Table 1. Overview of the Currently Characterized LysR-type Transcriptional Regulators and the Different Elements Required for Converting Them into Transcription Factor-Based Biosensorsa.
| identifier | origin | biological relevance | target ligand | regulatory target | reference |
|---|---|---|---|---|---|
| AalR | Acinetobacter baylyi ADP1 | aspartate metabolism | l-aspartate | PaspA, PaspT, PaspY, PracD | (81) |
| AceR | Acinetobacter baumannii | multidrug efflux pump regulation | chlorhexidine | PaceI | (82, 83) |
| AdmX | Serratia plymuthica A153 | antibiotic synthesis regulation | indole-3-acetic acid | PadmV (operon) | (84−86) |
| AllS | Escherichia coli | anaerobic allantoin metabolism | allantoin | PallD | (87−89) |
| AlsR | Bacillus subtilis | acetoin synthesis | acetate | PalsS | (73, 90−92) |
| AmpR | Citrobacter freundii | β-lactamase synthesis | 1,6-anhydro-MurNAc-peptides | PampC | (73, 93−98) |
| AphB | Vibrio cholerae | virulence | unknown | PtcpPH | (99−103) |
| AphT | Comamonas testosteroni TA441 | aromatic compound degradation | 2-hydroxymuconic semialdehyde | PaphCEFGHJI | (104) |
| ArgP | Escherichia coli | arginine transport | arginine | PargK | (105−107) |
| AtzR | Pseudomonas spp. | cyanuric acid catabolism | cyanuric acid | PatzDEF | (25, 108, 109) |
| BauR | Pseudomonas aeruginosa | polyamine utilization | β-alanine | PbauABCD | (110) |
| BenM | Acinetobacter spp. | aromatic compound degradation | cis,cis-muconate or benzoate | PbenABCDE, PbenPK | (111−118) |
| BlaA | Streptomyces spp. | β-lactamase synthesis | β-lactam compounds | PblaL | (119) |
| CatM | Acinetobacter calcolaceticus | catechol catabolism | cis,cis-muconate | PcatBCIJFD, PcatA, PbenPK | (71, 112, 120, 121) |
| CatR | Pseudomonas putida | catechol catabolism | cis,cis-muconate | PcatBCA, PpheBA | (71, 122−126) |
| CbbR | Xanthobacter flavus | carbon dioxide fixing | ribulose 1,5-bisphosphate | PcbbLSXFPTAE | (74, 127, 128) |
| Cbl | Escherichia coli | sulfur acquisition and reduction | thiosulfate | PcysP, PcysT, PtauABCD, PssuEADCB | (129−131) |
| CbnR | Ralstonia spp. | chlorocatechol catabolism | 2-chloro-cis,cis-muconate | PcbnABCD | (17, 71, 132−134) |
| CcpC | Bacillus subtilis | carbon catabolite control | citrate | PcitB, PcitZ | (135, 136) |
| CcpE | Staphylococcus aureus | carbon catabolite control | unknown | PcitE | (30, 137) |
| CfxR | Alcaligenes eutrophus | carbon dioxide fixing | unknown | PcfxLSXYEFP | (138) |
| ChiR | Serratia marcescens | chitin degradation | unknown | PCBP21 | (139) |
| CidR | Staphylococcus aureus | murein hydrolase regulation | acetic acid | PcidABC | (140) |
| CitR | Bacillus subtilis | citrate metabolism | unknown | PcitA | (141) |
| ClcR | Pseudomonas putida | chlorocatechol catabolism | 2-chloro-cis,cis-Muconate | PclcABD | (71, 123, 142, 143) |
| CmpR | Synechococcus elongatus | CO2 fixing | ribulose 1,5-bisphosphate | PcmpABCD | (144−146) |
| CrgA | Neisseria meningitidis | pili/capsule synthesis and oxidative stress response | α-methylene-γ-butyrolactone | PmdaB | (147−149) |
| CynR | Escherichia coli | cyanate detoxification | cyanate | PcynTSX | (150) |
| CysB | Salmonella enterica serovar Typhimurium | cysteine biosynthesis | N-Acetylserine | PcysI | (130, 151−155) |
| CysL | Bacillus subtilis | sulphite reductase | sulfate, sulfite, thiosulfate | PcysJI | (156) |
| DarR | Acinetobacter baylyi ADP1 | aspartate metabolism | d-aspartate | PaspA, PaspT, PaspY, PracD | (157) |
| DbdR | Thauera aromatica AR-1 | aromatic compound degradation | 3,5-dihydroxybenzoate | PdbhL | (158) |
| DntR | Burkholeria spp. | aromatic compound degradation | 2,4-dinitrotoluene, salicylate | PdntA | (50, 159−161) |
| FdeR | Herbaspirillum seropedicae | aromatic compound degradation | naringenin | PfdeA | (162, 163) |
| FinR | Pseudomonas putida | ferredoxin-NADP+ reductase regulation | oxidative and osmotic stresses | Pfpr | (164) |
| GcvA | Escherichia coli | glycine metabolism | glycine and adenine | PgcvTHP, PgcvB | (165, 166) |
| GigC | Acinetobacter baumannii | cysteine metabolism and virulence | l-cysteine | PcysI | (167) |
| GltC | Bacillus subtilis | glutamate synthase | α-ketoglutarate | PgltA | (168−170) |
| HexA | Photorhabdus luminescens | phenotypic heterogeneity, pathogen–symbiont transition | unknown | PpcfABCDEF | (171) |
| HsdR | Comamonas testosteroni | aromatic compound degradation | testosterone | PhsdA | (172, 173) |
| HupR | Vibrio vulnificus | haem uptake | haemin | PhupA | (174) |
| HvrB | Rhodobacter capsulatus | S-adenosyl-l-homocysteine hydrolase expression | light sensitivity | PahcY | (175) |
| HypT | Salmonella enterica serovar Typhimurium | HOCl response | HOCl | PfhuA | (176) |
| IlvR | Caulobacter crescentus | isoleucine/valine biosynthesis | unknown | PilvD | (177) |
| IlvY | Escherichia coli | isoleucine/valine biosynthesis | α-acetolactate, α-acetohydroxy-butyrate | PilvC | (178) |
| IrgB | Vibrio cholerae | iron-regulated virulence factor | unknown | PirgA | (179) |
| KaeR | Lactobacillus brevis | flavonoid response | kaempferol | PLVIS1988 | (180) |
| LeuO | Salmonella enterica serovar Typhimurium | bacterial stringent response | unknown | PompS1, PompS2, PassT | (70, 181−183) |
| LinR | Sphingomonas spp. | aromatic compound degradation | 2,5-dichlorohydroquinone, 2,6-dichlorohydroquinone, chlorohydroquinone | PlinE | (71, 184, 185) |
| LrhA | Escherichia coli | flagella, motility and chemotaxis | unknown | PflhDC | (186) |
| LttR | Lactobacillus plantarum | conjugated linoleic acid production | linoleic acids | Pcla-dh (operon) | (187) |
| LysG | Corynebacterium glutamicum | amino acid export | l-lysine and other amino acids | PlysE | (188, 189) |
| LysR | Escherichia coli | lysine biosynthesis | diaminopimelate | PlysA | (55) |
| MdcR | Klebsiella pneumoniae | malonate catabolism | malonate | PmdcABCDEGHLM | (190, 191) |
| MetR | Streptococcus spp. | methionine and cysteine transport/biosynthesis | homocysteine | PmetE | (192−198) |
| MleR | Streptococcus mutans | malolactic fermentation | l-malate | PmleSP | (199) |
| MvfR (= PqsR) | Pseudomonas aeruginosa | pathogenicity regulator | 4-hydroxy-2-heptylquinone | PpqsA | (200−205) |
| NagR | Ralstonia eutropha | naphthalene catabolism | salicylate | PnagA | (206, 207) |
| NahR | Pseudomonas putida | naphthalene/salicylate catabolism | salicylate | PnahABCFDE, PsalGHINL | (208−210) |
| NdhR (= CcmR) | Synechocystis spp. | CO2-concentrating mechanism | 2-phosphoglycolate, 2-oxoglutarate | Pndh3 (operon) | (72, 211) |
| NhaR | Escherichia coli | Na+/H+ antiporter regulation | Na+ | PnhaA | (212) |
| NocR | Agrobacterium tumefaciens | nopaline catabolism | octopine | PnocPTQM | (213) |
| NodD | Rhizobium spp. | nitrogen fixation/symbiosis | flavonoids | PnodABCIJ, PnodFEL, PnodMNT, PnodO | (78, 214−217) |
| NtdR | Acidovorax spp. | aromatic compound degradation | 2,4-dinitrotoluene, 2,6-dinitrotoluene, salicylate, anthranilate | PntdA | (71) |
| OccR | Agrobacterium tumefaciens | octopine catabolism | octopine | PoccQMPT | (218−222) |
| OdcR | Pigmentiphaga spp. | 3,5-dibromo-4-hydroxybenozate catabolism | 3-bromo-4-hydroxybenzoate, 3,5-dibromo-4-hydroxybenozate | PodcA, PodcB, PodcC | (223) |
| OxyR | Escherichia coli | oxidative stress response | redox changes | PkatG, PaphCF, PoxyS, PgorA, PgrxA | (224−231) |
| PA2206 | Pseudomonas aeruginosa | oxidative stress response | redox changes | PpvdS | (232) |
| PcaQ | Agrobacterium spp. | protocatechuate catabolism | β-carboxy-cis,cis-muconate, γ-carboxymuconate | PpcaDCHGB | (71) |
| PecT | Dickeya dadantii | virulence | temperature changes | PpelB, PpelC, PpelD, PpelE | (233, 234) |
| PhcA | Pseudomonas solanacearum | virulence | unknown | PT3SS | (235, 236) |
| PltR | Pseudomonas protegens | pyoluteorin synthesis | pyoluteorin | PpltLABCDEFG | (237, 238) |
| QuiR | Listeria monocytogenes | protocatechuate biosynthesis | shikimate | Plmo0489 (operon) | (239) |
| RbcR | Chromatium vinosum | carbon dioxide fixing | unknown | PrbcAB | (240) |
| RipR | Salmonella enterica | itaconic acid resistance | isocitrate | PripCBA | (241,242) |
| RovM | Yersinia pseudotuberculosis | invasion/motility, virulence | unknown | ProvA | (243, 244) |
| S cmR | Burkholderia thailandensis | secundary metabolism regulation | unknown | Phmq (operon) | (68, 69) |
| SpvR | Salmonella typhimurium | virulence | unknown | PspvABCD | (245, 246) |
| SyrM | Rhizobium meliloti | exopolysaccharide synthesis | unknown | PsyrA | (247) |
| TcbR | Pseudomonas spp. | chlorocatechol metabolism | 2-chloro-cis,cis-muconate | PtcbCDEF | (71, 248) |
| TfdR | Ralstonia spp. | chlorophenol catabolism | 2-chloro-cis,cis-muconate | PtfdCDEFB, PtfdA | (71) |
| TfdT | Burkholderia spp. | aromatic compound degradation | 3-chlorocatechol, 4-chlorocatechol, 2-chlorobenzoate, 3-chlorobenzoate | PtfdC | (71) |
| ThnR | Sphingopyxis granuli | aromatic compound degradation | tetralin | PthnB, PthnC | (249, 250) |
| ToxR | Burkholderia glumae | toxoflavin biosynthesis | toxoflavin | PtoxABCDE, PtoxFGHI | (251) |
| TsaR | Comamonas testosteroni | aromatic compound degradation | p-tolunesulfonate | PtsaMBCD | (252−254) |
| TtuA | Agrobacterium vitis | tartrate metabolism | l-tartrate | PttuB | (255) |
| VirR | Rhodococcus equi | virulence | unknown | Porf5 (virR operon) | (190) |
| VqsA | Vibrio alginolyticus | virulence | unknown | PaphA, PluxR | (256) |
| VtlR (= LsrB) | Agrobacterium tumefaciens | regulation of motility and biofilm formation | unknown | PabcR2 | (257−259) |
| YbeF | Escherichia coli | flagella biosynthesis, putative citrate utilization related 2 | unknown | unknown | (260) |
| YbdO | Escherichia coli | citrate utilization related, flagella biosynthesis | unknown | PybdO | (260) |
| YbhD | Escherichia coli | l-malate utilization related | unknown | PybhH, PybhI | (260) |
| YcaN | Escherichia coli | unknown | unknown | PycaC, PycaD | (260) |
| YeiE | Cronobacter sakazakii | sulfite resistance | sulfite | PcysJI | (261) |
| YgfI | Escherichia coli | dihydroxyacetone, glycerol or Thr utilization | unknown | PdhaK PyjiT, PpflB, PadhE, PhycBCDEF, PnarZ | (260) |
| YiaU | Escherichia coli | membrane modification and LPS biosynthesis | unknown | PwaaPSBOJYZU PyjiT, PadeP, PyiaT, PgltD | (260) |
| YneJ | Escherichia coli | putrescine utilization related | unknown | Psad,PfnrS | (260) |
| YofA | Bacillus subtilis | cell division | unknown | PftsW | (79) |
| YtxR | Yersinia entercolitica | ADP-ribosyl-transferase toxin | unknown | PytxAB | (262) |
a
For each regulator, the organism of origin is given, as well as the biological context in which it is active. When available, a ligand recognized by the regulator is provided, as well as target promoters. As these transcription factors often function as global regulators, the “regulatory target” column does not represent all target promoters.