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Abstract

LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor–activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.

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2023-09-15
2024-10-13
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Literature Cited

  1. 1.
    Akakura R, Winans SC. 2002. Mutations in the occQ operator that decrease OccR-induced DNA bending do not cause constitutive promoter activity. J. Biol. Chem. 277:15773–80
    [Google Scholar]
  2. 2.
    Alanazi AM, Neidle EL, Momany C. 2013. The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators. Acta Crystallogr. D 69:1995–2007
    [Google Scholar]
  3. 3.
    Altuvia S, Weinstein-Fischer D, Zhang A, Powstow L, Storz G. 1997. A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 90:43–53
    [Google Scholar]
  4. 4.
    Ambri F, Snoek T, Skjoedt ML, Jensen MK, Keasling JD. 2018. Design, engineering, and characterization of prokaryotic ligand-binding transcriptional activators as biosensors in yeast. Methods Mol. Biol. 1671:269–90
    [Google Scholar]
  5. 5.
    Anderssen S, Naome A, Jadot C, Brans A, Tocquin P, Rigali S. 2022. AURTHO: autoregulation of transcription factors as facilitator of cis-acting element discovery. Biochim. Biophys. Acta Gene Regul. Mech. 1865:194847
    [Google Scholar]
  6. 6.
    Aslund F, Zheng M, Beckwith J, Storz G. 1999. Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol-disulfide status. PNAS 96:6161–65
    [Google Scholar]
  7. 7.
    Barnett MJ, Solow-Cordero DE, Long SR. 2019. A high-throughput system to identify inhibitors of Candidatus Liberibacter asiaticus transcription regulators. PNAS 116:18009–14
    [Google Scholar]
  8. 8.
    Bedore SR, Schmidt AL, Slarks LE, Duscent-Maitland CV, Elliott KT et al. 2022. Regulation of l- and d-aspartate transport and metabolism in Acinetobacter baylyi ADP1. Appl. Environ. Microbiol. 88:e0088322
    [Google Scholar]
  9. 9.
    Bender RA. 2010. A NAC for regulating metabolism: the nitrogen assimilation control protein (NAC) from Klebsiella pneumoniae. J. Bacteriol. 192:4801–11
    [Google Scholar]
  10. 10.
    Bentley GJ, Narayanan N, Jha RK, Salvachua D, Elmore JR et al. 2020. Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440. Metab. Eng. 59:64–75
    [Google Scholar]
  11. 11.
    Bishop RE, Weiner JH. 1993. Overproduction, solubilization, purification and DNA-binding properties of AmpR from Citrobacter freundii. Eur. J. Biochem. 213:405–12
    [Google Scholar]
  12. 12.
    Browning DF, Busby SJ. 2016. Local and global regulation of transcription initiation in bacteria. Nat. Rev. Microbiol. 14:638–50
    [Google Scholar]
  13. 13.
    Budnick JA, Sheehan LM, Ginder MJ, Failor KC, Perkowski JM et al. 2020. A central role for the transcriptional regulator VtlR in small RNA–mediated gene regulation in Agrobacterium tumefaciens. Sci. Rep. 10:14968
    [Google Scholar]
  14. 14.
    Bundy BM, Collier LS, Hoover TR, Neidle EL. 2002. Synergistic transcriptional activation by one regulatory protein in response to two metabolites. PNAS 99:7693–98
    [Google Scholar]
  15. 15.
    Byrne GA, Russell DA, Chen X, Meijer WG. 2007. Transcriptional regulation of the virR operon of the intracellular pathogen Rhodococcus equi. J. Bacteriol. 189:5082–89
    [Google Scholar]
  16. 16.
    Chen J, Boyaci H, Campbell EA. 2021. Diverse and unified mechanisms of transcription initiation in bacteria. Nat. Rev. Microbiol. 19:95–109
    [Google Scholar]
  17. 17.
    Chen J, Byun H, She Q, Liu Z, Ruggeberg KG et al. 2022. S-Nitrosylation of the virulence regulator AphB promotes Vibrio cholerae pathogenesis. PLOS Pathog. 18:e1010581
    [Google Scholar]
  18. 18.
    Chen J, Shang F, Wang L, Zou L, Bu T et al. 2018. Structural and biochemical analysis of the citrate-responsive mechanism of the regulatory domain of catabolite control protein E from Staphylococcus aureus. Biochemistry 57:6054–60
    [Google Scholar]
  19. 19.
    Chen JX, Steel H, Wu YH, Wang Y, Xu J et al. 2019. Development of aspirin-inducible biosensors in Escherichia coli and SimCells. Appl. Environ. Microbiol. 85:e02959
    [Google Scholar]
  20. 20.
    Chen K, Ke Z, Wang S, Wang S, Yang K et al. 2022. Precise regulation of differential transcriptions of various catabolic genes by OdcR via a single nucleotide mutation in the promoter ensures the safety of metabolic flux. Appl. Environ. Microbiol. 88:e0118222
    [Google Scholar]
  21. 21.
    Choi H, Kim S, Mukhopadhyay P, Cho S, Woo J et al. 2001. Structural basis of the redox switch in the OxyR transcription factor. Cell 105:103–13
    [Google Scholar]
  22. 22.
    Coco WM, Parsek MR, Chakrabarty AM. 1994. Purification of the LysR family regulator, ClcR, and its interaction with the Pseudomonas putida clcABD chlorocatechol operon promoter. J. Bacteriol. 176:5530–33
    [Google Scholar]
  23. 23.
    Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL. 2009. Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1. Mol. Microbiol. 72:881–94
    [Google Scholar]
  24. 24.
    Craven SH, Ezezika OC, Momany C, Neidle EL. 2008. LysR homologs in Acinetobacter: insights into a diverse and prevalent family of transcriptional regulators. Acinetobacter Molecular Biology U Gerischer 163–202. Norfolk, UK: Caister Acad.
    [Google Scholar]
  25. 25.
    Cress BF, Trantas EA, Ververidis F, Linhardt RJ, Koffas MA. 2015. Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways. Curr. Opin. Biotechnol. 36:205–14
    [Google Scholar]
  26. 26.
    Dangel AW, Luther A, Tabita FR. 2014. Amino acid residues of RegA important for interactions with the CbbR-DNA complex of Rhodobacter sphaeroides. J. Bacteriol. 196:3179–90
    [Google Scholar]
  27. 27.
    De Paepe B, Maertens J, Vanholme B, De Mey M. 2019. Chimeric LysR-type transcriptional biosensors for customizing ligand specificity profiles toward flavonoids. ACS Synth. Biol. 8:318–31
    [Google Scholar]
  28. 28.
    Deghmane AE, Giorgini D, Maigre L, Taha MK. 2004. Analysis in vitro and in vivo of the transcriptional regulator CrgA of Neisseria meningitidis upon contact with target cells. Mol. Microbiol. 53:917–27
    [Google Scholar]
  29. 29.
    Devesse L, Smirnova I, Lonneborg R, Kapp U, Brzezinski P et al. 2011. Crystal structures of DntR inducer binding domains in complex with salicylate offer insights into the activation of LysR-type transcriptional regulators. Mol. Microbiol. 81:354–67
    [Google Scholar]
  30. 30.
    Dickey SW, Cheung GYC, Otto M. 2017. Different drugs for bad bugs: antivirulence strategies in the age of antibiotic resistance. Nat. Rev. Drug Discov. 16:457–71
    [Google Scholar]
  31. 31.
    Dorman CJ, Schumacher MA, Bush MJ, Brennan RG, Buttner MJ. 2020. When is a transcription factor a NAP?. Curr. Opin. Microbiol. 55:26–33
    [Google Scholar]
  32. 32.
    Eisfeld J, Kraus A, Ronge C, Jagst M, Brandenburg VB, Narberhaus F. 2021. A LysR-type transcriptional regulator controls the expression of numerous small RNAs in Agrobacterium tumefaciens. Mol. Microbiol. 116:126–39
    [Google Scholar]
  33. 33.
    Ezezika OC, Haddad S, Clark TJ, Neidle EL, Momany C. 2007. Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator. J. Mol. Biol. 367:616–29
    [Google Scholar]
  34. 34.
    Ezezika OC, Haddad S, Neidle EL, Momany C. 2007. Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family. Acta Crystallogr. F 63:361–68
    [Google Scholar]
  35. 35.
    Fan C, Davison PA, Habgood R, Zeng H, Decker CM et al. 2020. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. PNAS 117:6752–61
    [Google Scholar]
  36. 36.
    Fan X, Zhao Z, Sun T, Rou W, Gui C et al. 2020. The LysR-type transcriptional regulator CrgA negatively regulates the flagellar master regulator flhDC in Ralstonia solanacearum GMI1000. J. Bacteriol. 203:e00419
    [Google Scholar]
  37. 37.
    Fernandez-López R, Ruiz R, de la Cruz F, Moncalián G. 2015. Transcription factor-based biosensors enlightened by the analyte. Front. Microbiol. 6:648
    [Google Scholar]
  38. 38.
    Floriano B, Santero E, Reyes-Ramirez F. 2019. Biodegradation of tetralin: genomics, gene function and regulation. Genes 10:339
    [Google Scholar]
  39. 39.
    Fragel SM, Montada A, Heermann R, Baumann U, Schacherl M, Schnetz K. 2019. Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli. Nucleic Acids Res. 47:7363–79
    [Google Scholar]
  40. 40.
    Fritsch PS, Urbanowski ML, Stauffer GV. 2000. Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH: important residues in the C-terminal domain and orientation requirements within RNA polymerase. J. Bacteriol. 182:5539–50
    [Google Scholar]
  41. 41.
    Gao Y, Lim HG, Verkler H, Szubin R, Quach D et al. 2021. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Res. 49:9696–710
    [Google Scholar]
  42. 42.
    Garcia-Tomsig NI, Robledo M, diCenzo GC, Mengoni A, Millan V et al. 2022. Pervasive RNA regulation of metabolism enhances the root colonization ability of nitrogen-fixing symbiotic α-rhizobia. mBio 13:e0357621
    [Google Scholar]
  43. 43.
    Gavira JA, Rico-Jiménez M, Ortega A, Petukhova NV, Bug DS et al. 2023. Emergence of an auxin sensing domain in plant-associated bacteria. mBio 14:e0336322
    [Google Scholar]
  44. 44.
    Giannopoulou EA, Senda M, Koentjoro MP, Adachi N, Ogawa N, Senda T. 2021. Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA. FEBS J. 288:4560–75
    [Google Scholar]
  45. 45.
    Gopalan-Nair R, Jardinaud MF, Legrand L, Landry D, Barlet X et al. 2021. Convergent rewiring of the virulence regulatory network promotes adaptation of Ralstonia solanacearum on resistant tomato. Mol. Biol. Evol. 38:1792–808
    [Google Scholar]
  46. 46.
    Gui Q, Lawson T, Shan S, Yan L, Liu Y. 2017. The application of whole cell–based biosensors for use in environmental analysis and in medical diagnostics. Sensors 17:1623
    [Google Scholar]
  47. 47.
    Hanko EKR, Minton NP, Malys N. 2019. Design, cloning and characterization of transcription factor–based inducible gene expression systems. Methods Enzymol. 621:153–69
    [Google Scholar]
  48. 48.
    Hanko EKR, Paiva AC, Jonczyk M, Abbott M, Minton NP, Malys N. 2020. A genome-wide approach for identification and characterisation of metabolite-inducible systems. Nat. Commun. 11:1213
    [Google Scholar]
  49. 49.
    Henikoff S, Haughn GW, Calvo JM, Wallace JC. 1988. A large family of bacterial activator proteins. PNAS 85:6602–6
    [Google Scholar]
  50. 50.
    Hernandez-Lucas I, Calva E. 2012. The coming of age of the LeuO regulator. Mol. Microbiol. 85:1026–28
    [Google Scholar]
  51. 51.
    Hong S, Kim J, Cho E, Na S, Yoo YJ et al. 2022. Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria. PNAS 119:e2118002119
    [Google Scholar]
  52. 52.
    Huang WE, Wang H, Zheng H, Huang L, Singer AC et al. 2005. Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environ. Microbiol. 7:1339–48
    [Google Scholar]
  53. 53.
    Huber M, Lippegaus A, Melamed S, Siemers M, Wucher BR et al. 2022. An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae. Nat. Commun. 13:7585
    [Google Scholar]
  54. 54.
    Ilangovan A, Fletcher M, Rampioni G, Pustelny C, Rumbaugh K et al. 2013. Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR). PLOS Pathog. 9:e1003508
    [Google Scholar]
  55. 55.
    Jang Y, Choi G, Hong S, Jo I, Ahn J et al. 2018. A novel tetrameric assembly configuration in VV2_1132, a LysR-type transcriptional regulator in Vibrio vulnificus. Mol. Cells 41:301–10
    [Google Scholar]
  56. 56.
    Javanpour AA, Liu CC. 2021. Evolving small-molecule biosensors with improved performance and reprogrammed ligand preference using OrthoRep. ACS Synth. Biol. 10:2705–14
    [Google Scholar]
  57. 57.
    Jha RK, Bingen JM, Johnson CW, Kern TL, Khanna P et al. 2018. A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution. Metab. Eng. Commun. 6:33–38
    [Google Scholar]
  58. 58.
    Jiang YL, Wang XP, Sun H, Han SJ, Li WF et al. 2018. Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR. PNAS 115:403–8
    [Google Scholar]
  59. 59.
    Jo I, Chung IY, Bae HW, Kim JS, Song S et al. 2015. Structural details of the OxyR peroxide-sensing mechanism. PNAS 112:6443–48
    [Google Scholar]
  60. 60.
    Jo I, Kim D, No T, Hong S, Ahn J et al. 2019. Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator. PNAS 116:3740–45
    [Google Scholar]
  61. 61.
    Jones RM Jr., Popham DL, Schmidt AL, Neidle EL, Stabb EV. 2018. Vibrio fischeri DarR directs responses to d-aspartate and represents a group of similar LysR-type transcriptional regulators. J. Bacteriol. 200:e00773
    [Google Scholar]
  62. 62.
    Jones RM, Pagmantidis V, Williams PA. 2000. sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in Acinetobacter sp. strain ADP1. J. Bacteriol. 182:2018–25
    [Google Scholar]
  63. 63.
    Kavita K, de Mets F, Gottesman S. 2018. New aspects of RNA-based regulation by Hfq and its partner sRNAs. Curr. Opin. Microbiol. 42:53–61
    [Google Scholar]
  64. 64.
    Ki N, Kim J, Jo I, Hyun Y, Ryu S, Ha NC 2022. Isocitrate binds to the itaconic acid–responsive LysR-type transcriptional regulator RipR in Salmonella pathogenesis. J. Biol. Chem. 298:102562
    [Google Scholar]
  65. 65.
    Kim Y, Chhor G, Tsai CS, Winans JB, Jedrzejczak R et al. 2018. Crystal structure of the ligand-binding domain of a LysR-type transcriptional regulator: transcriptional activation via a rotary switch. Mol. Microbiol. 110:550–61
    [Google Scholar]
  66. 66.
    Kitao T, Lepine F, Babloudi S, Walte F, Steinbacher S et al. 2018. Molecular insights into function and competitive inhibition of Pseudomonas aeruginosa multiple virulence factor regulator. mBio 9:02158
    [Google Scholar]
  67. 67.
    Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T. 2018. Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region. FEBS J. 285:977–89
    [Google Scholar]
  68. 68.
    Koentjoro MP, Ogawa N. 2018. Structural studies of transcriptional regulation by LysR-type transcriptional regulators in bacteria. Rev. Agric. Sci. 6:105–18
    [Google Scholar]
  69. 69.
    Kovacikova G, Lin W, Skorupski K. 2010. The LysR-type virulence activator AphB regulates the expression of genes in Vibrio cholerae in response to low pH and anaerobiosis. J. Bacteriol. 192:4181–91
    [Google Scholar]
  70. 70.
    Langer A, Moldovan A, Harmath C, Joyce SA, Clarke DJ, Heermann R. 2017. HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens. PLOS ONE 12:e0176535
    [Google Scholar]
  71. 71.
    Latorre M, Quenti D, Travisany D, Singh KV, Murray BE et al. 2018. The role of Fur in the transcriptional and iron homeostatic response of Enterococcus faecalis. Front. Microbiol. 9:1580
    [Google Scholar]
  72. 72.
    Le Guillouzer S, Groleau MC, Mauffrey F, Deziel E 2020. ScmR, a global regulator of gene expression, quorum sensing, pH homeostasis, and virulence in Burkholderia thailandensis. J. Bacteriol. 202:e00776
    [Google Scholar]
  73. 73.
    Lee H-M, Vo PN, Na D. 2018. Advancement of metabolic engineering assisted by synthetic biology. Catalysts 8:619
    [Google Scholar]
  74. 74.
    Lehnen D, Blumer C, Polen T, Wackwitz B, Wendisch VF, Unden G. 2002. LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli. Mol. Microbiol. 45:521–32
    [Google Scholar]
  75. 75.
    Lemmens L, Maklad HR, Bervoets I, Peeters E. 2019. Transcription regulators in archaea: homologies and differences with bacterial regulators. J. Mol. Biol. 431:4132–46
    [Google Scholar]
  76. 76.
    Lerche M, Dian C, Round A, Lonneborg R, Brzezinski P, Leonard GA. 2016. The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors. Sci. Rep. 6:19988
    [Google Scholar]
  77. 77.
    Liu XX, Xiong ZQ, Wang GQ, Wang LF, Xia YJ et al. 2021. LysR family regulator LttR controls conjugated linoleic acid production by directly activating the cla operon in Lactobacillus plantarum. Appl. Environ. Microbiol. 87:e02798
    [Google Scholar]
  78. 78.
    Liu Z, Yang M, Peterfreund GL, Tsou AM, Selamoglu N et al. 2011. Vibrio cholerae anaerobic induction of virulence gene expression is controlled by thiol-based switches of virulence regulator AphB. PNAS 108:810–15
    [Google Scholar]
  79. 79.
    Lochowska A, Iwanicka-Nowicka R, Zaim J, Witkowska-Zimny M, Bolewska K, Hryniewicz MM. 2004. Identification of activating region (AR) of Escherichia coli LysR-type transcription factor CysB and CysB contact site on RNA polymerase α subunit at the cysP promoter. Mol. Microbiol. 53:791–806
    [Google Scholar]
  80. 80.
    Maddocks SE, Oyston PC. 2008. Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609–23
    [Google Scholar]
  81. 81.
    Mandal RS, Ta A, Sinha R, Theeya N, Ghosh A et al. 2016. Ribavirin suppresses bacterial virulence by targeting LysR-type transcriptional regulators. Sci. Rep. 6:39454
    [Google Scholar]
  82. 82.
    Mao D, Bushin LB, Moon K, Wu Y, Seyedsayamdost MR. 2017. Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264. PNAS 114:E2920–28
    [Google Scholar]
  83. 83.
    Matilla MA, Velando F, Martin-Mora D, Monteagudo-Cascales E, Krell T. 2022. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol. Rev. 46:fuab043
    [Google Scholar]
  84. 84.
    Maura D, Drees SL, Bandyopadhaya A, Kitao T, Negri M et al. 2017. Polypharmacology approaches against the Pseudomonas aeruginosa MvfR regulon and their application in blocking virulence and antibiotic tolerance. ACS Chem. Biol. 12:1435–43
    [Google Scholar]
  85. 85.
    Maxon ME, Wigboldus J, Brot N, Weissbach H. 1990. Structure-function studies on Escherichia coli MetR protein, a putative prokaryotic leucine zipper protein. PNAS 87:7076–79
    [Google Scholar]
  86. 86.
    McFall SM, Chugani SA, Chakrabarty AM. 1998. Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 223:257–67
    [Google Scholar]
  87. 87.
    Mittal M, Singh AK, Kumaran S. 2017. Structural and biochemical characterization of ligand recognition by CysB, the master regulator of sulfate metabolism. Biochimie 142:112–24
    [Google Scholar]
  88. 88.
    Modrzejewska M, Kawalek A, Bartosik AA. 2021. The LysR-type transcriptional regulator BsrA (PA2121) controls vital metabolic pathways in Pseudomonas aeruginosa. mSystems 6:e0001521
    [Google Scholar]
  89. 89.
    Momany C, Neidle EL. 2012. Defying stereotypes: the elusive search for a universal model of LysR-type regulation. Mol. Microbiol. 83:453–56
    [Google Scholar]
  90. 90.
    Monferrer D, Tralau T, Kertesz MA, Dix I, Sola M, Uson I. 2010. Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold. Mol. Microbiol. 75:1199–214
    [Google Scholar]
  91. 91.
    Muraoka S, Okumura R, Ogawa N, Nonaka T, Miyashita K, Senda T. 2003. Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol. 328:555–66
    [Google Scholar]
  92. 92.
    Nandineni MR, Gowrishankar J. 2004. Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli. J. Bacteriol. 186:3539–46
    [Google Scholar]
  93. 93.
    Nguyen LMP, Velazquez Ruiz C, Vandermeeren S, Abwoyo P, Bervoets I, Charlier D. 2018. Differential protein–DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli. Microbiol. Res. 206:141–58
    [Google Scholar]
  94. 94.
    Oliver P, Peralta-Gil M, Tabche ML, Merino E 2016. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model. BMC Genom. 17:686
    [Google Scholar]
  95. 95.
    Pardo I, Jha RK, Bermel RE, Bratti F, Gaddis M et al. 2020. Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1. Metab. Eng. 62:260–74
    [Google Scholar]
  96. 96.
    Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R. 2006. ExtraTrain: a database of extragenic regions and transcriptional information in prokaryotic organisms. BMC Microbiol. 6:29
    [Google Scholar]
  97. 97.
    Parsek MR, Shinabarger DL, Rothmel RK, Chakrabarty AM. 1992. Roles of CatR and cis,cis-muconate in activation of the catBC operon, which is involved in benzoate degradation in Pseudomonas putida. J. Bacteriol. 174:7798–806
    [Google Scholar]
  98. 98.
    Pedre B, Young D, Charlier D, Mourenza A, Rosado LA et al. 2018. Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2 sensing. PNAS 115:E11623–32
    [Google Scholar]
  99. 99.
    Perez-Rueda E, Hernandez-Guerrero R, Martinez-Nunez MA, Armenta-Medina D, Sanchez I, Ibarra JA. 2018. Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. PLOS ONE 13:e0195332
    [Google Scholar]
  100. 100.
    Perrier A, Barlet X, Peyraud R, Rengel D, Guidot A, Genin S. 2018. Comparative transcriptomic studies identify specific expression patterns of virulence factors under the control of the master regulator PhcA in the Ralstonia solanacearum species complex. Microb. Pathog. 116:273–78
    [Google Scholar]
  101. 101.
    Platero AI, López-Sánchez A, Tomás-Gallardo L, Santero E, Govantes F. 2016. Mechanism of antiactivation at the Pseudomonas sp. strain ADP σN-dependent PatzT promoter. Appl. Environ. Microbiol. 82:4350–62
    [Google Scholar]
  102. 102.
    Prezioso SM, Xue K, Leung N, Gray-Owen SD, Christendat D. 2018. Shikimate induced transcriptional activation of protocatechuate biosynthesis genes by QuiR, a LysR-type transcriptional regulator, in Listeria monocytogenes. J. Mol. Biol. 430:1265–83
    [Google Scholar]
  103. 103.
    Pu W, Chen J, Liu P, Shen J, Cai N et al. 2023. Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors. Biosens. Bioelectron. 222:115004
    [Google Scholar]
  104. 104.
    Reen FJ, Haynes JM, Mooij MJ, O'Gara F. 2013. A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa. PLOS ONE 8:e54479
    [Google Scholar]
  105. 105.
    Rodionov DA. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467–97
    [Google Scholar]
  106. 106.
    Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N et al. 2022. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Sci. Rep. 12:7274
    [Google Scholar]
  107. 107.
    Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG et al. 2021. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. Commun. Biol. 4:991
    [Google Scholar]
  108. 108.
    Rosenfeld N, Elowitz MB, Alon U. 2002. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323:785–93
    [Google Scholar]
  109. 109.
    Ruangprasert A, Craven SH, Neidle EL, Momany C. 2010. Full-length structures of BenM and two variants reveal different oligomerization schemes for LysR-type transcriptional regulators. J. Mol. Biol. 404:568–86
    [Google Scholar]
  110. 110.
    Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO. 2021. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res. 49:D112–20
    [Google Scholar]
  111. 111.
    Sainsbury S, Lane LA, Ren J, Gilbert RJ, Saunders NJ et al. 2009. The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators. Nucleic Acids Res. 37:4545–58
    [Google Scholar]
  112. 112.
    Sainsbury S, Ren J, Nettleship JE, Saunders NJ, Stuart DI, Owens RJ. 2010. The structure of a reduced form of OxyR from Neisseria meningitidis. BMC Struct. Biol. 10:10
    [Google Scholar]
  113. 113.
    Sanchez-Popoca D, Serrano-Fujarte I, Fernandez-Mora M, Calva E. 2022. The LeuO regulator and quiescence: about transcriptional roadblocks, multiple promoters, and CRISPR-Cas. Mol. Microbiol. 118:503–9
    [Google Scholar]
  114. 114.
    Schell MA. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597–626
    [Google Scholar]
  115. 115.
    Shin SM, Jha RK, Dale T. 2022. Tackling the Catch-22 situation of optimizing a sensor and a transporter system in a whole-cell microbial biosensor design for an anthropogenic small molecule. ACS Synth. Biol. 11:3996–4008
    [Google Scholar]
  116. 116.
    Singh VK, Almpani M, Maura D, Kitao T, Ferrari L et al. 2022. Tackling recalcitrant Pseudomonas aeruginosa infections in critical illness via anti-virulence monotherapy. Nat. Commun. 13:5103
    [Google Scholar]
  117. 117.
    Skjoedt ML, Snoek T, Kildegaard KR, Arsovska D, Eichenberger M et al. 2016. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat. Chem. Biol. 12:951–58
    [Google Scholar]
  118. 118.
    Smirnova IA, Dian C, Leonard GA, McSweeney S, Birse D, Brzezinski P. 2004. Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR. J. Mol. Biol. 340:405–18
    [Google Scholar]
  119. 119.
    Snoek T, Chaberski EK, Ambri F, Kol S, Bjorn SP et al. 2020. Evolution-guided engineering of small-molecule biosensors. Nucleic Acids Res. 48:e3
    [Google Scholar]
  120. 120.
    Stauffer LT, Stauffer GV. 2005. GcvA interacts with both the α and σ subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon. FEMS Microbiol. Lett. 242:333–38
    [Google Scholar]
  121. 121.
    Stoudenmire JL, Schmidt AL, Tumen-Velasquez MP, Elliott KT, Laniohan NS et al. 2017. Malonate degradation in Acinetobacter baylyi ADP1: operon organization and regulation by MdcR. Microbiology 163:789–803
    [Google Scholar]
  122. 122.
    Taylor JL, De Silva RS, Kovacikova G, Lin W, Taylor RK et al. 2012. The crystal structure of AphB, a virulence gene activator from Vibrio cholerae, reveals residues that influence its response to oxygen and pH. Mol. Microbiol. 83:457–70
    [Google Scholar]
  123. 123.
    Tierney ARP, Chin CY, Weiss DS, Rather PN. 2021. A LysR-type transcriptional regulator controls multiple phenotypes in Acinetobacter baumannii. Front. Cell Infect. Microbiol. 11:778331
    [Google Scholar]
  124. 124.
    Tropel D, van der Meer JR. 2004. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68:474–500
    [Google Scholar]
  125. 125.
    Tumen-Velasquez MP, Laniohan NS, Momany C, Neidle EL. 2019. Engineering CatM, a LysR-type transcriptional regulator, to respond synergistically to two effectors. Genes 10:421
    [Google Scholar]
  126. 126.
    Tyrrell R, Verschueren KH, Dodson EJ, Murshudov GN, Addy C, Wilkinson AJ. 1997. The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement. Structure 5:1017–32
    [Google Scholar]
  127. 127.
    van Keulen G, Girbal L, van den Bergh ER, Dijkhuizen L, Meijer WG. 1998. The LysR-type transcriptional regulator CbbR controlling autotrophic CO2 fixation by Xanthobacter flavus is an NADPH sensor. J. Bacteriol. 180:1411–17
    [Google Scholar]
  128. 128.
    Vieira TF, Magalhães RP, Simões M, Sousa SF. 2022. Drug repurposing targeting Pseudomonas aeruginosa MvfR using docking, virtual screening, molecular dynamics, and free-energy calculations. Antibiotics 11:185
    [Google Scholar]
  129. 129.
    Wang T, Sun W, Fan L, Hua C, Wu N et al. 2021. An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence. eLife 10:e61885
    [Google Scholar]
  130. 130.
    Wang W, Wu H, Xiao Q, Zhou H, Li M et al. 2021. Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism. Int. J. Biol. Macromol. 183:2354–63
    [Google Scholar]
  131. 131.
    Wang Z, Huang X, Nie C, Xiang T, Zhang X. 2022. The Lon protease negatively regulates pyoluteorin biosynthesis through the Gac/Rsm-RsmE cascade and directly degrades the transcriptional activator PltR in Pseudomonas protegens H78. Environ. Microbiol. Rep. 14:506–19
    [Google Scholar]
  132. 132.
    Xu N, Yu S, Moniot S, Weyand M, Blankenfeldt W. 2012. Crystallization and preliminary crystal structure analysis of the ligand-binding domain of PqsR (MvfR), the Pseudomonas quinolone signal (PQS) responsive quorum-sensing transcription factor of Pseudomonas aeruginosa. Acta Crystallogr. F 68:1034–39
    [Google Scholar]
  133. 133.
    Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE. 2016. The rare codon AGA is involved in regulation of pyoluteorin biosynthesis in Pseudomonas protegens Pf-5. Front. Microbiol. 7:497
    [Google Scholar]
  134. 134.
    Yang Y, Lin Y, Wang J, Wu Y, Zhang R et al. 2018. Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis. Nat. Commun. 9:3043
    [Google Scholar]
  135. 135.
    Yilmaz C, Schnetz K. 2022. High abundance of transcription regulators compacts the nucleoid in Escherichia coli. J. Bacteriol. 204:e0002622
    [Google Scholar]
  136. 136.
    Yuan X, Zeng Q, Khokhani D, Tian F, Severin GB et al. 2019. A feed-forward signalling circuit controls bacterial virulence through linking cyclic di-GMP and two mechanistically distinct sRNAs, ArcZ and RsmB. Environ. Microbiol. 21:2755–71
    [Google Scholar]
  137. 137.
    Zender M, Witzgall F, Kiefer A, Kirsch B, Maurer CK et al. 2020. Flexible fragment growing boosts potency of quorum-sensing inhibitors against Pseudomonas aeruginosa virulence. ChemMedChem 15:188–94
    [Google Scholar]
  138. 138.
    Zheng M, Storz G. 2000. Redox sensing by prokaryotic transcription factors. Biochem. Pharmacol. 59:1–6
    [Google Scholar]
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