Regulatory RNAs in Bacteria, Cell, vol.136, issue.4, pp.615-628, 2009. ,
DOI : 10.1016/j.cell.2009.01.043
URL : https://doi.org/10.1016/j.cell.2009.01.043
A Decade of Riboswitches, Cell, vol.152, issue.1-2, pp.17-24, 2013. ,
DOI : 10.1016/j.cell.2012.12.024
Identification of regulatory RNAs in Bacillus subtilis, Nucleic Acids Research, vol.38, issue.19, pp.6637-6651, 2010. ,
DOI : 10.1093/nar/gkq454
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes, Genome Biology, vol.11, issue.3, p.31, 2010. ,
DOI : 10.1186/gb-2010-11-3-r31
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2010-11-3-r31?site=genomebiology.biomedcentral.com
Dual-acting riboswitch control of translation initiation and mRNA decay, Proc. Natl Acad. Sci. USA, pp.3444-3453, 2012. ,
DOI : 10.1101/gad.1348805
Riboswitch control of Rho-dependent transcription termination, Proc. Natl Acad. Sci. USA, pp.5376-5381, 2012. ,
DOI : 10.1016/j.jmb.2010.11.006
URL : http://www.pnas.org/content/109/14/5376.full.pdf
Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator, Proc. Natl Acad. Sci. USA 111, pp.1999-2007, 2014. ,
DOI : 10.1016/j.ymeth.2008.10.006
Global analysis of Escherichia coli RNA degradosome function using DNA microarrays, Proc. Natl Acad. Sci. USA 101, pp.2758-2763, 2004. ,
DOI : 10.1074/jbc.M303381200
Rho and NusG suppress pervasive antisense transcription in Escherichia coli, Genes & Development, vol.26, issue.23, pp.2621-2633, 2012. ,
DOI : 10.1101/gad.196741.112
URL : http://genesdev.cshlp.org/content/26/23/2621.full.pdf
A pause sequence enriched at translation start sites drives transcription dynamics in vivo, Science, vol.115, issue.4, pp.1042-1047, 2014. ,
DOI : 10.1016/S0092-8674(03)00845-6
Thiamin biosynthesis in prokaryotes, Archives of Microbiology, vol.171, issue.5, pp.293-300, 1999. ,
DOI : 10.1007/s002030050713
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature, vol.53, issue.6910, pp.952-956, 2002. ,
DOI : 10.1016/0378-1119(87)90095-3
Comparative Genomics of Thiamin Biosynthesis in Procaryotes, Journal of Biological Chemistry, vol.175, issue.50, pp.48949-48959, 2002. ,
DOI : 10.1126/science.287.5454.820
Molecular basis of gene regulation by the THI-box riboswitch, Molecular Microbiology, vol.31, issue.4, pp.793-803, 2008. ,
DOI : 10.1128/jb.179.22.6887-6893.1997
RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli., Journal of Bacteriology, vol.178, issue.13, pp.3917-3925, 1996. ,
DOI : 10.1128/jb.178.13.3917-3925.1996
The Molecular Basis for the Mode of Action of Bicyclomycin, Current Drug Target -Infectious Disorders, vol.5, issue.3, pp.273-295, 2005. ,
DOI : 10.2174/1568005054880136
Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho, Nucleic Acids Research, vol.42, issue.15, pp.9677-9690, 2014. ,
DOI : 10.1093/nar/gku690
Elongation factor NusG interacts with termination factor rho to regulate termination and antitermination of transcription., Genes & Development, vol.7, issue.1, pp.161-172, 1993. ,
DOI : 10.1101/gad.7.1.161
A consensus motif common to all rho-dependent prokaryotic transcription terminators, Cell, vol.64, issue.3, pp.553-563, 1991. ,
DOI : 10.1016/0092-8674(91)90239-U
Crystal structure of the RNA-binding domain from transcription termination factor rho, Nature Structural Biology, vol.4, issue.5, pp.352-356, 1998. ,
DOI : 10.1107/S0021889891004399
The Structural Basis for Terminator Recognition by the Rho Transcription Termination Factor, Molecular Cell, vol.3, issue.4, pp.487-493, 1999. ,
DOI : 10.1016/S1097-2765(00)80476-1
An RNA motif advances transcription by preventing Rho-dependent termination, Proc. Natl Acad. Sci. USA, pp.6835-6843, 2015. ,
DOI : 10.1093/nar/gkg595
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687561/pdf
Protein synthesis by pure translation systems, Methods, vol.36, issue.3, pp.299-304, 2005. ,
DOI : 10.1016/j.ymeth.2005.04.006
Isolation and Characterization of New Thiamine-Deregulated Mutants of Bacillus subtilis, Journal of Bacteriology, vol.187, issue.23, pp.8127-8136, 2005. ,
DOI : 10.1128/JB.187.23.8127-8136.2005
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, Proc. Natl Acad. Sci. USA, pp.3323-3328, 2012. ,
DOI : 10.1111/j.1365-2958.1995.tb02251.x
Riboswitch Ligand Sensing and Regulatory Control, Journal of Biological Chemistry, vol.2, issue.44, pp.26739-26751, 2015. ,
DOI : 10.1126/science.1251871
The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch, Molecular Cell, vol.18, issue.1, pp.49-60, 2005. ,
DOI : 10.1016/j.molcel.2005.02.032
Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms, PLoS Genetics, vol.20, issue.1, p.1001278, 2011. ,
DOI : 10.1371/journal.pgen.1001278.s005
URL : https://doi.org/10.1371/journal.pgen.1001278
Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures, Proc. Natl Acad. Sci. USA, pp.17995-18000, 2007. ,
DOI : 10.1093/nar/25.24.4876
Rho-dependent termination of transcription. II. Kinetics of mRNA elongation during transcription from the bacteriophage lambda PR promoter, J. Biol. Chem, vol.258, pp.9565-9574, 1983. ,
Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch, Science, vol.399, issue.1, pp.397-400, 2012. ,
DOI : 10.1016/j.jmb.2010.03.051
Functional topography of nascent RNA in elongation intermediates of RNA polymerase, Proc. Natl Acad. Sci. USA 95, pp.14699-14704, 1998. ,
DOI : 10.1016/0014-5793(82)80323-2
RNA Structure Analysis at Single Nucleotide Resolution by Selective 2???-Hydroxyl Acylation and Primer Extension (SHAPE), Journal of the American Chemical Society, vol.127, issue.12, pp.4223-4231, 2005. ,
DOI : 10.1021/ja043822v
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation, Nucleic Acids Research, vol.39, issue.8, pp.3373-3387, 2010. ,
DOI : 10.1093/nar/gkq1247
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch, Nature Chemical Biology, vol.54, issue.6, pp.384-392, 2011. ,
DOI : 10.1107/S0907444998003254
Ligand-dependent folding of the three-way junction in the purine riboswitch, RNA, vol.14, issue.4, pp.675-684, 2008. ,
DOI : 10.1261/rna.736908
Tuning a riboswitch response through structural extension of a pseudoknot, Proc. Natl Acad. Sci. USA, pp.3256-3264, 2013. ,
DOI : 10.1529/biophysj.103.037531
B12 cofactors directly stabilize an mRNA regulatory switch, Nature, vol.40, issue.7427, pp.133-137, 2012. ,
DOI : 10.1107/S0021889807021206
Selective 2???-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA, Nature Protocols, vol.468, issue.11, pp.1683-1694, 2011. ,
DOI : 10.1038/nprot.2006.4
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection, Nucleic Acids Research, vol.39, issue.19, pp.8586-8598, 2011. ,
DOI : 10.1093/nar/gkr565
Selective 2???-Hydroxyl Acylation Analyzed by Protection from Exoribonuclease, Journal of the American Chemical Society, vol.132, issue.29, pp.9940-9943, 2010. ,
DOI : 10.1021/ja103781u
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912424/pdf
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
URL : https://doi.org/10.1016/j.cell.2014.02.033
Riboswitches as antibacterial drug targets, Nature Biotechnology, vol.306, issue.12, pp.1558-1564, 2006. ,
DOI : 10.4161/rna.3.2.3102
Selective small-molecule inhibition of an RNA structural element, Nature, vol.55, issue.7575, pp.672-677, 2015. ,
DOI : 10.1107/S0907444998006684
Regulation of Transcript Elongation, Annual Review of Microbiology, vol.69, issue.1, pp.49-69, 2015. ,
DOI : 10.1146/annurev-micro-091014-104047
Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12, J. Biol. Chem, vol.269, pp.18185-18191, 1994. ,
13892 | DOI: 10.1038/ncomms13892 | www.nature.com/naturecommunications 47. Guedich, S. et al. Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches, NATURE COMMUNICATIONS ARTICLE NATURE COMMUNICATIONS | RNA Biol, vol.8, issue.13, pp.10-1038, 2016. ,
Bacterial Transcription Terminators: The RNA 3???-End Chronicles, Journal of Molecular Biology, vol.412, issue.5, pp.793-813, 2011. ,
DOI : 10.1016/j.jmb.2011.03.036
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622210/pdf
Effect of Rho on Transcription of Bacterial Operons, Nature New Biology, vol.241, issue.113, pp.260-264, 1973. ,
DOI : 10.1038/newbio241260a0
A NusE:NusG Complex Links Transcription and Translation, Science, vol.461, issue.7268, pp.501-504, 2010. ,
DOI : 10.1038/nature08403
The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators, The EMBO Journal, vol.31, issue.14, pp.2805-2816, 2011. ,
DOI : 10.1093/nar/gkg595
URL : https://hal.archives-ouvertes.fr/hal-00720713
An efficient recombination system for chromosome engineering in Escherichia coli, Proc. Natl Acad. Sci. USA 97, pp.5978-5983, 2000. ,
DOI : 10.1016/0378-1119(87)90167-3
The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis, Molecular Microbiology, vol.9, issue.5, pp.1260-1273, 2007. ,
DOI : 10.1128/jb.172.4.1930-1938.1990
Folding of the Adenine Riboswitch, Chemistry & Biology, vol.13, issue.8, pp.857-868, 2006. ,
DOI : 10.1016/j.chembiol.2006.06.010
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering, PLoS Computational Biology, vol.22, issue.4, pp.680-691, 2007. ,
DOI : 10.1371/journal.pcbi.0030065.sd001
CMfinder--a covariance model based RNA motif finding algorithm, Bioinformatics, vol.22, issue.4, pp.445-452, 2006. ,
DOI : 10.1093/bioinformatics/btk008
URL : https://academic.oup.com/bioinformatics/article-pdf/22/4/445/449573/btk008.pdf
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements, International Journal of Bioinformatics Research and Applications, vol.10, issue.4/5, pp.498-518, 2014. ,
DOI : 10.1504/IJBRA.2014.062997
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156590/pdf
Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, vol.29, issue.22, pp.2933-2935, 2013. ,
DOI : 10.1093/bioinformatics/btt509
Finding Instances of Riboswitches and Ribozymes by Homology Search of Structured RNA with Infernal, Methods Mol. Biol, vol.1103, pp.113-126, 2014. ,
DOI : 10.1007/978-1-62703-730-3_9
URL : https://hal.archives-ouvertes.fr/pasteur-01135590
Quantitative analysis of transcriptional pausing by Escherichia coli RNA polymerase: his leader pause site as paradigm, Methods Enzym, vol.274, pp.334-353, 1996. ,
DOI : 10.1016/S0076-6879(96)74029-6
Methods of Walking with the RNA Polymerase, Methods Enzymol, vol.371, pp.160-169, 2003. ,
DOI : 10.1016/S0076-6879(03)71011-8
Evidence for two functional gal promoters in intact Escherichia coli cells, J. Biol. Chem, vol.256, pp.11905-11910, 1981. ,