Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum

Unleashing potential of Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 for chlorpyrifos biodegradation by genome analysis and kinetic studies

Chlorpyrifos (CP) is an extensively used organophosphate (OP) pesticide that inhibits the biogeochemical cycle with subsequent loss of soil fertility. In this view, indigenous soil bacteria with significant CP degradation capacity were identified as Pseudomonas aeruginosa RNC3 and Stenotrophomonas maltophilia RNC7 through 16 S rRNA. The optimum values of independent variables for CP degradation were found to be 30 ℃, pH 7, 100 mgL-1 of CP, and 1 OD600 cell culture. RNC3 and RNC7 showed 82.5 mgL-1 and 77.1 mgL-1 CP degradation within 5 days. A Michaelis-Menten kinetic model estimated the degradation rate (Vmax) and substrate binding affinity (Ks) for RNC3 were 1.23 mgL-1h-1 and 123 mgL-1 whereas for RNC7 as 1.19 mgL-1h -1 and 124.3 mgL-1, respectively. The major metabolites 3,5,6-trichloro-2-pyridinol (TCP) and 2-hydroxy pyridine were identified during CP degradation by RNC3 whereas, only TCP by RNC7 using GC-MS. Key enzymes encoded by opd and opch2 genes were annotated in the genomes of RNC3 and RNC7 along with the set of putative degradation genes (tcp, yieH, pho, prp). Protein-ligand docking between OPCH2 and CP found - 7.9 kcal mol -1 as a high binding affinity with the conserved catalytic triad (Ser155-Asp251-His281) in the active site. The study suggests that RNC3 can completely mineralize CP, whereas both strains have shown robust degradation ability of OP group of pesticides. The potential of rapid acclimatization to natural soil environment and non-virulent nature of the selected strains are beneficial for in situ application. Thus, selected indigenous strains can be applied for the bioremediation of OP-contaminated soil.

Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B

The dehaloperoxidase-hemoglobin (DHP), first isolated from the coelom of a marine terebellid polychaete, Amphitrite ornata, is an example of a multi-functional heme enzyme. Long known for its reversible oxygen (O2) binding, further studies have established DHP activity as a peroxidase, oxidase, oxygenase, and peroxygenase. The specific reactivity depends on substrate binding at various internal and external binding sites. This study focuses on comparison of the binding and reactivity of the substrate 2,4-dichlorophenol (DCP) in the isoforms DHPA and B. There is strong interest in the degradation of DCP because of its wide use in the chemical industry, presence in waste streams, and particular reactivity to form dioxins, some of the most toxic compounds known. The catalytic efficiency is 3.5 times higher for DCP oxidation in DHPB than DHPA by a peroxidase mechanism. However, DHPA and B both show self-inhibition even at modest concentrations of DCP. This phenomenon is analogous to the self-inhibition of 2,4,6-trichlorophenol (TCP) at higher concentration. The activation energies of the electron transfer steps in DCP in DHPA and DHPB are 19.3 ± 2.5 and 24.3 ± 3.2 kJ/mol, respectively, compared to 37.2 ± 6.5 kJ/mol in horseradish peroxidase (HRP), which may be a result of the more facile electron transfer of an internally bound substrate in DHPA. The x-ray crystal structure of DHPA bound with DCP determined at 1.48 Å resolution, shows tight substrate binding inside the heme pocket of DHPA (PDB 8EJN). This research contributes to the studies of DHP as a naturally occurring bioremediation enzyme capable of oxidizing a wide range of environmental pollutants.

LysR-type transcriptional regulators: state of the art

The LysR-type transcriptional regulators (LTTRs) are DNA-binding proteins present in bacteria, archaea, and in algae. Knowledge about their distribution, abundance, evolution, structural organization, transcriptional regulation, fundamental roles in free life, pathogenesis, and bacteria-plant interaction has been generated. This review focuses on these aspects and provides a current picture of LTTR biology.

The Operon Encoding Hydrolytic Dehalogenation of 4-Chlorobenzoate Is Transcriptionally Regulated by the TetR-Type Repressor FcbR and Its Ligand 4-Chlorobenzoyl Coenzyme A

The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a coenzyme A (CoA)-activation-type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and inducibly expressed in response to 4CBA. However, the associated molecular mechanism remains unknown. In this study, a gene (fcbR) adjacent to the fcb operon was predicted to encode a TetR-type transcriptional regulator in Comamonas sediminis strain CD-2. The fcbR knockout strain exhibited constitutive expression of the fcb cluster. In the host Escherichia coli, the expression of the P_fcb -fused green fluorescent protein (gfp) reporter was repressed by the introduction of the fcbR gene, and genetic studies combining various catabolic genes suggest that the ligand for FcbR may be an intermediate metabolite. Purified FcbR could bind to the P_fcb DNA probe in vitro, and the metabolite 4-chlorobenzyl-CoA (4CBA-CoA) prevented FcbR binding to the P _fcb DNA probe. Isothermal titration calorimetry (ITC) measurements showed that 4CBA-CoA could bind to FcbR at a 1:1 molar ratio. DNase I footprinting showed that FcbR protected a 42-bp DNA motif (5'-GGAAATCAATAGGTCCATAGAAAATCTATTGACTAATCGAAT-3') that consists of two sequence repeats containing four pseudopalindromic sequences (5'-TCNATNGA-3'). This binding motif overlaps with the -35 box of P_fcb and was proposed to prevent the binding of RNA polymerase. This study characterizes a transcriptional repressor of the fcb operon, together with its ligand, thus identifying halogenated benzoyl-CoA as belonging to the class of ligands of transcriptional regulators.IMPORTANCE The bacterial hydrolytic dehalogenation of 4CBA is a special CoA-activation-type catabolic pathway that plays an important role in the biodegradation of polychlorinated biphenyls and some herbicides. With genetic and biochemical approaches, the present study identified the transcriptional repressor and its cognate effector of a 4CBA hydrolytic dehalogenation operon. This work extends halogenated benzoyl-CoA as a new member of CoA-derived effector compounds that mediate allosteric regulation of transcriptional regulators.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Assembly and regulation of the chlorhexidine-specific efflux pump AceI

Acinetobacter baumannii has become challenging to treat due to its multidrug resistance mediated by active drug efflux pumps. The prototype member of the proteobacterial antimicrobial compound efflux (PACE) family, AceI of A. baumannii, is implicated in the transport of widely used antiseptic chlorhexidine, while AceR is associated with regulating the expression of the aceI gene. Here we apply native mass spectrometry to show that AceI forms dimers at high pH, and that chlorhexidine binding facilitates the functional form of the protein. Also, we demonstrate how AceR affects the interaction between RNA polymerase and promoter DNA both in the presence and in the absence of chlorhexidine. Overall, these results provide insight into the assembly and regulation of the PACE family.

Few antibiotics are effective against Acinetobacter baumannii, one of the most successful pathogens responsible for hospital-acquired infections. Resistance to chlorhexidine, an antiseptic widely used to combat A. baumannii, is effected through the proteobacterial antimicrobial compound efflux (PACE) family. The prototype membrane protein of this family, AceI (Acinetobacter chlorhexidine efflux protein I), is encoded for by the aceI gene and is under the transcriptional control of AceR (Acinetobacter chlorhexidine efflux protein regulator), a LysR-type transcriptional regulator (LTTR) protein. Here we use native mass spectrometry to probe the response of AceI and AceR to chlorhexidine assault. Specifically, we show that AceI forms dimers at high pH, and that binding to chlorhexidine facilitates the functional form of the protein. Changes in the oligomerization of AceR to enable interaction between RNA polymerase and promoter DNA were also observed following chlorhexidine assault. Taken together, these results provide insight into the assembly of PACE family transporters and their regulation via LTTR proteins on drug recognition and suggest potential routes for intervention.

Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii

Objectives

To investigate the function of AceR, a putative transcriptional regulator of the chlorhexidine efflux pump gene aceI in Acinetobacter baumannii.

Methods

Chlorhexidine susceptibility and chlorhexidine induction of aceI gene expression were determined by MIC and quantitative real-time PCR, respectively, in A. baumannii WT and ΔaceR mutant strains. Recombinant AceR was prepared as both a full-length protein and as a truncated protein, AceR (86–299), i.e. AceRt, which has the DNA-binding domain deleted. The binding interaction of the purified AceR protein and its putative operator region was investigated by electrophoretic mobility shift assays and DNase I footprinting assays. The binding of AceRt with its putative ligand chlorhexidine was examined using surface plasmon resonance and tryptophan fluorescence quenching assays.

Results

MIC determination assays indicated that the ΔaceI and ΔaceR mutant strains both showed lower resistance to chlorhexidine than the parental strain. Chlorhexidine-induced expression of aceI was abolished in a ΔaceR background. Electrophoretic mobility shift assays and DNase I footprinting assays demonstrated chlorhexidine-stimulated binding of AceR with two sites upstream of the putative aceI promoter. Surface plasmon resonance and tryptophan fluorescence quenching assays suggested that the purified ligand-binding domain of the AceR protein was able to bind with chlorhexidine with high affinity.

Conclusions

This study provides strong evidence that AceR is an activator of aceI gene expression when challenged with chlorhexidine. This study is the first characterization, to our knowledge, of a regulator controlling expression of a PACE family multidrug efflux pump.

The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants

The multifunctional catalytic hemoglobin dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata was found to catalyze the H₂O₂-dependent oxidation of EPA Priority Pollutants (4-Me-o-cresol, 4-Cl-m-cresol and pentachlorophenol) and EPA Toxic Substances Control Act compounds (o-, m-, p-cresol and 4-Cl-o-cresol). Biochemical assays (HPLC/LC-MS) indicated formation of multiple oxidation products, including the corresponding catechol, 2-methylbenzoquinone (2-MeBq), and oligomers with varying degrees of oxidation and/or dehalogenation. Using 4-Br-o-cresol as a representative substrate, labeling studies with ¹⁸O confirmed that the O-atom incorporated into the catechol was derived exclusively from H₂O₂, whereas the O-atom incorporated into 2-MeBq was from H₂O, consistent with this single substrate being oxidized by both peroxygenase and peroxidase mechanisms, respectively. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the peroxygenase mechanism leading to catechol formation, and for Compounds I and ES in the peroxidase mechanism that yields the 2-MeBq product. The X-ray crystal structures of DHP bound with 4-F-o-cresol (1.42 Å; PDB 6ONG), 4-Cl-o-cresol (1.50 Å; PDB 6ONK), 4-Br-o-cresol (1.70 Å; PDB 6ONX), 4-NO₂-o-cresol (1.80 Å; PDB 6ONZ), o-cresol (1.60 Å; PDB 6OO1), p-cresol (2.10 Å; PDB 6OO6), 4-Me-o-cresol (1.35 Å; PDB 6ONR) and pentachlorophenol (1.80 Å; PDB 6OO8) revealed substrate binding sites in the distal pocket in close proximity to the heme cofactor, consistent with both oxidation mechanisms. The findings establish cresols as a new class of substrate for DHP, demonstrate that multiple oxidation mechanisms may exist for a given substrate, and provide further evidence that different substituents can serve as functional switches between the different activities performed by dehaloperoxidase. More broadly, the results demonstrate the complexities of marine pollution where both microbial and non-microbial systems may play significant roles in the biotransformations of EPA-classified pollutants, and further reinforces that heterocyclic compounds of anthropogenic origin should be considered as environmental stressors of infaunal organisms.

Regulation of organohalide respiration

Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.

Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum

Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The alphaproteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of completely degrading PCP. This pathway produces four toxic intermediates, including a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that react with O2 to produce reactive oxygen species (ROS). RNA-seq analysis revealed that PCP causes a global stress response that resembles responses to proton motive force uncoupling and membrane disruption, while surprisingly, little of the response resembles the responses expected to be produced by the PCP degradation intermediates. Tn-seq was used to identify genes important for fitness in the presence of PCP. By comparing the genes that are important for fitness in wild-type S. chlorophenolicum and a non-PCP-degrading mutant, we identified genes that are important only when the PCP degradation intermediates are produced. These include genes encoding two enzymes that are likely to be involved in protection against ROS. In addition to these enzymes, the endogenous levels of other enzymes that protect cells from oxidative stress appear to mitigate the toxic effects of the chlorinated benzoquinone and hydroquinone metabolites of PCP. The combination of RNA-seq and Tn-seq results identify important mechanisms for defense against the toxicity of PCP. IMPORTANCE Phenolic compounds such as pentachlorophenol (PCP), triclosan, and 2,4-dichlorophenoxyacetic acid (2,4-D) represent a common class of anthropogenic biocides. Despite the novelty of these compounds, many can be degraded by microbes isolated from contaminated sites. However, degradation of this class of chemicals often generates toxic intermediates, which may contribute to their recalcitrance to biodegradation. We have addressed the stresses associated with degradation of PCP by Sphingobium chlorophenolicum by examining the transcriptional response after PCP exposure and identifying genes necessary for growth during both exposure to and degradation of PCP. This work identifies some of the mechanisms that protect cells from this toxic compound and facilitate its degradation. This information could be used to engineer strains capable of improved biodegradation of PCP or similar phenolic pollutants.

Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1

Maleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k _cat /K _m ) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.

Identification of a Small Molecule Activator for AphB, a LysR-Type Virulence Transcriptional Regulator in Vibrio cholerae

AphB is a LysR-type transcriptional regulator (LTTR) that cooperates with a second transcriptional activator, AphA, at the tcpPH promoter to initiate expression of the virulence cascade in Vibrio cholerae. Because it is not yet known whether AphB responds to a natural ligand in V. cholerae that influences its ability to activate transcription, we used a computational approach to identify small molecules that influence its activity. In silico docking was used to identify potential ligands for AphB, and saturation transfer difference nuclear magnetic resonance was subsequently employed to access the validity of promising targets. We identified a small molecule, BP-15, that specifically binds the C-terminal regulatory domain of AphB and increases its activity. Interestingly, molecular docking predicts that BP-15 does not bind in the putative primary effector-binding pocket located at the interface of RD-I and RD-II as in other LTTRs, but rather at the dimerization interface. The information gained in this study helps us to further understand the mechanism by which transcriptional activation by AphB is regulated by suggesting that AphB has a secondary ligand binding site, as observed in other LTTRs. This study also lays the groundwork for the future design of inhibitory molecules to block the V. cholerae virulence cascade, thereby preventing the devastating symptoms of cholera infection.

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric CO2 to be reduced to usable forms of organic carbon. This process, especially the Calvin-Bassham-Benson (CBB) pathway of CO2 fixation, provides the bulk of organic carbon found on earth. The enzyme ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) performs the key and rate-limiting step whereby CO2 is reduced and incorporated into a precursor organic metabolite. This is a highly regulated process in diverse organisms, with the expression of genes that comprise the CBB pathway (the cbb genes), including RubisCO, specifically controlled by the master transcriptional regulator protein CbbR. Many organisms have two or more cbb operons that either are regulated by a single CbbR or employ a specific CbbR for each cbb operon. CbbR family members are versatile and accommodate and bind many different effector metabolites that influence CbbR's ability to control cbb transcription. Moreover, two members of the CbbR family are further posttranslationally modified via interactions with other transcriptional regulator proteins from two-component regulatory systems, thus augmenting CbbR-dependent control and optimizing expression of specific cbb operons. In addition to interactions with small effector metabolites and other regulator proteins, CbbR proteins may be selected that are constitutively active and, in some instances, elevate the level of cbb expression relative to wild-type CbbR. Optimizing CbbR-dependent control is an important consideration for potentially using microbes to convert CO2 to useful bioproducts.

Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants

Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.

Amino acid substitutions in the transcriptional regulator CbbR lead to constitutively active CbbR proteins that elevate expression of the cbb CO2 fixation operons in Ralstonia eutropha (Cupriavidus necator) and identify regions of CbbR necessary for gene activation

CbbR is a LysR-type transcriptional regulator that activates expression of the operons containing (cbb) genes that encode the CO2 fixation pathway enzymes in Ralstonia eutropha (Cupriavidus necator) under autotrophic growth conditions. The cbb operons are stringently downregulated during chemoheterotrophic growth on organic acids such as malate. CbbR constitutive proteins (CbbR*s), typically with single amino acid substitutions, were selected and isolated that activate expression of the cbb operons under chemoheterotrophic growth conditions. A large set of CbbR*s from all major domains of the CbbR molecule were identified, except for the DNA-binding domain. The level of gene expression conferred for many of these CbbR*s under autotrophic growth was greater than that conferred by wild-type CbbR. Several of these CbbR*s increase transcription two- to threefold more than wild-type CbbR. One particular CbbR*, a truncated protein, was useful in identifying the regions of CbbR that are necessary for transcriptional activation and, by logical extension, necessary for interaction with RNA polymerase. The reductive assimilation of carbon via CO2 fixation is an important step in the cost-effective production of useful biological compounds. Enhancing CO2 fixation in Ralstonia eutropha through greater transcriptional activation of the cbb operons could prove advantageous, and the use of CbbR*s is one way to enhance product formation.

Transcription factor-based biosensors enlightened by the analyte

Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.