{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T01:00:27Z","timestamp":1790816427625,"version":"4.1.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Vector-borne pathogens must adapt to sharply distinct host environments, yet the regulatory logic that coordinates transitions between opposing host-specific programs remains poorly defined. Here, we identify a minimal regulatory module in the flea-borne pathogen\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    that integrates vector transmission with resistance to mammalian innate immunity. Screening of flea-induced genes uncovered the regulator HdfR, which acts primarily through activation of\n                    <jats:italic>maoP<\/jats:italic>\n                    , encoding a nucleoid-associated protein. This HdfR-MaoP module promotes biofilm-dependent foregut blockage in the flea while coordinating baseline envelope adaptations that limit complement recognition and inducible responses that confer resistance to antimicrobial peptides under mammalian host-like conditions. Functional interchangeability of HdfR and MaoP homologs reveals evolutionary conservation of this regulatory logic, and pharmacological perturbation of the module sensitizes\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    to antimicrobial peptides. Together, these findings define a parsimonious and evolutionarily conserved regulatory hub that orchestrates bacterial success across abrupt environmental transitions and exposes a tractable point of intervention.\n                  <\/jats:p>","DOI":"10.1038\/s41467-026-77307-4","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T07:04:31Z","timestamp":1788246271000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A dual-host regulatory hub integrating biofilm formation and innate immunity resistance"],"prefix":"10.1038","volume":"17","author":[{"given":"Alexandre","family":"Baillez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Am\u00e9lie","family":"Dewitte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Pierre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mounia","family":"Kortebi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5366-0462","authenticated-orcid":false,"given":"Virginia S.","family":"Lioy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2973-6153","authenticated-orcid":false,"given":"M\u00e9lanie","family":"Hillion","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4588-9811","authenticated-orcid":false,"given":"Julie","family":"Hardouin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6736-3162","authenticated-orcid":false,"given":"S\u00e9bastien","family":"Janel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Thuru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Clarisse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0909-8585","authenticated-orcid":false,"given":"Hassiba","family":"Bouafia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine Robbe","family":"Masselot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00e9bastien","family":"Bontemps-Gallo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3811-9691","authenticated-orcid":false,"given":"Florent","family":"Sebbane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"77307_CR1","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1016\/j.cell.2015.10.005","volume":"163","author":"AH Yona","year":"2015","unstructured":"Yona, A. H., Frumkin, I. & Pilpel, Y. A relay race on the evolutionary adaptation spectrum. Cell 163, 549\u2013559 (2015).","journal-title":"Cell"},{"key":"77307_CR2","doi-asserted-by":"publisher","first-page":"RP86636","DOI":"10.7554\/eLife.86636","volume":"12","author":"AL Sapiro","year":"2023","unstructured":"Sapiro, A. L. et al. Longitudinal map of transcriptome changes in the Lyme pathogen Borrelia burgdorferi during tick-borne transmission. Elife 12, RP86636 (2023).","journal-title":"Elife"},{"key":"77307_CR3","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nri.2016.72","volume":"16","author":"P Scott","year":"2016","unstructured":"Scott, P. & Novais, F. O. Cutaneous leishmaniasis: immune responses in protection and pathogenesis. Nat. Rev. Immunol. 16, 581\u2013592 (2016).","journal-title":"Nat. Rev. Immunol."},{"key":"77307_CR4","doi-asserted-by":"publisher","first-page":"e1012965","DOI":"10.1371\/journal.ppat.1012965","volume":"21","author":"SA Saab","year":"2025","unstructured":"Saab, S. A., Cardoso-Jaime, V., Kefi, M. & Dimopoulos, G. Advances in the dissection of Anopheles-Plasmodium interactions. PLoS Pathog. 21, e1012965 (2025).","journal-title":"PLoS Pathog."},{"key":"77307_CR5","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1146\/annurev-micro-090816-093521","volume":"71","author":"BJ Hinnebusch","year":"2017","unstructured":"Hinnebusch, B. J., Jarrett, C. O. & Bland, D. M. \u201cFleaing\u201d the plague: adaptations of Yersinia pestis to its insect vector that lead to transmission. Annu Rev. Microbiol. 71, 215\u2013232 (2017).","journal-title":"Annu Rev. Microbiol."},{"key":"77307_CR6","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1128\/CMR.10.1.35","volume":"10","author":"RD Perry","year":"1997","unstructured":"Perry, R. D. & Fetherston, J. D. Yersinia pestis-etiologic agent of plague. Clin. Microbiol Rev. 10, 35\u201366 (1997).","journal-title":"Clin. Microbiol Rev."},{"key":"77307_CR7","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1126\/science.273.5273.367","volume":"273","author":"BJ Hinnebusch","year":"1996","unstructured":"Hinnebusch, B. J., Perry, R. D. & Schwan, T. G. Role of the Yersinia pestis hemin storage (hms) locus in the transmission of plague by fleas. Science 273, 367\u2013370 (1996).","journal-title":"Science"},{"key":"77307_CR8","doi-asserted-by":"publisher","first-page":"e1008440","DOI":"10.1371\/journal.ppat.1008440","volume":"16","author":"A Dewitte","year":"2020","unstructured":"Dewitte, A. et al. A refined model of how Yersinia pestis produces a transmissible infection in its flea vector. PLoS Pathog. 16, e1008440 (2020).","journal-title":"PLoS Pathog."},{"key":"77307_CR9","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1099\/13500872-145-1-197","volume":"145","author":"JW Lillard Jr.","year":"1999","unstructured":"Lillard, J. W. Jr., Bearden, S. W., Fetherston, J. D. & Perry, R. D. The haemin storage (Hms+) phenotype of Yersinia pestis is not essential for the pathogenesis of bubonic plague in mammals. Microbiology 145, 197\u2013209 (1999).","journal-title":"Microbiology"},{"key":"77307_CR10","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1126\/science.1114580","volume":"309","author":"MM Marketon","year":"2005","unstructured":"Marketon, M. M., DePaolo, R. W., DeBord, K. L., Jabri, B. & Schneewind, O. Plague bacteria target immune cells during infection. Science 309, 1739\u20131741 (2005).","journal-title":"Science"},{"key":"77307_CR11","doi-asserted-by":"publisher","first-page":"1427","DOI":"10.1016\/S0002-9440(10)62360-7","volume":"166","author":"F Sebbane","year":"2005","unstructured":"Sebbane, F., Gardner, D., Long, D., Gowen, B. B. & Hinnebusch, B. J. Kinetics of disease progression and host response in a rat model of bubonic plague. Am. J. Pathol. 166, 1427\u20131439 (2005).","journal-title":"Am. J. Pathol."},{"key":"77307_CR12","doi-asserted-by":"publisher","first-page":"1907","DOI":"10.1086\/429931","volume":"191","author":"EA Lorange","year":"2005","unstructured":"Lorange, E. A., Race, B. L., Sebbane, F. & Hinnebusch, B. J. Poor vector competence of fleas and the evolution of hypervirulence in Yersinia pestis. J. Infect. Dis. 191, 1907\u20131912, https:\/\/doi.org\/10.1086\/429931 (2005).","journal-title":"J. Infect. Dis."},{"key":"77307_CR13","doi-asserted-by":"publisher","first-page":"e1000783","DOI":"10.1371\/journal.ppat.1000783","volume":"6","author":"V Vadyvaloo","year":"2010","unstructured":"Vadyvaloo, V., Jarrett, C., Sturdevant, D. E., Sebbane, F. & Hinnebusch, B. J. Transit through the flea vector induces a pretransmission innate immunity resistance phenotype in Yersinia pestis. PLoS Pathog. 6, e1000783 (2010).","journal-title":"PLoS Pathog."},{"key":"77307_CR14","doi-asserted-by":"publisher","first-page":"210","DOI":"10.3390\/biom11020210","volume":"11","author":"BJ Hinnebusch","year":"2021","unstructured":"Hinnebusch, B. J., Jarrett, C. O. & Bland, D. M. Molecular and genetic mechanisms that mediate transmission of Yersinia pestis by fleas. Biomolecules 11, 210 (2021).","journal-title":"Biomolecules"},{"key":"77307_CR15","doi-asserted-by":"publisher","first-page":"146","DOI":"10.3389\/fcimb.2014.00146","volume":"4","author":"AK Heroven","year":"2014","unstructured":"Heroven, A. K. & Dersch, P. Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae. Front. Cell Infect. Microbiol. 4, 146 (2014).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"77307_CR16","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.3390\/pathogens9121039","volume":"9","author":"HS Fukuto","year":"2020","unstructured":"Fukuto, H. S., Viboud,, G. I. & Vadyvaloo, V. The diverse roles of the global transcriptional regulator PhoP in the lifecycle of Yersinia pestis. Pathogens 9, 1039 (2020).","journal-title":"Pathogens"},{"key":"77307_CR17","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1093\/infdis\/jiu274","volume":"210","author":"A Reboul","year":"2014","unstructured":"Reboul, A. et al. Yersinia pestis requires the 2-component regulatory system OmpR-EnvZ to resist innate immunity during the early and late stages of plague. J. Infect. Dis. 210, 1367\u20131375 (2014).","journal-title":"J. Infect. Dis."},{"key":"77307_CR18","doi-asserted-by":"publisher","first-page":"13514","DOI":"10.1073\/pnas.0603456103","volume":"103","author":"JS Cathelyn","year":"2006","unstructured":"Cathelyn, J. S., Crosby, S. D., Lathem, W. W., Goldman, W. E. & Miller, V. L. RovA, a global regulator of Yersinia pestis, specifically required for bubonic plague. Proc. Natl. Acad. Sci. USA 103, 13514\u201313519 (2006).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"77307_CR19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137508","volume":"10","author":"V Vadyvaloo","year":"2015","unstructured":"Vadyvaloo, V. & Hinz, A. K. A LysR-type transcriptional regulator, RovM, senses nutritional cues, suggesting that it is involved in metabolic adaptation of Yersinia pestis to the flea gut. PLoS ONE 10, e0137508 (2015).","journal-title":"PLoS ONE"},{"key":"77307_CR20","doi-asserted-by":"publisher","first-page":"e02613","DOI":"10.1128\/mBio.02613-19","volume":"10","author":"JT Ritzert","year":"2019","unstructured":"Ritzert, J. T., Minasov, G., Embry, R., Schipma, M. J. & Satchell, K. J. F. The cyclic AMP receptor protein regulates quorum sensing and global gene expression in Yersinia pestis during planktonic growth and growth in biofilms. mBio 10, e02613\u2013e02619 (2019).","journal-title":"mBio"},{"key":"77307_CR21","doi-asserted-by":"publisher","first-page":"2036","DOI":"10.1128\/JB.06568-11","volume":"194","author":"KA Rempe","year":"2012","unstructured":"Rempe, K. A., Hinz, A. K. & Vadyvaloo, V. Hfq regulates biofilm gut blockage that facilitates flea-borne transmission of Yersinia pestis. J. Bacteriol. 194, 2036\u20132040 (2012).","journal-title":"J. Bacteriol."},{"key":"77307_CR22","doi-asserted-by":"publisher","first-page":"35796","DOI":"10.1074\/jbc.M112.379156","volume":"287","author":"N Quade","year":"2012","unstructured":"Quade, N. et al. Structural basis for intrinsic thermosensing by the master virulence regulator RovA of Yersinia. J. Biol. Chem. 287, 35796\u201335803 (2012).","journal-title":"J. Biol. Chem."},{"key":"77307_CR23","first-page":"299","volume":"34","author":"B Ni","year":"2021","unstructured":"Ni, B., Wu, H. S., Xin, Y. Q., Zhang, Q. W. & Zhang, Y. Q. Reciprocal regulation between fur and two RyhB homologs in Yersinia pestis, and roles of RyhBs in biofilm formation. Biomed. Environ. Sci. 34, 299\u2013308 (2021).","journal-title":"Biomed. Environ. Sci."},{"key":"77307_CR24","doi-asserted-by":"publisher","first-page":"685","DOI":"10.3389\/fmicb.2014.00685","volume":"5","author":"N Fang","year":"2014","unstructured":"Fang, N. et al. HmsB enhances biofilm formation in Yersinia pestis. Front. Microbiol 5, 685 (2014).","journal-title":"Front. Microbiol"},{"key":"77307_CR25","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1186\/s12866-016-0793-5","volume":"16","author":"Z Liu","year":"2016","unstructured":"Liu, Z. et al. Plasmid pPCP1-derived sRNA HmsA promotes biofilm formation of Yersinia pestis. BMC Microbiol. 16, 176 (2016).","journal-title":"BMC Microbiol."},{"key":"77307_CR26","doi-asserted-by":"publisher","first-page":"82","DOI":"10.3389\/fcimb.2016.00082","volume":"6","author":"CJ Kuo","year":"2016","unstructured":"Kuo, C. J. et al. Mutation of the enterohemorrhagic Escherichia coli Core LPS biosynthesis enzyme RfaD confers hypersusceptibility to host intestinal innate immunity in vivo. Front. Cell Infect. Microbiol 6, 82 (2016).","journal-title":"Front. Cell Infect. Microbiol"},{"key":"77307_CR27","doi-asserted-by":"publisher","first-page":"7236","DOI":"10.1128\/IAI.73.11.7236-7242.2005","volume":"73","author":"C Darby","year":"2005","unstructured":"Darby, C., Ananth, S. L., Tan, L. & Hinnebusch, B. J. Identification of gmhA, a Yersinia pestis gene required for flea blockage, by using a Caenorhabditis elegans biofilm system. Infect. Immun. 73, 7236\u20137242 (2005).","journal-title":"Infect. Immun."},{"key":"77307_CR28","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00301-25","volume":"16","author":"CF Bosio","year":"2025","unstructured":"Bosio, C. F., Jarrett, C. O. & Hinnebusch, B. J. Evidence of a role for the F1 capsule of Yersinia pestis in enhancing transmission from mammals to fleas in a mouse model of bubonic plague. mBio 16, e0030125 (2025).","journal-title":"mBio"},{"key":"77307_CR29","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/0014-5793(92)80650-6","volume":"305","author":"AV Karlyshev","year":"1992","unstructured":"Karlyshev, A. V., Galyov, E. E., Abramov, V. M. & Zav\u2019yalov, V. P. caf1R gene and its role in the regulation of capsule formation of Y. pestis. FEBS Lett. 305, 37\u201340 (1992).","journal-title":"FEBS Lett."},{"key":"77307_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23666-z","volume":"12","author":"S Lenz","year":"2021","unstructured":"Lenz, S. et al. Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat. Commun. 12, 3564 (2021).","journal-title":"Nat. Commun."},{"key":"77307_CR31","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/nar\/gkad216","volume":"51","author":"TS Stenum","year":"2023","unstructured":"Stenum, T. S. et al. RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins. Nucleic Acids Res. 51, 4572\u20134587 (2023).","journal-title":"Nucleic Acids Res."},{"key":"77307_CR32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006309","volume":"12","author":"M Valens","year":"2016","unstructured":"Valens, M., Thiel, A. & Boccard, F. The MaoP\/maoS site-specific system organizes the ori region of the E. coli chromosome into a macrodomain. PLoS Genet. 12, e1006309 (2016).","journal-title":"PLoS Genet."},{"key":"77307_CR33","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1038\/s41586-025-09396-y","volume":"645","author":"AA Gavrilov","year":"2025","unstructured":"Gavrilov, A. A. et al. Elementary 3D organization of the active and silenced E. coli genome. Nature 645, 1060\u20131070 (2025).","journal-title":"Nature"},{"key":"77307_CR34","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1038\/nrmicro2261","volume":"8","author":"SC Dillon","year":"2010","unstructured":"Dillon, S. C. & Dorman, C. J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol 8, 185\u2013195 (2010).","journal-title":"Nat. Rev. Microbiol"},{"key":"77307_CR35","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1016\/j.cell.2017.12.027","volume":"172","author":"VS Lioy","year":"2018","unstructured":"Lioy, V. S. et al. Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins. Cell 172, 771\u2013783 (2018).","journal-title":"Cell"},{"key":"77307_CR36","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature05283","volume":"444","author":"RT Dame","year":"2006","unstructured":"Dame, R. T., Noom, M. C. & Wuite, G. J. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444, 387\u2013390 (2006).","journal-title":"Nature"},{"key":"77307_CR37","doi-asserted-by":"publisher","first-page":"7929","DOI":"10.1093\/nar\/gkz530","volume":"47","author":"L Garcia-Pastor","year":"2019","unstructured":"Garcia-Pastor, L., Sanchez-Romero, M. A., Jakomin, M., Puerta-Fernandez, E. & Casadesus, J. Regulation of bistability in the std fimbrial operon of Salmonella enterica by DNA adenine methylation and transcription factors HdfR, StdE and StdF. Nucleic Acids Res. 47, 7929\u20137941 (2019).","journal-title":"Nucleic Acids Res."},{"key":"77307_CR38","doi-asserted-by":"publisher","first-page":"7406","DOI":"10.1128\/JB.01136-08","volume":"190","author":"M Jakomin","year":"2008","unstructured":"Jakomin, M., Chessa, D., Baumler, A. J. & Casadesus, J. Regulation of the Salmonella enterica std fimbrial operon by DNA adenine methylation, SeqA, and HdfR. J. Bacteriol. 190, 7406\u20137413 (2008).","journal-title":"J. Bacteriol."},{"key":"77307_CR39","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1111\/j.1462-2920.2011.02669.x","volume":"14","author":"CA Easom","year":"2012","unstructured":"Easom, C. A. & Clarke, D. J. HdfR is a regulator in Photorhabdus luminescens that modulates metabolism and symbiosis with the nematode Heterorhabditis. Environ. Microbiol 14, 953\u2013966 (2012).","journal-title":"Environ. Microbiol"},{"key":"77307_CR40","first-page":"673","volume":"7","author":"ER Holden","year":"2021","unstructured":"Holden, E. R. et al. Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli. Microb. Genom. 7, 673 (2021).","journal-title":"Microb. Genom."},{"key":"77307_CR41","doi-asserted-by":"publisher","first-page":"1344","DOI":"10.1126\/science.1226683","volume":"338","author":"AA Al Mamun","year":"2012","unstructured":"Al Mamun, A. A. et al. Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338, 1344\u20131348 (2012).","journal-title":"Science"},{"key":"77307_CR42","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1128\/IAI.72.5.2922-2938.2004","volume":"72","author":"LS Burall","year":"2004","unstructured":"Burall, L. S. et al. Proteus mirabilis genes that contribute to pathogenesis of urinary tract infection: identification of 25 signature-tagged mutants attenuated at least 100-fold. Infect. Immun. 72, 2922\u20132938 (2004).","journal-title":"Infect. Immun."},{"key":"77307_CR43","doi-asserted-by":"publisher","first-page":"e00715","DOI":"10.1128\/msphere.00715-20","volume":"5","author":"KR Eichelberger","year":"2020","unstructured":"Eichelberger, K. R. et al. Tn-seq analysis identifies genes important for Yersinia pestis adherence during primary pneumonic plague. mSphere 5, e00715\u2013e00720 (2020).","journal-title":"mSphere"},{"key":"77307_CR44","doi-asserted-by":"publisher","first-page":"4670","DOI":"10.1128\/JB.182.16.4670-4672.2000","volume":"182","author":"M Ko","year":"2000","unstructured":"Ko, M. & Park, C. H-NS-Dependent regulation of flagellar synthesis is mediated by a LysR family protein. J. Bacteriol. 182, 4670\u20134672 (2000).","journal-title":"J. Bacteriol."},{"key":"77307_CR45","doi-asserted-by":"publisher","first-page":"e00202","DOI":"10.1128\/JB.00202-17","volume":"199","author":"J Bartoli","year":"2017","unstructured":"Bartoli, J. et al. The long hunt for pssR: Looking for a phospholipid synthesis transcriptional regulator, finding the ribosome. J. Bacteriol. 199, e00202\u2013e00217 (2017).","journal-title":"J. Bacteriol."},{"key":"77307_CR46","doi-asserted-by":"publisher","first-page":"e1004029","DOI":"10.1371\/journal.ppat.1004029","volume":"10","author":"E Pradel","year":"2014","unstructured":"Pradel, E. et al. New insights into how Yersinia pestis adapts to its mammalian host during bubonic plague. PLoS Pathog. 10, e1004029 (2014).","journal-title":"PLoS Pathog."},{"key":"77307_CR47","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nmeth765","volume":"2","author":"KH Choi","year":"2005","unstructured":"Choi, K. H. et al. A Tn7-based broad-range bacterial cloning and expression system. Nat. Methods 2, 443\u2013448 (2005).","journal-title":"Nat. Methods"},{"key":"77307_CR48","doi-asserted-by":"crossref","unstructured":"Morgan, B. P. Complement Methods and Protocols. Vol. 150, 259 (Humana, Totowa, NJ, 2000).","DOI":"10.1385\/159259056X"},{"key":"77307_CR49","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1111\/j.1365-2958.2004.04253.x","volume":"54","author":"O Kirillina","year":"2004","unstructured":"Kirillina, O., Fetherston, J. D., Bobrov, A. G., Abney, J. & Perry, R. D. HmsP, a putative phosphodiesterase, and HmsT, a putative diguanylate cyclase, control Hms-dependent biofilm formation in Yersinia pestis. Mol. Microbiol. 54, 75\u201388 (2004).","journal-title":"Mol. Microbiol."},{"key":"77307_CR50","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1074\/mcp.M116.061044","volume":"16","author":"T Kentache","year":"2017","unstructured":"Kentache, T., Ben Abdelkrim, A., Jouenne, T., De, E. & Hardouin, J. Global dynamic proteome study of a pellicle-forming Acinetobacter baumannii Strain. Mol. Cell Proteom. 16, 100\u2013112 (2017).","journal-title":"Mol. Cell Proteom."},{"key":"77307_CR51","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/bs.mie.2015.05.016","volume":"561","author":"GM Mackay","year":"2015","unstructured":"Mackay, G. M., Zheng, L., van den Broek, N. J. & Gottlieb, E. Analysis of cell metabolism using LC-MS and isotope tracers. Methods Enzymol. 561, 171\u2013196 (2015).","journal-title":"Methods Enzymol."},{"key":"77307_CR52","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48009-6","volume":"15","author":"Z Pang","year":"2024","unstructured":"Pang, Z. et al. MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics. Nat. Commun. 15, 3675 (2024).","journal-title":"Nat. Commun."},{"key":"77307_CR53","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1038\/s41396-020-00839-0","volume":"15","author":"T Bouvenot","year":"2021","unstructured":"Bouvenot, T. et al. Interplay between Yersinia pestis and its flea vector in lipoate metabolism. ISME J. 15, 1136\u20131149 (2021).","journal-title":"ISME J."},{"key":"77307_CR54","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1046\/j.1365-2958.1999.01285.x","volume":"31","author":"M Skurnik","year":"1999","unstructured":"Skurnik, M., Venho, R., Bengoechea, J. A. & Moriyon, I. The lipopolysaccharide outer core of Yersinia enterocolitica serotype O:3 is required for virulence and plays a role in outer membrane integrity. Mol. Microbiol. 31, 1443\u20131462 (1999).","journal-title":"Mol. Microbiol."},{"key":"77307_CR55","doi-asserted-by":"publisher","first-page":"998671","DOI":"10.3389\/fmicb.2022.998671","volume":"13","author":"F Al-Marzooq","year":"2022","unstructured":"Al-Marzooq, F., Ghazawi, A., Tariq, S., Daoud, L. & Collyns, T. Discerning the role of polymyxin B nonapeptide in restoring the antibacterial activity of azithromycin against antibiotic-resistant Escherichia coli. Front. Microbiol. 13, 998671 (2022).","journal-title":"Front. Microbiol."},{"key":"77307_CR56","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2025.2493926","volume":"14","author":"F Pierre","year":"2025","unstructured":"Pierre, F., Baillez, A., Dewitte, A., Rolandelli, A. & Sebbane, F. Proteins of the SubB family provide multiple mechanisms of serum resistance in Yersinia pestis. Emerg. Microbes Infect. 14, 2493926 (2025).","journal-title":"Emerg. Microbes Infect."},{"key":"77307_CR57","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-39072-x","volume":"9","author":"L Koch","year":"2019","unstructured":"Koch, L. et al. Transcriptomic studies and assessment of Yersinia pestis reference genes in various conditions. Sci. Rep. 9, 2501 (2019).","journal-title":"Sci. Rep."},{"key":"77307_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-67746-w","volume":"17","author":"M Kortebi","year":"2026","unstructured":"Kortebi, M. et al. Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands. Nat. Commun. 17, 161 (2026).","journal-title":"Nat. Commun."},{"key":"77307_CR59","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-44761-x","volume":"15","author":"J Serizay","year":"2024","unstructured":"Serizay, J., Matthey-Doret, C., Bignaud, A., Baudry, L. & Koszul, R. Orchestrating chromosome conformation capture analysis with Bioconductor. Nat. Commun. 15, 1072 (2024).","journal-title":"Nat. Commun."},{"key":"77307_CR60","doi-asserted-by":"publisher","first-page":"100776","DOI":"10.1016\/j.xpro.2021.100776","volume":"2","author":"C Yao","year":"2021","unstructured":"Yao, C., Shao, X., Li, J. & Deng, X. Optimized protocols for ChIP-seq and deletion mutant construction in Pseudomonas syringae. STAR Protoc. 2, 100776 (2021).","journal-title":"STAR Protoc."},{"key":"77307_CR61","doi-asserted-by":"crossref","first-page":"W1","DOI":"10.1093\/nar\/gkae492","volume":"52","author":"C Galaxy","year":"2024","unstructured":"Galaxy, C. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Res. 52, W1\u2013W6 (2024).","journal-title":"Nucleic Acids Res."},{"key":"77307_CR62","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"77307_CR63","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"77307_CR64","doi-asserted-by":"publisher","first-page":"e19267","DOI":"10.1371\/journal.pone.0019267","volume":"6","author":"YC Sun","year":"2011","unstructured":"Sun, Y. C. et al. Differential control of Yersinia pestis biofilm formation in vitro and in the flea vector by two c-di-GMP diguanylate cyclases. PLoS ONE 6, e19267 (2011).","journal-title":"PLoS ONE"},{"key":"77307_CR65","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1007\/978-1-0716-2221-6_5","volume":"2476","author":"PJ Haynes","year":"2022","unstructured":"Haynes, P. J., Main, K. H. S., Akpinar, B. & Pyne, A. L. B. Atomic force microscopy of DNA and DNA-protein interactions. Methods Mol. Biol. 2476, 43\u201362 (2022).","journal-title":"Methods Mol. Biol."},{"key":"77307_CR66","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","volume":"50","author":"Y Perez-Riverol","year":"2022","unstructured":"Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidence. Nucleic Acids Res. 50, D543\u2013D552 (2022).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77307-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77307-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77307-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:03:12Z","timestamp":1790812992000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-026-77307-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":66,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["77307"],"URL":"https:\/\/doi.org\/10.1038\/s41467-026-77307-4","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]},"assertion":[{"value":"28 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"AB and FS are involved in the filing of a patent application related to a compound identified in this study for modulation of the HdfR-MaoP regulatory system. All other authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"10385"}}