J. Slager and J. Veening, Hard-Wired Control of Bacterial Processes by Chromosomal Gene Location, Trends in Microbiology, vol.24, issue.10, pp.788-800, 2016.
DOI : 10.1016/j.tim.2016.06.003

J. Bryant, L. Sellars, S. Busby, and D. Lee, Chromosome position effects on gene expression in Escherichia coli K-12, Nucleic Acids Research, vol.514, issue.Pt 6, pp.11383-11392, 2014.
DOI : 10.1016/j.gene.2012.11.011

M. Campos and C. Jacobs-wagner, Cellular organization of the transfer of genetic information, Current Opinion in Microbiology, vol.16, issue.2, pp.171-176, 2013.
DOI : 10.1016/j.mib.2013.01.007

E. Couturier and E. Rocha, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Molecular Microbiology, vol.52, issue.5, pp.1506-1518, 2006.
DOI : 10.1073/pnas.52.4.973

R. Dryselius, K. Izutsu, T. Honda, and T. Iida, Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location, BMC Genomics, vol.9, issue.1, pp.559-1471, 2008.
DOI : 10.1186/1471-2164-9-559

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-559?site=bmcgenomics.biomedcentral.com

V. Gerganova, M. Berger, E. Zaldastanishvili, P. Sobetzko, C. Lafon et al., Chromosomal position shift of a regulatory gene alters the bacterial phenotype, Nucleic Acids Research, vol.245, issue.17, pp.8215-8226, 2015.
DOI : 10.1007/s00018-013-1394-1

T. Emonet and C. Jacobs-wagner, Spatial organization of the flow of genetic information in bacteria, Nature, vol.466, pp.77-81, 2010.

J. Narula, A. Kuchina, D. Lee, M. Fujita, G. Süel et al., Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication, Cell, vol.162, issue.2, pp.328-337, 2015.
DOI : 10.1016/j.cell.2015.06.012

E. Rocha, The Organization of the Bacterial Genome, Annual Review of Genetics, vol.42, issue.1, pp.211-233, 2008.
DOI : 10.1146/annurev.genet.42.110807.091653

J. Slager, M. Kjos, L. Attaiech, and J. Veening, Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin, Cell, vol.157, issue.2, pp.395-406, 2014.
DOI : 10.1016/j.cell.2014.01.068

P. Sobetzko, M. Glinkowska, A. Travers, and G. Muskhelishvili, DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle, Molecular BioSystems, vol.95, issue.4, pp.1643-1651, 2013.
DOI : 10.1073/pnas.95.4.1460

P. Sobetzko, A. Travers, and G. Muskhelishvili, Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle, Proceedings of the National Academy of Sciences, vol.2, issue.21, pp.42-50, 2012.
DOI : 10.1038/sj.emboj.7600434

S. Vieira-silva and E. Rocha, The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics, PLoS Genetics, vol.24, issue.1, p.1000808, 2010.
DOI : 10.1371/journal.pgen.1000808.s012

URL : https://hal.archives-ouvertes.fr/pasteur-00488678

G. Muskhelishvili and A. Travers, Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome, Journal of Molecular Microbiology and Biotechnology, vol.24, issue.5-6, pp.332-343, 2014.
DOI : 10.1159/000368852

S. Fitzgerald, S. Dillon, T. Chao, H. Wiencko, K. Hokamp et al., Re-engineering cellular physiology by rewiring high-level global regulatory genes. Sci Rep 5:17653. https, 2015.
DOI : 10.1038/srep17653

URL : http://www.nature.com/articles/srep17653.pdf

M. Berger, V. Gerganova, P. Berger, R. Rapiteanu, V. Lisicovas et al., Genes on a wire: the nucleoid-associated protein HU insulates transcription units in Escherichia coli. Sci Rep 6:31512. https, 2016.

H. Bremer and P. Dennis, posting date. Modulation of chemical composition and other parameters of the cell at different exponential growth rates, EcoSal Plus, 2008.

E. Rocha, The replication-related organization of bacterial genomes, Microbiology, vol.150, issue.6, pp.1609-1627, 2004.
DOI : 10.1099/mic.0.26974-0

A. Soler-bistué, J. Mondotte, M. Bland, M. Val, M. Saleh et al., Genomic Location of the Major Ribosomal Protein Gene Locus Determines Vibrio cholerae Global Growth and Infectivity, PLOS Genetics, vol.26, issue.24, 2015.
DOI : 10.1371/journal.pgen.1005156.s023

M. Val, A. Soler-bistué, M. Bland, and D. Mazel, Management of multipartite genomes: the Vibrio cholerae model, Current Opinion in Microbiology, vol.22, pp.120-126, 2014.
DOI : 10.1016/j.mib.2014.10.003

URL : https://hal.archives-ouvertes.fr/pasteur-01163283

T. Rasmussen, R. Jensen, and O. Skovgaard, The two chromosomes of Vibrio cholerae are initiated at different time points in the cell cycle, The EMBO Journal, vol.100, issue.13, pp.3124-3131, 2007.
DOI : 10.1099/00221287-18-2-382

E. Nelson, J. Harris, J. Morris, . Jr, S. Calderwood et al., Cholera transmission: the host, pathogen and bacteriophage dynamic, Nature Reviews Microbiology, vol.45, issue.10, pp.693-702, 2009.
DOI : 10.1093/infdis/148.6.998

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842031/pdf

M. Chao, J. Pritchard, Y. Zhang, E. Rubin, J. Livny et al., High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model???based analyses of transposon-insertion sequencing data, Nucleic Acids Research, vol.35, issue.19, pp.9033-9048, 2013.
DOI : 10.1016/0092-8674(83)90117-4

B. Stoebe and K. Kowallik, Gene-cluster analysis in chloroplast genomics, Trends in Genetics, vol.15, issue.9, pp.344-347, 1999.
DOI : 10.1016/S0168-9525(99)01815-6

T. Le, M. Imakaev, L. Mirny, and M. Laub, High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome, Science, vol.110, issue.5, pp.731-734, 2013.
DOI : 10.1073/pnas.1220824110

T. Le and M. Laub, Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries, The EMBO Journal, vol.35, issue.14, pp.1582-1595, 2016.
DOI : 10.15252/embj.201593561

J. Spitzer, From Water and Ions to Crowded Biomacromolecules: In Vivo Structuring of a Prokaryotic Cell, Microbiology and Molecular Biology Reviews, vol.75, issue.3, pp.491-50600010, 2011.
DOI : 10.1128/MMBR.00010-11

G. Rivas and A. Minton, Macromolecular Crowding In Vitro , In Vivo , and In Between, Trends in Biochemical Sciences, vol.41, issue.11, pp.970-981, 2016.
DOI : 10.1016/j.tibs.2016.08.013

M. Mourão, J. Hakim, and S. Schnell, Connecting the Dots: The Effects of Macromolecular Crowding on Cell Physiology, Biophysical Journal, vol.107, issue.12, pp.2761-2766, 2014.
DOI : 10.1016/j.bpj.2014.10.051

A. Vendeville, D. Larivière, and E. Fourmentin, An inventory of the bacterial macromolecular components and their spatial organization, FEMS Microbiology Reviews, vol.61, issue.2, pp.395-414, 2011.
DOI : 10.1111/j.1365-2958.2006.05309.x

B. Parry, I. Surovtsev, M. Cabeen, O. Hern, C. Dufresne et al., The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity, Cell, vol.156, issue.1-2, pp.183-194, 2014.
DOI : 10.1016/j.cell.2013.11.028

URL : https://doi.org/10.1016/j.cell.2013.11.028

J. Concepción-acevedo, H. Weiss, W. Chaudhry, and B. Levin, Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput, PLOS ONE, vol.108, issue.6, 2015.
DOI : 10.1371/journal.pone.0126915.s010

O. Skovgaard, M. Bak, A. Løbner-olesen, and N. Tommerup, Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing, Genome Research, vol.21, issue.8, pp.1388-1393, 2011.
DOI : 10.1101/gr.117416.110

D. Block, R. Hussein, L. Liang, and H. Lim, Regulatory consequences of gene translocation in bacteria, Nucleic Acids Research, vol.108, issue.18, pp.8979-8992, 2012.
DOI : 10.1073/pnas.1010082108

A. Mandlik, J. Livny, W. Robins, J. Ritchie, J. Mekalanos et al., RNA-Seq-Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression, Cell Host & Microbe, vol.10, issue.2, pp.165-174, 2011.
DOI : 10.1016/j.chom.2011.07.007

M. Kaczanowska and M. Rydén-aulin, Ribosome Biogenesis and the Translation Process in Escherichia coli, Microbiology and Molecular Biology Reviews, vol.71, issue.3, pp.477-49400013, 2007.
DOI : 10.1128/MMBR.00013-07

Z. Shajani, M. Sykes, and J. Williamson, Assembly of Bacterial Ribosomes, Annual Review of Biochemistry, vol.80, issue.1, pp.501-526, 2011.
DOI : 10.1146/annurev-biochem-062608-160432

J. Moffitt, S. Pandey, A. Boettiger, S. Wang, and X. Zhuang, Spatial organization shapes the turnover of a bacterial transcriptome Elife 5:e13065. https, 2016.

C. Hutchison, I. Chuang, R. Noskov, V. Assad-garcia, N. Deerinck et al., Design and synthesis of a minimal bacterial genome, Science, vol.181, issue.24, p.6253, 2016.
DOI : 10.1016/S0147-619X(02)00121-X

G. Li, D. Burkhardt, C. Gross, and J. Weissman, Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources, Cell, vol.157, issue.3, pp.624-635, 2014.
DOI : 10.1016/j.cell.2014.02.033

T. Allen, T. Watkins, L. Lindahl, and J. Zengel, Regulation of Ribosomal Protein Synthesis in Vibrio cholerae, Journal of Bacteriology, vol.186, issue.17, pp.5933-5937, 2004.
DOI : 10.1128/JB.186.17.5933-5937.2004

Z. Gyorfy, G. Draskovits, V. Vernyik, F. Blattner, T. Gaal et al., Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number, Nucleic Acids Research, vol.10, issue.3, pp.1783-1794, 2015.
DOI : 10.15252/msb.20145379

K. Søgaard and M. Nørholm, Side effects of extra tRNA supplied in a typical bacterial protein production scenario, Protein Science, vol.28, issue.11, pp.2102-2108, 2016.
DOI : 10.1093/nar/28.1.292

P. Schlax, K. Xavier, T. Gluick, and D. Draper, ?? Operon mRNA, Journal of Biological Chemistry, vol.236, issue.42, pp.38494-38501, 2001.
DOI : 10.1093/nar/13.11.3891

URL : http://www.jbc.org/content/276/42/38494.full.pdf

M. Nomura, R. Gourse, and G. Baughman, Regulation of the Synthesis of Ribosomes and Ribosomal Components, Annual Review of Biochemistry, vol.53, issue.1, pp.75-117, 1984.
DOI : 10.1146/annurev.bi.53.070184.000451

R. Reyes-lamothe, E. Nicolas, and D. Sherratt, Chromosome Replication and Segregation in Bacteria, Annual Review of Genetics, vol.46, issue.1, pp.121-143, 2012.
DOI : 10.1146/annurev-genet-110711-155421

E. Toro and L. Shapiro, Bacterial Chromosome Organization and Segregation, Cold Spring Harbor Perspectives in Biology, vol.2, issue.2, p.349, 2010.
DOI : 10.1101/cshperspect.a000349

P. Nikel, M. Chavarría, A. Danchin, and V. De-lorenzo, From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions, Current Opinion in Chemical Biology, vol.34, pp.20-29, 2016.
DOI : 10.1016/j.cbpa.2016.05.011

B. Hall, H. Acar, A. Nandipati, and M. Barlow, Growth Rates Made Easy, Molecular Biology and Evolution, vol.20, issue.1, pp.232-238, 2014.
DOI : 10.1002/yea.931

URL : https://academic.oup.com/mbe/article-pdf/31/1/232/3572663/mst187.pdf

A. San-millan, K. Heilbron, and R. Maclean, Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations, The ISME Journal, vol.87, issue.3, pp.601-612, 2014.
DOI : 10.1128/AAC.01284-08

J. Andersen, C. Sternberg, L. Poulsen, S. Bjorn, M. Givskov et al., New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria, Appl Environ Microbiol, vol.64, pp.2240-2246, 1998.

M. Val, O. Skovgaard, M. Ducos-galand, M. Bland, and D. Mazel, Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues, PLoS Genetics, vol.163, issue.1, p.1002472, 2012.
DOI : 10.1371/journal.pgen.1002472.s005

URL : https://hal.archives-ouvertes.fr/inserm-01285625

D. Souza-silva, O. Blokesch, and M. , Genetic manipulation of Vibrio cholerae by combining natural transformation with FLP recombination, Plasmid, vol.64, issue.3, pp.186-195, 2010.
DOI : 10.1016/j.plasmid.2010.08.001

R. Marvig and M. Blokesch, Natural transformation of Vibrio cholerae as a tool - Optimizing the procedure, BMC Microbiology, vol.10, issue.1, p.155, 2010.
DOI : 10.1186/1471-2180-10-155

M. Blokesch, TransFLP &#x2014; A Method to Genetically Modify <em>Vibrio cholerae</em> Based on Natural Transformation and FLP-recombination, Journal of Visualized Experiments, issue.68, p.3761, 2012.
DOI : 10.3791/3761