Emergence of novel functions in transcriptional regulators by regression to stem protein types

Highly multiplexed design of an allosteric transcription factor to sense novel ligands

Allosteric transcription factors (aTF), widely used as biosensors, have proven challenging to design for detecting novel molecules because mutation of ligand-binding residues often disrupts allostery. We developed Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screened a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures - four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone - as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identified novel biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design showed shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we developed cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid, scalable design of new biosensors, overcoming constraints of natural biosensors.

Water potential governs the effector specificity of the transcriptional regulator XylR of Pseudomonas putida

The biodegradative capacity of bacteria in their natural habitats is affected by water availability. In this work, we have examined the activity and effector specificity of the transcriptional regulator XylR of the TOL plasmid pWW0 of Pseudomonas putida mt-2 for biodegradation of m-xylene when external water potential was manipulated with polyethylene glycol PEG8000. By using non-disruptive luxCDEAB reporter technology, we noticed that the promoter activated by XylR (Pu) restricted its activity and the regulator became more effector-specific towards head TOL substrates when cells were grown under water subsaturation. Such a tight specificity brought about by water limitation was relaxed when intracellular osmotic stress was counteracted by the external addition of the compatible solute glycine betaine. With these facts in hand, XylR variants isolated earlier as effector-specificity responders to the non-substrate 1,2,4-trichlorobenzene under high matric stress were re-examined and found to be unaffected by water potential in vivo. All these phenomena could be ultimately explained as the result of water potential-dependent conformational changes in the A domain of XylR and its effector-binding pocket, as suggested by AlphaFold prediction of protein structures. The consequences of this scenario for the evolution of specificities in regulators and the emergence of catabolic pathways are discussed.

Directed Evolution of Transcription Factor-Based Biosensors for Altered Effector Specificity

Transcription factor-based biosensors are important tools in Synthetic Biology for the sensing of industrially valuable molecules and clinically important metabolites, therefore presenting applications in the bioremediation, industrial biotechnology, and biomedical fields. The directed evolution of allosteric transcription factors (aTFs) with the aim of altering effector specificity has the potential for the development of new biosensors to detect natural and nonnatural molecules, expanding the scope of available aTF-based biosensors. In this chapter, we delineate a general method for the directed evolution of aTFs. The theory of library design is discussed, along with the detailed methodology for an improved transformation of combined libraries, and the experimental search space by counterselection using fluorescence-activated cell sorting (FACS) is presented.

Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis

The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.

Modular tuning engineering and versatile applications of genetically encoded biosensors

Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.

An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors

A revised model of the aromatic binding A domain of the σ⁵⁴ -dependent regulator XylR of Pseudomonas putida mt-2 was produced based on the known 3D structures of homologous regulators PoxR, MopR and DmpR. The resulting frame was instrumental for mapping a number of mutations known to alter effector specificity, which were then reinterpreted under a dependable spatial reference. Some of these changes involved the predicted aromatic binding pocket but others occurred in distant locations, including dimerization interfaces and putative zinc binding site. The effector pocket was buried within the protein structure and accessible from the outside only through a narrow tunnel. Yet, several loop regions of the A domain could provide the flexibility required for widening such a tunnel for passage of aromatic ligands. The model was experimentally validated by treating the cells in vivo and the purified protein in vitro with benzyl bromide, which reacts with accessible nucleophilic residues on the protein surface. Structural and proteomic analyses confirmed the predicted in/out distribution of residues but also supported two additional possible scenarios of interaction of the A domain with aromatic effectors: a dynamic interaction of the fully structured yet flexible protein with the aromatic partner and/or inducer-assisted folding of the A domain.

Engineering Alternate Ligand Recognition in the PurR Topology: A System of Novel Caffeine Biosensing Transcriptional Antirepressors

Recent advances in synthetic biology and protein engineering have increased the number of allosteric transcription factors used to regulate independent promoters. These developments represent an important increase in our biological computing capacity, which will enable us to construct more sophisticated genetic programs for a broad range of biological technologies. However, the majority of these transcription factors are represented by the repressor phenotype (BUFFER), and require layered inversion to confer the antithetical logical function (NOT), requiring additional biological resources. Moreover, these engineered transcription factors typically utilize native ligand binding functions paired with alternate DNA binding functions. In this study, we have advanced the state-of-the-art by engineering and redesigning the PurR topology (a native antirepressor) to be responsive to caffeine, while mitigating responsiveness to the native ligand hypoxanthine-i.e., a deamination product of the input molecule adenine. Importantly, the resulting caffeine responsive transcription factors are not antagonized by the native ligand hypoxanthine. In addition, we conferred alternate DNA binding to the caffeine antirepressors, and to the PurR scaffold, creating 38 new transcription factors that are congruent with our current transcriptional programming structure. Finally, we leveraged this system of transcription factors to create integrated NOR logic and related feedback operations. This study represents the first example of a system of transcription factors (antirepressors) in which both the ligand binding site and the DNA binding functions were successfully engineered in tandem.

Engineered protein switches for exogenous control of gene expression

There is an ongoing need in the synthetic biology community for novel ways to regulate gene expression. Protein switches, which sense biological inputs and respond with functional outputs, represent one way to meet this need. Despite the fact that there is already a large pool of transcription factors and signaling proteins available, the pool of existing switches lacks the substrate specificities and activities required for certain applications. Therefore, a large number of techniques have been applied to engineer switches with novel properties. Here we discuss some of these techniques by broadly organizing them into three approaches. We show how novel switches can be created through mutagenesis, domain swapping, or domain insertion. We then briefly discuss their use as biosensors and in complex genetic circuits.

Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli

Bacterial transcription factors (TFs) are key devices for the engineering of complex circuits in many biotechnological applications, yet there are few well-characterized inducer-responsive TFs that could be used in the context of an animal or human host. We have deciphered the inducer recognition mechanism of two AraC/XylS regulators from Pseudomonas putida (BenR and XylS) for creating a novel expression system responsive to acetyl salicylate (i.e., aspirin). Using protein homology modeling and molecular docking with the cognate inducer benzoate and a suite of chemical analogues, we identified the conserved binding pocket of BenR and XylS. By means of site-directed mutagenesis, we identified a single amino acid position required for efficient inducer recognition and transcriptional activation. Whereas this modification in BenR abolishes protein activity, in XylS, it increases the response to several inducers, including acetyl salicylic acid, to levels close to those achieved by the canonical inducer. Moreover, by constructing chimeric proteins with swapped N-terminal domains, we created novel regulators with mixed promoter and inducer recognition profiles. As a result, a collection of engineered TFs was generated with an enhanced response to benzoate, 3-methylbenzoate, 2-methylbenzoate, 4-methylbenzoate, salicylic acid, aspirin, and acetylsalicylic acid molecules for eliciting gene expression in E. coli.

Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids

Transcriptional biosensors enable key applications in both metabolic engineering and synthetic biology. Due to nature's immense variety of metabolites, these applications require biosensors with a ligand specificity profile customized to the researcher's needs. In this work, chimeric biosensors were created by introducing parts of a donor regulatory circuit from Sinorhizobium meliloti, delivering the desired luteolin-specific response, into a nonspecific biosensor chassis from Herbaspirillum seropedicae. Two strategies were evaluated for the development of chimeric LysR-type biosensors with customized ligand specificity profiles toward three closely related flavonoids, naringenin, apigenin, and luteolin. In the first strategy, chimeric promoter regions were constructed at the biosensor effector module, while in the second strategy, chimeric transcription factors were created at the biosensor detector module. Via both strategies, the biosensor repertoire was expanded with luteolin-specific chimeric biosensors demonstrating a variety of response curves and ligand specificity profiles. Starting from the nonspecific biosensor chassis, a shift from 27.5% to 95.3% luteolin specificity was achieved with the created chimeric biosensors. Both strategies provide a compelling, faster, and more accessible route for the customization of biosensor ligand specificity, compared to de novo design and construction of each biosensor circuit for every desired ligand specificity.

Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications

Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.

Tailor-made transcriptional biosensors for optimizing microbial cell factories

Monitoring cellular behavior and eventually properly adapting cellular processes is key to handle the enormous complexity of today's metabolic engineering questions. Hence, transcriptional biosensors bear the potential to augment and accelerate current metabolic engineering strategies, catalyzing vital advances in industrial biotechnology. The development of such transcriptional biosensors typically starts with exploring nature's richness. Hence, in a first part, the transcriptional biosensor architecture and the various modi operandi are briefly discussed, as well as experimental and computational methods and relevant ontologies to search for natural transcription factors and their corresponding binding sites. In the second part of this review, various engineering approaches are reviewed to tune the main characteristics of these (natural) transcriptional biosensors, i.e., the response curve and ligand specificity, in view of specific industrial biotechnology applications, which is illustrated using success stories of transcriptional biosensor engineering.

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10⁷ variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (∼2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.

Engineering an allosteric transcription factor to respond to new ligands

Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.

Transcription factor-based biosensors in biotechnology: current state and future prospects

Living organisms have evolved a plethora of sensing systems for the intra- and extracellular detection of small molecules, ions or physical parameters. Several recent studies have demonstrated that these principles can be exploited to devise synthetic regulatory circuits for metabolic engineering strategies. In this context, transcription factors (TFs) controlling microbial physiology at the level of transcription play a major role in biosensor design, since they can be implemented in synthetic circuits controlling gene expression in dependency of, for example, small molecule production. Here, we review recent progress on the utilization of TF-based biosensors in microbial biotechnology highlighting different areas of application. Recent advances in metabolic engineering reveal TF-based sensors to be versatile tools for strain and enzyme development using high-throughput (HT) screening strategies and adaptive laboratory evolution, the optimization of heterologous pathways via the implementation of dynamic control circuits and for the monitoring of single-cell productivity in live cell imaging studies. These examples underline the immense potential of TF-based biosensor circuits but also identify limitations and room for further optimization.

Identification of a missing link in the evolution of an enzyme into a transcriptional regulator

The evolution of transcriptional regulators through the recruitment of DNA-binding domains by enzymes is a widely held notion. However, few experimental approaches have directly addressed this hypothesis. Here we report the reconstruction of a plausible pathway for the evolution of an enzyme into a transcriptional regulator. The BzdR protein is the prototype of a subfamily of prokaryotic transcriptional regulators that controls the expression of genes involved in the anaerobic degradation of benzoate. We have shown that BzdR consists of an N-terminal DNA-binding domain connected through a linker to a C-terminal effector-binding domain that shows significant identity to the shikimate kinase (SK). The construction of active synthetic BzdR-like regulators by fusing the DNA-binding domain of BzdR to the Escherichia coli SKI protein strongly supports the notion that an ancestral SK domain could have been involved in the evolutionary origin of BzdR. The loss of the enzymatic activity of the ancestral SK domain was essential for it to evolve as a regulatory domain in the current BzdR protein. This work also supports the view that enzymes precede the emergence of the regulatory systems that may control their expression.

Increasing signal specificity of the TOL network of Pseudomonas putida mt-2 by rewiring the connectivity of the master regulator XylR

Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants) often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA). We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system). XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops.

It is generally taken for granted that promoters regulated by transcriptional factors (TFs) that respond to small molecules control their specificity to given effectors by tightening or relaxing the intrinsic dual interaction between the TF and the particular inducer. One such promoter is Pu, which drives expression of an operon for the biodegradation of m-xylene by the soil bacterium P. putida mt-2. While XylR, the chief TF of this system, binds this substrate and activates Pu, the same regulator responds, to a lesser extent, to 3-methylbenzylalcohol and thus also activates the promoter. This work provides evidence that such natural effector promiscuity of the system can be altogether suppressed by replacing the naturally occurring negative autoregulation loop that governs XylR expression with an equivalent positive feedback loop. Based on this result, we argue that signal specificity of a given regulatory device depends not only on the TF involved but also on TF connectivity to upstream signals and downstream targets.

Evolution of a new function in an esterase: simple amino acid substitutions enable the activity present in the larger paralog, BioH

Gene duplication and divergence are essential processes for the evolution of new activities. Divergence may be gradual, involving simple amino acid residue substitutions, or drastic, such that larger structural elements are inserted, deleted or rearranged. Vast protein sequence comparisons, supported by some experimental evidence, argue that large structural modifications have been necessary for certain catalytic activities to evolve. However, it is not clear whether these activities could not have been attained by gradual changes. Interestingly, catalytic promiscuity could play a fundamental evolutionary role: a preexistent secondary activity could be increased by simple amino acid residue substitutions that do not affect the enzyme's primary activity. The promiscuous profile of the enzyme may be modified gradually by genetic drift, making a pool of potentially useful activities that can be selected before duplication. In this work, we used random mutagenesis and in vivo selection to evolve the Pseudomonas aeruginosa PAO1 carboxylesterase PA3859, a small protein, to attain the function of BioH, a much larger paralog involved in biotin biosynthesis. BioH was chosen as a target activity because it provides a highly sensitive selection for evolved enzymatic activities by auxotrophy complementation. After only two cycles of directed evolution, mutants with the ability to efficiently complement biotin auxotrophy were selected. The in vivo and in vitro characterization showed that the activity of one of our mutant proteins was similar to that of the wild-type BioH enzyme. Our results demonstrate that it is possible to evolve enzymatic activities present in larger proteins by discrete amino acid substitutions.

Directed evolution of the transcriptional regulator DntR: isolation of mutants with improved DNT-response

The transcriptional regulator DntR, which previously has been isolated from bacterial strains capable of degrading 2,4-dinitrotoluene (DNT), was engineered in order to improve the ability to detect DNT. A directed evolution strategy was employed, where sequence diversity first was created by random mutagenesis in three subsequent rounds, followed by recombination of previously selected mutants. A gfp gene was used as a reporter for transcriptional activity mediated by DntR and cells with higher GFP expression after addition of DNT were sorted out using fluorescence-activated cell sorting (FACS). A DntR mutant, which displayed 10 times higher induction levels than wild-type DntR in response to DNT was isolated. This mutant still maintained low levels of gfp expression in the absence of DNT. The detection limit was ∼10 µM, a 25-fold improvement compared to wild-type DntR. The functional role of some substitutions found in this clone is discussed in the framework of the structural changes observed when comparing the recently determined structures of DntR with and without bound inducer ligand.

The Crp regulator of Pseudomonas putida: evidence of an unusually high affinity for its physiological effector, cAMP

Although the genome of Pseudomonas putida KT2440 encodes an orthologue of the crp gene of Escherichia coli (encoding the cAMP receptor protein), the regulatory scope of this factor seems to be predominantly co-opted in this bacterium for controlling non-metabolic functions. In order to investigate the reasons for such a functional divergence in otherwise nearly identical proteins, the Crp regulator of P. putida (Crp(P. putida)) was purified to apparent homogeneity and subject to a battery of in vitro assays aimed at determining its principal physicochemical properties. Analytical ultracentrifugation indicated effector-free Crp(P. putida) to be a dimer in solution that undergoes a significant change in its hydrodynamic shape in the presence of cAMP. Such a conformational transition was confirmed by limited proteolysis of the protein in the absence or presence of the inducer. Thermodynamic parameters calculated by isothermal titration calorimetry revealed a tight cAMP-Crp(P. putida) association with an apparent K(D) of 22.5 ± 2.8 nM, i.e. much greater affinity than that reported for the E. coli's counterpart. The regulator also bound cGMP, but with a K(D) = 2.6 ± 0.3 µM. An in vitro transcription system was then set up with purified P. putida's RNA polymerase for examining the preservation of the correct protein-protein architecture that makes Crp to activate target promoters. These results, along with cognate gel retardation assays indicated that all basic features of the reference Crp(E. coli) protein are kept in the P. putida's counterpart, albeit operating under a different set of parameters, the extraordinarily high affinity for cAMP being the most noticeable.

Protein and RNA engineering to customize microbial molecular reporting

Nature takes advantage of the malleability of protein and RNA sequence and structure to employ these macromolecules as molecular reporters whose conformation and functional roles depend on the presence of a specific ligand (an "effector" molecule). By following nature's example, ligand-responsive proteins and RNA molecules are now routinely engineered and incorporated into customized molecular reporting systems (biosensors). Microbial small-molecule biosensors and endogenous molecular reporters based on these sensing components find a variety of applications that include high-throughput screening of biosynthesis libraries, environmental monitoring, and novel gene regulation in synthetic biology. Here, we review recent advances in engineering small-molecule recognition by proteins and RNA and in coupling in vivo ligand binding to reporter-gene expression or to allosteric activation of a protein conferring a detectable phenotype. Emphasis is placed on microbial screening systems that serve as molecular reporters and facilitate engineering the ligand-binding component to recognize new molecules.

Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation

The regulation of the DNT pathway for biodegradation of 2,4-dinitrotoluene of Burkholderia sp. DNT has been examined by exporting each of its components to Pseudomonas putida KT2440. The cognate regulator DntR does not respond to the pathway substrate, but to the non-substrate salicylate. In order to examine whether such a response to an unrelated inducer was specific or rather a vestige of a previous evolutionary stage, the complete dnt complement or parts of it were expressed functionally for accumulation of various metabolic intermediates. Their effect on expression of dnt genes was then followed both biochemically and by means of a luminescent reporter engineered in the surrogate host. DntR was not only unresponsive to DNT biodegradation products, but it also failed to influence expression of dnt genes at all. Comparison of the dntR/dntA divergent promoter region with similar ones found in various catabolic systems indicated that the leading segment of the DNT biodegradation pathway evolved from a matching portion of naphthalene biodegradation routes existing in other bacteria. That a useless but still active transcriptional factor occurs along enzymes that have already evolved a new substrate specificity suggests that emergence of novel catalytic abilities precedes their submission to cognate regulatory devices, not vice versa.

Evolution of catabolic pathways and their regulatory systems in synthetic nitroaromatic compounds degrading bacteria

Evolution of catabolic pathways for the degradation of synthetic nitroaromatic compounds is currently ongoing process because these compounds have been in nature only for a short time. Bacteria isolated from contaminated areas contain pathways for the degradation of nitroaromatic compounds at different stages of progression. Therefore, the emergence of pathways for the degradation of such chemicals provides a good opportunity to investigate evolutionary processes leading to the emergence of new metabolic routes and their regulatory systems. In Burkholderia sp. strain DNT the regulatory gene encoding the LysR-type transcriptional regulator DntR is placed divergently of the dinitrotoluene (DNT) dioxygenase genes. This regulator still recognizes salicylate, an effector of its NagR-like ancestor but not DNT. In this issue of Molecular Microbiology, de las Heras et al. demonstrate that the DntR does not respond to any metabolic intermediates of the DNT catabolic pathway. The results of this study suggest that the catabolic pathway for the degradation of DNT has reached to an early stage of evolution when novel specificities of the catabolic enzymes have already acquired but the cognate regulatory system is still missing. This research addresses some fundamental questions about bottlenecks to be solved during evolution of new catabolic operons.

Tracing explosives in soil with transcriptional regulators of Pseudomonas putida evolved for responding to nitrotoluenes

Although different biological approaches for detection of anti-personnel mines and other unexploded ordnance (UXO) have been entertained, none of them has been rigorously documented thus far in the scientific literature. The industrial 2,4,6 trinitrotoluene (TNT) habitually employed in the manufacturing of mines is at all times tainted with a small but significant proportion of the more volatile 2,4 dinitrotoluene (2,4 DNT) and other nitroaromatic compounds. By using mutation-prone PCR and DNA sequence shuffling we have evolved in vitro and selected in vivo variants of the effector recognition domain of the toluene-responsive XylR regulator of the soil bacterium Pseudomonas putida that responds to mono-, bi- and trinitro substituted toluenes. Re-introduction of such variants in P. putida settled the transcriptional activity of the cognate promoters (Po and Pu) as a function of the presence of nitrotoluenes in the medium. When strains bearing transcriptional fusions to reporters with an optical output (luxAB, GFP) were spread on soil spotted with nitrotoluenes, the signal triggered by promoter activation allowed localization of the target compounds on the soil surface. Our data provide a proof of concept that non-natural transcription factors evolved to respond to nitroaromatics can be engineered in soil bacteria and inoculated on a target site to pinpoint the presence of explosives. This approach thus opens new ways to tackle this gigantic humanitarian problem.

Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis

Bacterial transcription activators of the XylR/DmpR subfamily exert their expression control via σ(54)-dependent RNA polymerase upon stimulation by a chemical effector, typically an aromatic compound. Where the chemical effector interacts with the transcription regulator protein to achieve activation is still largely unknown. Here we focus on the HbpR protein from Pseudomonas azelaica, which is a member of the XylR/DmpR subfamily and responds to biaromatic effectors such as 2-hydroxybiphenyl. We use protein structure modeling to predict folding of the effector recognition domain of HbpR and molecular docking to identify the region where 2-hydroxybiphenyl may interact with HbpR. A large number of site-directed HbpR mutants of residues in- and outside the predicted interaction area was created and their potential to induce reporter gene expression in Escherichia coli from the cognate P(C) promoter upon activation with 2-hydroxybiphenyl was studied. Mutant proteins were purified to study their conformation. Critical residues for effector stimulation indeed grouped near the predicted area, some of which are conserved among XylR/DmpR subfamily members in spite of displaying different effector specificities. This suggests that they are important for the process of effector activation, but not necessarily for effector specificity recognition.

Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family

Each family of signal transduction systems requires specificity determinants that link individual signals to the correct regulatory output. In Bacillus subtilis, a family of four anti-terminator proteins controls the expression of genes for the utilisation of alternative sugars. These regulatory systems contain the anti-terminator proteins and a RNA structure, the RNA anti-terminator (RAT) that is bound by the anti-terminator proteins. We have studied three of these proteins (SacT, SacY, and LicT) to understand how they can transmit a specific signal in spite of their strong structural homology. A screen for random mutations that render SacT capable to bind a RNA structure recognized by LicT only revealed a substitution (P26S) at one of the few non-conserved residues that are in contact with the RNA. We have randomly modified this position in SacT together with another non-conserved RNA-contacting residue (Q31). Surprisingly, the mutant proteins could bind all RAT structures that are present in B. subtilis. In a complementary approach, reciprocal amino acid exchanges have been introduced in LicT and SacY at non-conserved positions of the RNA-binding site. This analysis revealed the key role of an arginine side-chain for both the high affinity and specificity of LicT for its cognate RAT. Introduction of this Arg at the equivalent position of SacY (A26) increased the RNA binding in vitro but also resulted in a relaxed specificity. Altogether our results suggest that this family of anti-termination proteins has evolved to reach a compromise between RNA binding efficacy and specific interaction with individual target sequences.

Reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator NtdR

Many toxic man-made compounds have been introduced into the environment, and bacterial strains that are able to grow on them are ideal model systems for studying the evolution of metabolic pathways and regulatory systems. Acidovorax sp. strain JS42 is unique in its ability to use 2-nitrotoluene as a sole carbon, nitrogen, and energy source for growth. The LysR-type transcriptional regulator NtdR activates expression of the 2-nitrotoluene degradation genes not only when nitroaromatic compounds are present, but also in the presence of a wide range of aromatic acids and analogues. The molecular determinants of inducer specificity were identified through comparative analysis with NagR, the activator of the naphthalene degradation pathway genes in Ralstonia sp. strain U2. Although NagR is 98% identical to NtdR, it does not respond to nitrotoluenes. Exchange of residues that differ between NagR and NtdR revealed that residues at positions 227 and 232 were key for the recognition of nitroaromatic compounds, while the amino acid at position 169 determined the range of aromatic acids recognized. Structural modelling of NtdR suggests that these residues are near the predicted inducer binding pocket. Based on these results, an evolutionary model is presented that depicts the stepwise evolution of NtdR.

Degradation of nitroaromatic compounds: a model to study evolution of metabolic pathways

Although many nitroaromatic compounds have been in nature for only a few decades, bacteria have already evolved the ability to metabolize them. Both horizontal transfer of genes and mutagenesis induced under stressful conditions might facilitate evolution of new catabolic pathways. Nitrotoluene degradation pathways are supposedly derived from an ancestral naphthalene degradation pathway. The 2-nitrotoluene degradation genes in Acidovorax sp. strain JS42 are controlled by the transcriptional activator NtdR, which differs from NagR, the activator of the naphthalene degradation operon in Ralstonia sp. strain U2, by only five amino acids. Both regulators respond to salicylate, an intermediate of naphthalene degradation, but NtdR also recognizes a wide range of nitroaromatic compounds. In this issue of Molecular Microbiology, Ju et al. present results of site-directed mutagenesis of NtdR and NagR and show how the nitrotoluene-responsive regulator NtdR can be generated from a NagR-like ancestor by only a few mutations. The reconstructed hypothetical pathway for the evolution of NtdR from NagR demonstrates stepwise broadening of the effector range of the evolving protein without loss of the original activity. These results provide strong evidence for the idea that promiscuity of proteins is an important step in the evolution of new functions.

Bionemo: molecular information on biodegradation metabolism

Bionemo (http://bionemo.bioinfo.cnio.es) stores manually curated information about proteins and genes directly implicated in the Biodegradation metabolism. When possible, the database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Thus, Bionemo is a unique resource that complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus more on the biochemical aspects of biodegradation than in the nature of the biomolecules carrying out the reactions. Bionemo has been built by manually associating sequences database entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network. In its current version, Bionemo contains sequence information for 324 reactions and transcription regulation information for more than 100 promoters and 100 transcription factors. The information in the Bionemo database is available via a web server and the full database is also downloadable as a PostgresSQL dump. To facilitate the programmatic use of the information contained in the database, an object-oriented Perl API is also provided.

Mining logic gates in prokaryotic transcriptional regulation networks

Prokaryotic transcriptional networks possess a large number of regulatory modules that formally implement many of the logic gates that are typical of digital, Boolean circuits. Yet, natural regulatory elements appear most often compressed and exaggeratedly context-dependent for any reliable circuit engineering barely comparable to electronic counterparts. To overcome this impasse, we argue that designing new functions with biological parts requires (i) the recognition of logic gates not yet assigned but surely present in the meta-genome, (ii) the orthogonalization and disambiguation of natural regulatory modules and (iii) the development of ways to tackle the connectivity and the definition of boundaries between minimal biological components.