P. Fawcett, P. Eichenberger, R. Losick, and P. Youngman, The transcriptional profile of early to middle sporulation in Bacillus subtilis, Proceedings of the National Academy of Sciences, vol.97, issue.14, pp.8063-8068, 2000.
DOI : 10.1073/pnas.140209597

D. Haeusser and P. Levin, The great divide: coordinating cell cycle events during bacterial growth and division, Current Opinion in Microbiology, vol.11, issue.2, pp.94-99, 2008.
DOI : 10.1016/j.mib.2008.02.008

L. Bowers, E. Shapland, and K. Ryan, Who's in charge here? Regulating cell cycle regulators, Current Opinion in Microbiology, vol.11, issue.6, pp.547-552, 2008.
DOI : 10.1016/j.mib.2008.09.019

E. Purcell, C. Boutte, and S. Crosson, Two-Component Signaling Systems and Cell Cycle Control in Caulobacter crescentus, Adv Exp Med Biol, vol.631, pp.122-130, 2008.
DOI : 10.1007/978-0-387-78885-2_8

J. Skerker and M. Laub, Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus, Nature Reviews Microbiology, vol.181, issue.4, pp.325-337, 2004.
DOI : 10.1073/pnas.1332764100

I. Domian, K. Quon, and L. Shapiro, Cell Type-Specific Phosphorylation and Proteolysis of a Transcriptional Regulator Controls the G1-to-S Transition in a Bacterial Cell Cycle, Cell, vol.90, issue.3, pp.415-424, 1997.
DOI : 10.1016/S0092-8674(00)80502-4

K. Quon, G. Marczynski, and L. Shapiro, Cell Cycle Control by an Essential Bacterial Two-Component Signal Transduction Protein, Cell, vol.84, issue.1, pp.83-93, 1996.
DOI : 10.1016/S0092-8674(00)80995-2

A. Reisenauer, K. Quon, and L. Shapiro, The CtrA response regulator mediates temporal control of gene expression during the Caulobacter cell cycle, J Bacteriol, vol.181, pp.2430-2439, 1999.

J. Collier, H. Mcadams, and L. Shapiro, A DNA methylation ratchet governs progression through a bacterial cell cycle, Proceedings of the National Academy of Sciences, vol.104, issue.43, pp.17111-17116, 2007.
DOI : 10.1073/pnas.0708112104

S. Jones, N. Ferguson, and M. Alley, New members of the ctrA regulon: the major chemotaxis operon in Caulobacter is CtrA dependent, Microbiology, vol.147, issue.4, pp.949-958, 2001.
DOI : 10.1099/00221287-147-4-949

M. Laub, S. Chen, L. Shapiro, and H. Mcadams, Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle, Proceedings of the National Academy of Sciences, vol.99, issue.7, pp.4632-4637, 2002.
DOI : 10.1073/pnas.062065699

J. Skerker and L. Shapiro, Identification and cell cycle control of a novel pilus system in Caulobacter crescentus, The EMBO Journal, vol.19, issue.13, pp.3223-3234, 2000.
DOI : 10.1093/emboj/19.13.3223

M. Wortinger, M. Sackett, and Y. Brun, CtrA mediates a DNA replication checkpoint that prevents cell division in Caulobacter crescentus, The EMBO Journal, vol.19, issue.17, pp.4503-4512, 2000.
DOI : 10.1093/emboj/19.17.4503

J. Collier, S. Murray, and L. Shapiro, DnaA couples DNA replication and the expression of two cell cycle master regulators, The EMBO Journal, vol.176, issue.2, pp.346-356, 2006.
DOI : 10.1006/jmbi.1994.1007

B. Gorbatyuk and G. Marczynski, Regulated degradation of chromosome replication proteins DnaA and CtrA in Caulobacter crescentus, Molecular Microbiology, vol.42, issue.4, pp.1233-1245, 2005.
DOI : 10.1111/j.1365-2958.2004.04459.x

A. Hottes, L. Shapiro, and H. Mcadams, DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus, Molecular Microbiology, vol.176, issue.5, pp.1340-1353, 2005.
DOI : 10.1111/j.1365-2958.2005.04912.x

J. Holtzendorff, D. Hung, P. Brende, A. Reisenauer, P. Viollier et al., Oscillating Global Regulators Control the Genetic Circuit Driving a Bacterial Cell Cycle, Science, vol.304, issue.5673, pp.983-987, 2004.
DOI : 10.1126/science.1095191

E. Biondi, S. Reisinger, J. Skerker, M. Arif, B. Perchuk et al., Regulation of the bacterial cell cycle by an integrated genetic circuit, Nature, vol.4, issue.7121, pp.899-904, 2006.
DOI : 10.1038/nature05321

C. Jacobs, I. Domian, J. Maddock, and L. Shapiro, Cell Cycle???Dependent Polar Localization of an Essential Bacterial Histidine Kinase that Controls DNA Replication and Cell Division, Cell, vol.97, issue.1, pp.111-120, 1999.
DOI : 10.1016/S0092-8674(00)80719-9

G. Burton, G. Hecht, and A. Newton, Roles of the histidine protein kinase pleC in Caulobacter crescentus motility and chemotaxis., Journal of Bacteriology, vol.179, issue.18, pp.5849-5853, 1997.
DOI : 10.1128/jb.179.18.5849-5853.1997

N. Ohta, T. Lane, E. Ninfa, J. Sommer, and A. Newton, A histidine protein kinase homologue required for regulation of bacterial cell division and differentiation., Proceedings of the National Academy of Sciences, vol.89, issue.21, pp.10297-10301, 1992.
DOI : 10.1073/pnas.89.21.10297

J. Sommer and A. Newton, Pseudoreversion analysis indicates a direct role of cell division genes in polar morphogenesis and differentiation in Caulobacter crescentus, Genetics, vol.129, pp.623-630, 1991.

J. Wu, N. Ohta, and A. Newton, An essential, multicomponent signal transduction pathway required for cell cycle regulation in Caulobacter, Proceedings of the National Academy of Sciences, vol.95, issue.4, pp.1443-1448, 1998.
DOI : 10.1073/pnas.95.4.1443

V. Weiss, G. Kramer, T. Dunnebier, and A. Flotho, Mechanism of regulation of the bifunctional histidine kinase NtrB in Escherichia coli, J Mol Microbiol Biotechnol, vol.4, pp.229-233, 2002.

C. Jacobs, D. Hung, and L. Shapiro, Dynamic localization of a cytoplasmic signal transduction response regulator controls morphogenesis during the Caulobacter cell cycle, Proceedings of the National Academy of Sciences, vol.98, issue.7, pp.4095-4100, 2001.
DOI : 10.1073/pnas.051609998

R. Wheeler and L. Shapiro, Differential Localization of Two Histidine Kinases Controlling Bacterial Cell Differentiation, Molecular Cell, vol.4, issue.5, pp.683-694, 1999.
DOI : 10.1016/S1097-2765(00)80379-2

S. Radhakrishnan, M. Thanbichler, and P. Viollier, The dynamic interplay between a cell fate determinant and a lysozyme homolog drives the asymmetric division cycle of Caulobacter crescentus, Genes & Development, vol.22, issue.2, pp.212-225, 2008.
DOI : 10.1101/gad.1601808

A. Iniesta, P. Mcgrath, A. Reisenauer, H. Mcadams, and L. Shapiro, A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression, Proceedings of the National Academy of Sciences, vol.103, issue.29, pp.10935-10940, 2006.
DOI : 10.1073/pnas.0604554103

U. Jenal and T. Fuchs, An essential protease involved in bacterial cell-cycle control, The EMBO Journal, vol.17, issue.19, pp.5658-5669, 1998.
DOI : 10.1093/emboj/17.19.5658

P. Mcgrath, A. Iniesta, K. Ryan, L. Shapiro, and H. Mcadams, A Dynamically Localized Protease Complex and a Polar Specificity Factor Control a Cell Cycle Master Regulator, Cell, vol.124, issue.3, pp.535-547, 2006.
DOI : 10.1016/j.cell.2005.12.033

K. Ryan, Partners in crime: phosphotransfer profiling identifies a multicomponent phosphorelay, Molecular Microbiology, vol.280, issue.2, pp.361-363, 2006.
DOI : 10.1111/j.1365-2958.2005.04980.x

K. Ryan, S. Huntwork, and L. Shapiro, Recruitment of a cytoplasmic response regulator to the cell pole is linked to its cell cycle-regulated proteolysis, Proceedings of the National Academy of Sciences, vol.101, issue.19, pp.7415-7420, 2004.
DOI : 10.1073/pnas.0402153101

R. Hallez, A. Bellefontaine, and J. Letesson, Morphological and functional asymmetry in ??-proteobacteria, Trends in Microbiology, vol.12, issue.8, pp.361-365, 2004.
DOI : 10.1016/j.tim.2004.06.002

A. Lang and J. Beatty, Genetic analysis of a bacterial genetic exchange element: The gene transfer agent of Rhodobacter capsulatus, Proceedings of the National Academy of Sciences, vol.97, issue.2, pp.859-864, 2000.
DOI : 10.1073/pnas.97.2.859

A. Lang and J. Beatty, A Bacterial Signal Transduction System Controls Genetic Exchange and Motility, Journal of Bacteriology, vol.184, issue.4, pp.913-918, 2002.
DOI : 10.1128/jb.184.4.913-918.2002

A. Bellefontaine, C. Pierreux, P. Mertens, J. Vandenhaute, J. Letesson et al., Plasticity of a transcriptional regulation network among alpha-proteobacteria is supported by the identification of CtrA targets in Brucella abortus, Molecular Microbiology, vol.43, issue.4, pp.945-960, 2002.
DOI : 10.1073/pnas.96.23.13068

G. Robertson, A. Reisenauer, R. Wright, R. Jensen, A. Jensen et al., The Brucella abortus CcrM DNA methyltransferase is Additional file 10 Figure S4

T. Miller and R. Belas, Motility is involved in Silicibacter sp. TM1040 interaction with dinoflagellates, Environmental Microbiology, vol.6, issue.9, pp.1648-1659, 2006.
DOI : 10.1128/AEM.67.11.5210-5218.2001

L. Kahng and L. Shapiro, The CcrM DNA Methyltransferase of Agrobacterium tumefaciens Is Essential, and Its Activity Is Cell Cycle Regulated, Journal of Bacteriology, vol.183, issue.10, pp.3065-3075, 2001.
DOI : 10.1128/JB.183.10.3065-3075.2001

R. Gupta and A. Mok, Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups, BMC Microbiology, vol.7, issue.1, p.106, 2007.
DOI : 10.1186/1471-2180-7-106

M. Pellegrini, E. Marcotte, M. Thompson, D. Eisenberg, and T. Yeates, Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles, Proceedings of the National Academy of Sciences, vol.96, issue.8, pp.4285-4288, 1999.
DOI : 10.1073/pnas.96.8.4285
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16324

M. Laub, H. Mcadams, T. Feldblyum, C. Fraser, and L. Shapiro, Global Analysis of the Genetic Network Controlling a Bacterial Cell Cycle, Science, vol.290, issue.5499, pp.2144-2148, 2000.
DOI : 10.1126/science.290.5499.2144

F. Roth, J. Hughes, P. Estep, and G. Church, Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation, Nature Biotechnology, vol.15, issue.10, pp.939-945, 1998.
DOI : 10.1038/nbt0698-566

A. Brassinga, R. Siam, W. Mcsween, H. Winkler, D. Wood et al., Conserved Response Regulator CtrA and IHF Binding Sites in the ??-Proteobacteria Caulobacter crescentus and Rickettsia prowazekii Chromosomal Replication Origins, Journal of Bacteriology, vol.184, issue.20, pp.5789-5799, 2002.
DOI : 10.1128/JB.184.20.5789-5799.2002

C. Stephens, A. Reisenauer, R. Wright, and L. Shapiro, A cell cycle-regulated bacterial DNA methyltransferase is essential for viability., Proceedings of the National Academy of Sciences, vol.93, issue.3, pp.1210-1214, 1996.
DOI : 10.1073/pnas.93.3.1210

R. Wright, C. Stephens, and L. Shapiro, The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus., Journal of Bacteriology, vol.179, issue.18, pp.5869-5877, 1997.
DOI : 10.1128/jb.179.18.5869-5877.1997

F. Hansen, B. Christensen, and T. Atlung, Sequence Characteristics Required for Cooperative Binding and Efficient in Vivo Titration of the Replication Initiator Protein DnaA in E. coli, Journal of Molecular Biology, vol.367, issue.4, pp.942-952, 2007.
DOI : 10.1016/j.jmb.2007.01.056

S. Ishikawa, Y. Ogura, M. Yoshimura, H. Okumura, E. Cho et al., Distribution of Stable DnaA-Binding Sites on the Bacillus Subtilis Genome Detected using a Modified ChIP-chip Method, DNA Research, vol.14, issue.4, pp.155-168, 2007.
DOI : 10.1093/dnares/dsm017

J. Collier and L. Shapiro, Spatial complexity and control of a bacterial cell cycle, Current Opinion in Biotechnology, vol.18, issue.4, pp.333-340, 2007.
DOI : 10.1016/j.copbio.2007.07.007

M. Barnett, D. Hung, A. Reisenauer, L. Shapiro, and S. Long, A Homolog of the CtrA Cell Cycle Regulator Is Present and Essential in Sinorhizobium meliloti, Journal of Bacteriology, vol.183, issue.10, pp.3204-3210, 2001.
DOI : 10.1128/JB.183.10.3204-3210.2001

P. Mcgrath, H. Lee, L. Zhang, A. Iniesta, A. Hottes et al., High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons, Nature Biotechnology, vol.177, issue.5, pp.584-592, 2007.
DOI : 10.1038/nbt1294

C. Sibley, S. Maclellan, and T. Finan, The Sinorhizobium meliloti chromosomal origin of replication, Microbiology, vol.152, issue.2, pp.443-455, 2006.
DOI : 10.1099/mic.0.28455-0

N. Ohta and A. Newton, The Core Dimerization Domains of Histidine Kinases Contain Recognition Specificity for the Cognate Response Regulator, Journal of Bacteriology, vol.185, issue.15, pp.4424-4431, 2003.
DOI : 10.1128/JB.185.15.4424-4431.2003

S. Reisinger, S. Huntwork, P. Viollier, and K. Ryan, DivL Performs Critical Cell Cycle Functions in Caulobacter crescentus Independent of Kinase Activity, Journal of Bacteriology, vol.189, issue.22, pp.8308-8320, 2007.
DOI : 10.1128/JB.00868-07

R. Gupta, Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for ?? ???Proteobacterial Evolution, Critical Reviews in Microbiology, vol.62, issue.2, pp.101-135, 2005.
DOI : 10.1073/pnas.221575398

B. Sallstrom and S. Andersson, Genome reduction in the ??-Proteobacteria, Current Opinion in Microbiology, vol.8, issue.5, pp.579-585, 2005.
DOI : 10.1016/j.mib.2005.08.002

J. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai et al., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092

T. Schneider, G. Stormo, L. Gold, and A. Ehrenfeucht, Information content of binding sites on nucleotide sequences, Journal of Molecular Biology, vol.188, issue.3, pp.415-431, 1986.
DOI : 10.1016/0022-2836(86)90165-8

X. Liu, D. Brutlag, and J. Liu, An algorithm for finding protein???DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments, Nature Biotechnology, vol.262, issue.8, pp.835-839, 2002.
DOI : 10.1038/nbt717

R. Tatusov, D. Natale, I. Garkavtsev, T. Tatusova, U. Shankavaram et al., The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-28, 2001.
DOI : 10.1093/nar/29.1.22

S. Whelan, P. Lio, and N. Goldman, Molecular phylogenetics: state-of-the-art methods for looking into the past, Trends in Genetics, vol.17, issue.5, pp.262-272, 2001.
DOI : 10.1016/S0168-9525(01)02272-7

. Brilli, The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis BMC Systems Biology, p.52, 2010.