEMS Microbiol. Lett, vol.352, pp.129-139, 2014.

M. Wojnowska, J. Yan, G. N. Sivalingam, A. Cryar, J. Gor et al., Autophosphorylation activity of a soluble hexameric histidine kinase correlates with the shift in protein conformational equilibrium, Chem. Biol, vol.20, pp.1411-1420, 2013.

A. J. Wolfe, Physiologically relevant small phosphodonors link metabolism to signal transduction, Curr. Opin. Microbiol, vol.13, pp.204-209, 2010.

K. Wuichet, B. J. Cantwell, and I. B. Zhulin, Evolution and phyletic distribution of two-component signal transduction systems, Curr. Opin. Microbiol, vol.13, pp.219-225, 2010.

E. A. Wunder, C. P. Figueira, N. Benaroudj, B. Hu, B. A. Tong et al., A novel flagellar sheath protein, FcpA, determines filament coiling, translational motility and virulence for the Leptospira spirochete, Mol. Microbiol, vol.101, pp.457-470, 2016.

S. Yamada, H. Sugimoto, M. Kobayashi, A. Ohno, H. Nakamura et al., Structure of PAS-linked histidine kinase and the response regulator complex, Structure, vol.17, pp.1333-1344, 2009.