Acknowledgements
Our research is supported by ANR-23-CE20-0042 CAGE. Sara Moutacharrif received a doctoral grant from the French Ministère de l’Éducation nationale de l’Énseignement Supérieur et de la Recherche (INSA de Lyon).
References
Ali Azam, T. et al. (1999) ‘Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid’, Journal of Bacteriology , 181(20), pp. 6361–6370. Available at: https://doi.org/10.1128/JB.181.20.6361-6370.1999.Amemiya, H.M., Schroeder, J. and Freddolino, P.L. (2021) ‘Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom’, Transcription , 12(4), pp. 182–218. Available at: https://doi.org/10.1080/21541264.2021.1973865.Arfin, S.M. et al. (2000) ‘Global Gene Expression Profiling in Escherichia coliK12: THE EFFECTS OF INTEGRATION HOST FACTOR * 210’, Journal of Biological Chemistry , 275(38), pp. 29672–29684. Available at: https://doi.org/10.1074/jbc.M002247200.Arluison, V. et al. (2006) ‘Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins’, Journal of Molecular Biology , 356(1), pp. 86–96. Available at: https://doi.org/10.1016/j.jmb.2005.11.010.Atlung, T. and Ingmer, H. (1997) ‘H‐NS: a modulator of environmentally regulated gene expression’, Molecular Microbiology , 24(1), pp. 7–17. Available at: https://doi.org/10.1046/j.1365-2958.1997.3151679.x.Azam, T.A., Hiraga, S. and Ishihama, A. (2000) ‘Two types of localization of the DNA‐binding proteins within the Escherichia coli nucleoid’,Genes to Cells , 5(8), pp. 613–626. Available at: https://doi.org/10.1046/j.1365-2443.2000.00350.x.Azam, T.A. and Ishihama, A. (1999) ‘Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity’, The Journal of Biological Chemistry , 274(46), pp. 33105–33113. Available at: https://doi.org/10.1074/jbc.274.46.33105.Bahloul, A., Boubrik, F. and Rouviere-Yaniv, J. (2001) ‘Roles of Escherichia coli histone-like protein HU in DNA replication:HU-beta suppresses the thermosensitivity of dnaA46ts’, Biochimie , 83(2), pp. 219–229. Available at: https://doi.org/10.1016/S0300-9084(01)01246-9.Bak, G. et al. (2014) ‘Roles of rpoS-activating small RNAs in pathways leading to acid resistance of Escherichia coli’, MicrobiologyOpen , 3(1), pp. 15–28. Available at: https://doi.org/10.1002/mbo3.143.Balandina, A., Kamashev, D. and Rouviere-Yaniv, J. (2002) ‘The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids’, The Journal of Biological Chemistry , 277(31), pp. 27622–27628. Available at: https://doi.org/10.1074/jbc.M201978200.Barrick, J.E. et al. (2005) ‘6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter’, RNA (New York, N.Y.) , 11(5), pp. 774–784. Available at: https://doi.org/10.1261/rna.7286705.Battesti, A., Majdalani, N. and Gottesman, S. (2011) ‘The RpoS-Mediated General Stress Response inEscherichia coli ’, Annual Review of Microbiology , 65(1), pp. 189–213. Available at: https://doi.org/10.1146/annurev-micro-090110-102946.Beaufay, F. et al. (2021) ‘Polyphosphate drives bacterial heterochromatin formation’,Science Advances , 7(52), p. eabk0233. Available at: https://doi.org/10.1126/sciadv.abk0233.Bensaid, A. et al. (1996) ‘Cross-talk Between Topoisomerase I and HU inEscherichia coli’,Journal of Molecular Biology , 256(2), pp. 292–300. Available at: https://doi.org/10.1006/jmbi.1996.0086.Bettridge, K. et al. (2021) ‘Single‐molecule tracking reveals that the nucleoid‐associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA’, Molecular Microbiology , 115(1), pp. 12–27. Available at: https://doi.org/10.1111/mmi.14572.Bonar, C.D. et al. (2022) ‘E. coli 6S RNA complexed to RNA polymerase maintains product RNA synthesis at low cellular ATP levels by initiation with non-canonical initiator nucleotides’, RNA , p. rna.079356.122. Available at: https://doi.org/10.1261/rna.079356.122.Bonnefoy, E. and Rouvière‐Yaniv, J. (1992) ‘HU, the major histone‐like protein of E. coli, modulates the binding of IHF to oriC.’, The EMBO Journal , 11(12), pp. 4489–4496. Available at: https://doi.org/10.1002/j.1460-2075.1992.tb05550.x.Boudreau, B.A.et al. (2018) ‘StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments’, Nucleic Acids Research , 46(11), pp. 5525–5546. Available at: https://doi.org/10.1093/nar/gky265.Brencic, A. et al. (2009) ‘The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs’, Molecular Microbiology , 73(3), pp. 434–445. Available at: https://doi.org/10.1111/j.1365-2958.2009.06782.x.Brownlee, G.G. (1971) ‘Sequence of 6S RNA of E. coli’, Nature: New Biology , 229(5), pp. 147–149. Available at: https://doi.org/10.1038/newbio229147a0.Castang, S. et al. (2008) ‘H-NS family members function coordinately in an opportunistic pathogen’, Proceedings of the National Academy of Sciences of the United States of America , 105(48), pp. 18947–18952. Available at: https://doi.org/10.1073/pnas.0808215105.Cech, G.M.et al. (2016) ‘The Escherichia Coli Hfq Protein: An Unattended DNA-Transactions Regulator’, Frontiers in Molecular Biosciences , 3. Available at: https://doi.org/10.3389/fmolb.2016.00036.Chae, H.et al. (2011) ‘Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3’ processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase)’, The Journal of Biological Chemistry , 286(1), pp. 114–122. Available at: https://doi.org/10.1074/jbc.M110.150201.Chen, K.-Y. et al. (2019) ‘The Transcriptional Regulator Lrp Contributes to Toxin Expression, Sporulation, and Swimming Motility in Clostridium difficile’,Frontiers in Cellular and Infection Microbiology , 9, p. 356. Available at: https://doi.org/10.3389/fcimb.2019.00356.Chen, S. et al. (2001) ‘Modulation of Lrp action in Escherichia coli by leucine: effects on non-specific binding of Lrp to DNA’, Journal of Molecular Biology , 314(5), pp. 1067–1075. Available at: https://doi.org/10.1006/jmbi.2000.5209.Claret, L. and Rouviere-Yaniv, J. (1997) ‘Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival’, Journal of Molecular Biology , 273(1), pp. 93–104. Available at: https://doi.org/10.1006/jmbi.1997.1310.Corcoran, C.P. et al. (2012) ‘Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA’, Mol Microbiol , 84(3), pp. 428–45. Available at: https://doi.org/10.1111/j.1365-2958.2012.08031.x.Cossa, A. et al. (2022) ‘Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator’, Journal of Structural Biology , 214(4), p. 107912. Available at: https://doi.org/10.1016/j.jsb.2022.107912.Dame, R.T., Wyman, C. and Goosen, N. (2000) ‘H-NS mediated compaction of DNA visualised by atomic force microscopy’, Nucleic Acids Research , 28(18), pp. 3504–3510. Available at: https://doi.org/10.1093/nar/28.18.3504.De Los Rios, S. and Perona, J.J. (2007) ‘Structure of the Escherichia coli Leucine-responsive Regulatory Protein Lrp Reveals a Novel Octameric Assembly’, Journal of Molecular Biology , 366(5), pp. 1589–1602. Available at: https://doi.org/10.1016/j.jmb.2006.12.032.Dean, C.R. and Goldberg, J.B. (2002) ‘Pseudomonas aeruginosa galU is required for a complete lipopolysaccharide core and repairs a secondary mutation in a PA103 (serogroup O11) wbpM mutant’, FEMS Microbiology Letters , 210(2), pp. 277–283. Available at: https://doi.org/10.1111/j.1574-6968.2002.tb11193.x.Dhavan, G.M. et al. (2002) ‘Concerted binding and bending of DNA by Escherichia coli integration host factor’, Journal of Molecular Biology , 315(5), pp. 1027–1037. Available at: https://doi.org/10.1006/jmbi.2001.5303.Diestra, E. et al. (2009) ‘Cellular electron microscopy imaging reveals the localization of the Hfq protein close to the bacterial membrane’, PloS One , 4(12), p. e8301. Available at: https://doi.org/10.1371/journal.pone.0008301.Doyle, M. et al. (2007) ‘An H-NS-like stealth protein aids horizontal DNA transmission in bacteria’, Science , 315(5809), pp. 251–2. Available at: https://doi.org/10.1126/science.1137550.Ferrario, M.et al. (1995) ‘The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF’, Journal of Bacteriology , 177(1), pp. 103–113. Available at: https://doi.org/10.1128/jb.177.1.103-113.1995.Fortas, E. et al. (2015) ‘New insight into the structure and function of Hfq C-terminus’,Bioscience Reports , 35(2), p. e00190. Available at: https://doi.org/10.1042/BSR20140128.Franze de Fernandez, M.T., Hayward, W.S. and August, J.T. (1972) ‘Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding protein’, The Journal of Biological Chemistry , 247(3), pp. 824–831.Freundlich, M. et al. (1992) ‘The role of integration host factor in gene expression in Escherichia coli’, Molecular Microbiology , 6(18), pp. 2557–2563. Available at: https://doi.org/10.1111/j.1365-2958.1992.tb01432.x.Friedman, D.I. (1988) ‘Integration host factor: a protein for all reasons’, Cell , 55(4), pp. 545–554. Available at: https://doi.org/10.1016/0092-8674(88)90213-9.Fröhlich, K.S. and Vogel, J. (2009) ‘Activation of gene expression by small RNA’, Current Opinion in Microbiology , 12(6), pp. 674–682. Available at: https://doi.org/10.1016/j.mib.2009.09.009.Geinguenaud, F. et al. (2011) ‘Conformational transition of DNA bound to Hfq probed by infrared spectroscopy’, Physical chemistry chemical physics: PCCP , 13(3), pp. 1222–1229. Available at: https://doi.org/10.1039/c0cp01084g.Gellert, M., Lipsett, M.N. and Davies, D.R. (1962) ‘Helix formation by guanylic acid’,Proceedings of the National Academy of Sciences of the United States of America , 48(12), pp. 2013–2018. Available at: https://doi.org/10.1073/pnas.48.12.2013.Georg, J. and Hess, W.R. (2011) ‘cis-antisense RNA, another level of gene regulation in bacteria’,Microbiology and molecular biology reviews: MMBR , 75(2), pp. 286–300. Available at: https://doi.org/10.1128/MMBR.00032-10.Gilson, E.et al. (1991) ‘Palindromic units are part of a new bacterial interspersed mosaic element (BIME)’, Nucleic Acids Research , 19(7), pp. 1375–1383. Available at: https://doi.org/10.1093/nar/19.7.1375.González, N. et al. (2008) ‘Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species’, BMC Genomics , 9, p. 167.Grainger, D.C. (2016) ‘Structure and function of bacterial H-NS protein’,Biochemical Society Transactions , 44(6), pp. 1561–1569. Available at: https://doi.org/10.1042/BST20160190.Guo, Y. et al. (2010) ‘Requirement of the galU Gene for Polysaccharide Production by and Pathogenicity and Growth In Planta ofXanthomonas citri subsp. citri ’, Applied and Environmental Microbiology , 76(7), pp. 2234–2242. Available at: https://doi.org/10.1128/AEM.02897-09.Hecht, R.M. and Pettijohn, D.E. (1976) ‘Studies of DNA bound RNA molecules isolated from nucleoids of Escherichia coli’, Nucleic Acids Research , 3(3), pp. 767–788. Available at: https://doi.org/10.1093/nar/3.3.767.Hillebrand, A.et al. (2005) ‘The seven E. coli ribosomal RNA operon upstream regulatory regions differ in structure and transcription factor binding efficiencies’, Biological Chemistry , 386(6), pp. 523–534. Available at: https://doi.org/10.1515/BC.2005.062.Hirsch, M. and Elliott, T. (2005) ‘Fis Regulates Transcriptional Induction of RpoS inSalmonella enterica ’, Journal of Bacteriology , 187(5), pp. 1568–1580. Available at: https://doi.org/10.1128/JB.187.5.1568-1580.2005.Hirvonen, C.A. et al. (2001) ‘Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli’,Journal of Bacteriology , 183(21), pp. 6305–6314. Available at: https://doi.org/10.1128/JB.183.21.6305-6314.2001.Ho, Y.-C. et al. (2017) ‘Lrp, a global regulator, regulates the virulence of Vibrio vulnificus’, Journal of Biomedical Science , 24(1), p. 54. Available at: https://doi.org/10.1186/s12929-017-0361-9.Holmqvist, E.et al. (2012) ‘A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp’, Molecular Microbiology , 84(3), pp. 414–427. Available at: https://doi.org/10.1111/j.1365-2958.2012.07994.x.Holmqvist, E. et al. (2016) ‘Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo ’, The EMBO Journal , 35(9), pp. 991–1011. Available at: https://doi.org/10.15252/embj.201593360.Holmqvist, E. et al. (2018) ‘Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3′ Ends’,Molecular Cell , 70(5), pp. 971-982.e6. Available at: https://doi.org/10.1016/j.molcel.2018.04.017.Hommais, F. et al. (2001) ‘Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS’,Mol Microbiol , 40(1), pp. 20–36. Available at: https://doi.org/mmi2358 [pii].Hommais, F. et al. (2004) ‘GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli’, Microbiology (Reading, England) , 150(Pt 1), pp. 61–72. Available at: https://doi.org/10.1099/mic.0.26659-0.Humair, B., Wackwitz, B. and Haas, D. (2010) ‘GacA-controlled activation of promoters for small RNA genes in Pseudomonas fluorescens’, Applied and Environmental Microbiology , 76(5), pp. 1497–1506. Available at: https://doi.org/10.1128/AEM.02014-09.Hustmyer, C.M. et al. (2022) ‘RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS–StpA Nucleoprotein Filaments in Pathogenic Escherichiacoli’, mBio . Edited by M.T. Laub, 13(6), pp. e02662-22. Available at: https://doi.org/10.1128/mbio.02662-22.Hustmyer, C.M. and Landick, R. (2024) ‘Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression’, Molecular Microbiology , 122(1), pp. 81–112. Available at: https://doi.org/10.1111/mmi.15283.Jiang, K. et al. (2015) ‘Effects of Hfq on the conformation and compaction of DNA’,Nucleic Acids Research , 43(8), pp. 4332–4341. Available at: https://doi.org/10.1093/nar/gkv268.Jousselin, A., Metzinger, L. and Felden, B. (2009) ‘On the facultative requirement of the bacterial RNA chaperone, Hfq’, Trends in Microbiology , 17(9), pp. 399–405. Available at: https://doi.org/10.1016/j.tim.2009.06.003.Kamashev, D. and Rouviere-Yaniv, J. (2000) ‘The histone-like protein HU binds specifically to DNA recombination and repair intermediates’, The EMBO journal , 19(23), pp. 6527–6535. Available at: https://doi.org/10.1093/emboj/19.23.6527.Karambelkar, S., Swapna, G. and Nagaraja, V. (2012) ‘Silencing of toxic gene expression by Fis’,Nucleic Acids Research , 40(10), pp. 4358–4367. Available at: https://doi.org/10.1093/nar/gks037.Kim, K. and Lee, Y. (2004) ‘Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases’, Nucleic Acids Research , 32(20), pp. 6057–6068. Available at: https://doi.org/10.1093/nar/gkh939.Koch, C. and Kahmann, R. (1986) ‘Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu’, The Journal of Biological Chemistry , 261(33), pp. 15673–15678.Kotlajich, M.V. et al. (2015) ‘Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria’, eLife , 4, p. e04970. Available at: https://doi.org/10.7554/eLife.04970.Kroner, G.M., Wolfe, M.B. and Freddolino, P.L. (2019) ‘Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes’,Journal of Bacteriology . Edited by V.J. DiRita, 201(3). Available at: https://doi.org/10.1128/JB.00411-18.Kubiak, K. et al. (2022) ‘Amyloid-like Hfq interaction with single-stranded DNA: involvement in recombination and replication in Escherichia coli’, QRB discovery , 3, p. e15. Available at: https://doi.org/10.1017/qrd.2022.15.Lalaouna, D. et al. (2015) ‘DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli’, Molecular Microbiology , 98(2), pp. 357–369. Available at: https://doi.org/10.1111/mmi.13129.Lalaouna, D. et al. (2019) ‘GcvB small RNA uses two distinct seed regions to regulate an extensive targetome’, Molecular Microbiology , 111(2), pp. 473–486. Available at: https://doi.org/10.1111/mmi.14168.Lalaouna, D. and Massé, E. (2016) ‘The spectrum of activity of the small RNA DsrA: not so narrow after all’,Current Genetics , 62(2), pp. 261–264. Available at: https://doi.org/10.1007/s00294-015-0533-7.Lang, B. et al. (2007) ‘High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes’, Nucleic Acids Research , 35(18), pp. 6330–6337. Available at: https://doi.org/10.1093/nar/gkm712.Lautier, T. and Nasser, W. (2007) ‘The DNA nucleoid-associated protein Fis co-ordinates the expression of the main virulence genes in the phytopathogenic bacterium Erwinia chrysanthemi’, Mol Microbiol , 66(6), pp. 1474–90. Available at: https://doi.org/10.1111/j.1365-2958.2007.06012.x.Le Berre, D. et al. (2022) ‘Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma?’, Microorganisms , 10(5), p. 846. Available at: https://doi.org/10.3390/microorganisms10050846.Lease, R.A. and Belfort, M. (2000) ‘Riboregulation by DsrA RNA: trans-actions for global economy’, Molecular Microbiology , 38(4), pp. 667–672. Available at: https://doi.org/10.1046/j.1365-2958.2000.02162.x.Lease, R.A., Cusick, M.E. and Belfort, M. (1998) ‘Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci’,Proceedings of the National Academy of Sciences of the United States of America , 95(21), pp. 12456–12461. Available at: https://doi.org/10.1073/pnas.95.21.12456.Lee, H.-J. and Gottesman, S. (2016) ‘sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs’, Nucleic Acids Research , 44(14), pp. 6907–6923. Available at: https://doi.org/10.1093/nar/gkw358.Lee, J.H. and Zhao, Y. (2016) ‘Integration Host Factor Is Required for RpoN-Dependent hrpL Gene Expression and Controls Motility by Positively Regulating rsmB sRNA in Erwinia amylovora’, Phytopathology , 106(1), pp. 29–36. Available at: https://doi.org/10.1094/PHYTO-07-15-0170-R.Lee, J.Y. et al. (2013) ‘Regulation of transcription from two ssrS promoters in 6S RNA biogenesis’, Molecules and Cells , 36(3), pp. 227–234. Available at: https://doi.org/10.1007/s10059-013-0082-1.Leonard, P.G. et al. (2009) ‘Investigation of the self-association and hetero-association interactions of H-NS and StpA from Enterobacteria’,Molecular Microbiology , 73(2), pp. 165–179. Available at: https://doi.org/10.1111/j.1365-2958.2009.06754.x.Leonard, S. et al. (2021) ‘RNA Chaperones Hfq and ProQ Play a Key Role in the Virulence of the Plant Pathogenic Bacterium Dickeya dadantii’,Frontiers in Microbiology , 12, p. 687484. Available at: https://doi.org/10.3389/fmicb.2021.687484.Liu, G., Ma, Q. and Xu, Y. (2018) ‘Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome’,Mathematical Biosciences , 301, pp. 50–58. Available at: https://doi.org/10.1016/j.mbs.2018.03.026.Livny, J. et al. (2006) ‘Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2’, Nucleic Acids Res , 34(12), pp. 3484–93.Lu, P.et al. (2016) ‘RpoS-dependent sRNA RgsA regulates Fis and AcpP in Pseudomonas aeruginosa’, Molecular Microbiology , 102(2), pp. 244–259. Available at: https://doi.org/10.1111/mmi.13458.Lu, Z.et al. (2019) ‘Engineering of leucine-responsive regulatory protein improves spiramycin and bitespiramycin biosynthesis’,Microbial Cell Factories , 18(1), p. 38. Available at: https://doi.org/10.1186/s12934-019-1086-0.Lukose, B. et al. (2024) ‘Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS’, Nucleic Acids Research , 52(5), pp. 2157–2173. Available at: https://doi.org/10.1093/nar/gkae090.Macvanin, M. et al. (2012) ‘Noncoding RNAs binding to the nucleoid protein HU in Escherichia coli’, Journal of Bacteriology , 194(22), pp. 6046–6055. Available at: https://doi.org/10.1128/JB.00961-12.Maki, K.et al. (2008) ‘RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA’, Proceedings of the National Academy of Sciences , 105(30), pp. 10332–10337. Available at: https://doi.org/10.1073/pnas.0803106105.Malabirade, A. et al. (2017) ‘Compaction and condensation of DNA mediated by the C-terminal domain of Hfq’, Nucleic Acids Research , 45(12), pp. 7299–7308. Available at: https://doi.org/10.1093/nar/gkx431.Malabirade, A. et al. (2018a) ‘Revised role for Hfq bacterial regulator on DNA topology’,Scientific Reports , 8(1), p. 16792. Available at: https://doi.org/10.1038/s41598-018-35060-9.Malabirade, A. et al. (2018b) ‘Revised role for Hfq bacterial regulator on DNA topology’,Scientific Reports , 8(1), p. 16792. Available at: https://doi.org/10.1038/s41598-018-35060-9.Martínez, L.C. et al. (2014) ‘In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes’, Journal of Bacteriology , 196(2), pp. 325–336. Available at: https://doi.org/10.1128/JB.00806-13.McFarland, K.A. and Dorman, C.J. (2008) ‘Autoregulated expression of the gene coding for the leucine-responsive protein, Lrp, a global regulator in Salmonella enterica serovar Typhimurium’, Microbiology (Reading, England) , 154(Pt 7), pp. 2008–2016. Available at: https://doi.org/10.1099/mic.0.2008/018358-0.Melamed, S. et al. (2020) ‘RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles’, Molecular Cell , 77(2), pp. 411-425.e7. Available at: https://doi.org/10.1016/j.molcel.2019.10.022.Miller, H.I. and Friedman, D.I. (1980) ‘An E. coli gene product required for lambda site-specific recombination’, Cell , 20(3), pp. 711–719. Available at: https://doi.org/10.1016/0092-8674(80)90317-7.Modi, S.R.et al. (2011) ‘Functional characterization of bacterial sRNAs using a network biology approach’, Proceedings of the National Academy of Sciences of the United States of America , 108(37), pp. 15522–15527. Available at: https://doi.org/10.1073/pnas.1104318108.Mohanty, B.K., Maples, V.F. and Kushner, S.R. (2004) ‘The Sm‐like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli ’, Molecular Microbiology , 54(4), pp. 905–920. Available at: https://doi.org/10.1111/j.1365-2958.2004.04337.x.Moll, I. et al. (2003) ‘Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs’, RNA , 9(11), pp. 1308–1314. Available at: https://doi.org/10.1261/rna.5850703.Muffler, A. et al. (1997) ‘The RNA-binding protein HF-I plays a global regulatory role which is largely, but not exclusively, due to its role in expression of the sigmaS subunit of RNA polymerase in Escherichia coli’, Journal of Bacteriology , 179(1), pp. 297–300. Available at: https://doi.org/10.1128/jb.179.1.297-300.1997.Mura, C. et al. (2013) ‘Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function’, RNA Biology , 10(4), pp. 636–651. Available at: https://doi.org/10.4161/rna.24538.Nash, H.A.et al. (1987) ‘Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits’, Journal of Bacteriology , 169(9), pp. 4124–4127. Available at: https://doi.org/10.1128/jb.169.9.4124-4127.1987.Navarre, W.W. et al. (2006) ‘Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella’, Science , 313(5784), pp. 236–8. Available at: https://doi.org/10.1126/science.1128794.Navarre, W.W.et al. (2007) ‘Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA’, Genes Dev , 21(12), pp. 1456–71. Available at: https://doi.org/10.1101/gad.1543107.Neusser, T. et al. (2008) ‘Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation’, Biological Chemistry , 389(3), pp. 285–297. Available at: https://doi.org/10.1515/BC.2008.023.Ninnemann, O., Koch, C. and Kahmann, R. (1992) ‘The E.coli fis promoter is subject to stringent control and autoregulation.’, The EMBO Journal , 11(3), pp. 1075–1083. Available at: https://doi.org/10.1002/j.1460-2075.1992.tb05146.x.Oberto, J. et al. (2009) ‘The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction’,PLOS ONE , 4(2), p. e4367. Available at: https://doi.org/10.1371/journal.pone.0004367.Ohniwa, R.L. et al. (2006) ‘Dynamic state of DNA topology is essential for genome condensation in bacteria’, The EMBO journal , 25(23), pp. 5591–5602. Available at: https://doi.org/10.1038/sj.emboj.7601414.Oshima, T. et al. (1995) ‘Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp’, Molecular & general genetics: MGG , 247(5), pp. 521–528. Available at: https://doi.org/10.1007/BF00290342.Papenfort, K. and Melamed, S. (2023) ‘Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria’, Annual Review of Microbiology , 77(1), pp. 23–43. Available at: https://doi.org/10.1146/annurev-micro-041320-025836.Parekh, V.J.et al. (2019) ‘Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli’, Microorganisms , 8(1), p. 28. Available at: https://doi.org/10.3390/microorganisms8010028.Parekh, V.J.et al. (2020) ‘Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability’, Microorganisms , 8(10), p. 1598. Available at: https://doi.org/10.3390/microorganisms8101598.Park, H.-S.et al. (2010) ‘Novel role for a bacterial nucleoid protein in translation of mRNAs with suboptimal ribosome-binding sites’,Genes & Development , 24(13), pp. 1345–1350. Available at: https://doi.org/10.1101/gad.576310.Park, S.H. et al. (2013) ‘Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000’, Microbiology , 159(Pt_2), pp. 296–306. Available at: https://doi.org/10.1099/mic.0.063826-0.Partouche, D. et al. (2019) ‘In Situ Characterization of Hfq Bacterial Amyloid: A Fourier-Transform Infrared Spectroscopy Study’, Pathogens (Basel, Switzerland) , 8(1), p. 36. Available at: https://doi.org/10.3390/pathogens8010036.Partridge, J.D. et al. (2009) ‘NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility’, Molecular Microbiology , 73(4), pp. 680–694. Available at: https://doi.org/10.1111/j.1365-2958.2009.06799.x.Pollak, A.J. and Reich, N.O. (2015) ‘DNA Adenine Methyltransferase Facilitated Diffusion Is Enhanced by Protein–DNA “Roadblock” Complexes That Induce DNA Looping’, Biochemistry , 54(13), pp. 2181–2192. Available at: https://doi.org/10.1021/bi501344r.Prieto, A.I. et al. (2012) ‘Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12’,Nucleic Acids Research , 40(8), pp. 3524–3537. Available at: https://doi.org/10.1093/nar/gkr1236.Pulvermacher, S.C., Stauffer, L.T. and Stauffer, G.V. (2008) ‘The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli: GcvB regulation of OppA and DppA’, FEMS Microbiology Letters , 281(1), pp. 42–50. Available at: https://doi.org/10.1111/j.1574-6968.2008.01068.x.Pulvermacher, S.C., Stauffer, L.T. and Stauffer, G.V. (2009) ‘Role of the sRNA GcvB in regulation of cycA in Escherichia coli’, Microbiology , 155(1), pp. 106–114. Available at: https://doi.org/10.1099/mic.0.023598-0.Qian, Z. et al. (2015) ‘A New Noncoding RNA Arranges Bacterial Chromosome Organization’, mBio , 6(4), pp. e00998-15. Available at: https://doi.org/10.1128/mBio.00998-15.Qian, Z., Zhurkin, V.B. and Adhya, S. (2017) ‘DNA–RNA interactions are critical for chromosome condensation in Escherichia coli’, Proceedings of the National Academy of Sciences , 114(46), pp. 12225–12230. Available at: https://doi.org/10.1073/pnas.1711285114.Quendera, A.P. et al. (2020) ‘RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria’, Frontiers in Molecular Biosciences , 7, p. 78. Available at: https://doi.org/10.3389/fmolb.2020.00078.Reddy, M.C.M. et al. (2008) ‘Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response’, Protein Science: A Publication of the Protein Society , 17(1), pp. 159–170. Available at: https://doi.org/10.1110/ps.073192208.Ren, J. et al. (2007) ‘The structure and transcriptional analysis of a global regulator from Neisseria meningitidis’, The Journal of Biological Chemistry , 282(19), pp. 14655–14664. Available at: https://doi.org/10.1074/jbc.M701082200.Repoila, F. and Darfeuille, F. (2009) ‘Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects’, Biology of the Cell , 101(2), pp. 117–131. Available at: https://doi.org/10.1042/BC20070137.Repoila, F. and Gottesman, S. (2001) ‘Signal transduction cascade for regulation of RpoS: temperature regulation of DsrA’, Journal of Bacteriology , 183(13), pp. 4012–4023. Available at: https://doi.org/10.1128/JB.183.13.4012-4023.2001.Reverchon, S. et al. (2021) ‘The nucleoid-associated protein IHF acts as a “transcriptional domainin” protein coordinating the bacterial virulence traits with global transcription’, Nucleic Acids Research , 49(2), pp. 776–790. Available at: https://doi.org/10.1093/nar/gkaa1227.Rouvière-Yaniv, J. and Gros, F. (1975) ‘Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli.’, Proceedings of the National Academy of Sciences , 72(9), pp. 3428–3432. Available at: https://doi.org/10.1073/pnas.72.9.3428.Sauer, E., Schmidt, S. and Weichenrieder, O. (2012) ‘Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition’, Proceedings of the National Academy of Sciences , 109(24), pp. 9396–9401. Available at: https://doi.org/10.1073/pnas.1202521109.Sauter, C. (2003) ‘Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli’, Nucleic Acids Research , 31(14), pp. 4091–4098. Available at: https://doi.org/10.1093/nar/gkg480.Schachterle, J.K. and Sundin, G.W. (2019) ‘The Leucine-Responsive Regulatory Protein Lrp Participates in Virulence Regulation Downstream of Small RNA ArcZ in Erwinia amylovora’,mBio , 10(3), pp. e00757-19. Available at: https://doi.org/10.1128/mBio.00757-19.Schneider, R. (2001) ‘An architectural role of the Escherichia coli chromatin protein FIS in organising DNA’, Nucleic Acids Research , 29(24), pp. 5107–5114. Available at: https://doi.org/10.1093/nar/29.24.5107.Schwab, S. and Dame, R.T. (2024) ‘Identification, characterization and classification of prokaryotic nucleoid‐associated proteins’, Molecular Microbiology , p. mmi.15298. Available at: https://doi.org/10.1111/mmi.15298.Sette, M. et al. (2009) ‘Sequence-specific Recognition of DNA by the C-terminal Domain of Nucleoid-associated Protein H-NS’, Journal of Biological Chemistry , 284(44), pp. 30453–30462. Available at: https://doi.org/10.1074/jbc.M109.044313.Shahul Hameed, U.F. et al. (2019) ‘H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing’, Nucleic Acids Research , 47(5), pp. 2666–2680. Available at: https://doi.org/10.1093/nar/gky1299.Sharma, C.M. et al. (2007) ‘A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites’, Genes & Development , 21(21), pp. 2804–2817. Available at: https://doi.org/10.1101/gad.447207.Sharma, C.M. et al. (2011) ‘Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA’, Molecular Microbiology , 81(5), pp. 1144–1165. Available at: https://doi.org/10.1111/j.1365-2958.2011.07751.x.Singh, S.S. et al. (2014) ‘Widespread suppression of intragenic transcription initiation by H-NS’, Genes & Development , 28(3), pp. 214–219. Available at: https://doi.org/10.1101/gad.234336.113.Sittka, A. et al. (2007) ‘The RNA chaperone Hfq is essential for the virulence ofSalmonella typhimurium ’, Molecular Microbiology , 63(1), pp. 193–217. Available at: https://doi.org/10.1111/j.1365-2958.2006.05489.x.Skoko, D. et al. (2006) ‘Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis’, Journal of Molecular Biology , 364(4), pp. 777–798. Available at: https://doi.org/10.1016/j.jmb.2006.09.043.Sledjeski, D. and Gottesman, S. (1995) ‘A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli’, Proceedings of the National Academy of Sciences of the United States of America , 92(6), pp. 2003–2007. Available at: https://doi.org/10.1073/pnas.92.6.2003.Sledjeski, D.D., Whitman, C. and Zhang, A. (2001) ‘Hfq is necessary for regulation by the untranslated RNA DsrA’, Journal of Bacteriology , 183(6), pp. 1997–2005. Available at: https://doi.org/10.1128/JB.183.6.1997-2005.2001.Song, N. et al. (2016) ‘New Targets and Cofactors for the Transcription Factor LrpA from Mycobacterium tuberculosis’, DNA and cell biology , 35(4), pp. 167–176. Available at: https://doi.org/10.1089/dna.2015.3040.Stella, S., Cascio, D. and Johnson, R.C. (2010) ‘The shape of the DNA minor groove directs binding by the DNA-bending protein Fis’, Genes & Development , 24(8), pp. 814–826. Available at: https://doi.org/10.1101/gad.1900610.Stoebel, D.M., Free, A. and Dorman, C.J. (2008) ‘Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria’, Microbiology , 154(9), pp. 2533–2545. Available at: https://doi.org/10.1099/mic.0.2008/020693-0.Storz, G., Vogel, J. and Wassarman, K.M. (2011) ‘Regulation by small RNAs in bacteria: expanding frontiers’, Mol Cell , 43(6), pp. 880–91. Available at: https://doi.org/Regulatory RNAs in bacteria.Sun, X. (2002) ‘Predicted structure and phyletic distribution of the RNA-binding protein Hfq’,Nucleic Acids Research , 30(17), pp. 3662–3671. Available at: https://doi.org/10.1093/nar/gkf508.Swinger, K.K. and Rice, P.A. (2004) ‘IHF and HU: flexible architects of bent DNA’, Current Opinion in Structural Biology , 14(1), pp. 28–35. Available at: https://doi.org/10.1016/j.sbi.2003.12.003.Talukder, A. and Ishihama, A. (2015) ‘Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli’, Science China. Life Sciences , 58(9), pp. 902–911. Available at: https://doi.org/10.1007/s11427-015-4898-0.Toledo-Arana, A. and Lasa, I. (2020) ‘Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept’, Molecular Microbiology , 113(3), pp. 593–602. Available at: https://doi.org/10.1111/mmi.14456.Torres Montaguth, O.E. et al. (2019) ‘Competitive Repression of the artPIQM Operon for Arginine and Ornithine Transport by Arginine Repressor and Leucine-Responsive Regulatory Protein in Escherichia coli’, Frontiers in Microbiology , 10, p. 1563. Available at: https://doi.org/10.3389/fmicb.2019.01563.Traxler, M.F. et al. (2011) ‘Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the “feast to famine” gradient in Escherichia coli’, Molecular Microbiology , 79(4), pp. 830–845. Available at: https://doi.org/10.1111/j.1365-2958.2010.07498.x.Trotochaud, A.E. and Wassarman, K.M. (2005) ‘A highly conserved 6S RNA structure is required for regulation of transcription’, Nature Structural & Molecular Biology , 12(4), pp. 313–319. Available at: https://doi.org/10.1038/nsmb917.Tsui, H.C., Feng, G. and Winkler, M.E. (1997) ‘Negative regulation of mutS and mutH repair gene expression by the Hfq and RpoS global regulators of Escherichia coli K-12’,Journal of Bacteriology , 179(23), pp. 7476–7487. Available at: https://doi.org/10.1128/jb.179.23.7476-7487.1997.Tsui, H.T., Leung, H.E. and Winkler, M.E. (1994) ‘Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation inEscherichia coli K‐12’, Molecular Microbiology , 13(1), pp. 35–49. Available at: https://doi.org/10.1111/j.1365-2958.1994.tb00400.x.Ueda, T. et al. (2013) ‘Functions of the Hha and YdgT Proteins in Transcriptional Silencing by the Nucleoid Proteins, H-NS and StpA, in Escherichia coli’,DNA Research , 20(3), pp. 263–271. Available at: https://doi.org/10.1093/dnares/dst008.Updegrove, T.B. et al. (2010) ‘E. coli DNA associated with isolated Hfq interacts with Hfq’s distal surface and C-terminal domain’, Biochimica Et Biophysica Acta , 1799(8), pp. 588–596. Available at: https://doi.org/10.1016/j.bbagrm.2010.06.007.Verma, S.C. et al. (2023) ‘Non‐specific and specific DNA binding modes of bacterial histone, HU , separately regulate distinct physiological processes through different mechanisms’, Molecular Microbiology , 119(4), pp. 439–455. Available at: https://doi.org/10.1111/mmi.15033.Vogel, J. and Luisi, B.F. (2011) ‘Hfq and its constellation of RNA’, Nature Reviews. Microbiology , 9(8), pp. 578–589. Available at: https://doi.org/10.1038/nrmicro2615.Wang, Q. et al. (1994) ‘Regulation of the Escherichia coli lrp gene’, Journal of Bacteriology , 176(7), pp. 1831–1839. Available at: https://doi.org/10.1128/jb.176.7.1831-1839.1994.Wassarman, K.M. et al. (2001) ‘Identification of novel small RNAs using comparative genomics and microarrays’, Genes & Development , 15(13), pp. 1637–1651. Available at: https://doi.org/10.1101/gad.901001.Wassarman, K.M. and Storz, G. (2000) ‘6S RNA Regulates E. coli RNA Polymerase Activity’, Cell , 101(6), pp. 613–623. Available at: https://doi.org/10.1016/S0092-8674(00)80873-9.Wilusz, C.J. and Wilusz, J. (2013) ‘Lsm proteins and Hfq: Life at the 3′ end’, RNA Biology , 10(4), pp. 592–601. Available at: https://doi.org/10.4161/rna.23695.Wright, P.R. et al. (2013) ‘Comparative genomics boosts target prediction for bacterial small RNAs’, Proceedings of the National Academy of Sciences of the United States of America , 110(37), pp. E3487-3496. Available at: https://doi.org/10.1073/pnas.1303248110.Wu, P. et al. (2017) ‘The important conformational plasticity of DsrA sRNA for adapting multiple target regulation’, Nucleic Acids Research , 45(16), pp. 9625–9639. Available at: https://doi.org/10.1093/nar/gkx570.Zghidi-Abouzid, O. et al. (2016) ‘Regulation of pel genes, major virulence factors in the plant pathogen bacterium Dickeya dadantii, is mediated by cooperative binding of the nucleoid-associated protein H-NS’, Research in Microbiology , 167(4), pp. 247–253. Available at: https://doi.org/10.1016/j.resmic.2016.02.001.Zhang, A. (1998) ‘The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein’, The EMBO Journal , 17(20), pp. 6061–6068. Available at: https://doi.org/10.1093/emboj/17.20.6061.Zhang, A. et al. (2003) ‘Global analysis of small RNA and mRNA targets of Hfq’, Molecular Microbiology , 50(4), pp. 1111–1124. Available at: https://doi.org/10.1046/j.1365-2958.2003.03734.x.Zhao, X. et al. (2021) ‘Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins’, eLife , 10, p. e57467. Available at: https://doi.org/10.7554/eLife.57467.Ziegler, C.A. and Freddolino, P.L. (2021) ‘The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea’, Critical Reviews in Biochemistry and Molecular Biology , 56(4), pp. 373–400. Available at: https://doi.org/10.1080/10409238.2021.1925215.Ziegler, C.A. and Freddolino, P.L. (2023) ‘Escherichia coli Leucine-Responsive Regulatory Protein Bridges DNA In Vivo and Tunably Dissociates in the Presence of Exogenous Leucine’, mBio . Edited by C.L. Stallings, 14(2), pp. e02690-22. Available at: https://doi.org/10.1128/mbio.02690-22.