M. Allert, J. C. Cox, and H. W. Hellinga, Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames, Journal of Molecular Biology, vol.402, issue.5, pp.905-918, 2010.

J. M. Andrade, R. F. Santos, I. Chelysheva, Z. Ignatova, and C. M. Arraiano, The RNAbinding protein Hfq is important for ribosome biogenesis and affects translation fidelity, The EMBO Journal, vol.37, issue.11, p.97631, 2018.

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. TL -100, vol.100, pp.3889-3894, 2003.

T. E. Arnold, J. Yu, and J. G. Belasco, mRNA stabilization by the ompA 5' untranslated region: two protective elements hinder distinct pathways for mRNA degradation, RNA, vol.4, pp.319-330, 1998.

I. Artsimovitch, Rebuilding the bridge between transcription and translation: NusG as a transcription-translation coupling factor, Molecular Microbiology, vol.108, issue.5, pp.467-472, 2018.

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, issue.2, p.8, 2006.

N. E. Baggett, Y. Zhang, and C. A. Gross, Global analysis of translation termination in E. coli, PLOS Genetics, vol.13, issue.3, p.1006676, 2017.

C. S. Baker, I. Morozov, K. Suzuki, T. Romeo, and P. Babitzke, CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli: Regulation of glycogen biosynthesis in E. coli, Molecular Microbiology, vol.44, issue.6, pp.1599-1610, 2002.

S. Bakshi, H. Choi, and J. Weisshaar, The Spatial Biology of Transcription and Translation in Rapidly Growing Escherichia Coli, Frontiers in Microbiology, vol.6, 2015.

S. Bakshi, A. Siryaporn, M. Goulian, and J. C. Weisshaar, , 2012.

, Superresolution Imaging of Ribosomes and RNA Polymerase in Live Escherichia Coli Cells, Molecular Microbiology, vol.85, issue.1, pp.21-38

D. Barrick, K. Villanueba, J. Childs, R. Kalil, T. D. Schneider et al., Quantitative analysis of ribosome binding sites in E.coli, Nucleic Acids Research, vol.22, issue.7, pp.1287-1295, 1994.

A. Bartholomäus, I. Fedyunin, P. Feist, C. Sin, G. Zhang et al., Bacteria differently regulate mRNA abundance to specifically respond to various stresses, Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences, vol.374, p.20150069, 2016.

L. Bastet, P. Turcotte, J. T. Wade, and D. A. Lafontaine, Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay, RNA Biology, pp.1-4, 2018.

K. Bentele, P. Saffert, R. Rauscher, Z. Ignatova, and N. Bluthgen, Efficient translation initiation dictates codon usage at gene start, Molecular Systems Biology, vol.9, issue.1, pp.675-675, 2014.

O. G. Berg and C. G. Kurland, Growth Rate-optimised tRNA Abundance and Codon Usage, Journal of Molecular Biology, vol.270, pp.544-550, 1997.

J. A. Bernstein, A. B. Khodursky, P. Lin, S. Lin-chao, and S. N. Cohen, Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays, Proceedings of the National Academy of Sciences, vol.99, issue.15, pp.9697-9702, 2002.

S. Berthoumieux, H. De-jong, G. Baptist, C. Pinel, C. Ranquet et al., Shared control of gene expression in bacteria by transcription factors and global physiology of the cell, Molecular Systems Biology, vol.9, issue.1, pp.634-634, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00793352

F. R. Blattner, G. Plunkett, C. Bloch, N. Perna, V. Burland et al., The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-1462, 1997.

Z. D. Blount, The unexhausted potential of E, 2015.

G. Boël, R. Letso, H. Neely, W. N. Price, K. Wong et al., Codon influence on protein expression in E. coli correlates with mRNA levels, Nature, vol.529, pp.358-363, 2016.

M. Bouvier and A. J. Carpousis, A tale of two mRNA degradation pathways mediated by RNase E: RNase E pathways, Molecular Microbiology, vol.82, issue.6, pp.1305-1310, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00666936

S. Brantl, Regulatory mechanisms employed by cis-encoded antisense RNAs, Current Opinion in Microbiology, vol.10, issue.2, pp.102-109, 2007.

H. Bremer and P. Dennis, Feedback control of ribosome function in Escherichia coli, Biochimie, vol.90, issue.3, pp.493-499, 2008.

H. Bremer and P. P. Dennis, Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate, pp.1553-1569, 1996.

M. Bulmer, The Selection-Mutation-DriftTheory of Synonymous Codon Usage, Genetics, vol.129, pp.897-907, 1991.

N. A. Burgess-brown, S. Sharma, F. Sobott, C. Loenarz, U. Oppermann et al., Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study, Protein Expression and Purification, vol.59, issue.1, pp.94-102, 2008.

D. H. Burkhardt, S. Rouskin, Y. Zhang, G. Li, J. S. Weissman et al., Operon mRNAs are organized into ORF-centric structures that predict translation efficiency, p.22037, 2017.

G. Cambray, J. C. Guimaraes, and A. P. Arkin, Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli, Nature Biotechnology, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01986590

R. A. Capaldi, B. Schulenberg, J. Murray, and R. Aggeler, Structure and function of E. coli ATP synthase, The Journal of Experimental Biology, vol.203, pp.29-33, 2000.

M. Caron, L. Bastet, A. Lussier, M. Simoneau-roy, E. Masse et al., Dualacting riboswitch control of translation initiation and mRNA decay, Proceedings of the National Academy of Sciences, vol.109, issue.50, pp.3444-3453, 2012.

A. J. Carpousis, The RNA Degradosome of Escherichia coli : An mRNA-Degrading Machine Assembled on RNase E, Annual Review of Microbiology, vol.61, issue.1, pp.71-87, 2007.

T. A. Carrier and J. D. Keasling, Controlling Messenger RNA Stability in Bacteria: Strategies for Engineering Gene Expression, Biotechnology Progress, vol.13, issue.6, pp.699-708, 1997.

L. Y. Chan, C. F. Mugler, S. Heinrich, P. Vallotton, and K. Weis, Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability, vol.7, p.32, 2018.

D. Chandu and D. Nandi, Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation, Research in Microbiology, vol.155, issue.9, pp.710-719, 2004.

B. Chang, S. Halgamuge, and S. Tang, Analysis of SD sequences in completed microbial genomes: Non-SD-led genes are as common as SD-led genes, Gene, vol.373, pp.90-99, 2006.

D. Chang, D. J. Smalley, D. L. Tucker, M. P. Leatham, W. E. Norris et al., Carbon nutrition of Escherichia coli in the mouse intestine, Proceedings of the National Academy of Sciences, vol.101, issue.19, pp.7427-7432, 2004.

H. Chassé, S. Boulben, V. Costache, P. Cormier, and J. Morales, Analysis of translation using polysome profiling, Nucleic Acids Research, vol.45, issue.3, p.15, 2016.

H. Chen, K. Shiroguchi, H. Ge, and X. S. Xie, Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli, Molecular Systems Biology, vol.11, issue.1, pp.781-781, 2015.

S. N. Cohen, A. C. Chang, H. W. Boyer, and R. B. Helling, Construction of Biologically Functional Bacterial Plasmids In Vitro, Proceedings of the National Academy of Sciences of the United States of America, vol.70, issue.11, pp.3240-3244, 1973.

J. R. Cole and M. Nomura, Changes in the half-life of ribosomal protein messenger RNA caused by translational repression, Journal of Molecular Biology, vol.188, issue.3, pp.383-392, 1986.

F. H. Crick, L. Barnett, S. Brenner, and R. J. Watts-tobin, General Nature of the Genetic Code for Proteins, Nature, vol.192, issue.4809, pp.1227-1232, 1961.

F. Darfeuille, C. Unoson, J. Vogel, and E. G. Wagner, An Antisense RNA Inhibits Translation by Competing with Standby Ribosomes, Molecular Cell, vol.26, issue.3, pp.381-392, 2007.

M. H. De-smit and J. Van-duin, Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis, Proceedings of the National Academy of Sciences, vol.87, issue.19, pp.7668-7672, 1990.

A. Deana and J. G. Belasco, Lost in translation: the influence of ribosomes on bacterial mRNA decay, Genes & Development, vol.19, issue.21, pp.2526-2533, 2005.

C. Del-campo, A. Bartholomäus, I. Fedyunin, and Z. Ignatova, Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function, PLoS Genetics, vol.11, issue.10, pp.1-24, 2015.

H. Dong, L. Nilsson, and C. G. Kurland, Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates, Journal of Molecular Biology, vol.260, issue.5, pp.649-663, 1996.

C. Dressaire, C. Gitton, P. Loubière, V. Monnet, I. Queinnec et al., Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis, PLoS Computational Biology, vol.5, issue.12, p.1000606, 2009.

M. Dreyfus, Chapter 11 Killer and Protective Ribosomes, Progress in Molecular Biology and Translational Science, vol.85, 2009.

M. Ehrenberg, H. Bremer, and P. P. Dennis, Medium-dependent control of the bacterial growth rate, Biochimie, vol.95, issue.4, pp.643-658, 2013.

T. Esquerré, S. Laguerre, C. Turlan, A. J. Carpousis, L. Girbal et al., Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates, Nucleic Acids Research, vol.42, issue.4, pp.2460-2472, 2014.

T. Esquerré, A. Moisan, H. Chiapello, L. Arike, R. Vilu et al., , 2015.

, Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates, BMC Genomics, vol.16, issue.1, p.275

S. A. Evfratov, I. A. Osterman, E. S. Komarova, A. M. Pogorelskaya, M. P. Rubtsova et al., Application of sorting and next generation sequencing to study 5?-UTR influence on translation efficiency in Escherichia coli, Nucleic Acids Research, vol.45, issue.6, pp.3487-3502, 2017.

L. D. Fernandes, A. P. Moura, and L. Ciandrini, Gene length as a regulator for ribosome recruitment and protein synthesis: Theoretical insights, Scientific Reports, vol.7, issue.1, pp.1-11, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01585262

N. Fluman, S. Navon, E. Bibi, and Y. Pilpel, mRNA-programmed translation pauses in the targeting of E. coli membrane proteins, ELife, vol.3, pp.1-19, 2014.

I. Frumkin, M. J. Lajoie, C. J. Gregg, G. Hornung, G. M. Church et al., Codon usage of highly expressed genes affects proteome-wide translation efficiency, Proceedings of the National Academy of Sciences, vol.115, issue.21, pp.4940-4949, 2018.

I. Frumkin, D. Schirman, A. Rotman, F. Li, L. Zahavi et al., Gene Architectures that Minimize Cost of Gene Expression, Molecular Cell, vol.65, issue.1, pp.142-153, 2017.

J. Gardin, R. Yeasmin, A. Yurovsky, Y. Cai, S. Skiena et al., Measurement of average decoding rates of the 61 sense codons in vivo, ELife, vol.3, pp.1-20, 2014.

L. Gerosa, K. Kochanowski, M. Heinemann, and U. Sauer, Dissecting specific and global transcriptional regulation of bacterial gene expression, Molecular Systems Biology, vol.9, issue.1, pp.658-658, 2014.

D. B. Goodman, G. M. Church, and S. Kosuri, Causes and Effects of N-Terminal Codon Bias in Bacterial Genes, Science, vol.342, issue.6157, pp.475-479, 2013.

T. E. Gorochowski, Z. Ignatova, R. A. Bovenberg, and J. A. Roubos, Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate, Nucleic Acids Research, vol.43, issue.6, pp.3022-3032, 2015.

J. C. Guimaraes, M. Rocha, and A. P. Arkin, Transcript level and sequence determinants of protein abundance and noise in Escherichia coli, Nucleic Acids Research, vol.42, issue.8, pp.4791-4799, 2014.

C. Gustafsson, S. Govindarajan, and J. Minshull, Codon bias and heterologous protein expression, Trends in Biotechnology, vol.22, issue.7, pp.346-353, 2004.

C. S. Hayes and R. T. Sauer, Cleavage of the A Site mRNA Codon during Ribosome Pausing Provides a Mechanism for Translational Quality Control, Molecular Cell, vol.12, issue.4, pp.903-911, 2003.

D. G. Hendrickson, D. J. Hogan, H. L. Mccullough, J. W. Myers, D. Herschlag et al., Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA, PLoS Biology, vol.7, issue.11, p.1000238, 2009.

A. J. Hockenberry, A. R. Pah, M. C. Jewett, and L. A. Amaral, Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency, Open Biology, vol.7, issue.1, p.160239, 2017.

E. Holmqvist and J. Vogel, RNA-binding proteins in bacteria, Nature Reviews Microbiology, vol.16, issue.10, pp.601-615, 2018.

X. Hu, Y. Yang, and B. Ma, Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability, Scientific Reports, vol.5, p.11113, 2015.

C. Huang, H. Lin, and X. Yang, Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements, Journal of Industrial Microbiology & Biotechnology, vol.39, issue.3, pp.383-399, 2012.

N. T. Ingolia, Ribosome profiling: new views of translation, from single codons to genome scale, Nature Reviews Genetics, vol.15, issue.3, pp.205-213, 2014.

N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, and J. S. Weissman, Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling, Science, issue.5924, pp.218-223, 2009.

I. Iost and M. Dreyfus, The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation, The EMBO Journal, vol.14, issue.13, pp.3252-3261, 1995.

F. Jacob and J. Monod, Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-356, 1961.

S. A. Joyce and M. Dreyfus, In the Absence of Translation, RNase E can Bypass 5H mRNA Stabilizers in Escherichia coli, Journal of Molecular Biology, vol.282, pp.241-254, 1998.

. Kaern, T. C. Mads, W. J. Elston, J. J. Blake, and . Collins, Stochasticity in Gene Expression: From Theories to Phenotypes, Nature Reviews Genetics, vol.6, issue.6, pp.451-64, 2005.

M. Kamionka, Engineering of Therapeutic Proteins Production in Escherichia coli, Current Pharmaceutical Biotechnology, vol.12, issue.2, pp.268-274, 2011.

P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker et al., Multidimensional annotation of the Escherichia coli K-12 genome, Nucleic Acids Research, vol.35, issue.22, pp.7577-7590, 2007.

M. Kertesz, Y. Wan, E. Mazor, J. L. Rinn, R. C. Nutter et al., Genomewide measurement of RNA secondary structure in yeast, Nature, vol.467, issue.7311, pp.103-107, 2010.

S. Klumpp and T. Hwa, Growth-rate-dependent partitioning of RNA polymerases in bacteria, Proceedings of the National Academy of Sciences, vol.105, issue.51, pp.20245-20250, 2008.

S. Klumpp, Z. Zhang, and T. Hwa, Growth-rate dependent global effects on gene expression in bacteria, Cell, vol.139, issue.7, p.1366, 2009.

S. Klumpp, M. Scott, S. Pedersen, and T. Hwa, Molecular Crowding Limits Translation and Cell Growth, Proceedings of the National Academy of Sciences, vol.110, issue.42, pp.16754-59, 2013.

R. Kohler, R. A. Mooney, D. J. Mills, R. Landick, and P. Cramer, Architecture of a transcribingtranslating expressome, Science, vol.356, issue.6334, pp.194-197, 2017.

E. Korkmazhan, H. Teimouri, N. Peterman, and E. Levine, Dynamics of translation can determine the spatial organization of membrane-bound proteins and their mRNA, Proceedings of the National Academy of Sciences, vol.114, issue.51, 2017.

S. Kosuri, D. B. Goodman, G. Cambray, V. K. Mutalik, Y. Gao et al., Composability of regulatory sequences controlling transcription and translation in Escherichia coli, Proceedings of the National Academy of Sciences, vol.110, issue.34, pp.14024-14029, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01422313

G. Kudla, A. W. Murray, D. Tollervey, and J. B. Plotkin, Coding-Sequence Determinants of, Gene Expression in Escherichia coli, vol.324, p.4, 2009.

K. M. Kuhn, J. L. Derisi, P. O. Brown, and P. Sarnow, Global and Specific Translational Regulation in the Genomic Response of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a Nonfermentable Carbon Source, Molecular and Cellular Biology, vol.21, issue.3, pp.916-927, 2001.

D. H. Lackner, T. H. Beilharz, S. Marguerat, J. Mata, S. Watt et al., A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast, Molecular Cell, vol.26, issue.1, pp.145-155, 2007.

J. R. Lacsina, G. Lamonte, C. V. Nicchitta, and J. Chi, Polysome profiling of the malaria parasite Plasmodium falciparum, Molecular and Biochemical Parasitology, vol.179, issue.1, pp.42-46, 2011.

C. Lange, M. Lehr, K. Zerulla, P. Ludwig, J. Schweitzer et al., Effects of Kasugamycin on the Translatome of Escherichia coli, PLOS ONE, vol.12, issue.1, p.168143, 2017.

C. Lange, A. Zaigler, M. Hammelmann, J. Twellmeyer, G. Raddatz et al., , 2007.

, Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea, BMC Genomics, vol.8, pp.1-17

B. S. Laursen, H. P. Sørensen, K. K. Mortensen, and H. U. Sperling-petersen, Initiation of Protein Synthesis in Bacteria, Microbiology and Molecular Biology Reviews, vol.69, issue.1, pp.101-123, 2005.

I. R. Lehman, S. B. Zimmerman, J. Adler, M. J. Bessman, E. S. Simms et al., Enzymatic synthesis of deoxyribonucleic acid, Proceedings of the National Academy of Sciences of the United States of America, vol.44, issue.12, pp.1191-1196, 1958.

A. Levin-karp, U. Barenholz, T. Bareia, M. Dayagi, L. Zelcbuch et al., Quantifying translational coupling in E. coli synthetic operons using RBS modulation and fluorescent reporters, ACS Synthetic Biology, vol.2, issue.6, pp.327-336, 2013.

G. W. Li, D. Burkhardt, C. Gross, and J. S. Weissman, Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources, Cell, vol.157, issue.3, pp.624-635, 2014.

G. Li, E. Oh, and J. S. Weissman, The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria, Nature, vol.484, issue.7395, pp.538-541, 2012.

S. Linn and W. Arber, Host specificity of DNA produced by Escherichia coli, X. In vitro restriction of phage fd replicative form, Proceedings of the National Academy of Sciences of the United States of America, vol.59, pp.1300-1306, 1968.

G. Lithwick, Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation, Genome Research, vol.13, issue.12, pp.2665-2673, 2003.

P. Lu, C. Vogel, R. Wang, X. Yao, and E. M. Marcotte, Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation, Nature Biotechnology, vol.25, issue.1, pp.117-124, 2007.

A. Martínez-antonio, Escherichia coli transcriptional regulatory network, Network Biology, vol.1, issue.1, pp.21-33, 2011.

K. Mcgary and E. Nudler, RNA polymerase and the ribosome: the close relationship, Current Opinion in Microbiology, vol.16, issue.2, pp.112-117, 2013.

D. Melamed, L. Pnueli, and Y. Arava, Yeast translational response to high salinity: global analysis reveals regulation at multiple levels, RNA, issue.7, pp.1337-1351, 2008.

M. Meselson and R. Yuan, DNA Restriction Enzyme from E. coli, Nature, vol.217, issue.5134, p.1110, 1968.

I. Moll, S. Grill, C. O. Gualerzi, and U. Bläsi, Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control, Molecular Microbiology, vol.43, issue.1, pp.239-246, 2002.

T. Møller, T. Franch, C. Udesen, K. Gerdes, and P. Valentin-hansen, Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon, Genes & Development, vol.16, issue.13, pp.1696-1706, 2002.

G. J. Morgan, D. H. Burkhardt, J. W. Kelly, and E. T. Powers, Translation efficiency is maintained at elevated temperature in Escherichia coli, Journal of Biological Chemistry, vol.293, issue.3, pp.777-793, 2018.

M. Mori, Quantifying the benefit of a proteome reserve in fluctuating environments, Nature Communications, vol.8, issue.1, 2017.

T. Morisaki, K. Lyon, K. F. Deluca, J. G. Deluca, B. P. English et al., Real-Time Quantification of Single RNA Translation Dynamics in Living Cells, Science, vol.352, issue.6292, pp.1425-1454, 2016.

K. Nakahigashi, Y. Takai, Y. Shiwa, M. Wada, M. Honma et al., Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo, BMC Genomics, vol.15, issue.1, p.1115, 2014.

L. Nie, G. Wu, and W. Zhang, Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency in Desulfovibrio vulgaris : A Quantitative Analysis, Genetics, vol.174, issue.4, pp.2229-2243, 2006.

E. J. O'brien, J. Utrilla, B. O. Palsson, E. Oh, A. H. Becker et al., Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments, PLOS Computational Biology, vol.12, issue.6, pp.1295-1308, 2011.

Y. Osada, R. Saito, and M. Tomita, Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes, Bioinformatics, vol.15, issue.7, pp.578-581, 1999.

F. Picard, C. Dressaire, L. Girbal, and M. Cocaign-bousquet, Examination of posttranscriptional regulations in prokaryotes by integrative biology, Comptes Rendus Biologies, vol.332, issue.11, pp.958-973, 2009.

F. Picard, P. Loubière, L. Girbal, and M. Cocaign-bousquet, The significance of translation regulation in the stress response, BMC Genomics, vol.14, issue.1, p.588, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268301

F. Picard, H. Milhem, P. Loubière, B. Laurent, M. Cocaign-bousquet et al., Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression, BMC Genomics, vol.13, issue.1, p.528, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01268281

J. B. Plotkin and G. Kudla, Synonymous but not the same: the causes and consequences of codon bias, Nature Reviews Genetics, vol.12, issue.1, pp.32-42, 2011.

C. Pop, S. Rouskin, N. T. Ingolia, L. Han, E. M. Phizicky et al., Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation, Molecular Systems Biology, vol.10, issue.12, pp.770-770, 2014.

V. Presnyak, N. Alhusaini, Y. H. Chen, S. Martin, N. Morris et al., Codon optimality is a major determinant of mRNA stability, Cell, vol.160, issue.6, pp.1111-1124, 2015.

M. N. Price, K. M. Wetmore, A. M. Deutschbauer, and A. P. Arkin, A Comparison of the Costs and Benefits of Bacterial Gene Expression, PLOS ONE, p.22, 2016.

S. Proshkin, R. Rahmouni, A. Mironov, and E. Nudler, Cooperation between Translating Ribosomes and RNA Polymerase in Transcription Elongation, Science, issue.5977, pp.504-508, 2010.

F. Qi, M. Motz, K. Jung, J. Lassak, and D. Frishman, Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation, PLOS Computational Biology, vol.14, issue.2, p.1005987, 2018.

W. Qian, J. Yang, N. M. Pearson, C. Maclean, and J. Zhang, Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency, PLOS Genetics, vol.8, issue.3, p.1002603, 2012.

T. E. Quax, Y. I. Wolf, J. J. Koehorst, O. Wurtzel, R. Vanderoost et al., Differential translation tunes uneven production of operon-encoded proteins, Cell Reports, vol.4, issue.5, pp.938-944, 2013.

V. Ramakrishnan, Ribosome Structure and the Mechanism of Translation, Cell, vol.108, issue.4, pp.557-572, 2002.

M. D. Reis, Solving the riddle of codon usage preferences: a test for translational selection, Nucleic Acids Research, vol.32, issue.17, pp.5036-5044, 2004.

A. Resch, T. Afonyushkin, T. B. Lombo, K. J. Mcdowall, U. Bläsi et al., Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5?-leader, RNA, vol.14, issue.3, pp.454-459, 2008.

M. Riley, T. Abe, M. Arnaud, M. Berlyn, F. Blattner et al., Escherichia coli K-12: a cooperatively developed annotation snapshot--2005, Nucleic Acids Research, vol.34, issue.1, pp.1-9, 2006.

S. Ringquist, S. Shinedling, D. Barrick, L. Green, J. Binkley et al., Translation initiation in Escherichia coli: sequences within the ribosome-binding site, Molecular Microbiology, vol.6, issue.9, pp.1219-1229, 1992.

E. P. Rocha, A. Danchin, and A. Viari, Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis, Nucleic Acids Research, vol.27, issue.17, pp.3567-3576, 1999.

O. Ruiz-larrabeiti, A. H. Plágaro, C. Gracia, E. Sevillano, L. Gallego et al., A new custom microarray for sRNA profiling in Escherichia coli, FEMS Microbiology Letters, vol.363, issue.13, p.131, 2016.

H. M. Salis, E. A. Mirsky, and C. A. Voigt, Automated design of synthetic ribosome binding sites to control protein expression, Nature Biotechnology, vol.27, issue.10, pp.946-950, 2009.

T. M. Schmeing and V. Ramakrishnan, What recent ribosome structures have revealed about the mechanism of translation, Nature, issue.7268, pp.1234-1242, 2009.

D. A. Schneider, W. Ross, and R. L. Gourse, Control of rRNA expression in Escherichia coli, Current Opinion in Microbiology, vol.6, issue.2, pp.151-156, 2003.

P. Shah, Y. Ding, M. Niemczyk, G. Kudla, and J. B. Plotkin, Rate-limiting steps in yeast protein translation, Cell, vol.153, issue.7, pp.1589-1601, 2013.

Z. Shajani, M. T. Sykes, and J. R. Williamson, Assembly of Bacterial Ribosomes, Annual Review of Biochemistry, vol.80, issue.1, pp.501-526, 2011.

P. M. Sharp and W. Li, The codon adaptation index -a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Research, vol.15, issue.3, pp.1281-1295, 1987.

J. Shine and L. Dalgarno, The 3?-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites, Proceedings of the National Academy of Sciences of the United States of America, vol.71, pp.1342-1346, 1974.

C. Sin, D. Chiarugi, and A. Valleriani, Quantitative assessment of ribosome drop-off in E. coli, Nucleic Acids Research, vol.44, issue.6, pp.2528-2537, 2016.

T. J. Soper and S. A. Woodson, The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA, RNA, vol.14, issue.9, pp.1907-1917, 2008.

M. A. Sorensen, A. O. Fehler, and S. Lo-svenningsen, Transfer RNA instability as a stress response in Escherichia coli : Rapid dynamics of the tRNA pool as a function of demand, RNA Biology, vol.15, issue.4-5, pp.586-593, 2018.

A. Stevens, Incorporation of the adenine ribonucleotide into RNA by cell fractions from, E. coli. Biochemical and biophysical research communications, vol.3, issue.1, p.5, 1960.

G. Storz, J. Vogel, and K. M. Wassarman, Regulation by Small RNAs in Bacteria: Expanding Frontiers, Molecular Cell, vol.43, issue.6, pp.880-891, 2011.

A. R. Subramaniam, B. M. Zid, and E. K. Shea, An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation, Cell, vol.159, issue.5, pp.1200-1211, 2014.

S. L. Svenningsen, M. Kongstad, T. S. Stenum, A. J. Muñoz-gómez, and M. A. Sørensen, , 2017.

, Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli, Nucleic Acids Research, vol.45, issue.2, pp.793-804

Y. Taniguchi, P. J. Choi, G. Li, H. Chen, M. Babu et al., Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Science, vol.329, issue.5991, pp.533-538, 2010.

T. Tian and H. M. Salis, A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons, Nucleic Acids Research, vol.43, issue.5, pp.1-15, 2015.

J. Timmermans and L. Van-melderen, Post-transcriptional global regulation by CsrA in bacteria, Cellular and Molecular Life Sciences, vol.67, issue.17, pp.2897-2908, 2010.

Y. Tsai, D. Du, L. Domínguez-malfavón, D. Dimastrogiovanni, J. Cross et al., Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli, Nucleic Acids Research, vol.40, issue.20, pp.10417-10431, 2012.

C. Vogel and E. M. Marcotte, Insights into the regulation of protein abundance from proteomic and transcriptomic analyses, Nat Rev Genet, vol.13, issue.4, pp.227-259, 2013.

M. Duval, A. Simonetti, I. Caldelari, and S. Marzi, Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics, Biochimie, vol.114, pp.18-29, 2015.

C. Lange, A. Zaigler, M. Hammelmann, J. Twellmeyer, G. Raddatz et al.,

, Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea, BMC Genomics, vol.8, pp.1-17, 2007.

G. Y. Fisunov, D. V. Evsyutina, I. A. Garanina, A. A. Arzamasov, I. O. Butenko et al., Ribosome profiling reveals an adaptation strategy of reduced bacterium to acute stress, Biochimie, vol.132, pp.66-74, 2017.

H. Chassé, S. Boulben, V. Costache, P. Cormier, and J. Morales, Analysis of translation using polysome profiling, Nucleic Acids Res, vol.45, issue.3, p.15, 2017.

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proc Natl Acad Sci, vol.100, issue.7, pp.3889-94, 2003.

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

M. Caron, L. Bastet, A. Lussier, M. Simoneau-roy, E. Masse et al., Dual-acting riboswitch control of translation initiation and mRNA decay, Proceedings of the National Academy of Sciences, vol.109, pp.3444-3453, 2012.

N. J. Croucher and N. R. Thomson, Studying bacterial transcriptomes using RNA-seq, Current Opinion in Microbiology, vol.13, pp.619-624, 2010.

C. Dressaire, B. Laurent, P. Loubière, P. Besse, and M. Bousquet, Linear covariance models to examine the determinants of protein levels in Lactococcus lactis, Molecular BioSystems, vol.6, p.1255, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00960013

H. Feng, X. Zhang, and C. Zhang, MRIN for direct assessment of genome-wide and genespecific mRNA integrity from large-scale RNA-sequencing data, Nature Communications, vol.6, pp.1-10, 2015.

J. A. Gagnon-bartsch and T. P. Speed, Using control genes to correct for unwanted variation in microarray data, Biostatistics, vol.13, pp.539-552, 2012.

L. C. Gandolfo and T. P. Speed, Genome wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, PLOS ONE, vol.13, pp.5095-5101, 2009.

D. Kim, J. S. Hong, .. Qiu, Y. Nagarajan, H. Seo et al., Comparative Analysis of Regulatory Elements between <italic>Escherichia coli</italic> and <italic>Klebsiella pneumoniae</italic> by Genome-Wide Transcription Start Site Profiling, PLoS Genet, vol.8, 2012.

S. Kosuri, D. B. Goodman, G. Cambray, V. K. Mutalik, Y. Gao et al., Composability of regulatory sequences controlling transcription and translation in Escherichia coli, Proceedings of the National Academy of Sciences, vol.110, pp.14024-14029, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01422313

H. Li, Exploring single-sample snp and indel calling with whole-genome de novo assembly, Bioinformatics, vol.28, pp.1838-1844, 2012.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, vol.25, pp.1754-1760, 2009.

K. D. Passalacqua, A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick et al., Structure and Complexity of a Bacterial Transcriptome, Journal of Bacteriology, vol.191, pp.3203-3211, 2009.

D. Risso, J. Ngai, T. P. Speed, and S. Dudoit, Normalization of RNA-seq data using factor analysis of control genes or samples, Nature Biotechnology, vol.32, pp.896-902, 2014.

J. T. Robinson, H. Thorvaldsdóttir, W. Winckler, M. Guttman, E. S. Lander et al., Integrative genomics viewer, Nature Biotechnology, vol.29, pp.24-26, 2011.

C. M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiß et al., The primary transcriptome of the major human pathogen Helicobacter pylori, Nature, vol.464, pp.250-255, 2010.

A. Sittka, S. Lucchini, K. Papenfort, C. M. Sharma, K. Rolle et al., Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genetics, vol.4, 2008.

G. Storz, J. Vogel, and K. M. Wassarman, Regulation by Small RNAs in Bacteria: Expanding Frontiers, Molecular Cell, vol.43, pp.880-891, 2011.

M. K. Thomason, T. Bischler, S. K. Eisenbart, K. U. Förstner, A. Zhang et al., Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli, Journal of Bacteriology, vol.197, pp.18-28, 2015.

M. K. Thomason, T. Bischler, S. K. Eisenbart, K. U. Förstner, A. Zhang et al., Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli, Journal of Bacteriology, vol.197, pp.18-28, 2015.

Z. Wang, M. Gerstein, and M. Snyder, RNA-Seq: a revolutionary tool for transcriptomics, Nature Reviews Genetics, vol.10, pp.57-63, 2009.

Y. Ah-seng, J. Rech, D. Lane, and J. Bouet, Defining the Role of ATP Hydrolysis in Mitotic Segregation of Bacterial Plasmids, PLOS Genetics, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00944950

I. Andreeva, R. Belardinelli, and M. Rodnina, Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA, Proceedings of the National Academy of Sciences of the United States of America, vol.115, pp.4411-4416, 2018.

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.100, pp.3889-3894, 2003.

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.2, 2006.

D. H. Burkhardt, S. Rouskin, Y. Zhang, G. Li, J. S. Weissman et al., Operon mRNAs are organized into ORF-centric structures that predict translation efficiency, vol.6, p.22037, 2017.

M. Castellana, -. Hsin, S. Li, and N. S. Wingreen, Spatial organization of bacterial transcription and translation, Proceedings of the National Academy of Sciences, vol.113, pp.9286-9291, 2016.

L. Y. Chan, C. F. Mugler, S. Heinrich, P. Vallotton, and K. Weis, Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability, vol.7, p.32, 2018.

A. Dana and T. Tuller, Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells, PLoS Comput Biol, vol.8, 2012.

E. Borujeni, A. Channarasappa, A. S. Salis, and H. M. , Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites, Nucleic Acids Research, vol.42, pp.2646-2659, 2014.

T. Esquerré, A. Moisan, H. Chiapello, L. Arike, R. Vilu et al., Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates, BMC Genomics, vol.16, p.275, 2015.

T. Esquerré, M. Bouvier, C. Turlan, A. J. Carpousis, L. Girbal et al., The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli, Scientific Reports, vol.6, 2016.

. Gallant, Stringent control in Escherichia coli, Annu. Rev. Genet, vol.13, pp.393-415, 1979.

J. C. Guimaraes, M. Rocha, and A. P. Arkin, Transcript level and sequence determinants of protein abundance and noise in Escherichia coli, Nucleic Acids Research, vol.42, pp.4791-4799, 2014.

. Ingolia, Genome wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, vol.29, pp.5095-5101, 2009.

D. Kim, J. S. Hong, .. Qiu, Y. Nagarajan, H. Seo et al., Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling, PLoS Genetics, vol.8, 2012.

. Kudla, Coding sequence determinants of gene expression, pp.255-258, 2009.

J. Kyte and R. F. Doolittle, A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, pp.105-132, 1982.

D. H. Lackner, T. H. Beilharz, S. Marguerat, J. Mata, S. Watt et al., A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast, Molecular Cell, vol.26, pp.145-155, 2007.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, vol.25, pp.1754-1760, 2009.

G. W. Li, D. Burkhardt, C. Gross, and J. S. Weissman, Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources, Cell, vol.157, pp.624-635, 2014.

B. Liu, Y. Han, and S. Qian, Co-Translational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes, Mol Cell, vol.49, pp.453-463, 2013.

M. Maligoy, M. Mercade, M. Cocaign-bousquet, and P. Loubiere, Transcriptome analysis of Lactococcus lactis in coculture with Saccharomyces cerevisiae, Applied and Environmental Microbiology, vol.74, pp.485-494, 2008.

D. Melamed, L. Pnueli, A. , and Y. , Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels, RNA, vol.14, pp.1337-1351, 2008.

N. Mitarai, K. Sneppen, and S. Pedersen, Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization, Journal of Molecular Biology, vol.382, pp.236-245, 2008.

J. R. Moffitt, S. Pandey, A. N. Boettiger, S. Wang, and X. Zhuang, Spatial organization shapes the turnover of a bacterial transcriptome, 2016.

G. J. Morgan, D. H. Burkhardt, J. W. Kelly, and E. T. Powers, Translation efficiency is maintained at elevated temperature in E. coli, Journal of Biological Chemistry, vol.293, 2017.

K. Nakahigashi, Y. Takai, Y. Shiwa, M. Wada, M. Honma et al., Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo, BMC Genomics, vol.15, p.1115, 2014.

H. L. Nguyen, M. Duviau, M. Cocaign-bousquet, S. Nouaille, and L. Girbal, Multiplexing polysome profiling experiments to study translation in Escherichia coli, PLOS ONE, vol.14, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02106750

S. Nouaille, S. Mondeil, A. L. Finoux, C. Moulis, L. Girbal et al., The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression, Nucleic Acids Research, vol.45, pp.11711-11724, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01882991

E. Oh, A. H. Becker, A. Sandikci, D. Huber, R. Chaba et al., Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo, Cell, vol.147, pp.1295-1308, 2011.

I. A. Osterman, S. A. Evfratov, P. V. Sergiev, and O. A. Dontsova, Comparison of mRNA features affecting translation initiation and reinitiation, Nucleic Acids Research, vol.41, pp.474-486, 2013.

M. W. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Research, vol.29, p.45, 2001.

F. Picard, H. Milhem, P. Loubière, B. Laurent, M. Cocaign-bousquet et al., Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression, BMC Genomics, vol.13, p.528, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01268281

F. Picard, P. Loubière, L. Girbal, and M. Bousquet, The significance of translation regulation in the stress response, BMC Genomics, vol.14, p.588, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268301

J. B. Plotkin and G. Kudla, Synonymous but not the same: the causes and consequences of codon bias, Nat Rev Genet, vol.12, pp.32-42, 2011.

T. Preiss, J. Baron-benhamou, W. Ansorge, and M. W. Hentze, Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock, Nature Structural & Molecular Biology, vol.10, pp.1039-1047, 2003.

S. Proshkin, A. R. Rahmouni, A. Mironov, and E. Nudler, Cooperation between translating ribosomes and RNA polymerase in transcription elongation, Science, vol.328, pp.504-508, 2010.

E. Redon, P. Loubière, and M. Bousquet, Role of mRNA stability during genomewide adaptation of Lactococcus lactis to carbon starvation, The Journal of Biological Chemistry, vol.280, pp.36380-36385, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682214

S. Reuveni, I. Meilijson, M. Kupiec, E. Ruppin, and T. Tuller, Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model, PLoS Computational Biology, vol.7, p.1002127, 2011.

M. Riley, Escherichia coli K-12: a cooperatively developed annotation snapshot--2005, Nucleic Acids Research, vol.34, pp.1-9, 2006.

J. B. Russell and G. M. Cook, Energetics of Bacterial Growth: Balance of Anabolic and Catabolic Reactions, 1995.

T. Sato, M. Terabe, H. Watanabe, T. Gojobori, C. Hori-takemoto et al., The Journal of biochemistry, 2001.

S. Aboulhouda, R. Di-santo, G. Therizols, and D. Weinberg, Accurate, Streamlined Analysis of mRNA Translation by Sucrose Gradient Fractionation, Bio Protoc, vol.7, 2017.

T. Ando and J. Skolnick, Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion, Proceedings of the National Academy of Sciences, vol.107, pp.18457-18462, 2010.

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.100, pp.3889-3894, 2003.

G. Boël, R. Letso, H. Neely, W. N. Price, K. Wong et al., Codon influence on protein expression in E. coli correlates with mRNA levels, Nature, vol.529, pp.358-363, 2016.

H. Chassé, S. Boulben, V. Costache, P. Cormier, and J. Morales, Analysis of translation using polysome profiling, Nucleic Acids Research, p.907, 2016.

G. Csárdi, A. Franks, D. S. Choi, E. M. Airoldi, and D. A. Drummond, Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast, PLOS Genetics, vol.11, p.1005206, 2015.

A. P. Darlington, J. Kim, J. I. Jiménez, and D. G. Bates, Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes, Nat Commun, vol.9, 2018.

G. Kudla, A. W. Murray, D. Tollervey, and J. B. Plotkin, Coding-Sequence Determinants of Gene Expression in Escherichia coli, vol.324, p.4, 2009.

D. H. Lackner, T. H. Beilharz, S. Marguerat, J. Mata, S. Watt et al., A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast, Molecular Cell, vol.26, pp.145-155, 2007.

C. Lange, M. Lehr, K. Zerulla, P. Ludwig, J. Schweitzer et al., Effects of Kasugamycin on the Translatome of Escherichia coli, PLOS ONE, vol.12, 2017.

G. Li, E. Oh, and J. S. Weissman, The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria, Nature, vol.484, pp.538-541, 2012.

G. Li, D. Burkhardt, C. Gross, and J. S. Weissman, Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources, Cell, vol.157, pp.624-635, 2014.

J. J. Li, G. Chew, and M. D. Biggin, Quantitating translational control: mRNA abundancedependent and independent contributions and the mRNA sequences that specify them, Nucleic Acids Research, vol.45, pp.11821-11836, 2017.

L. Marschall, P. Sagmeister, and C. Herwig, Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints, Applied Microbiology and Biotechnology, vol.101, pp.501-512, 2017.

D. Melamed, L. Pnueli, A. , and Y. , Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels, RNA, vol.14, pp.1337-1351, 2008.

N. Mitarai, K. Sneppen, and S. Pedersen, Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization, Journal of Molecular Biology, vol.382, pp.236-245, 2008.

S. Nouaille, S. Mondeil, A. Finoux, C. Moulis, L. Girbal et al., The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression, Nucleic Acids Research, vol.45, pp.11711-11724, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01882991

F. Picard, H. Milhem, P. Loubière, B. Laurent, M. Cocaign-bousquet et al., Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression, BMC Genomics, vol.13, p.528, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01268281

V. Presnyak, N. Alhusaini, Y. Chen, S. Martin, N. Morris et al., Codon Optimality Is a Major Determinant of mRNA Stability, Cell, vol.160, pp.1111-1124, 2015.

M. N. Price, K. M. Wetmore, A. M. Deutschbauer, and A. P. Arkin, A Comparison of the Costs and Benefits of Bacterial Gene Expression, PLOS ONE, vol.22, 2016.

J. Racle, F. Picard, L. Girbal, M. Cocaign-bousquet, V. Hatzimanikatis et al., A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data, PLoS Computational Biology, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651947

M. Sauert, M. T. Wolfinger, O. Vesper, C. Müller, K. Byrgazov et al., The MazFregulon: a toolbox for the post-transcriptional stress response in Escherichia coli, Nucleic Acids Res, vol.44, pp.6660-6675, 2016.

S. W. Seo, J. Yang, J. , and G. Y. , Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli, Biotechnology and Bioengineering, vol.104, pp.611-616, 2009.

G. Shaham and T. Tuller, Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation, DNA Research, vol.25, pp.195-205, 2018.

L. Spangenberg, P. Shigunov, A. P. Abud, A. R. Cofré, M. A. Stimamiglio et al., Polysome profiling shows extensive posttranscriptional regulation during human adipocyte stem cell differentiation into adipocytes, Stem Cell Research, vol.11, pp.902-912, 2013.

A. R. Subramaniam, B. M. Zid, and E. K. Shea, An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation, Cell, vol.159, pp.1200-1211, 2014.

T. Tuller, Y. Y. Waldman, M. Kupiec, and E. Ruppin, Translation efficiency is determined by both codon bias and folding energy, Proceedings of the National Academy of Sciences, vol.107, pp.3645-3650, 2010.

Y. Zarai, M. Margaliot, and T. Tuller, On the Ribosomal Density that Maximizes Protein Translation Rate, PLOS ONE, vol.11, 2016.

H. Zouridis and V. Hatzimanikatis, A Model for Protein Translation: Polysome Self-Organization Leads to Maximum Protein Synthesis Rates, 176 -Multiplexing polysome profiling Citation: Nguyen HL, Duviau M-P, Cocaign, vol.92, pp.717-730, 2007.

M. Bousquet, S. Nouaille, and L. Girbal, Multiplexing polysome profiling experiments to study translation in Escherichia coli, PLoS ONE, vol.14, issue.2, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02106750

C. Vogel and E. M. Marcotte, Insights into the regulation of protein abundance from proteomic and transcriptomic analyses, Nat Rev Genet, vol.13, issue.4, pp.227-259, 2013.

M. Duval, A. Simonetti, I. Caldelari, and S. Marzi, Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics, Biochimie, vol.114, pp.18-29, 2015.

C. Lange, A. Zaigler, M. Hammelmann, J. Twellmeyer, G. Raddatz et al., Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea, BMC Genomics, vol.8, pp.1-17, 2007.

H. Chasse´, S. Boulben, V. Costache, P. Cormier, and J. Morales, Analysis of translation using polysome profiling, Nucleic Acids Res, vol.45, issue.3, p.15, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01389711

Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown et al., Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, vol.100, issue.7, pp.3889-94, 2003.

S. Yamasaki, H. Matsuura, T. Demura, and K. Kato, Changes in Polysome Association of mRNA Throughout Growth and Development in Arabidopsis thaliana, Plant Cell Physiol, 2015.

H. Chasse´, A. J. Boulben, S. , L. Corguille´, G. Corre et al., Translatome analysis at the egg-to-embryo transition in sea urchin, Nucleic Acids Res, vol.46, issue.9, pp.4607-4628, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01803500

S. Pytharopoulou, K. Grintzalis, E. Sazakli, M. Leotsinidis, C. D. Georgiou et al., Translational responses and oxidative stress of mussels experimentally exposed to Hg, Cu and Cd: One pattern does not fit at all, Aquat Toxicol, vol.105, issue.1-2, pp.157-65, 2011.

D. Melamed, L. Pnueli, and Y. Arava, Yeast translational response to high salinity: global analysis reveals regulation at multiple levels, RNA, vol.14, issue.7, pp.1337-51, 2008.

H. Matsuura, Y. Ishibashi, A. Shinmyo, S. Kanaya, and K. Kato, Genome-Wide Analyses of Early Translational Responses to Elevated Temperature and High Salinity in Arabidopsis thaliana, Plant Cell Physiol, vol.51, issue.3, pp.448-62, 2010.

Y. Wu, J. Taggart, P. X. Song, C. Macdiarmid, and D. J. Eide, An MSC2 Promoter-lacZ Fusion Gene Reveals Zinc-Responsive Changes in Sites of Transcription Initiation That Occur across the Yeast Genome, PLoS One, vol.11, issue.9, p.163256, 2016.

J. B. Smirnova, J. N. Selley, F. Sanchez-cabo, C. K. Eddy, A. A. Mccarthy et al., Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways, Mol Cell Biol, vol.25, issue.21, pp.9340-9349, 2005.

L. R. Alves, C. Oliveira, and S. Goldenberg, Eukaryotic translation elongation factor-1 alpha is associated with a specific subset of mRNAs in Trypanosoma cruzi, BMC Microbiol, vol.15, p.25986694, 2015.

B. Liu and C. Chen, Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes, Antimicrob Agents Chemother, vol.62, issue.8, pp.2356-2373, 2018.

F. A. Saglioccos, M. R. Vega-lasoj, D. Zhull, M. F. Tuitell, J. Mccarthyj et al., The Influence of 5'-Secondary Structures upon Ribosome Binding to mRNA during Translation in Yeast, J Biol Chem, vol.268, issue.35, pp.26522-26552, 1993.

V. Presnyak, N. Alhusaini, Y. H. Chen, S. Martin, N. Morris et al., Codon optimality is a major determinant of mRNA stability, Cell, vol.160, issue.6, pp.1111-1135, 2015.

H. Matsuura, S. Takenami, Y. Kubo, K. Ueda, A. Ueda et al., A Computational and Experimental Approach Reveals that the 5 0 -Proximal Region of the 5 0 -UTR has a Cis-Regulatory Signature Responsible for Heat Stress-Regulated mRNA Translation in Arabidopsis, Plant Cell Physiol, vol.54, issue.4, pp.474-83, 2013.

H. A. King and A. P. Gerber, Translatome profiling: Methods for genome-scale analysis of mRNA translation, Brief Funct Genomics, vol.15, issue.1, pp.22-31, 2016.

Y. Ah-seng, J. Rech, D. Lane, and J. Bouet, Defining the Role of ATP Hydrolysis in Mitotic Segregation of Bacterial Plasmids, PLoS Genet, vol.9, issue.12, p.1003956, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00944950

T. Esquerre´, S. Laguerre, C. Turlan, A. J. Carpousis, L. Girbal et al., Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates, Nucleic Acids Res, vol.42, issue.4, pp.2460-72, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02129879

S. Nouaille, S. Mondeil, A. L. Finoux, C. Moulis, L. Girbal et al., The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression, Nucleic Acids Res, vol.45, issue.20, pp.11711-11735, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01882991

E. Redon, P. Loubière, and M. Cocaign-bousquet, Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation, J Biol Chem, vol.280, issue.43, pp.36380-36385, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02682214

M. Maligoy, M. Mercade, M. Cocaign-bousquet, and P. Loubiere, Transcriptome analysis of Lactococcus lactis in coculture with Saccharomyces cerevisiae, Appl Environ Microbiol, vol.74, issue.2, pp.485-94, 2008.

M. W. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res, vol.29, issue.9, 2001.

M. Morin, D. Ropers, E. Cinquemani, J. C. Portais, B. Enjalbert et al., The Csr system regulates Escherichia coli fitness by controlling glycogen accumulation and energy levels, MBio, vol.8, issue.5, pp.1628-1645, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01672038

L. Zhang, W. Jiang, J. Nan, J. Almqvist, and Y. Huang, The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite, Biochim Biophys Acta, vol.1838, pp.1809-1825, 2014.

F. Jacob and J. Monod, Genetic regulatory mechanisms in the synthesis of proteins, J Mol Biol, vol.3, issue.3, pp.318-56, 1961.

C. H. Yu, Y. Dang, Z. Zhou, C. Wu, F. Zhao et al., Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding, Mol Cell, vol.59, issue.5, pp.744-54, 2015.

G. W. Li, E. Oh, and J. S. Weissman, The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria, Nature, vol.484, issue.7395, pp.538-579, 2012.

S. A. Evfratov, I. A. Osterman, E. S. Komarova, A. M. Pogorelskaya, M. P. Rubtsova et al., Application of sorting and next generation sequencing to study 5 0 -UTR influence on translation efficiency in Escherichia coli, Nucleic Acids Res, vol.45, issue.6, pp.3487-502, 2017.

A. M. Giuliodori, D. Pietro, F. Marzi, S. Masquida, B. Wagner et al., The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA, Mol Cell, vol.37, issue.1, pp.21-33, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00475727

S. Gottesman and G. Storz, Bacterial small RNA regulators: versatile roles and rapidly evolving variations, Cold Spring Harb Perspect Biol, vol.3, issue.12, p.3798, 2011.

A. H. Potts, C. A. Vakulskas, A. Pannuri, H. Yakhnin, P. Babitzke et al., Global role of the bacterial posttranscriptional regulator CsrA revealed by integrated transcriptomics, Nat Commun, vol.8, issue.1, p.29150605, 2017.

C. G. Artieri and H. B. Fraser, Evolution at two levels of gene expression in yeast, Genome Res, vol.24, issue.3, pp.411-432, 2014.

Z. Wang, X. Sun, Y. Zhao, X. Guo, H. Jiang et al., Evolution of gene regulation during transcription and translation, Genome Biol Evol, vol.7, issue.4, pp.1155-67, 2015.