{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T20:30:14Z","timestamp":1791923414087,"version":"4.3.4"},"reference-count":74,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T00:00:00Z","timestamp":1631232000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004541","name":"Ministry of Human Resource Development","doi-asserted-by":"publisher","award":["11015\/4\/2009-SCDV"],"award-info":[{"award-number":["11015\/4\/2009-SCDV"]}],"id":[{"id":"10.13039\/501100004541","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The bacterial pathogen, Yersinia pestis, has caused three historic pandemics and continues to cause small outbreaks worldwide. During infection, Y. pestis assembles a capsule-like protective coat of thin fibres of Caf1 subunits. This F1 capsular antigen has attracted much attention due to its clinical value in plague diagnostics and anti-plague vaccine development. Expression of F1 is tightly regulated by a transcriptional activator, Caf1R, of the AraC\/XylS family, proteins notoriously prone to aggregation. Here, we have optimised the recombinant expression of soluble Caf1R. Expression from the native and synthetic codon-optimised caf1R cloned in three different expression plasmids was examined in a library of E. coli host strains. The functionality of His-tagged Caf1R was demonstrated in vivo, but insolubility was a problem with overproduction. High levels of soluble MBP-Caf1R were produced from codon optimised caf1R. Transcriptional-lacZ reporter fusions defined the PM promoter and Caf1R binding site responsible for transcription of the cafMA1 operon. Use of the identified Caf1R binding caf DNA sequence in an electrophoretic mobility shift assay (EMSA) confirmed correct folding and functionality of the Caf1R DNA-binding domain in recombinant MBP-Caf1R. Availability of functional recombinant Caf1R will be a valuable tool to elucidate control of expression of F1 and Caf1R-regulated pathophysiology of Y. pestis.<\/jats:p>","DOI":"10.3390\/ijms22189805","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T10:31:34Z","timestamp":1631269894000},"page":"9805","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Optimised Heterologous Expression and Functional Analysis of the Yersinia pestis F1-Capsular Antigen Regulator Caf1R"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6963-0009","authenticated-orcid":false,"given":"Dharmender K.","family":"Gahlot","sequence":"first","affiliation":[{"name":"School of Biological Sciences, University of Reading, Reading RG6 6UR, UK"},{"name":"Department of Molecular Biology, Ume\u00e5 University, 901 87 Ume\u00e5, Sweden"},{"name":"Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, 901 87 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gyles","family":"Ifill","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Reading, Reading RG6 6UR, UK"},{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheila","family":"MacIntyre","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Reading, Reading RG6 6UR, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,10]]},"reference":[{"key":"ref_1","first-page":"289","article-title":"Plague around the world in 2019","volume":"94","author":"Bertherat","year":"2019","journal-title":"WHO Wkly. Epidemiol. Rec."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Stenseth, N.C., Atshabar, B.B., Begon, M., Belmain, S.R., Bertherat, E., Carniel, E., Gage, K.L., Leirs, H., and Rahalison, L. (2008). Plague: Past, present, and future. PLoS Med., 5.","DOI":"10.1371\/journal.pmed.0050003"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1128\/iai.64.6.2180-2187.1996","article-title":"Fraction 1 capsular antigen (F1) purification from Yersinia pestis CO92 and from an Escherichia coli recombinant strain and efficacy against lethal plague challenge","volume":"64","author":"Andrews","year":"1996","journal-title":"Infect. Immun."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/S0092-8674(03)00351-9","article-title":"Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: Preserved folding energy drives fiber formation","volume":"113","author":"Zavialov","year":"2003","journal-title":"Cell"},{"key":"ref_5","unstructured":"Carniel, E., and Hinnenbusch, B.J. (2004). Structure, assembly and applications of the polymeric F1 antigen of Yersinia pestis. Yersinia: Molecular and Cellular Biology, Horizon Bioscience."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/cei.12044","article-title":"Protecting against plague: Towards a next-generation vaccine","volume":"172","author":"Williamson","year":"2013","journal-title":"Clin. Exp. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.jmb.2012.01.020","article-title":"Large is fast, small is tight: Determinants of speed and affinity in subunit capture by a periplasmic chaperone","volume":"417","author":"Xiao","year":"2012","journal-title":"J. Mol. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1861","DOI":"10.1016\/j.str.2012.08.016","article-title":"Allosteric mechanism controls traffic in the chaperone\/usher pathway","volume":"20","author":"Xiao","year":"2012","journal-title":"Structure"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1926","DOI":"10.1128\/iai.65.5.1926-1930.1997","article-title":"Expression of the Yersinia pestis capsular antigen (F1 antigen) on the surface of an aroA mutant of Salmonella typhimurium induces high levels of protection against plague","volume":"65","author":"Titball","year":"1997","journal-title":"Infect. Immun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1128\/IAI.70.3.1453-1460.2002","article-title":"Role of fraction 1 antigen of Yersinia pestis in inhibition of phagocytosis","volume":"70","author":"Du","year":"2002","journal-title":"Infect. Immun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"299","DOI":"10.2147\/ITT.S267077","article-title":"Development of Anti-Yersinia pestis Human Antibodies with Features Required for Diagnostic and Therapeutic Applications","volume":"9","author":"Lillo","year":"2020","journal-title":"Immunotargets Ther."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Hsu, H.-L., Chuang, C.-C., Liang, C.-C., Chiao, D.-J., Wu, H.-L., Wu, Y.-P., Lin, F.-P., and Shyu, R.-H. (2018). Rapid and sensitive detection of Yersinia pestis by lateral-flow assay in simulated clinical samples. BMC Infect. Dis., 18.","DOI":"10.1186\/s12879-018-3315-2"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Simon, S., Demeure, C., Lamourette, P., Filali, S., Plaisance, M., Cr\u00e9minon, C., Volland, H., and Carniel, E. (2013). Fast and simple detection of Yersinia pestis applicable to field investigation of plague foci. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0054947"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41435-019-0065-0","article-title":"Yersinia pestis and plague: An updated view on evolution, virulence determinants, immune subversion, vaccination, and diagnostics","volume":"20","author":"Demeure","year":"2019","journal-title":"Genes Immun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41541-020-00275-3","article-title":"A new generation needle- and adjuvant-free trivalent plague vaccine utilizing adenovirus-5 nanoparticle platform","volume":"6","author":"Kilgore","year":"2021","journal-title":"NPJ Vaccines"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41541-020-0156-y","article-title":"Flagellin adjuvanted F1\/V subunit plague vaccine induces T cell and functional antibody responses with unique gene signatures","volume":"5","author":"Hamzabegovic","year":"2020","journal-title":"NPJ Vaccines"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/s41541-018-0087-z","article-title":"Targeting of the Yersinia pestis F1 capsular antigen by innate-like B1b cells mediates a rapid protective response against bubonic plague","volume":"3","author":"Levy","year":"2018","journal-title":"NPJ Vaccines"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/0014-5793(92)80650-6","article-title":"Caf1R gene and its role in the regulation of capsule formation of Y. pestis","volume":"305","author":"Karlyshev","year":"1992","journal-title":"FEBS Lett."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Cort\u00e9s-Avalos, D., Mart\u00ednez-P\u00e9rez, N., Ortiz-Moncada, M.A., Ju\u00e1rez-Gonz\u00e1lez, A., Ba\u00f1os-Vargas, A.A., Estrada-de Los Santos, P., P\u00e9rez-Rueda, E., and Ibarra, J.A. (2021). An update of the unceasingly growing and diverse AraC\/XylS family of transcriptional activators. FEMS Microbiol. Rev., fuab020.","DOI":"10.1093\/femsre\/fuab020"},{"key":"ref_20","first-page":"393","article-title":"Arac\/XylS family of transcriptional regulators","volume":"61","author":"Gallegos","year":"1997","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Perez-Rueda, E., Hernandez-Guerrero, R., Martinez-Nu\u00f1ez, M.A., Armenta-Medina, D., Sanchez, I., and Ibarra, J.A. (2018). Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0195332"},{"key":"ref_22","first-page":"101","article-title":"MarA, SoxS and Rob of Escherichia coli\u2013Global regulators of multidrug resistance, virulence and stress response","volume":"2","author":"Duval","year":"2013","journal-title":"Int. J. Biotechnol. Wellness Ind."},{"key":"ref_23","first-page":"103132","article-title":"Computer-based annotation of putative AraC\/XylS-family transcription factors of known structure but unknown function","volume":"2012","author":"Slater","year":"2012","journal-title":"J. Biomed. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/75213","article-title":"Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA","volume":"7","author":"Kwon","year":"2000","journal-title":"Nat. Struct. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"10413","DOI":"10.1073\/pnas.95.18.10413","article-title":"A novel DNA-binding motif in MarA: The first structure for an AraC family transcriptional activator","volume":"95","author":"Rhee","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S0003-2697(03)00059-9","article-title":"Detection and prevention of protein aggregation before, during, and after purification","volume":"316","author":"Bondos","year":"2003","journal-title":"Anal. Biochem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1002\/pro.3668","article-title":"New tools for recombinant protein production in Escherichia coli: A 5-year update","volume":"28","author":"Rosano","year":"2019","journal-title":"Protein Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"172","DOI":"10.3389\/fmicb.2014.00172","article-title":"Recombinant protein expression in Escherichia coli: Advances and challenges","volume":"5","author":"Rosano","year":"2014","journal-title":"Front. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4867","DOI":"10.1128\/JB.00680-12","article-title":"Transcriptional cross talk within the mar-sox-rob regulon in Escherichia coli is limited to the rob and marRAB operons","volume":"194","author":"Chubiz","year":"2012","journal-title":"J. Bacteriol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1093\/nar\/gks1207","article-title":"Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: An AraC DNA-binding family member with a LacI\/GalR ligand-binding domain","volume":"41","author":"Ni","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1111\/j.1365-2958.2005.04599.x","article-title":"Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS\/MarA\/Rob regulon","volume":"56","author":"Griffith","year":"2005","journal-title":"Mol. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1111\/j.1365-2958.1994.tb01305.x","article-title":"Purification of a MalE-SoxS fusion protein and identification of the control sites of Escherichia coli superoxide-inducible genes","volume":"14","author":"Fawcett","year":"1994","journal-title":"Mol. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1046\/j.1365-2958.2000.01957.x","article-title":"Rns, a virulence regulator within the AraC family, requires binding sites upstream and downstream of its own promoter to function as an activator","volume":"36","author":"Munson","year":"2000","journal-title":"Mol. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1007\/s10534-013-9676-5","article-title":"In vitro-binding of the natural siderophore enantiomers pyochelin and enantiopyochelin to their AraC-type regulators PchR in Pseudomonas","volume":"26","author":"Lin","year":"2013","journal-title":"Biometals"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"377","DOI":"10.18388\/pb.2016_41","article-title":"The remarkable solubility-enhancing power of Escherichia coli maltose-binding protein","volume":"62","author":"Waugh","year":"2016","journal-title":"Postepy Biochem."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Kotecka, K., Kawalek, A., Kobylecki, K., and Bartosik, A.A. (2021). The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22105066"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1177\/00220345211000668","article-title":"EpsR Negatively Regulates Streptococcus mutans Exopolysaccharide Synthesis","volume":"100","author":"Chen","year":"2021","journal-title":"J. Dent. Res."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Park, M., Hwang, S., Ryu, S., and Jeon, B. (2021). CosR Regulation of perR Transcription for the Control of Oxidative Stress Defense in Campylobacter jejuni. Microorganisms, 9.","DOI":"10.3390\/microorganisms9061281"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"4947","DOI":"10.1038\/s41467-020-18744-7","article-title":"A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae","volume":"11","author":"Fan","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1111\/j.1574-6976.2010.00226.x","article-title":"AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action","volume":"34","author":"Schleif","year":"2010","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1111\/j.1365-2958.2008.06164.x","article-title":"Differences in the mechanism of the allosteric l-rhamnose responses of the AraC\/XylS family transcription activators RhaS and RhaR","volume":"68","author":"Kolin","year":"2008","journal-title":"Mol. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2356","DOI":"10.1128\/jb.178.8.2356-2361.1996","article-title":"Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and alpha 54-dependent tandem promoters according to the compound used for growth","volume":"178","author":"Gallegos","year":"1996","journal-title":"J. Bacteriol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"37349","DOI":"10.1074\/jbc.M203462200","article-title":"Urea-dependent signal transduction by the virulence regulator UreR","volume":"277","author":"Gendlina","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1107\/S2053230X1601298X","article-title":"1.65 A resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae","volume":"72","author":"Li","year":"2016","journal-title":"Acta Cryst. F Struct. Biol. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1073\/pnas.0915021107","article-title":"Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes","volume":"107","author":"Lowden","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1046\/j.1365-2958.2003.03531.x","article-title":"Bile salts and fatty acids induce the expression of Escherichia coli AcrAB multidrug efflux pump through their interaction with Rob regulatory protein","volume":"48","author":"Rosenberg","year":"2003","journal-title":"Mol. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/s42003-019-0686-x","article-title":"Structural basis for virulence regulation in Vibrio cholerae by unsaturated fatty acid components of bile","volume":"2","author":"Cruite","year":"2019","journal-title":"Commun. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e02170-e15","DOI":"10.1128\/mBio.02170-15","article-title":"Intestinal Long-Chain Fatty Acids Act as a Direct Signal to Modulate Expression of the Salmonella Pathogenicity Island 1 Type III Secretion System","volume":"7","author":"Golubeva","year":"2016","journal-title":"MBio"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/nar\/gkv236","article-title":"IntFOLD: An integrated server for modelling protein structures and functions from amino acid sequences","volume":"43","author":"McGuffin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1046\/j.1365-2958.2002.03066.x","article-title":"Donor strand complementation mechanism in the biogenesis of non-pilus systems","volume":"45","author":"Zavialov","year":"2002","journal-title":"Mol. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1046\/j.1365-2958.2002.02721.x","article-title":"Regulation of gene expression in Vibrio cholerae by ToxT involves both antirepression and RNA polymerase stimulation","volume":"43","author":"Yu","year":"2002","journal-title":"Mol. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.jmb.2004.05.018","article-title":"Biochemical and physiological properties of the DNA binding domain of AraC protein","volume":"340","author":"Timmes","year":"2004","journal-title":"J. Mol. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1002\/prot.22431","article-title":"Solution structure of the DNA binding domain of AraC protein","volume":"77","author":"Rodgers","year":"2009","journal-title":"Proteins"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1006\/jmbi.2001.5106","article-title":"Structure and dynamics of MarA-DNA complexes: An NMR investigation","volume":"314","author":"Dangi","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1475-2859-8-41","article-title":"Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain","volume":"8","author":"Rosano","year":"2009","journal-title":"Microb. Cell Fact."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1186\/s12934-015-0393-3","article-title":"Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway","volume":"14","author":"Dvorak","year":"2015","journal-title":"Microb. Cell Fact."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1128\/JB.183.8.2586-2594.2001","article-title":"Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid","volume":"183","author":"Prentice","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref_59","unstructured":"Kumar, D. (2016). Caf1R-Mediated Regulation of the F1 Surface Antigen of Yersinia Pestis. [Ph.D. Thesis, University of Reading]. British Library, UK (EthoS ID: 690097)."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1093\/nar\/21.7.1507","article-title":"Compilation of E. coli mRNA promoter sequences","volume":"21","author":"Lisser","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","article-title":"Genome sequence of Yersinia pestis, the causative agent of plague","volume":"413","author":"Parkhill","year":"2001","journal-title":"Nature"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Starmer, J., Stomp, A., Vouk, M., and Bitzer, D. (2006). Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput. Biol., 2.","DOI":"10.1371\/journal.pcbi.0020057"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.mib.2004.02.011","article-title":"Regulation at complex bacterial promoters: How bacteria use different promoter organizations to produce different regulatory outcomes","volume":"7","author":"Barnard","year":"2004","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1038\/s41576-020-0254-8","article-title":"Redefining fundamental concepts of transcription initiation in bacteria","volume":"21","author":"Busby","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/0378-1119(87)90095-3","article-title":"Improved single and multicopy lac-based cloning vectors for protein and operon fusions","volume":"53","author":"Simons","year":"1987","journal-title":"Gene"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"7100","DOI":"10.1128\/jb.177.24.7100-7104.1995","article-title":"Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters","volume":"177","author":"Jair","year":"1995","journal-title":"J. Bacteriol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1128\/jb.178.9.2507-2513.1996","article-title":"Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication","volume":"178","author":"Jair","year":"1996","journal-title":"J. Bacteriol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1128\/jb.184.4.1196-1199.2002","article-title":"In Vitro identification of Rns-regulated genes","volume":"184","author":"Munson","year":"2002","journal-title":"J. Bacteriol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nrmicro.2016.103","article-title":"Local and global regulation of transcription initiation in bacteria","volume":"14","author":"Browning","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1099\/mic.0.000783","article-title":"Transcription activation in bacteria: Ancient and modern","volume":"165","author":"Busby","year":"2019","journal-title":"Microbiology"},{"key":"ref_71","unstructured":"Li, R.W. (2011). Automatic Annotation of Microbial Genomes and Metagenomic Sequences. Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies 1, Nova Science."},{"key":"ref_72","first-page":"14","article-title":"Basic image analysis and manipulation in ImageJ","volume":"104","author":"Hartig","year":"2013","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.jmb.2010.08.034","article-title":"Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly","volume":"403","author":"Dubnovitsky","year":"2010","journal-title":"J. Mol. Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1111\/j.1365-2958.2007.05802.x","article-title":"EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7","volume":"65","author":"Cao","year":"2007","journal-title":"Mol. Microbiol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/18\/9805\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:00:34Z","timestamp":1760166034000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/18\/9805"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,10]]},"references-count":74,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2021,9]]}},"alternative-id":["ijms22189805"],"URL":"https:\/\/doi.org\/10.3390\/ijms22189805","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,10]]}}}