# Patent

## Title
Receptor/histidine kinase fusion constructs and uses thereof

## Abstract

The present disclosure provides compositions and methods for sensing a target substance of interest in the environment and inducing gene expression in response thereto, useful for detection of biological and chemical agents and environmental pollutants.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the priority of U.S. Provisional Appl. Ser. No. 62/701,396, filed Jul. 20, 2018, the entire disclosure of which is incorporated herein by reference.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under grant W911NF-09-1-0526 awarded by Army Research Office and grant N00014-07-1-0180 awarded by the Office of Naval Research. The government has certain rights in the invention.


INCORPORATION OF SEQUENCE LISTING
A sequence listing contained in the file named “CSUV004US.txt” which is 172 kilobytes (measured in MS-Windows®) and created on Jun. 18, 2019, is filed electronically herewith and incorporated by reference in its entirety.
FIELD OF THE INVENTION
The present disclosure relates to the field of molecular biology, more specifically compositions and methods involved in signal transduction from outside of a cell to the nucleus and to systems for sensing a target substance of interest in the environment and inducing gene expression in response thereto, useful for detection of biological and chemical agents, pathogens and their products and environmental pollutants especially with plants and plant sentinels.
BACKGROUND
Current detectors of biological and chemical agents and environmental pollutants involve electronic and/or vacuum-like mechanisms to sample the air or the environment. All current means to detect harmful biological or chemical agents and environmental pollutants are costly and require continuous maintenance. The high and continuous cost significantly limits the ability to detect biological and chemical agents, pathogens and their products, as well as environmental pollutants.
Therefore there is an increasing need for simple and robust detectors for harmful biological or chemical agents, pathogens and their products, and environmental pollutants.
SUMMARY OF THE INVENTION
The present disclosure provides a fusion protein comprising a chemotactic receptor protein, or a receptor involved in quorum sensing, or a receptor from a receptor histidine kinase operably linked at the A/D position to a histidine kinase protein, wherein the fusion protein comprises a kinase activation region. In certain embodiments the chemotactic receptor protein is Trg, Tar, Tap or Tsr. In other embodiments the receptor involved in quorum sensing is the Xylella DSF receptor RpfC or the LuxPQ receptor LuxP. In additional embodiments the histidine kinase protein is PhoR or EnvZ, while in further embodiments the histidine kinase protein is a EnvZ/PhoR chimera. In some embodiments the kinase activation region of the fusion protein has been engineered to restore inducible kinase activity or engineered to allow the interaction of maltose-bound maltose binding protein with the receptor to functionally activate kinase activity.
In particular embodiments the histidine kinase protein is activated when the chemotactic receptor protein or the receptor involved in quorum sensing binds to a sensor protein bound to a target substance or a target substance itself. Because of the diversity that nature provides from histidine kinases and with the ability afforded by computational design of proteins such as demonstrated here, in certain embodiments the fusions can be made where the target substance is a chemical agent, a heavy metal, a poison, a pollutant, a toxin, an herbicide, a polycyclic aromatic hydrocarbon, a benzene, a toluene, a xylene, a halogenated hydrocarbon, a steroid or other hormone, an explosive, or a degradation product of one of the foregoing compounds, most small molecules as enabled with computational design. In further embodiments the fusion protein further comprises a plasma membrane targeting signal sequence operably linked to an N-terminus of the chemotactic receptor protein or receptor involved in quorum sensing. Quorum sensing molecules are found in pathogen and their related products as demonstrated here and expanded with computational design abilities, hence our embodiments here and with computational abilities provide means to sense and respond to pathogens.
The present disclosure also provides a DNA construct comprising a nucleic acid segment that encodes a fusion protein comprising a chemotactic receptor protein, a receptor involved in quorum sensing, or a receptor from a receptor histidine kinase operably linked at the A/D position to a histidine kinase protein, wherein the fusion protein comprises a kinase activation region. In some embodiments the nucleic acid segment is operably linked to a heterologous or homologous promoter. In further embodiments the chemotactic receptor protein or the receptor involved in quorum sensing are or can be computationally designed.
The present disclosure further provides a transgenic plant or a plant cell comprising a first DNA construct comprising a first plant operable promoter operably linked to a nucleic acid segment encoding a sensor protein, the protein comprising a secretory sequence for directing the protein to the extracellular space of a plant cell and a binding region specific for a target substance of interest, wherein the protein undergoes a conformational change when the target substance is bound, a second DNA construct comprising a second plant operable promoter operably linked to a nucleic acid segment encoding a protein that comprises the following domains: a plasma membrane targeting signal sequence, an extracellular domain for binding the sensor protein, a transmembrane domain and a histidine kinase domain for phosphorylating a protein with nuclear shuttling or transcriptional activating functions, wherein the histidine kinase is activated when the sensor protein binds to the extracellular domain, and a third DNA construct comprising a third plant operable promoter operably linked to a nucleic acid segment encoding a detectable marker or a response gene, wherein the third plant operative promoter is responsive to the transcriptional activator protein, and wherein the detectable marker is expressed when the external target substance of interest is bound to the sensor protein. In particular embodiments the extracellular domain for binding the sensor protein comprises a chemotactic receptor protein, a receptor involved in quorum sensing, or a receptor from a receptor histidine kinase, and the extracellular domain or the transmembrane domain is operably linked at the A/D position to a histidine kinase protein, wherein the second DNA construct encodes a fusion protein comprising a kinase activation region.
In certain embodiments the extracellular domain, the transmembrane domain and/or the histidine kinase domain of the second DNA construct are derived from one or more bacterial genes, and the membrane targeting signal sequence of the second DNA construct is derived from a plant gene. The derived bacterial genes can be subjected to refactoring (codon optimization, removal of splice sites, post-translational regulatory elements, etc.) as is typical for one skilled in the field. In some embodiments the detectable marker of the third DNA construct is a chlorophyll degradation enzyme or a functional fragment thereof. In other embodiments the plant loses detectable green color when the detectable marker is expressed. In yet other embodiments the chlorophyll degradation enzyme is selected from the group consisting of red chlorophyll catabolite reductase (RCCR), pheophorbide a oxygenase (PaO), and chlorophyllase. In still other embodiments the third DNA construct comprises a plant operable promoter responsive to a transcription activator protein operably linked to a nucleic acid sequence encoding an interfering RNA molecule specific for a chlorophyll biosynthesis coding sequence. In further embodiments the chlorophyll biosynthesis coding sequence encodes chlorophyll synthetase, protochlorophyllide oxidoreductase (POR) or GUN4. In other embodiments the response or readout is non-visible but detectable by various systems including webcams and high altitude platforms.
In particular embodiments the secretory sequence is from pollen extension-like protein (PEX). In certain embodiments the membrane targeting signal sequence is from FLS2. In further embodiments the histidine kinase domain comprises segments derived from a non-plant organism or segments derived from a non-plant organism and a plant. In additional embodiments the plant operable promoter comprises a PhoB binding sequence.
In further embodiments the transgenic plant or plant cell further comprises a fourth DNA construct comprising a nucleic acid encoding a chlorophyll degradation enzyme or a functional fragment thereof operably linked to a plant operable promoter responsive to the transcription activator protein, and wherein the promoter is not in nature associated with the sequence encoding a chlorophyll degradation enzyme. In yet further embodiments the transgenic plant or plant cell further comprises a fourth DNA construct comprising a plant operable promoter operably linked to a nucleic acid sequence encoding a plant operable transcriptional activator, wherein the transcriptional activator is activated when phosphorylated by a histidine kinase.
In certain embodiments the detectable marker is a functional RNA. In some embodiments the functional RNA is an interfering RNA molecule. In other embodiments the functional RNA inhibits expression of a chlorophyll biosynthesis coding sequence. In particular embodiments the chlorophyll biosynthesis coding sequence encodes chlorophyll synthetase, protochlorophyllide oxidoreductase (POR) or GUN4. In additional embodiments the detectable marker is a chlorophyll degradation enzyme. In certain embodiments the chlorophyll degradation enzyme is red chlorophyll catabolite reductase (RCCR), pheophorbide a oxygenase (PaO), or chlorophyllase. In yet other embodiments the detectable marker is a β-glucuronidase, a β-galactosidase or a green or yellow fluorescent protein.
In some embodiments the transcription activator protein comprises a response regulator domain. In certain embodiments the response regulator domain is derived from PhoB. In particular embodiments the transcription activator protein is a PhoB:VP64 translational fusion protein. In further embodiments the detectable marker is a functional RNA that inhibits expression of a chlorophyll biosynthesis coding sequence. In still further embodiments the plant loses green color due to inhibition of chlorophyll biosynthesis and enhanced breakdown of chlorophyll upon induction of a gene encoding a chlorophyll degradation enzyme. In other embodiments the enhanced breakdown of chlorophyll is achieved by expressing at least one enzyme selected from the group consisting of red chlorophyll catabolite reductase (RCCR), pheide a oxygenase (PaO), and chlorophyllase. In yet other embodiments the inhibition of chlorophyll biosynthesis is achieved by inhibiting expression of at least one enzyme selected from the group consisting of protochlorophyllide oxidoreductase (POR), chlorophyll synthetase and GUN4. In certain embodiments the inhibition of POR is achieved by producing an interfering RNA molecule that contains a sequence derived from the coding sequence of POR. In further embodiments the plant loses green color by inhibiting POR and stimulating RCCR and chlorophyllase. In other embodiments the response or readout is non-visible but detectable by various systems including webcams and high altitude platforms.
The present disclosure additionally provides a plant cell comprising a first DNA construct comprising a first promoter functional in a plant operably linked to a recombinant nucleic acid encoding a first repressor, a second DNA construct comprising a second promoter functional in a plant operably linked to a nucleic acid encoding a detectable marker or response gene encoding a fusion protein comprising a chemotactic receptor protein, a receptor involved in quorum sensing, or a receptor from a receptor histidine kinase operably linked at the A/D position to a histidine kinase protein, wherein the fusion protein comprises a kinase activation region, wherein the second promoter is repressible by a second repressor, and a third DNA construct comprising a third promoter functional in a plant operably linked to a nucleic acid encoding the first repressor, wherein the third promoter is constitutive and repressible by the second repressor, wherein the first repressor or second repressor comprise at least one EAR 1 or EAR 2 repressor domain, or a transgenic plant comprising the plant cell. In further embodiments the plant cell comprises a fourth DNA construct comprising a fourth promoter operable in a plant operably linked to a nucleic acid encoding the second repressor, wherein the fourth promoter is constitutive and repressible.
In certain embodiments the fourth promoter is repressible by the first repressor. In some embodiments repression of the fourth promoter by the first repressor reduces expression of the second repressor. In other embodiments reduced expression of the second repressor increases expression of the detectable marker or response gene. In yet other embodiments the fourth promoter is a recombinant polynucleotide comprising nucleic acid sequence from a non-plant organism. In still other embodiments the nucleic acid encoding the first repressor is a recombinant polynucleotide. In particular embodiments the nucleic acid encoding the first repressor comprises nucleic acid sequences encoding at least one GAL4 DNA binding domain. In further embodiments the nucleic acid encoding the second repressor is a recombinant polynucleotide. In yet further embodiments the first promoter is a recombinant polynucleotide. In still further embodiments the first promoter is induced by a transcription activator protein activated by an external signal.
In additional embodiments the transcription activator protein is a fusion protein encoded by a polynucleotide sequence derived from a non-plant organism. In other embodiments the polynucleotide sequence encoding the fusion protein comprises at least one nucleic acid sequence encoding a PhoB binding domain. In some embodiments the fusion protein is encoded by a polynucleotide sequence comprising a nucleic acid sequence encoding a polypeptide sequence of VP64. In further embodiments the plant cell comprises a fifth DNA construct comprising a plant operable promoter operably linked to a nucleic acid sequence encoding a sensor protein that recognizes the external signal. In certain embodiments the second promoter is a recombinant polynucleotide.
The present disclosure also provides a method for detecting an external substance of interest, the method comprising exposing a transgenic plant or a plant cell comprising a first DNA construct comprising a first plant operable promoter operably linked to a nucleic acid segment encoding a sensor protein, the protein comprising a secretory sequence for directing the protein to the extracellular space of a plant cell and a binding region specific for a target substance of interest, wherein the protein undergoes a conformational change when the target substance is bound, a second DNA construct comprising a second plant operable promoter operably linked to a nucleic acid segment encoding a protein that comprises the following domains: a plasma membrane targeting signal sequence, an extracellular domain for binding the sensor protein, a transmembrane domain and a histidine kinase domain for phosphorylating a protein with nuclear shuttling and/or transcriptional activating functions, wherein the histidine kinase is activated when the sensor protein binds to the extracellular domain, and a third DNA construct comprising a third plant operable promoter operably linked to a nucleic acid segment encoding a detectable marker or a response gene, wherein the third plant operative promoter is responsive to the transcriptional activator protein, and wherein the detectable marker is expressed when the external target substance of interest is bound to the sensor protein, wherein the extracellular domain for binding the sensor protein comprises a chemotactic receptor protein, a receptor involved in quorum sensing, or a receptor from a receptor histidine kinase, and the extracellular domain or the transmembrane domain is operably linked at the A/D position to a histidine kinase protein, wherein the second DNA construct encodes a fusion protein comprising a kinase activation region to an external substance of interest, and detecting a change resulting from expression of the detectable marker.
In certain embodiments the detectable marker is a functional RNA. In some embodiments the functional RNA is an interfering RNA molecule. In other embodiments the functional RNA inhibits expression of a chlorophyll biosynthesis coding sequence. In yet other embodiments the chlorophyll biosynthesis coding sequence encodes chlorophyll synthetase, protochlorophyllide oxidoreductase (POR) or GUN4. In still other embodiments the detectable marker is a chlorophyll degradation enzyme. In further embodiments the chlorophyll degradation enzyme is red chlorophyll catabolite reductase (RCCR), pheophorbide a oxygenase (PaO), or chlorophyllase. In still further embodiments the detectable marker is a β-glucuronidase, a β-galactosidase or a green or yellow fluorescent protein. In other embodiments the response or readout is non-visible but detectable by various systems including webcams and high altitude platforms. In additional embodiments the transcription activator protein is a PhoB protein or is derived from a PhoB protein. In some embodiments the transcription activator protein is a PhoB:VP64 translational fusion protein.
In certain embodiments the change is degreening of the transgenic plant. In some embodiments the degreening of the transgenic plant is detected visually or by detecting properties selected from the group consisting of chlorophyll fluorescence, photosynthetic properties and properties related to reactive oxygen species and their damage. In other embodiments the degreening is detected by imaging selected from the group consisting of hyper-spectral imaging, infra-red imaging, near-infra-red imaging and multi-spectral imaging. In further embodiments the transgenic plant regreens after removal of the external substance of interest. In other embodiments the response or readout is non-visible but detectable by various systems including webcams and high altitude platforms. In another embodiment the external signal is detectable after a single exposure of the transgenic plant or plant cell to the external signal.



BRIEF DESCRIPTION OF THE DRAWINGS
For a more complete understanding of the features and advantages of the present disclosure, reference is now made to the detailed description of the disclosure along with the accompanying figures. The drawings described herein are for illustration purposes only and are not intended to limit the scope of the present teachings in any way.
FIG. 1A, FIG. 1B and FIG. 1C: Diagrams of two component systems (TCS). FIG. 1A. “Simple” bacterial TCS—Extracellular input is provided by a transmembrane histidine kinase (HK). In the HK molecule a histidine residue in the dimerization and histidine phosphorylation (DHP) domain auto-phosphorylates in response to ligand binding. The high energy phosphoryl group is then transferred to a cytoplasmically localized response regulator (RR). FIG. 1B. Hybrid HK signaling found in plants and bacteria—These systems have more complex HKs and signaling components. In response to a ligand binding on the HK, a histidine residue in the DHP domain auto-phosphorylates. The high energy phosphoryl group is then transferred internally to an aspartate in the receiver domain, and subsequently to a histidine in a cytoplasmic Hpt protein which then phosphorylates an RR on its aspartate residue. FIG. 1C. Bacterial chemotactic TCS—A chemotactic receptor (e.g., Trg) binds a PBP-ligand complex or directly binds a ligand. This binding event initiates a signal that is transmitted to a cytoplasm-localized histidine kinase CheA. CheW acts as an adaptor protein for the chemotactic receptor/CheA complex. CheA then phosphorylates RRs that do not activate transcription.
FIG. 2. Synthetic Signaling System Used In Detector Plants. In the apoplast, computationally re-designed PBPs bind TNT. The PBP-TNT complex interacts with a membrane-localized Trg-PhoR (DHP8) fusion, causing it to auto-phosphorylate and transfer the high energy phosphate to PhoB-VP64. PhoB-VP64 translocates to the nucleus and activates the PlantPho promoter.
FIG. 3A, FIG. 3B and FIG. 3C. Interaction between the two α-helices in the tropomyosin coiled-coil. Each α-helix is shown with seven residues (a-g) in two turns. FIG. 3A. End-on view looking from N terminus. The interface between the α-helices derives primarily from hydrophobic residues in core positions a and d, although there are also some salt bridges formed between residues e and g. FIG. 3B. The core interface viewed parallel to the coiled-coil axis shows how residues from one chain occupy the spaces between the corresponding residues from the second chain to give “knobs in holes” packing. FIG. 3C. Representation of a coiled coil structure.
FIG. 4. Predicted HK coiled coil element in Trz (SEQ ID NO:48) and PhoR (SEQ ID NO:53). Note that the methionine used in the HAMP fusion between Trg and EnvZ (underlined) is adjacent to the start of coiled coil heptad number 3.
FIG. 5. Predicted coiled coil and fusions junctions from coiled coil test constructs. Proteins used in the fusions (EnvZ—SEQ ID NO:50; Trg—SEQ ID NO:51; Trz—SEQ ID NO:52; PhoR—SEQ ID NO:53) highlighted in blue. Sequence junctions from the 4 coiled coil test constructs (Trg′′CC′′Pho—SEQ ID NO:54; TrzEnvZCC—SEQ ID NO:55; TrzEnvZcc2&3—SEQ ID NO:56; TrgPhoRcc3—SEQ ID NO:57) are shown along with the signaling phenotype. The autophosphorylated Histidine from the DHP domain is shown in bold. The position of the HAMP helices, if found in the protein, are shown above the alignments.
FIG. 6. pACYC177 based fusion testing plasmid.
FIG. 7. Refining the TrzPhoR functional fusion point. Proteins used in the fusions are Trg (SEQ ID NO:51); EnvZ (SEQ ID NO:50); Trg′′cc1′′PhoR (SEQ ID NO:54); and PhoR (SEQ ID NO:53). TrzHAMP+VK (SEQ ID NO:60) recapitulates the original coiled coil based TrzPhoR fusion (SEQ ID NO:58). Residues efg of the Trg HAMP domain (QHS vs AAG in EnvZ) can functionally substitute for the EnvZ efg residues from the original TrzHAMP fusion as seen in TrgHAMP+V (SEQ ID NO:61) and TrzHAMP+V PhoR (SEQ ID NO:59).
FIG. 8. Coiled coil D position mutants TrzHAMP+M (SEQ ID NO:62), TrzHAMP+V (SEQ ID NO:63), TrgHAMP+V (SEQ ID NO:64), TrgHAMP+G (SEQ ID NO:65), TrgHAMP+A (SEQ ID NO:66), TrgHAMP+L (SEQ ID NO:67), TrgHAMP+I (SEQ ID NO:68), TrgHAMP+E (SEQ ID NO:69), and TrgHAMP+T (SEQ ID NO:70). Proteins used in the fusions are Trz (SEQ ID NO:52); Trg (SEQ ID NO:51); and PhoR (SEQ ID NO:53). TrgHAMP+G and TrgHAMP+A tested the effect of putting a smaller hydrophobic D position residue in place of the Valine. TrgHAMP+L,I,E or T tested the effect of placing a naturally occurring A/D residue from the 10 HKs found in E. coli that have the HAMP position A/D position HK Coiled coil architecture.
FIG. 9A and FIG. 9B. Imaging of a luciferase gene reporter in transgenic Arabidopsis with the signaling circuit Ribose Binding Protein (RBP)→TrzPhoR→PhoBVP64 activating a plant pho promoter: luciferase reporter gene FIG. 9A. Four transgenic Arabidopsis lines at 0 hours (no exposure to ribose) top panel and 24 hours after exposure to ribose bottom panel. FIG. 9B. Quantification of luciferase activity from FIG. 9A.
FIG. 10. β-galactosidase assay showing diffusible signaling factor signaling via the RpfCPhoR fusion. Yellow=control, Blue=DSF.
FIG. 11A and FIG. 11B. FIG. 11A. Paired detached leaf assay on a split plate with luciferase reporter readout, 24 hour exposure to DSF. Two leaves from 7 independent RpfCTrzPhoR transgenic lines were detached and placed on media without (left side) and with (right side) DSF extracted from Xylella. The signaling circuit is DSF→RpfCTrzPhoR→PhoBVP64 activating a plant pho promoter. FIG. 11B. Quantification of luciferase activity. Mean activity of all 7 leaves.
FIG. 12A and FIG. 12B. FIG. 12A. Split plate assay showing Mg2+ induction of PhoQTrzPhoR. Left=background signaling from 2 mM MgSO4 present in media, Right=signaling increase seen with addition of 10 mM MgCl2. FIG. 12B. β-galactosidase activity of PhoQTrzPhoR. Yellow=background signaling from Mg2+ in media, Blue=signaling with additional 10 mM Mg2+.
FIG. 13A and FIG. 13B. β-galactosidase activity of TrzChim3 and the TrzChim3 ADD→EGA mutant. FIG. 13A. β-galactosidase activity of TrzChim3. Yellow=control, Blue=ribose. FIG. 13B. β-galactosidase activity of the TrzChim3 ADD→EGA mutant. Yellow=control, Blue=ribose.
FIG. 14. Alignment between EnvZ (SEQ ID NO:71) and PhoR (SEQ ID NO:72) indicating the ADD residues (275-277) of EnvZ and the corresponding EGA residues of PhoR in bold underline.
FIG. 15. Split plate assay showing ribose induction of the TrzChim variants 8 and 10. Left side=control, right side=ribose.
FIG. 16. β-galactosidase activity of TrzChim3, TrzChim3-8 and TrzChim3-10. Yellow=control, Blue=ribose.
FIG. 17A and FIG. 17B. Normalized GFP reporter gene fluorescence showing maltose induction of the TarHK fusion variants TazPhoR (FIG. 17A) and TAC (FIG. 17B).
FIG. 18. Data showing function of computationally designed protein to fentanyl with histidine kinase fusions and synthetic signal transduction system. Plants without (Control) and with exposure to the ligand (fentanyl) were evaluated.
FIG. 19. Means to engineer plant sensing and response systems. Left portion shows means to produce a rapid response in a plant. A computationally designed protein is located in the apoplast. When this protein binds a ligand, there is a conformational change that produces a response or readout. Right portion shows two means to use the synthetic histidine kinase systems. In one case (center) the computationally designed protein, partially or entirely, functions as a periplasmic protein (e.g., MBP). When the ligand binds the protein, there is high affinity for the external domain of the synthetic or computationally designed histidine kinase (chemotactic receptor/HK protein). A conformational change takes places that activates that transmembrane molecule, specifically, the internal kinase domain. This initiates a phosphoryl relay with a modified response regulator (e.g., engineered PhoB, OmpR) or computational designs of these, that translocates in the plant nucleus, binds a receptive promoter and activates a transcriptional response. The response can produce a direct readout, or the response can be regulated or tuned as shown schematically in FIG. 20 and demonstrated in FIG. 18. The second means to initiate a response is shown on the far right. A transmembrane fusion is made with a pathogen receptor-histidine kinase as shown with RpfC. The pathogen or pathogen factor activates the receptor-HK fusion protein and initiates a response as shown for the MBP protein (center).
FIG. 20. Genetic means to regulate or tune a plant sensing signal as used in FIG. 18. Once the transcriptional signal is received by the receptive promoter, in this case the PlantPho promoter, a quantitatively tuned response cascade is initiated. Transcription from the PlantPho promoter activates a second transcription factor, Tal-Gal4, that activates the pUAS promoter driving GAL4-VP64. Expression of GAL4-VP64 feeds-back and produces more of its own expression and feeds-forward to initiate expression of any response, readout or reporter gene.



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1—DNA coding sequence of TrzPhoR coiled coil based fusion of Trz (Trg chemotactic receptor/EnvZ histidine kinase fusion) to PhoR histidine kinase Escherichia coli sequence.
SEQ ID NO:2—Protein sequence of TrzPhoR coiled coil based fusion of Trz (Trg chemotactic receptor/EnvZ histidine kinase fusion) to PhoR histidine kinase Escherichia coli sequence.
SEQ ID NO:3—DNA coding sequence of TrzPhoR: Trz HAMP domain+Valine A/D fusion to PhoR histidine kinase Escherichia coli sequence.
SEQ ID NO:4—Protein sequence of TrzPhoR: Trz HAMP domain+Valine A/D fusion (SEQ ID NO:48) to PhoR histidine kinase Escherichia coli sequence (SEQ ID NO:49).
SEQ ID NO:5—DNA coding sequence of RpfCPhoR Fusion of Xylella fastidiosa RpfC quorum sensing receptor to PhoR HK at A/D valine position, Arahidopsis codon optimized sequence.
SEQ ID NO:6—Protein sequence of RpfCPhoR Fusion of Xylella fastidiosa RpfC quorum sensing receptor to PhoR HK at A/D valine position, Arabidopsis codon optimized sequence.
SEQ ID NO:7—DNA coding sequence of TrzChim3: Trz with partial substitution of PhoR DHP domain Escherichia coli sequence.
SEQ ID NO:8—Protein sequence of TrzChim3: Trz with partial substitution of PhoR DHP domain Escherichia coli sequence.
SEQ ID NO:9—DNA coding sequence of TrzChim3 ADD to EGA variant Escherichia coli sequence.
SEQ ID NO:10—Protein sequence of TrzChim3 ADD to EGA variant Escherichia coli sequence.
SEQ ID NO:11—DNA coding sequence of TrzChim3-8 Directed evolution variant of TrzChim3 with restored on/off functionality Escherichia coli sequence.
SEQ ID NO:12—Protein sequence of TrzChim3-8 Directed evolution variant of TrzChim3 with restored on/off functionality Escherichia coli sequence.
SEQ ID NO:13—DNA coding sequence of TrzChim3-10 Directed evolution variant of TrzChim3 with restored on/off functionality Escherichia coli sequence.
SEQ ID NO:14—Protein sequence of TrzChim3-10 Directed evolution variant of TrzChim3 with restored on/off functionality Escherichia coli sequence.
SEQ ID NO:15—DNA coding sequence of TazPhoR: TrzPhoR fusion with the Tar chemotactic receptor replacing the Trg chemotactic receptor Escherichia coli sequence.
SEQ ID NO:16—Protein sequence of TazPhoR: TrzPhoR fusion with the Tar chemotactic receptor replacing the Trg chemotactic receptor Escherichia coli sequence.
SEQ ID NO:17—DNA coding sequence of TazPhoR 61: Maltose inducible directed evolution variant of TazPhoR Escherichia coli sequence.
SEQ ID NO:18—Protein sequence of TazPhoR 61: Maltose inducible directed evolution variant of TazPhoR Escherichia coli sequence.
SEQ ID NO:19—DNA coding sequence of TazPhoR 86: Maltose inducible directed evolution variant of TazPhoR Escherichia coli sequence.
SEQ ID NO:20—Protein sequence of TazPhoR 86: Maltose inducible directed evolution variant of TazPhoR Escherichia coli sequence.
SEQ ID NO:21—DNA coding sequence of Tac8: TrzChim3-8 with the chemotactic receptor Tar replacing the chemotactic receptor Trg Escherichia coli sequence.
SEQ ID NO:22—Protein sequence of Tac8: TrzChim3-8 with the chemotactic receptor Tar replacing the chemotactic receptor Trg Escherichia coli sequence.
SEQ ID NO:23—DNA coding sequence of Tac40: Maltose inducible directed evolution variant of Tac8.
SEQ ID NO:24—Protein sequence of Tac40: Maltose inducible directed evolution variant of Tac8.
SEQ ID NO:25—DNA coding sequence of PhoR Phosphate regulon sensor Histidine Kinase from Escherichia coli. 
SEQ ID NO:26—Protein sequence of PhoR Phosphate regulon sensor Histidine Kinase from Escherichia coli. 
SEQ ID NO:27—DNA coding sequence of Trg Ribose responsive chemotactic receptor that interacts with ribose binding protein (RBP) from Escherichia coli. 
SEQ ID NO:28—Protein sequence of Trg Ribose responsive chemotactic receptor that interacts with ribose binding protein (RBP) from Escherichia coli. 
SEQ ID NO:29—DNA coding sequence of Tar Aspartate and Maltose responsive chemotactic receptor that interacts with maltose binding protein from Escherichia coli. 
SEQ ID NO:30—Protein sequence of Tar Aspartate and Maltose responsive chemotactic receptor that interacts with maltose binding protein from Escherichia coli. 
SEQ ID NO:31—DNA coding sequence of EnvZ Histidine kinase involved in osmotic sensing from Escherichia coli. 
SEQ ID NO:32—Protein sequence of EnvZ Histidine kinase involved in osmotic sensing from Escherichia coli. 
SEQ ID NO:33—DNA coding sequence of RpfC Quorum sensing histidine kinase that senses diffusible signaling factor DSF from Xylella fastidiosa. 
SEQ ID NO:34—Protein sequence of RpfC Quorum sensing histidine kinase that senses diffusible signaling factor DSF from Xylella fastidiosa. 
SEQ ID NO:35—DNA coding sequence of Trz-Trg chemotactic receptor fused to EnvZ histidine kinase at conserved HAMP domain: Trg nt 1-801_EnvZ nt 802-end.
SEQ ID NO:36—Protein sequence of Trz-Trg chemotactic receptor fused to EnvZ histidine kinase at conserved HAMP domain: Trg aa 1-275_EnvZ aa 276-end.
SEQ ID NO:37—DNA coding sequence of Taz-Tar chemotactic receptor fused to EnvZ histidine kinase at conserved HAMP domain:Tar nt 1-778_EnvZ nt 779-end.
SEQ ID NO:38—Protein sequence of Taz-Tar chemotactic receptor fused to EnvZ histidine kinase at conserved HAMP domain:Tar aa 1-262_EnvZ aa 263-end.
SEQ ID NO:39—DNA coding sequence of PhoQTrzPhoR: Mg2+ responsive PhoQ receptor fused to TzyPhoR at the D position. Escherichia coli sequence.
SEQ ID NO:40—Protein sequence of PhoQTrzPhoR: Mg2+ responsive PhoQ receptor fused to TzyPhoR at the D position. Escherichia coli sequence.
SEQ ID NO:41—DNA coding sequence of LuxQTrzPhoR: D position fusion of receptor histidine kinase LuxA which quorum senses AI-2 and TrzPhoR LuxQ codon optimized for Escherichia coli. TrzPhoR Escherichia coli sequence.
SEQ ID NO:42—Protein sequence of LuxQTrzPhoR: D position fusion of receptor histidine kinase LuxA which quorum senses AI-2 and TrzPhoR LuxQ codon optimized for Escherichia coli. TrzPhoR Escherichia coli sequence.
SEQ ID NO:43—PhoQ DNA coding sequence from Escherichia coli. 
SEQ ID NO:44—PhoQ protein sequence from Escherichia coli. 
SEQ ID NO:45—DNA coding sequence of LuxQ Receptor Histidine Kinase involved in quorum sensing from Vibrio harveyi. 
SEQ ID NO:46—Protein sequence of LuxQ Receptor Histidine Kinase involved in quorum sensing from Vibrio harveyi. 
SEQ ID NO:47—DNA recognition sequence for PhoB.
SEQ ID NO:48—Partial protein sequence of TrzPhoR: Trz HAMP domain+Valine A/D fusion.
SEQ ID NO:49—Partial protein sequence of PhoR histidine kinase Escherichia coli sequence.
SEQ ID NO:50—Partial EnvZ protein sequence spanning fusion region.
SEQ ID NO:51—Partial Trg protein sequence spanning fusion region.
SEQ ID NO:52—Partial Trz protein sequence spanning fusion region.
SEQ ID NO:53—Partial PhoR protein sequence spanning fusion region.
SEQ ID NO:54—Partial protein sequence of coiled coil test construct Trg′′CC′′Pho.
SEQ ID NO:55—Partial protein sequence of coiled coil test construct TrzEnvZCC.
SEQ ID NO:56—Partial protein sequence of coiled coil test construct TrzEnvZcc2&3.
SEQ ID NO:57—Partial protein sequence of coiled coil test construct TrgPhoRcc3.
SEQ ID NO:58—Partial protein sequence of coiled coil test construct TrzHAMPPhoR fusion.
SEQ ID NO:59—Partial protein sequence of coiled coil test construct TrzHAMP+V PhoR.
SEQ ID NO:60—Partial protein sequence of coiled coil test construct TrzHAMP+VK.
SEQ ID NO:61—Partial protein sequence of coiled coil test construct TrgHAMP+V.
SEQ ID NO:62—Partial protein sequence of coiled coil D position mutants TrzHAMP+M.
SEQ ID NO:63—Partial protein sequence of coiled coil D position mutants TrzHAMP+V.
SEQ ID NO:64—Partial protein sequence of coiled coil D position mutants TrgHAMP+V.
SEQ ID NO:65—Partial protein sequence of coiled coil D position mutants TrgHAMP+G.
SEQ ID NO:66—Partial protein sequence of coiled coil D position mutants TrgHAMP+A.
SEQ ID NO:67—Partial protein sequence of coiled coil D position mutants TrgHAMP+L.
SEQ ID NO:68—Partial protein sequence of coiled coil D position mutants TrgHAMP+I.
SEQ ID NO:69—Partial protein sequence of coiled coil D position mutants TrgHAMP+E.
SEQ ID NO:70—Partial protein sequence of coiled coil D position mutants TrgHAMP+T.
SEQ ID NO:71—Partial protein sequence of EnvZ (SEQ ID NO:71) spanning the ADD residues (275-277) of EnvZ.
SEQ ID NO:72—Partial protein sequence of PhoR (SEQ ID NO:72) spanning the EGA residues corresponding to the ADD residues (275-277) of EnvZ.
SEQ ID NO:73—DNA coding sequence of MBP 6.1-5.
SEQ ID NO:74—DNA coding sequence for TAL transcription factor engineered to bind Gal4 binding sites.
SEQ ID NO:75—DNA coding sequence for Gal4VP64 codon optimized for Arabidopsis. 
SEQ ID NO:76—DNA coding sequence for Firefly luciferase codon optimized for Arabidopsis. 
DETAILED DESCRIPTION
The present disclosure provides novel receptor fusions with the histidine kinase PhoR for use in synthetic signaling systems with both high throughput systems (e.g., bacteria) and in plants. The source of the receptors may be other histidine kinase receptors such as those from pathogenic bacteria, e.g., the quorum sensing receptor RpfC. Because of the inventors' robust abilities with computational protein design, the receptor component can now be computationally designed. Alternatively, the receptors may be derived from chemoreceptor involved in periplasmic binding protein (PBPs) mediated chemotaxis such as Trg or Tar. Either the PBPs or the receptors have computationally re-designed binding pockets or are able to be entirely computationally redesigned, allowing the detection of novel, man-made substances in the environment and/or metabolic products of pathogens and/or metabolic products of biological organisms in general. The present disclosure also establishes the ability to convert nonfunctioning receptor histidine kinase fusions into functional fusions by manipulating a specific region of the histidine kinase, the CA interacting region. One application of the present disclosure is for use in detecting novel environmental signals using detector plants enabled with the present synthetic signaling system.
Plants, bacteria, and fungi can sense aspects of their environment through two-component or histidine kinase (HK) signal transduction systems that transmit information via protein to protein phosphoryl-transfer. Two component signal transduction systems respond to specific inputs such as the presence of ligands, osmotic conditions, oxidative conditions, or factors contributing to pathogenesis. The simplest two-component systems (TCS) use a plasma membrane localized histidine kinase and an intracellular response regulator (RR) protein. The RR functions to both receive the phosphoryl signal at an aspartate residue and initiate a transcriptional response upon becoming phosphorylated (FIG. 1A). More complex hybrid two component systems found in bacteria and plants involve additional components (FIG. 1B). TCS have been used in synthetic biology and biotechnology applications, primarily as components in synthetic signaling pathways.
Typically sensing of an environmental aspect through a TCS consists of three distinct phases, signal transmission, signal dependent kinase activation and signal transduction. In signal transmission a membrane localized receptor senses an environmental stimulus or binds to a molecular signal (ligand). The sensing event causes a conformational change in the receptor and the conformational change propagates across the membrane (trans-membrane signaling) to the cytoplasmically localized portion of the histidine kinase. Signal dependent kinase activation occurs when the receptor signal acts upon a distinct region of the histidine kinase causing a conformational change. The conformational change triggers a switch from a kinase “off” to a kinase “on” configuration of the HK. Activation of kinase activity results in autophosphorylation of a conserved Histidine residue. Signal transduction occurs when a RR interacts with the HK, resulting in a transfer of the phosphoryl group from the HK to the RR. The phosphorylated RR undergoes a conformational change which allows it to activate transcription of genes that will allow the plant, bacteria or fungus to respond to the environmental stimulus.
The inventors previously described a synthetic two-component signaling system in plants based on bacterial derived histidine kinases and the bacterial RR PhoB (U.S. Pat. Nos. 8,148,605 and 9,062,320, both of which are incorporated herein by reference in their entirety). In this synthetic system, computationally designed receptors based on bacterial periplasmic binding proteins bind a substance of interest e.g., the explosive TNT. Periplasmic binding proteins (PBPs) are involved in binding of a wide variety of substances in gram negative bacteria. A subset of PBPs interact with the chemotactic receptors Trg, Tar, and Tap and initiate a signaling cascade (FIG. 1C) that allows the bacteria to respond to the presence of certain sugars (glucose, ribose, maltose, galactose) and amino acids (dipeptides, asp, glu, ser, ala and gly) by directing the cells to environments containing these nutrients. The ligand binding sites of ribose binding protein (RBP) and maltose binding protein (MBP) have been computationally re-designed to bind a variety of substances, among them a nerve toxin agent surrogate, the metal zinc and 2,4,6 trinitrotoluene (TNT) (Looger, et al., Nature 423:185-190, 2003; Feng, et al., eLife 4:e10606, 2015; Bick, et al., eLife 6; e28909, 2017; Strauch, et al., Nat. Biotechnol. 35:667-671, 2017). When a PBP binds its ligand a conformational change is produced, leading to increased affinity of the PBP-ligand complex for the extracellular domain of a bacterial chemotactic receptor, Trg in the case of RBP and Tar in the case of MBP. In this synthetic signaling system a chimeric fusion between the chemotactic receptor Trg with the cognate HK for PhoB, PhoR allows direction of the signal through PhoB. The inventors discovered that PhoB translocates to the plant's nucleus in a signal dependent manner. In this plant system PhoB has been modified to activate the transcription of plant genes (FIG. 2). In one aspect of the system, this synthetic two component signal transduction pathway activates a set of genes which breaks down chlorophyll (de-greening circuit). This results in the ability to produce a monitor or detector plant which de-greens specifically in the presence of a substance of interest. This synthetic signal transduction system allows one to artificially control biological input-output in plants as well as test, monitor and perfect components in bacteria.
The present disclosure exploits cells or plants' sensing mechanisms for extracellular signals, with the development of cells or plants that respond to a variety of biological, chemical, and environmental pollutants for substances of interest to produce a readily detectable response or phenotype. In a particular embodiment the plants disclosed herein lose green color when exposed to a specific substance; the degreening is an easily detectable biomarker and does not require sophisticated instrumentation. The modularity of the system allows a wide variety of responses, both visible and non-visible, to be produced in response to a detection event. These plants function as “sentinels” and are especially useful for widespread monitoring of substances in the environment whether interior or exterior.
For the plants to be useful as degreening biomarkers to detect specific chemical agents or to monitor environmental factors, an appropriate input circuit was produced. This input circuit is useful for linking detection to response. The modularity of the system allows a wide variety of responses, both visible and non-visible, to be produced in response to a detection event. When the input circuit is linked to the degreening circuit, a plant detector is produced. In addition, the ability to control response of plants and biological organisms to specific substances provides a useful tool for biotechnology allowing, for example, co-ordination of crop plants, facilitating harvesting and controlling other developmental, tissue or environmental responses.
The present disclosure provides a highly specific and sensitive method for cells or plants to detect a target substance of interest in their environment, transmit the sensing from outside the cell or plant to the nucleus, induce a specific transcriptional response and a type of output (for example controlled degreening) that provides detection to humans. In one embodiment of the present disclosure, the regulatory circuits have two components, referred to herein as input and output circuits. In another embodiment of the present disclosure, the input circuit has an ability to specifically recognize (bind) the target substance of interest and transmit a signal to the nucleus, where a specific response is initiated. The response can be a phenotypic and/or metabolic change of interest or a visible response to produce a plant sentinel. The modularity of the system allows a wide variety of responses, both visible and non-visible, to be produced in response to a detection event. In one embodiment of the present disclosure, one output circuit produces a degreening or other detectable phenotype in the transgenic plant containing the circuits. In one embodiment of the present disclosure the output circuit is also modular in that a variety of genes can be placed under control of the signal-inducible promoter. In one embodiment the input circuit is modular in that the receptor that is targeted to the extracellular space can be designed to provide specificity and selectivity for binding a given target substance of interest. One specific input circuit specifically exemplified herein provides detection of the explosive trinitrotoluene. One specific output circuit specifically exemplified herein serves as a simple and sensitive marker that can easily be recognized directly (visually), or by remote sensing and/or by monitoring changes in chlorophyll fluorescence, by changes in photosystem I and/or photosystem II, electron transport, by changes in hyper-spectral imaging, and/or by changes in spectral properties. The modular nature of the system provides the ability to produce numerous types of responses or readouts including non-visible readouts that are detectable by webcam and high altitude platforms.
The input circuit comprises a sensor protein specifically targeted to the extracellular space of the cell or plant with a binding site specific for recognizing a target agent or a target substance of interest, a transmembrane histidine kinase protein, a nuclear shuttling protein, and a synthetically designed signal responsive promoter. Variations and elaborations described herein are found in various research publications, and known to those skilled in the art. One type of output circuit described herein activates the expression of one or more genes, which results in a degreening phenotype in transgenic plants containing the circuits.
The present disclosure provides a sensor protein or receptor at the cell surface, such that the sensor protein or receptor has a binding site specific for the target substance of interest. The transmembrane protein, a second component of the input circuit has three parts: an interacting domain, a transmembrane domain and a histidine kinase domain. Binding of the target substance of interest causes a conformational change in the sensor protein or receptor, so that it then binds to an interacting domain of the transmembrane protein on the exterior surface. The interaction of the sensor protein:target substance of interest complex results in activation of the histidine kinase, typically by an autophosphorylation mechanism. The interaction of the sensor protein or receptor with the interacting domain produces a conformational change in the transmembrane protein and/or transmembrane histidine kinase. The autophosphorylated histidine kinase domain of the transmembrane protein transfers a high energy phosphate group to a cytoplasmically located protein. A variety of proteins will function as shuttling proteins, including, but not limited to, a synthetically adapted shuttling protein such as PhoB:VP64, other shuttling proteins such as histidine phosphotransferases, Arabidopsis histidine phosphotransferase, and other natural proteins such as response regulators from plants, bacteria, fungi, and cyanobacteria systems, including adapted or synthetic proteins, or computationally designed proteins, that function in histidine kinase mediated signaling systems.
The shuttling protein typically has several functions including reception of the signal from the transmembrane protein, relay of this signal to the nucleus, or specific responding component, and/or activation of transcription. The protein may directly, or indirectly, bring about a cellular response. The typical cellular response is activation of transcription; however, other responses are possible including changes in membrane potential, cell expansion (in the case of engineering a response that would allow expansion of the xylem), or changes in the accumulation of a plant-derived product. At least some proteins are phosphorylated (directly) by the histidine kinase domain of the transmembrane protein. The phosphorylation of the proteins or protein components can cause an increase in binding affinity for a specific sequence of DNA as is the case for OmpR, or in the case of PhoB, allow a conformational change that removes repression, allowing the DNA binding domain to function. One type of response of this is a readout circuit that includes expression of the specifically regulated gene located in the nucleus of the plant and the production of a detectable phenotype, appearance or function of lack thereof or the readout can include activation of a gene controlling a trait of interest, for example, flowering or ripening.
The sensor protein or receptor can be derived from a bacterial (e.g., Escherichia coli) periplasmic binding protein (PBP), such as a maltose, ribose or galactose PBP, and the binding site for the target substance of interest can be a naturally occurring binding site or one that is the result of computational design. At the N-terminus there is also a signal peptide sequence for targeting the sensor protein to the exterior of the cell, plant or plant cell, such as, but not limited to, the signal peptide of the pollen PEX protein (Baumberger, et al., Plant Physiol. 131:1313-1326, 2003). Substances of interest can include, without limitation, plant hormones, explosives, chemical agents, products of industrial manufacturing, metabolites of biological organism(s), environmental pollutants including all currently listed environmental pollutants on the Environmental Protection Agency (EPA) superfund site, halogenated hydrocarbons, or degradation products, metal ions such as zinc, a heavy metal, a sugar, neurotransmitter, herbicides, pathogenic products, or an amino acid. The ability to computationally design the PBP, partially or entirely, expands this list of detectable substances to most molecules.
When the target substance of interest is bound to the sensor protein or receptor, there is an interaction with the protein that transmits a signal from the exterior of the plant to the interior of the plant by autophosphorylation and activation of the histidine kinase. Upon binding of the target substance of interest, there is an interaction between or within the sensor protein or receptor and the transmembrane protein (which contains the histidine kinase domain). This interaction causes autophosphorylation of a histidine residue located on the interior portion of the transmembrane protein. The phosphoryl group is then transferred (a mechanism called phosphor-relay or phosphotransfer) to a shuttling protein or transcription activator protein domain, allowing it to translocate to the nucleus or otherwise initiate a response. The phosphorylated protein, protein domain or secondary protein then binds a DNA recognition sequence present in a promoter of a gene (or genes) in the nucleus, which can be a genetically engineered gene, with the result that transcriptional expression of that gene occurs.
The transmembrane protein can be genetically engineered as a translational fusion consisting of plant and/or bacterial proteins, derived from one or more bacterial or plant proteins, derived from one or more proteins containing histidine kinase-like features, or synthetically synthesized features, or computationally designed features, provided that it functions in plants in conjunction with a protein or protein domain to transmit the signal to a response unit. The intracellular receptive protein or protein domain can be a plant protein, a bacterial protein or a synthetically designed protein, with the proviso that it receives the signal from the transmembrane protein. The receptive protein can either transmit the signal to another protein that initiates a response, or translocate to the nucleus in response to the signal. In one example, the signal receptive protein itself moves to the nucleus, binds DNA and activates gene expression. Specific examples include a plant histidine phosphotransferase or a bacterial protein such as the E. coli proteins OmpR or PhoB. Where the signal receptive protein is also a transcriptional activation protein, PhoB, the DNA recognition sequence is CTGTCATAYAYCTGTCACAYYN (SEQ ID NO:47), and it can occur from 2 to 12 times, for example 4 or 8 times in the region upstream of the transcription start site, and includes a plant transcriptional start site such as defined by a minimal transcriptional promoter.
The sequence that is expressed in response to detection of, or the presence of, a target substance of interest in the plant environment can be a protein coding sequence or it can be a functional nucleic acid sequence (such as a RNA interfering molecule, diRNA or an antisense RNA to inhibit synthesis of a related coding sequence) or it can be a combination of these. The associated expressed sequence can be a plant gene that is, in nature, expressed constitutively or in a tissue or condition specific fashion, but in the present disclosure, it is expressed when the target substance of interest or substance that binds to the sensing protein or sensing proteins is present or after the target substance of interest is present. The expressed sequence can be virtually any sequence of interest: a detectable marker such as green or yellow fluorescent protein or another fluorescent protein, β-glucuronidase or β-glucosidase, among others, a positive regulator of flowering or a sterility protein preferably selectively expressed in the appropriate tissue, a bioremediation coding sequence such as mercury reductase, a phytochelatin or metal sequestering protein, an enzyme for detoxifying a contaminant or harmful material, and the production of a specific nutritive or pharmaceutical substance, among others. The expressed sequence can also be a functional nucleic acid (antisense or diRNA to inhibit expression of a related nucleic acid sequence). There can be more than one target substance-regulated gene within a single cell or plant and more than one readout or response in a single cell or plant.
In an embodiment of the present disclosure, the sensing circuitry can be used to control features of interest, such as the timing of flowering of a plant or ripening of a fruit such that harvesting is more synchronized, coordination of crops such as cotton, soybean and corn and hence an ability to predict harvest time, and thus, make harvesting more efficient and economical or so that plants are in flower for a particular occasion. Such a gene or response unit is operably linked to a promoter containing the recognition sequence of the specific sensing system or systems. In another embodiment, the target substance of interest-dependent transcription regulatory system can be used to render plants exposed to the target substance sterile, when a sterility inducing protein is expressed under the regulatory control of the control system of the present disclosure.
Within the scope of the present disclosure are one or more DNA constructs containing a plant operable sensor protein as described above, a plant transmembrane protein, a plant operable signal reception and/or transcription activation protein that is activated by the histidine kinase portion of the sensing circuit (via an intermediary endogenous protein, or directly by the membrane bound kinase), and a plant operable sequence operably linked to transcription regulatory sequences, which include the recognition sequence of the particular transcription activating protein of the disclosure. Similarly, the present disclosure provides transgenic plant cells, transgenic plant parts, transgenic plant tissue and transgenic plants containing one or more constructs of the present disclosure.
The present disclosure provides transgenic (sentinel) plants useful for environmental monitoring and for detecting particular biological and chemical agents, environmental pollutants, and/or a specific substance such as herbicides or trigger compounds. Trigger compounds are substances that bind to the natural or computationally designed sensor proteins and thereby increase the sensor proteins affinity for an extracellular protein domain (for example Trg). In a specific embodiment, the plants disclosed herein lose green color within hours of exposure to particular target biological/chemical agents or environmental pollutants. The loss of green color (or a change in the fluorescence of chlorophyll or a change in photosynthetic electron transport, or other types of responses) in plants are easily detectable, either by direct observation, with simple hand-held machines, or remotely by aircraft, satellite, or other varieties of sensors, including webcams and high altitude platforms. The sentinel plants of the present disclosure comprise genetically engineered DNA constructs that direct the expression of both the input and output circuits, as described herein, with the result that the plants lose color, or otherwise respond, when they “sense” the presence of the target substance of interest. An important advantage of the degreening system in these sentinel plants is that they are capable of regreening. They either regreen naturally or at an enhanced rate with treatment of hormones, i.e., the sentinels can be reset for renewed surveillance for the target substance to which they respond. In one aspect of the present disclosure a transgenic plant wherein degreening has occurred due to the presence of a target substance of interest is able to regreen after removal of the external target substance of interest. Other responses or readouts allow rapid response time or ability to detect signals remotely with webcams or high altitude platforms.
The transgenic plants (sentinel plants) of the present disclosure can be indoor plants, for example, any of a number of species that are commonly used as decorative accent plants, such as peace lily (Spathiphyllum), philodendron, pothos (Epipremnum), spider plant (Chlorophytum), Tradescantia and Dracaena, and the like. In addition, the sentinel plants can be crop plants such as corn, wheat, soy, cotton, soybeans and others, or they can be grasses or trees, either deciduous (poplars, aspens, maple, oak, cottonwood, and the like) or evergreen (pines, spruce, junipers and the like) or they can be annuals or perennials used in various types of plantings, or they can be a variety of native species, or they can be aquatic plants including, but not limited to, algae. Nearly all plants and/or plant cells can be readily transformed and transformed seed directly formed or plants produced from the transformed cells, as is well known to the art. The sentinel plants of the present disclosure can provide a warning of current presence of a target substance of interest or they can provide notice to responders to a scene to allow for appropriate protective measures and/or to prevent exposure to a dangerous condition. In addition, the sentinel plants provide the ability to remotely monitor for the presence of substances. Moreover, the sentinel plants allow for continuous environmental monitoring over extremely large scales (e.g., hundreds or thousands of square kilometers) that is not currently possible with any other publicly known method.
The sentinel plants of the present disclosure contain a genetically engineered signaling pathway consisting of two functional parts referred to herein as “input” and “output” wherein one embodiment of the output is the “degreening” circuit”. The input gene circuit is a natural or genetically engineered system, or computationally designed system, that recognizes a biological or chemical agent, explosive, or an environmental pollutant or target substance of interest specifically and selectively, then activates an output gene circuit that results in the desired response. In the case of a plant sentinel, one example of an output gene circuit is the degreening circuit, so that the degreening phenotype i.e., white plants, are produced in response to an agent or pollutant. The degreening can be visually detected as a loss of green color or it can be detected as a change in chlorophyll fluorescence or in photosynthetic electron transport or it can be detected with a variety of spectroscopic methods such as hyper-spectral imaging and other methods. Other responses or readouts allow rapid response time or ability to detect signals remotely with webcams or high altitude platforms.
The output and input circuits of the present disclosure are generated by expressing DNA constructs specifically designed to provide a functional system. Examples of methodologies well-known to people in the field include CRISPR-Cas9 methods, where the endogenous genes can be changed to produce plants with these properties. The input circuit is a system comprising a receptor or a binding protein designed to recognize (e.g., by binding) a signal (e.g., analyte or ligand), and this binding event ultimately activates a response, one of which is transcription of a gene of the output (degreening) circuit to produce a plant sentinel. Thus, the specificity and selectivity of a given response is determined by the input circuit. An example of the input circuit is a receptor or binding protein (sensor protein) that specifically binds a particular explosive, chemical agent or a pollutant, or pathogen or pathogen product, the target substance of interest, which, upon binding of such explosive, agent or pollutant, or pathogen or pathogen product, can transmit a signal via the transmembrane protein to activate transcription of a gene(s) in the output circuit. As specifically exemplified the sensor protein:target substance complex interacts with the exterior domain of the transmembrane protein, with the result that the histidine kinase becomes active.
In one method, the response system (output, as exemplified by degreening) circuit is generated by transforming a plant with DNA constructs (i.e., expression vectors) comprising one or more nucleic acids encoding, or complementary to, a nucleic acid encoding key enzymes or functional fragments thereof in chlorophyll biosynthesis and/or degradation pathway under the control of a promoter that responds to a signal from the input circuit. The term “functional fragment” as used herein, is intended to indicate that the product (i.e., enzyme) can be a truncated protein as long as it retains its enzymatic activity to cause degreening (chlorophyll degradation). One skilled in the art would know that a truncated protein may be able to maintain enzyme activity. Examples of chlorophyll degradation enzymes include, but are not limited to, RCCR, PaO and chlorophyllase. The output/degreening circuit can also comprises a target-substance-regulated inhibition of chlorophyll biosynthesis. As specifically exemplified, this is achieved by expression of either antisense, or preferably, interfering RNA molecule (such as diRNA, siRNA) sequences specific to a coding sequence for an enzyme in the chlorophyll biosynthetic pathway. These interfering RNA molecules are examples of functional nucleic acids, and in the context of inhibition of gene expression, a functional fragment of a coding sequence or gene is one that specifically interacts with a transcript of the coding sequence or gene so as to reduce expression of the product of that gene or coding sequence. Examples of the enzymes involved in chlorophyll biosynthesis include, but are not limited to, protochlorophyllide oxidoreductase (POR), GUN4, other GUN genes (genome uncoupling), Mg chelatase and chlorophyll synthetase. It is understood that other targets in the chlorophyll synthesis or degradation pathway can be substituted for those specifically set forth. It is further understood that the input system allows a wide variety of outputs, responses or readouts, as long as the output, response or readout is operationally linked to the input. These include rapid response time or ability to detect signals remotely with webcams or high altitude platforms.
The DNA construct for transforming the readout or degreening gene circuit into a plant or plant cell typically contains a nucleic acid encoding at least one chlorophyll degradation enzyme (or a fragment thereof that functions to effect chlorophyll degradation) and/or desirably also a nucleic acid whose expression product inhibits chlorophyll synthesis operably linked to a promoter with transcription regulatory sequences that bind a transcription activator protein that receives the signal from the input gene circuit. Typically it can be a transcriptional activator protein that solely receives the signal from the transmembrane histidine kinase and shuttles to the nucleus or a nuclear localized transcriptional activator protein that receives the signal from the transmission protein that relays the signal from the transmembrane histidine kinase and shuttles to the nucleus. The exterior component of the transmembrane histidine kinase has bound the sensor protein substance complex therefore relaying an input signal generated by an explosive, a chemical or biological agent, a pollutant, a pathogen or pathogen product, or a specific substance. In response to the input signal, this dual modulation, i.e., inhibition of synthesis and stimulation of degradation of chlorophyll ensures loss of green color in plants when exposed to a variety of chemical agents or environmental pollutants. As described herein, chlorophyll synthesis can be inhibited by producing interfering RNA or antisense RNA derived from at least one of the genes encoding chlorophyll synthetic enzymes.
Accordingly, a transgenic plant containing the input and output circuits disclosed herein loses its green color when exposed to a substance in the environment that activates the input circuit by binding to a specific receptor site (i.e., sensor protein) outside the plant. The substance can be, for example, a chemical agent, mercury, lead, arsenic, uranium, cadmium, selenium, polycyclic aromatic hydrocarbon, a benzene, a toluene, a xylene, or a halogenated (chloro, fluoro, and chlorofluoro) hydrocarbon, a by-product of industrial manufacturing, a metabolite of biological organisms, explosives, any substance listed on the EPA superfund website, specific compounds involved in manufacture of compounds of interest, a pathogen or pathogen product, or a trigger substance to bring about a desired change in the plant or crop. It is also possible to wire the genetic circuitry to enable detection of multiple substances. In addition, the target substance that binds to a specifically engineered sensor protein and input circuit via the extracellular receptor could be an explosive such as trinitrotoluene, other types of explosives, or a degradation product of one of the foregoing compounds specifically bound by the sensor protein, including computationally designed sensor proteins.
The sensing and response system of this disclosure is modular in that it can be coupled with a variety of input circuits (sensor proteins) to provide specificity and selectivity for a particular chemical agent and/or other environmental factor of interest that is recognized by an available sensor protein that effectively interacts with the exterior domain of the transmembrane protein when the target substance is bound. Likewise, the input circuits can be combined with Logic Gates (e.g., AND, OR, NOT gates organized, for example, as detect substance “a” AND detect substance “b”; detect substance “a” OR substance “b”; detect substance “a” OR substance “b” but NOT substance “c,” etc.) to further increase the present technology's uses. Similarly, the readout gene that is expressed via the histidine kinase system or systems of this disclosure can be selected for a desired result, with the proviso that it is operably linked to a promoter and associated control sequences that interact positively with a transcription regulatory protein activated directly or indirectly by the histidine kinase and/or PhoB or OmpR, described herein. Specifically, receptors that are engineered to bind site specifically to the target substance of interest (including but not limited to heavy metals, chemical agents, explosives and certain degradation products thereof, environmental pollutants such as MTBE, herbicides such as glyphosate and the like. The sensing circuit further includes the transmembrane protein with an external binding domain that interacts with the sensing protein-target substance complex and an intracellular portion which directs the phosphorylation of a transcriptional activator protein, as specifically exemplified by PhoB and/or modified and/or an adapted version of the PhoB protein. PhoB can also be phosphorylated by an endogenous plant histidine phosphotransferase. The phosphorylated PhoB (activated form) then binds to the PhoB cognate binding sequences which are part of the synthetic promoter operably liked to a chlorophyll degradation enzyme coding sequence (such as chlorophyllase). The transcriptional activator protein can also be a hybrid protein including, but not limited to, PhoB:VP64 translational fusion protein and it is expressed in a transgenic plant expressing its coding sequence operably linked to a plant expressible promoter, which can be constitutive or which can include sequences for tissue-specific or condition-specific expression. The activator protein can be any eukaryotic transcriptional activator including, but not limited to, VP16, VP64 and GAL4. The signal-dependent nuclear translocating PhoB protein could also be fused to synthetic repressors, including LexA-EAR (LEAR) or Gal4-EAR (GEAR) (U.S. Patent Application Publication Number 2018/0105825), or OfpX (Wang, et al., PLoS One 6:e23896, 2011).
Histidine Kinase Signal Transduction System
Two component histidine kinase signal transduction systems are conserved between plants and bacteria, and this conservation was the basis of forming a functional input (sensing) circuit. In bacteria, sensitive chemotactic sensors exist to direct motile bacteria to nutrients, e.g., ribose. When a periplasmic binding protein such as the ribose binding protein binds its ligand, it develops a high affinity for the extracellular domain of bacterial chemotactic receptors such as Trg. Upon binding of the ligand/binding protein complex, a cytoplasmic histidine kinase is activated. Normally in the bacterium, this results in chemotaxis toward the food source. Hybrid histidine kinases have been expressed in bacteria where the cell surface PBP binding domain of Trg has been combined with the interior histidine kinase domain from proteins such as EnvZ. This hybrid protein activates transcription via phosphorylated transcription activator proteins. In the hybrid histidine kinases, the target substance is bound by the sensor protein, and the substance:protein complex binds to the interacting domain of the hybrid histidine kinase at the exterior side of the cell membrane, and that initiates activation of the histidine kinase (HK). The HK starts a phospho-relay (phosphorylation relay) through a bacteria response regulator (e.g., OmpR or PhoB) to activate transcription of bacterial genes. The phospho-relay always goes His→Asp→His, etc. In addition, at least some transcription activator proteins are phosphorylated (activated) by that same kinase domain.
Chemotactic binding proteins (periplasmic binding proteins) have been redesigned using computer-run computational design methods so that instead of binding substances such as ribose or galactose or maltose, the engineered proteins specifically bind a target substance of interest such as TNT, chemical agents, heavy metals, or other environmental pollutants or harmful substances.
Plants also use a two-component or histidine kinase signaling system that responds to cytokinin (a plant hormone). Plant signal transduction is more complex. The histidine kinases are “hybrid types”. The plant HKs in Arabidopsis are known as AHKs. Upon sensing cytokinin, plant HKs phosphorylate an internal histidine kinase and initiate a phospho-relay internally to an aspartate residue located in the receiver domain of the same protein. The receiver domain transfers the phosphate group to an independent protein. The independent protein moves into the plant cell nucleus upon phosphorylation and then transfers the phosphate group to a nuclear localized protein, ARR Type B, transcription factors that then initiate transcription of ARR Type A genes. Examples of ARR type A genes useful in the present disclosure include, but are not limited to, ARR5 and ARR7, or any Type A ARR gene. Other functionally equivalent sequences may also be used in the systems described herein.
Computer design enables the design of sensor proteins to bind with great specificity and sensitivity, a variety of compounds or substances. In bacteria, the engineered receptors were targeted to the periplasmic space to sense various substances of interest. In plant cells, it is necessary to add (desirably at the N-terminus) a secretory sequence functional in plant cells so that the sensor protein is at the exterior of the cell and can bind the particular target substance of interest and it is necessary to delete the bacterial periplasmic targeting leader. The starting point is the engineered periplasmic binding protein, and the ending point is a detectable change resulting from a transcriptional response in the nucleus; computer-designed sensor proteins and molecular biological techniques allows for the combination. Hybrids at both the starting point and ending point allowed functional signaling.
To obtain information from outside the plant cell and transmit a signal to the nucleus of the plant cell, specifically engineered target sensing receptors were positioned outside of plant cells. Receptors that have been computationally designed include, but are not limited to, the periplasmic binding proteins RBP, MBP (maltose binding protein) and GBP (galactose binding protein). Importantly, at least in part because the system is modular, PCR or DNA synthesis can be used to change the receptor/sensor protein portion from a receptor/sensor protein specific for TNT to a target substance of interest (explosives, chemical agents, zinc, heavy metal, environmental pollutant).
Plant Extracellular Space
Plants are not known to have a functional periplasmic space. However, evidence indicates that there is a functional space between the plant plasma membrane and the outside. Small proteins can freely move and/or diffuse in the plant cell wall, better understood as a complex matrix, and even move and/or diffuse in the plant cuticle, the waxy coating that is found outside some plant organs. In bacteria, the periplasmic binding protein contains a leader peptide portion that targets the protein to the periplasm. In plants, proteins are targeted to the extra-cellular space by way of the endoplasmic reticulum. Because of the different targeting mechanisms, a plant extracellular targeting sequence is needed and the bacterial periplasmic targeting leader must be removed.
Genetically Engineered Plants Capable of Losing Green Color
The present disclosure also provides genetically engineered plants capable of losing green color in response to a signal (analyte or ligand) by simultaneously controlling expression of genes involved in chlorophyll biosynthesis and/or degradation. These plants are capable of receiving input from cytoplasmic and extracellular analytes and linking these components to the degreening circuit resulting in the loss of green color. Thus, the plants of this disclosure serve as a simple and easily detectable biomarker for adverse environmental input.
The degreening circuit is assembled in a “plug and play” manner. Hence, the sensor protein for TNT, which initiates the input, can be replaced by a different computationally designed sensor protein allowing the degreening circuit to respond to a specific target substance or target substances of interest. The model plant species Arabidopsis, which allows rapid optimization of the degreening circuit and its response, can be used in the presently disclosed compositions and methods. However, the circuits described herein are readily introduced into other plant species such as those typical of shopping malls, office buildings, landscapes, forested areas, cropland or aquatic systems.
The plants of this disclosure that lose their green color in response to a target substance can serve as untiring sentinels reporting on adverse input from the environment (e.g., chemical weapons or pollutants). Plant sentinels would be unthreatening to the general public and can be deployed in shopping malls and office buildings and at special events where most people can recognize a loss of green color and security personnel could easily detect the changes within a short period with inexpensive hand-held machines. In addition, loss of green color or other disruption of chlorophyll, such as chlorophyll fluorescence, or photosystem electron transport or hyper-spectral imaging can be rapidly quantified by authorities with either portable hand-held equipment or simple laboratory equipment (spectrophotometers). In vast geographic areas, detector systems could be introduced into plants typical for landscapes and aquatic systems, allowing satellites to identify adverse environments.
The degreening circuit of the present disclosure induces genes that are involved in chlorophyll breakdown and synthetic genes for inhibiting chlorophyll synthesis. Simultaneous expression of the genes that initiate chlorophyll breakdown and inhibit new chlorophyll biosynthesis would yield the most efficient degreening phenotype. For this reason, the degreening circuit can be created using three genes, two in the chlorophyll degradation pathway and one inhibitory gene in the chlorophyll biosynthesis pathway. A person of ordinary skill in the art understands that other combinations of the genes that are known to be involved in chlorophyll synthesis and degradation can be used to obtain the degreening phenotype demonstrated herein. In addition, a person of ordinary skill in the art understands that the reactive oxygen species (ROS) generated in the chloroplast could be used to initiate and generate the degreening within plastids.
The degreening circuit of the present disclosure can respond in two different ways; it can respond to target substances within the cytoplasm as well as those that are extracellular. To test the ability of the degreening circuit to function with cytoplasmic input in plants, a synthetic cytoplasmic receptor is linked to the circuit. In response to binding an analyte, the cytoplasmic receptor is transported to the nucleus where it activates synthetic transcriptional promoter(s) fused to genes whose products degrade chlorophyll while preventing new chlorophyll biosynthesis. To test the ability of the degreening circuit to function with input from outside the plant, an input circuit containing a chimeric receptor or binding protein can be linked to the degreening circuit. In response to binding an analyte, the extracellular receptor initiates a signal transduction pathway and activates a signal receptive synthetic transcriptional promoter fused to genes whose products degrade chlorophyll while preventing new chlorophyll biosynthesis.
Normal time periods for notable loss of green color in plants varies widely from days to weeks depending on whether the loss is triggered from environmental changes, development (e.g., flower petals) or stress (e.g., pathogens). To develop a system that can lose green color rapidly in response to a signal, both the chlorophyll biosynthesis and chlorophyll breakdown pathways were modified to construct a “degreening circuit”. In addition to genes involved in chlorophyll metabolism, a redundant marker, green fluorescent protein (GFP) can be included in the degreening circuit as a control. The GFP marker is similarly (optionally) linked to the input part of the circuit and serves to eliminate false positives that might arise.
To ensure that the degreening phenotype appears rapidly, two genes (for example, chlorophyllase and RCCR) were used in the degreening circuit exemplified herein. Although it was not measured, the turnover in chlorophyll is strongly believed to have stimulated feedback induction of new chlorophyll biosynthesis. To prevent this from occurring in the degreening circuit, expression of the protochlorophyllide oxidoreductase (POR) gene, the rate-limiting enzyme in chlorophyll biosynthesis, was inhibited.
One approach to prevent expression of (silence) a specific gene involves the production of an interfering RNA molecule that contains a sequence identical to the gene of interest. Typically, the plants are genetically engineered to express inverted repeats (500-700 bp) to the gene of interest. The resulting double-stranded RNA is homologous to an endogenous transcript. Transgenic plants containing diRNA show high turnover rates of the homologous transcript and complete silencing of the endogenous gene expression. An interfering RNA molecule has been shown to be more efficient than antisense RNA in blocking the expression of a desired gene with silencing frequency between 90-100%. Thus the initial degreening circuit was generated using double stranded RNAs to silence the POR gene in a transgenic plant and hence prevent the de novo synthesis of chlorophyll after input from an analyte. A series of convenient Arabidopsis vectors for making dsRNA constructs are publicly available. These vectors contain a cassette for cloning a desired gene or gene portion in the sense and antisense orientations. The cassette has two pairs of unique restriction enzyme recognition sites flanking a 335 base pair GUS (β-glucuronidase) fragment that separates sense and antisense regions of the inverted repeat and facilitates formation of the dsRNA. The vectors are a series of plasmids that replicate in both E. coli and Agrobacterium tumefaciens allowing easy cloning and plant transformation, respectively. Vectors are available carrying the Bar or NptII genes, the plants containing the introduced genes can be selected with the herbicide BASTA (glufosinate ammonium) or the antibiotic kanamycin, respectively. A chloamphenicol or spectinomycin gene provides bacterial selection. For example, the conserved region of protochlorophyllide oxidoreductase (POR) gene can be cloned in the sense and antisense direction to produce the diRNA molecule specific for the POR genes. The vectors are designed to direct expression of the diRNA molecule with a strong constitutive promoter (CaMV 35S). To place the diRNA vector in the degreening circuit, this promoter, which is flanked with unique restriction sites, is replaced with promoters that place expression under control of perception of cytoplasmic or extracellular analytes for example, using the Pho promoter described.
Assembly and Testing of Degreening Gene Circuits
In many biological responses, sensing of a specific substance leads to a transcriptional response. The synthetic sensing system for plant sentinels links input to transcriptional output, hence, a test readout system was created that is triggered by a transcriptional response (signal-regulated induction of gene expression). Numerous transcriptional induction systems are available that provide a model in which to test the chlorophyll reporter system. A synthetically designed, steroid inducible system was modified to function in plants. In the presence of a synthetic steroid (4-hydroxytamoxifen, 4-OHT), a chimeric transcriptional regulator relocates to the nucleus and induces expression of a promoter made up of specific response elements and the −46 region of the CaMV35S promoter, designated 10XN1P. The 4-OHT induction system is essentially analogous to other transcriptional inducible systems.
In order to use plants to monitor large areas for pollution or terrorist agents, a reporter or readout system is needed. Prior gene reporter systems were developed for laboratory use and do not provide characteristics needed for a plant sentinel. A synthetic degreening circuit was developed that allows the green pigment chlorophyll to be used as a biosensor readout system. Induction of the degreening circuit allows remote detection, displays a rapid response, provides a reset capacity, and results in a phenotype readily recognized by the general public. Because the degreening circuit produces a white phenotype, it is easy to distinguish it from plants stressed from biotic or abiotic conditions, which produce yellow (or other color) phenotypes via senescence-related pathways. The inability to reset biosensors has been the major limitation to their use. The degreening circuit provides a simple capacity to be reset. Plants regreened after removal of the inducer, and this regreening was enhanced by a brief cytokinin treatment. Because the transcriptional inducer used (4-OHT) is relatively stable, the degreening circuit may not fully switch to an “off” position immediately following removal of the inducer, and the regreening process may not start until the inducer within the plant degrades. Hence, it should be possible to substantially reduce the time needed for regreening, currently about 3 days.
The degreening circuit, combining “stop-synthesis” with an “initiate breakdown” function, caused loss of chlorophyll with unprecedented speed. When each function was introduced separately, plants did not visibly degreen in the 48 hour timeframe except in the cotyledons. Expression of the “initiate degradation” circuits (CHLASE and PAO, or CHLASE and RCCR) failed to produce rapid degreening, suggesting that plants can enhance chlorophyll biosynthesis when needed. Likewise, the “stop synthesis” circuits (diRNA specific to POR or GUN4) failed to produce rapid degreening, supporting the concept of a large amount of metabolically stable chlorophyll within the plant. The rational combination of these two functions in one T-DNA construct produced a synthetic “degreening circuit”. The designed gene circuit is successful with respect to signal responsiveness, as indicated by three types of data: response of excised leaves to dark-induced senescence, distinctive ultrastructural changes, and microarray data showing a difference in genes regulated by the degreening circuit and normal chlorophyll loss in senescence.
Light was shown to be important for the rapid degreening process to occur, as induced plants incubated in the dark failed to turn white, even after 72 hours of induction. When induced plants were transferred to light, degreening proceeded at an enhanced rate. These results suggest that the degreening circuit is poised to respond in darkness, but not able to initiate rapid degreening without light. Chlorophyll biosynthesis and breakdown intermediates are potentially phototoxic. Because the degreening circuit interferes with the normal balance of chlorophyll and likely its metabolic intermediates, it is possible that, upon light exposure, these molecules cause photo-oxidation of pigments. A similar light requirement for degreening was observed for detached leaves. Under standard light conditions degreening induction caused detached leaves to fully degreen within 48 hours. However, darkness failed to induce full degreening in detached leaves, even after 72 hours of induction. Because darkness has been shown to induce senescence in Arabidopsis detached leaves, these results suggest that chlorophyll loss from the degreening circuit is distinct from senescence.
The degreening circuit provides an effective means to control chlorophyll levels in plants. The trigger for the degreening circuit is a specific input, resulting from sensing of the binding of a target substance of interest outside the plant, with signal transduction via histidine kinase within the cell and nuclear transcription activation. The steroid-inducible 10XN1P promoter used with the degreening circuit as a model can be replaced with other promoter elements, such as those responsive to signal transduction or the synthetic PlantPho promoter, as readily understood in the art. By combining the controlled chlorophyll loss as a reporting element with a sensing system such as computationally designed receptors or sensor proteins that provide input via transmembrane histidine kinases, plants are produced to serve as inexpensive monitors for terrorist agents, environmental pollutants or other target substances of interest. Degreening indicating presence of the target substance can be observed visually at close range or detected from a distance by remote sensing, as known to the art.
All DNA constructs, transgenic plant cells, tissue and plants, and methods for detecting a target substance of interest or for obtaining gene expression in response to the presence of the target substance of interest are within the scope of the present disclosure. It is further understood that other evolutionarily conserved signal transduction components and systems, and transcription regulatory components can be substituted for those recited herein, provided that there are functional input and/or output circuits responsive to the presence of a target substance.
Definitions
In general the terms and phrases used herein have their art-recognized meaning, which can be found by reference to standard texts, journal references and contexts known to those skilled in the art. The following definitions are provided to clarify their specific use in the context of the present disclosure.
The term “transgenic plant” is used herein to indicate a plant, or photosynthetic organism including algae, that has been genetically modified to contain exogenous or heterologous DNA to obtain a desired phenotype. Examples of the exogenous DNA molecules that have been transformed into the plants of the present disclosure include those encoding segments of DNA encoding the sensor protein, the transmembrane protein, a shuttling and/or response protein, and a receptive promoter, collectively known as the response circuits and/or those encoding segments of chlorophyll biosynthetic and/or complete degradation enzymes and a promoter that is responsive to a signal.
The term, “plant,” as used in the present disclosure, is intended to cover any plant, vascular or nonvascular, aquatic or terrestrial; algae, and organisms formally and informally recognized as algae now more properly known as cyanobacteria are included within this definition.
The term “non-plant organism” includes, but is not limited to, Archea, bacteria, fungi including yeast and cyanobacteria and the like and other organisms containing two-component signaling systems.
The term “degreening,” also referred to as a “loss of green color,” is intended to indicate a loss of chlorophyll and photosynthetic pigments in the transgenic plants that is distinguishable from normal plants (non-transgenic plants). The degreening can be detected visibly, or with a variety of instruments that measure properties including, but not limited to, chlorophyll fluorescence, hyper-spectral imaging, infra-red and near-infra-red imaging, multi-spectral imaging, photosynthetic properties and properties related to reactive oxygen species and their damage. The measurement instruments can be hand-held, or instruments that function at a distance, the distance being from aircraft or satellites.
The term “external signal,” or “environmental signal,” or “target substance of interest,” is intended to mean a signal typically in the form of an analyte or ligand that triggers the signaling pathway in the transgenic plants of the present disclosure and results in the degreening phenotype and/or a change such as induction of gene expression of interest. In this sense, the signal can be any biological or chemical agent including environmental pollutants. The substance can be, for example, sugars, herbicides, a poison, a pollutant, a toxin, heavy metals such as mercury, lead, arsenic, uranium, cadmium, selenium, polycyclic aromatic hydrocarbon, a benzene, a toluene, a xylene, or a halogenated (chloro, fluoro, and chlorofluoro) hydrocarbon, a steroid or other hormone. In addition, the target substance that binds to a specifically engineered input circuit via the extracellular receptor could be an explosive such as TNT (trinitrotoluene) or other explosive, or a degradation product of one of the foregoing compounds recognized by the input circuit via specific receptor site binding by the sensor protein. Any target substance for which a sensor protein can be computationally designed (Looger, et al., Nature 423:185-190, 2003; Dwyer, et al., Curr. Opin. Struct. Biol. 14:495-504, 2004) can serve as an external signal in the context of the present disclosure.
The term “detectable marker” is a change brought about in a plant that is perceivable or capable of being sensed by humans, other organisms such as, but not limited to, dogs, and/or machines. The change can be visible or invisible to humans. The sensing can involve non-destructive (for example, multi-spectral imaging) or destructive methods (for example, analysis of protein, DNA, RNA or metabolic product).
The term “response regulator domain” is a protein or portion of a protein that contains conserved amino acids collectively functioning to perceive a phosphor-relay from an activated histidine kinase. The conserved domain may contain a phosphor-accepting Asp or His residue, or it may contain other residues that can be made capable of accepting the activated phosphate.
The term “response gene” is a gene whose expression is linked to input from the sensor protein or proteins.
The term “sensor protein” is used interchangeably with “receptor.”
The term “transmembrane protein” is used interchangeably with “histidine kinase”.
The terms “expression construct” or “DNA construct” are used interchangeably herein and indicate a DNA construct comprising particular sequences necessary for transcription of an associated downstream sequence. An expression vector is a plasmid containing an expression construct. If appropriate and desired for the associated sequence, the term expression also encompasses translation (protein synthesis) of the transcribed RNA. The particular sequences contained in the expression vector include a promoter, enhancer, termination signal, transcriptional block and the like. To prevent transcriptional interference from multiple transgenes, a transcriptional block can be placed between appropriate genes on a plant transformation plasmid. A promoter is a DNA region that includes sequences sufficient to cause transcription of an associated (downstream) sequence. The promoter may be regulated, i.e., not constitutively acting to cause transcription of the associated sequence. If inducible, there are sequences present therein that mediate regulation of expression so that the associated sequence is transcribed only when an inducer molecule is present. In the present context, the inducer molecule is analogous to the signal transmitted by an input circuit.
The term “derived from” includes genes, nucleic acids, and proteins when they include fragments or elements assembled in such a way that they produce a functional unit. The fragments or elements can be assembled from multiple organisms provided that they retain evolutionarily conserved function. Elements or domains could be assembled from various organisms and/or synthesized partially or entirely, provided that they retain evolutionarily conserved function, elements or domains. In some cases the derivation could include changes so that the codons are optimized for expression in a particular organism.
“Expression control sequences” are DNA sequences involved in any way in the control of transcription or translation. Suitable expression control sequences and methods of making and using them are well-known in the art. The expression control sequences must include a promoter. The promoter may be any DNA sequence that shows transcriptional activity in the chosen organism, plant cells, plant parts, or plants. The promoter may be inducible or constitutive. It may be naturally-occurring, may be composed of portions of various naturally-occurring promoters, or may be partially or totally synthetic. Also, the location of the promoter relative to the transcription start may be optimized. Many suitable promoters for use in plants are well-known in the art as are nucleotide sequences that enhance expression of an associated expressible sequence.
The term “RNA interfering molecule” includes, but is not limited to, diRNA, siRNA miRNA, or an antisense RNA to inhibit synthesis of a related coding sequence. It is part of a mechanism for RNA-guided regulation of gene expression in which double-stranded ribonucleic acid (RNA) inhibits the expression of genes with complementary nucleotide sequences.
The DNA constructs of the present disclosure can be used to transform any type of cell, plant or plant cell. A genetic marker can be used for selecting transformed cells (“a selection marker”). Selection markers typically allow transformed cells to be recovered by negative selection (i.e., inhibiting growth of cells that do not contain the selection marker) or by screening for a product encoded by the selection marker.
EXAMPLES
The following examples are included to demonstrate preferred embodiments of the present disclosure. It should be appreciated by those of skill in the art that the techniques disclosed in the examples, which follow represent techniques discovered by the inventors to function well in the practice of the present disclosure, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments, which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the present disclosure.
Example 1: Using the N-Terminal End of the Signal Dependent Histidine Kinase Activation Region to Engineer Novel Receptor Histidine Kinase Fusions
Most of the reported functional chimeric receptor/HK fusions utilize a common signaling domain, the HAMP domain, which is found in chemotactic receptors and some HKs. The first reported chimeric receptor/HK fusion was made by fusing a chemotactic receptor Tar to the HK EnvZ at the shared HAMP domain. However, there are a large number of receptors and HKs that lack a HAMP domain. PhoR lacks a HAMP domain which made determining a functional fusion point (functional=off in the absence of ligand and on in presence of the ligand) with previous knowledge and technology difficult. Previous fusions of Trg to PhoR showed a high basal activity (kinase on) in the absence of signaling.
A computational learning algorithm can be used to show a protein structural feature, a coiled-coil like element, in the dimerization and histidine phosphorylation (DHP) domain of HKs (Singh, et al., Proc. Natl. Acad. Sci. USA 95:2738-2743). As diagramed in FIG. 3, coiled-coils result from protein-protein interactions between 2 or more alpha helices somewhat resembling the coiled strands in a springs. There are seven amino acids per coiled coil alpha helix and the amino acids are designated A-G. The interfaces between helices of coiled coils are characterized by interactions of the residues located at the A position of one helix with the D position of a second helix. The interface of the two helices typically has hydrophobic residues at the A and D positions. When the alpha helices interact to form a coiled coil, residues from one helix occupy the spaces between corresponding residues from the second helix, producing a “knobs in holes” packing.
The inventors reasoned that because this coiled-coil like element was a common motif in histidine kinases it would be possible to make fusions utilizing this element. In addition to strict fusions between Trg and PhoR, coiled coil elements were also incorporated from a functional fusion between Trg and EnvZ (Trz) with the idea that it may contain structural elements that allow proper HAMP signaling activation of an HK whereas PhoR, which lacks a HAMP domain, may not be able to be properly activated in the absence of these elements. The sequences of PhoR and Trz fusion were submitted to the HK coiled coil prediction program (groups.csail.mit.edu/cb/learncoil/cgi-bin/learncoil.cgi) (FIG. 4). Fusions incorporating the coiled-coil helices from Trz were designed as well as a fusion using the PhoR coiled-coil and the equivalent region of Trg which lacks the HK coiled coil (FIG. 5). These fusions were tested in E. coli. An expression plasmid was constructed in the plasmid pACYC177 with a LacI promoter driving RBP and a LacI promoter driving an operon consisting of the PhoB response regulator and the chimeric receptor:PhoR fusion to be tested. The operon was modeled after the naturally occurring PhoB/PhoR operon (FIG. 6). The expression constructs were transformed into the E. coli cell line BW23423, which has a PhoB responsive promoter driving a β-galactosidase reporter gene. The functionality of the fusions was tested by a split plate assay with X-Gal present to monitor β-galactosidase activity. One side of the split plate contained medium with maltose as a control; the other side of the split plate had medium containing ribose, the ligand being used to test functionality. A functional fusion should show no signaling on maltose (white colonies) whereas colonies growing on ribose should be blue. The blue color indicates the ligand activates the HK receptor fusion, which then transfers a phosphoryl group to PhoB leading to the activation of the β-galactosidase reporter gene. Three of the coiled coil based fusions showed high basal activity, but the fusion incorporating a coiled coil heptad of EnvZ (heptad repeat 3) was functional.
Functional analysis within the 7 amino acids of the EnvZ coiled-coil element revealed the key point of the fusion wasn't the first amino acid of the seven amino acids of the EnvZ coiled coil region (residue A) but the 4th amino acid (residue D), a valine (FIG. 7). Because the ground state of a histidine kinase is such that the kinase is active, “kinase on” and the predominate signaling phenotype seen in non-functional fusions is “kinase on,” the inventors reasoned that the valine at the D position is essential in maintaining the “kinase off” state in the absence of ligand dependent signaling. Fusions where the D position valine is replaced by alanine, glycine (the two hydrophobic amino acids smaller than valine) or a methionine (the D position residue of PhoR) results in constitutive activation (FIG. 8). E. coli has 10 HKs, including EnvZ, with HAMP domains adjacent to the HK coiled coil (FIG. 8). EnvZ is the only HK with a valine in the A/D position. There are 4 other amino acids, glutamate, isoleucine, leucine and threonine that occupy the A/D position in the 9 other E. coli HKs with a HAMP/HK coiled coil A/D overlap. Fusions testing whether any of these amino acids can functionally substitute for the valine were produced. All fusions resulted in the high basal phenotype or “kinase on” suggesting that the valine at the D position is essential in creating functional receptor/PhoR fusions. The A/D position represents the point at which the signal from the receptor acts to initiate histidine kinase activity. This position defines the N-terminal end of the signal dependent histidine kinase activation region. The functional TrzPhoR fusion represents an improvement in the synthetic signaling system that enables detector plants allowing for a cleaner signaling system. In addition, the TrzPhoR fusion has been introduced into the plant detector system and it was shown to be highly functional (FIG. 9).
To test the utility of the A/D position as a fusion point for engineering novel receptor/histidine kinase fusions, a fusion between the RpfC receptor and PhoR was made. RpfC is a sensor HK involved in quorum sensing found in many species of Xylella and Xanthomonas that are bacterial pathogens of plants (Chatterjee, et al., Proc. Natl. Acad. Sci. USA 105:2670-2675, 2008). RpfC senses Diffusible Signaling Factor (DSF) mediating the control of virulence factor synthesis, and hence start the virulence response. RpfC does not have a HAMP domain only a cytoplasmic linker between the final transmembrane helix and the DHp domain. RpfC has a predicted HK coiled coil in the same register as the one predicted for PhoR. The RpfC DSF sensor and cytoplasmic linker was fused to PhoR at the A/D position. Both the D position of wild-type PhoR and the TrzPhoR fusion D position were used. The RpfCPhoR D position fusion containing a methionine at the D position had a high basal phenotype. The RpfCTrzPhoR D position fusion containing a valine at the D position showed inducible signaling in the presence of DSF extract (FIG. 10). This result showed the efficacy of using the A/D position as a fusion point for receptor/histidine kinase fusions. These results also showed how important the amino acid occupying the A/D position is in obtaining a functional fusion. In addition, when the RpfCTrzPhoR D position fusion was expressed in transgenic Arabidopsis plants, the presence of DSF was detected using a luciferase reporter gene readout (FIG. 11A and FIG. 11B). An additional test of the D position fusion point was implemented by fusing the PhoQ receptor to PhoR. PhoQ is a Mg2+ responsive receptor histidine kinase that mediates adaptation to Mg2+ limiting environments (Groisman, J. Bacteriol. 183:1835-1842, 2001). PhoQ also lacks a cytoplasmic HAMP domain. FIG. 12 demonstrates PhoQTrzPhoR showing an increase in Mg2+ signaling (above that seen from the Mg2+ already present in the media) with exposure to additional Mg2+.
Example 2: Using the C-Terminal End of the Signal Dependent Histidine Kinase Activation Region to Engineer Inducible Kinase Activity in Non-Functional Receptor/Histidine Kinase Fusions
An engineered an EnvZ variant that interacts with PhoB was previously engineered by substituting twenty-eight amino acids from the helix-loop-helix region of the PhoR DHp domain into the corresponding positions of the EnvZ DHp domain. This version of EnvZ, called Chim3, was able to phosphorylate PhoB in an in vitro assay (Skerker, et al., Cell 133:1043-1054, 2008). The changes in EnvZ that allowed it to interact with PhoB were incorporated into the Trg receptor EnvZ fusion Trz (Baumgartner, et al., J. Bacteriol. 176:1157-1163, 1994). This chimeric version of Trz was named TrzChim3. When TrzChim3 was tested in-vivo for the ability to signal through PhoB, high basal activity was found and no evidence of induction (FIG. 13A). This is termed as a kinase “locked-ON” phenotype. PhoR and EnvZ differ in three amino acids that are located directly upstream from a conserved arginine found in the DHp domain of both PhoR and EnvZ. The conserved arginine is in a region proposed to be involved in the interaction between the CA domain and the DHp domain in the kinase OFF/phosphatase ON state. The inventors reasoned that this area was important in activating histidine kinase activity and that this region of TrzChim3, which evolved to control EnvZ kinase activation, was unable to control the activity of the chimeric EnvZ/PhoR. In EnvZ the three amino acids are alanine, aspartate and aspartate (ADD) (residues 275-277, FIG. 14), while in PhoR the amino acids are glutamate, glycine and alanine (EGA) (see PhoR alignment with Trz, FIG. 14). A version of TrzChim3 was constructed with EGA substituting for ADD. This substitution allowed for the determination of whether the three residues have a function in controlling the CA/DHp interaction involved in the kinase off/phosphatase on state. Replacing the three putative CA interaction region EnvZ amino acids with those of PhoR did not restore ligand inducible function (FIG. 13B). However, the substitution did result in a change from a kinase “locked ON” phenotype to a kinase “locked OFF” phenotype, suggesting that this region could indeed be involved in the signal inducible activation of kinase activity.
The inventors reasoned that the chimeric nature of the DHp helix-loop-helix region in TrzChim3 results in a structure that does not correctly position the CA domain in the same way that the native EnvZ or PhoR CA domains are positioned. Further alterations to the putative CA interaction region were tested to determine if these could provide a functional HK. All three amino acid positions were randomly mutagenized and screened for functionality by plating on media with the ribose ligand and X-gal. Blue colonies were selected and re-tested for ribose inducibility on the split plates. Two mutants were isolated, TrzChim3-8 and TrzChim3-10, that showed ligand inducible signaling with the split plate assay (FIG. 15). The mutants were sequenced and it was found that the putative CA domain interaction region amino acids were mutated from EGA to RGV in TrzChim3-8 and EGA to AGG in TrzChim3-10. FIG. 16 shows quantification of the kinase function for TrzChim3, TrzChim3-8 and TrzChim3-10. The ability to restore in vivo inducibility to TrzChim3 suggests that the original TrzChim3 kinase “locked-ON” phenotype is due to a perturbation of the CA/DHp domain interaction. This experiment allowed for the identification and manipulation of the C-terminal end of the signal dependent histidine kinase activation region.
Example 3—Development of a Maltose Inducible Tar HK Fusion
In E. coli, the chemotactic receptor Tar mediates chemotaxis towards the amino acid aspartate and the disaccharide sugar maltose via an interaction between Tar and Maltose Binding Protein (MBP). When Tar is fused to the histidine kinase EnvZ to form Taz, the fusion retains the ability to be induced by aspartate, however it no longer shows a response to maltose. Trg was replaced with Tar in either the TrzPhoR fusion to form TazPhoR or in TrzChim3-8 to form Tac8. When TazPhoR or Tac8 was tested with maltose no maltose inducibility was observed. However, aspartate inducibility of both fusions was observed. In E. coli, aspartate mediates a stronger chemotactic response than maltose. The inventors reasoned that the transmembrane signal mediated by Tar when it binds aspartate is strong enough to activate histidine kinase activity in a Tar/HK fusion but the transmembrane signal mediated by Tar when it interacts with MBP is not strong enough to activate histidine kinase activity. Based on the ability to manipulate histidine kinase activity in TrzChim3, the inventors reasoned that targeting the same three amino acids in TazPhoR or Tac8 may results in variants whose kinase activation threshold is lowered enough to be activated by maltose. Amino acids 265, 266 and 267 in both Tac8 and TazPhoR were mutagenized by site directed mutagenesis. The site directed mutagenesis libraries were screened using fluorescent activated cell sorting (FACS). Initial sorting for Tac and TazPhoR functionality showed populations of cells with significant maltose ligand induction. From this screen two TazPhoR variants (TazPhoR 61 and 86; FIG. 17A) and one Tac8 variant (Tac40; FIG. 17B) were selected for further testing and development. This is the first reported example of MBP/maltose signaling via a TarHK fusion.
Example 4—Using TazPhoR61 and a Maltose Binding Protein with a Computationally Designed Binding Pocket to Detect a Fentanyl Ligand
The ability to computationally design proteins partially or entirely, including the ligand binding pockets of several Periplasmic Binding Proteins, e.g., Maltose Binding Protein, Ribose Binding Protein, and Glucose Binding Protein, offers powerful means to produce new types of protein sensors and enable them in plants to serve as plant sentinels. Because previous TarHK fusions (Tar/EnvZ and Tar/PhoR) were unresponsive to maltose signaling through MBP it was not possible to test whether MBPs with computationally redesigned binding pockets could use HK signaling to report the presence of a ligand of interest. Using an MBP redesigned to bind a Fentanyl ligand, the inventors tested whether the maltose inducible TazPhoR61 could be used to detect the presence of Fentanyl in the environment. Two genetic circuits were used in this experiment. A Fentanyl Detection circuit consisting of the redesigned Maltose Binding Protein (MBP 6.1-5), TazPhoR61 and PhoB was co-transformed with a PhoB Signal Amplifying circuit consisting of a PhoB responsive promoter driving a Tal transcription factor engineered to bind Gal4 binding sites, a Gal4 responsive promoter driving a Gal4VP64 transcription factor (Gal4VP64 can bind its own promoter resulting in a positive feedback) and a Gal4 responsive promoter driving a luciferase reporter gene. Transformed plants were exposed to 500 μM Fentanyl and responded by inducing expression of luciferase (FIG. 18). The system described above is diagrammed in FIG. 19 with the quantitative controllers (positive feedback system) shown in FIG. 20.
The term “about” is used herein to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value. The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and to “and/or.” When not used in conjunction closed wording in the claims or specifically noted otherwise, the words “a” and “an” denote “one or more.”
The terms “comprise,” “have,” and “include” are open-ended linking verbs. Any forms or tenses of one or more of these verbs, such as “comprises,” “comprising,” “has,” “having,” “includes,” and “including,” are also open-ended. For example, any method that “comprises,” “has” or “includes” one or more steps is not limited to possessing only those one or more steps and also covers other unlisted steps. Similarly, any cell that “comprises,” “has” or “includes” one or more traits is not limited to possessing only those one or more traits and covers other unlisted traits.
While the disclosure has been described in connection with specific embodiments thereof, it will be understood that the present disclosure is capable of further modifications by one of skill in the art. It is to be understood that, unless otherwise indicated, the present disclosure is not limited to particular materials, reagents, reaction materials, manufacturing processes, or the like, as such can vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It is also possible in the present disclosure that steps can be executed in different sequence where this is logically possible. The present disclosure is therefore intended to encompass any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth.
All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
All publications, patents, and patent publications cited are incorporated by reference herein in their entirety for all purposes.

## Claims

1. A fusion protein comprising a receptor protein selected from the group consisting of a chemotactic receptor, a quorum sensing receptor, a histidine kinase receptor, and a computationally designed receptor, operably linked to a histidine kinase protein at the A/D fusion point wherein the A/D fusion point is a hydrophobic amino acid located at the overlapping interface between a coiled coil alpha helix of an extracellular receptor signal transmission domain of said receptor and an N-terminal coiled coil alpha helix of the internal dimerization and histidine phosphorylation (DHP) domain of said histidine kinase, wherein the fusion of said receptor and histidine kinase at the A/D fusion point results in inducible histidine kinase activity, and wherein said fusion protein further comprises a kinase activation region that has been engineered to activate said inducible histidine kinase activity through ligand binding.

2. The fusion protein of claim 1, wherein the chemotactic receptor protein is Trg, Tar, Tap or Tsr or a computationally redesigned receptor.

3. The fusion protein of claim 1, wherein the receptor involved in quorum sensing is the Xylella DSF receptor RpfC or the LuxPQ receptor LuxP or a computationally redesigned receptor.

4. The fusion protein of claim 1, wherein the histidine kinase protein is PhoR or EnvZ.

5. The fusion protein of claim 1, wherein the histidine kinase protein is a EnvZ/PhoR chimera.

6. The fusion protein of claim 1, wherein the histidine kinase protein is activated when the chemotactic receptor protein or the receptor involved in quorum sensing binds to a sensor protein, or a computationally designed receptor bound to a target substance.

7. The fusion protein of claim 6, wherein the target substance is a chemical agent, a heavy metal, a poison, a pollutant, a toxin, an herbicide, a polycyclic aromatic hydrocarbon, a benzene, a toluene, a xylene, a halogenated hydrocarbon, a steroid or other hormone, an explosive, or a degradation product of one of the foregoing compounds.

8. The fusion protein of claim 1, further comprising a plasma membrane targeting signal sequence operably linked to an N-terminus of the chemotactic receptor protein or receptor involved in quorum sensing, or a computationally designed receptor.

9. The fusion protein of claim 1, wherein the kinase activation region comprises a maltose binding protein and maltose is the ligand which activates the inducible histidine kinase activity.

10. A DNA construct comprising a nucleic acid segment that encodes the fusion protein of claim 1.

11. The DNA construct of claim 10, wherein the nucleic acid segment is operably linked to a promoter.