# Patent

## Title
Luciferase biosensors for cAMP

## Abstract

A modified luciferase protein which is a sensor for molecules including cAMP is provided. The modified luciferase protein includes one or more heterologous amino acid sequences, at least one of which directly or indirectly interacts with cAMP.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of U.S. application Ser. No. 12/454,643 filed May 19, 2009, now U.S. Pat. No. 9,045,730 which claims priority to U.S. Provisional Application No. 61/054,374 filed on May 19, 2008 and U.S. Provisional Application No. 61/119,983 filed on Dec. 4, 2008, all of which are incorporated herein by reference in their entirety.


FIELD OF THE INVENTION
This invention relates to the field of biochemical assays and reagents. More specifically, this invention relates to modified luciferases and to methods for their use.
BACKGROUND
Luciferases are enzymes that catalyze the oxidation of a substrate (e.g., luciferin) with the concomitant release of photons of light. Luciferases have been isolated from numerous species, including Coleopteran arthropods and many sea creatures. Because it is easily detectable and its activity can be quantified with high precision, luciferases have been used widely to study gene expression and protein localization. Unlike green fluorescent protein (GFP), which requires up to 30 minutes to form its chromophore, the products of luciferases can be detected immediately upon completion of synthesis of the polypeptide chain (if substrate and oxygen are also present). In addition, no post-translational modifications are required for enzymatic activity, and the enzyme contains no prosthetic groups, bound cofactors, or disulfide bonds. Luciferases are useful reporters in numerous species and in a wide variety of cells.
Luciferases possess additional features that render them particularly useful as reporter molecules for biosensing, i.e., molecules which reveal molecular properties of a system. Biosensors (i.e., sensors which comprise a biological component) generally function by means of a two-step process: signal generation mediated through a biological component, and signal transduction and/or amplification through an electrical component. Signal generation is typically achieved through binding, energy transfer or catalysis. Signal generation by enzymatic catalysis can be particularly useful due to the inherent efficiency and specificity of these chemical processes. Most catalytic reactions generate less than the energy of hydrolysis for two molecules of ATP, or about 70 kJ/mole. However, the luminescence elicited by luciferases has much higher energy content. For instance, the reaction catalyzed by firefly luciferase (560 nm) emits 214 kJ/mole of energy. Furthermore, luciferases are also highly efficient at converting chemical energy into photons, i.e., they have high quantum yields. Luciferases are thus extremely efficient for generating detectable signals.
Luciferase biosensors have been described. For example, Sala-Newby et al. (Biochem J. 279:727 (1991)) disclose that a Photinus pyralis luciferase cDNA was modified to generate cyclic AMP-dependent protein kinase phosphorylation sites. In particular, a valine at position 217 was mutated to arginine to generate a site, RRFS (SEQ ID NO:1), and the heptapeptide kemptide, the phosphorylation site of the porcine pyruvate kinase, was added at the N- or C-terminus of the luciferase. Sala-Newby et al. relate that the proteins carrying phosphorylation sites were characterized for their specific activity, pI, effect of pH on the color of the light emitted, and effect of the catalytic subunit of protein kinase A in the presence of ATP. They found that only one of the recombinant proteins (RRFS; SEQ ID NO:1) was significantly different from wild-type luciferase and that the RRFS (SEQ ID NO:1) mutant had a lower specific activity, lower pH optimum, emitted greener light at low pH and, when phosphorylated, decreased its activity by up to 80%. It is disclosed that the latter effect was reversed by phosphatase.
Waud et al. (BBA 1292: 89 (1996)) engineered protein kinase recognition sequences and proteinase sites into a Photinus pyralis luciferase cDNA. Two domains of the luciferase were modified by Waud et al.; one between amino acids 209 and 227 and the other at the C-terminus between amino acids 537 and 550. Waud et al. disclose that the mutation of amino acids between residues 209 and 227 reduced bioluminescent activity to less than 1% of wild-type recombinant, while engineering peptide sequences at the C-terminus resulted in specific activities ranging from 0.06%-120% of the wild-type recombinant luciferase. Waud et al. also disclose that addition of a cyclic AMP dependent protein kinase catalytic subunit to a variant luciferase incorporating the kinase recognition sequence, LRRASLG (SEQ ID NO:2), with a serine at amino acid position 543, resulted in a 30% reduction activity. Alkaline phosphatase treatment restored activity. Waud et al. further disclose that the bioluminescent activity of a variant luciferase containing a thrombin recognition sequence, LVPRES (SEQ ID NO:3), with the cleavage site positioned between amino acids 542 and 543, decreased by 50% when incubated in the presence of thrombin.
Ozawa et al. (Analytical Chemistry 73: 2516 (2001)) describe a biosensor based on protein splicing-induced complementation of rationally designed fragments of firefly luciferase. Protein splicing is a posttranslational protein modification through which inteins (internal proteins) are excised out from a precursor fusion protein, ligating the flanking exteins (external proteins) into a contiguous polypeptide. It is disclosed that the N- and C-terminal intein DnaE from Synechocystis sp. PCC6803 were each fused respectively to N- and C-terminal fragments of a luciferase. Protein-protein interactions trigger the folding of DnaE intein, resulting in protein splicing, and thereby the extein of ligated luciferase recovers its enzymatic activity. Ozawa et al. disclose that the interaction between known binding partners, phosphorylated insulin receptor substrate 1 (IRS-1) and its target N-terminal SH2 domain of PI 3-kinase, was monitored using a split luciferase in the presence insulin.
Paulmurugan et al. (PNAS USA 99: 3105 (2002)) employed a split firefly luciferase-based assay to monitor the interaction of two proteins, i.e., MyoD and Id, in cell cultures and in mice using both complementation strategy and an intein-mediated reconstitution strategy. To retain reporter activity, in the complementation strategy, fusion proteins need protein interaction, i.e., via the interaction of the protein partners MyoD and Id, while in the reconstitution strategy, the new complete beetle luciferase formed via intein-mediated splicing maintains it activity even in the absence of a continuing interaction between the protein partners.
A protein fragment complementation assay is disclosed in Michnick et al. (U.S. Pat. Nos. 6,270,964, 6,294,330 and 6,428,951). Specifically, Michnick describe a split murine dihydrofolate reductase (DHFR) gene-based assay in which an N-terminal fragment of DHFR and a C-terminal fragment of DHFR are each fused to a GCN4 leucine zipper sequence. DHFR activity was detected in cells which expressed both fusion proteins. Michnick et al. also describe another complementation approach in which nested sets of Si nuclease generated deletions in the aminoglycoside kinase (AK) gene are introduced into a leucine zipper construct, and the resulting sets of constructs introduced to cells and screened for AK activity.
SUMMARY OF THE INVENTION
The invention provides an improved gene product, e.g., a modified luciferase such as a modified beetle luciferase, for instance, a modified firefly or click beetle luciferase, a modified anthozoan luciferase such as a Renilla luciferase, or a modified copepod or decapod luciferase comprising a heterologous, non-native mutant cAMP binding site having one or more altered activities.
cAMP binding sites (domains) useful to prepare mutant cAMP binding domain for use in the modified luciferases of the invention include but are not limited to cAMP binding domain in exchange protein directly activated by cAMP (Epac) (Bos et al., Nat. Rev. Mol. Cell. Biol. 4:733 (2003); NCBI Accession No. AF115480; SEQ ID NO:123)), including Epac 2B, Epac 1 (Nikolav, J. Biol. Chem. 279:372 (2004)), and Epac IIA; human RIα residues 245-381 (Genbank Accession No. BL036285; SEQ ID NO:124); cyclic nucleotide gated ion channels such as hyperpolarization-activated cyclic nucleotide modulated channel (Zagotta et al., Nature 425: 730 (2003)); neuropathy target esterase (Dremier et al., FEBS Lett. 546:163 (2003)); PKA regulatory type IIβ subunit (see, e.g., NCBI Accession No. M124921), e.g., PKA IIβA and PKA IIβB; PKA regulatory type Iα subunit, e.g., PKA IαA and PKA IαB, PKG IIA, PKG IIB; GAF A domain from Trypanosoma brucei PDE residues 241-375 (Genbank Accession No. AF192755; SEQ ID NO:125); and catabolite activating protein. In one embodiment, the cAMP binding domain includes a protein fold from a native protein which protein fold has substantially the same three-dimensional structure as the cAMP binding site of, for instance, RIIβB, and an amino acid residue that is different than the residue at a position corresponding to residue 266, 282, 284, 286, 296, 316, 333, 338, 382, 389, 404 or 407 of RIIβB having SEQ ID NO:4, which different residue results in an altered affinity for cAMP. In one embodiment, the cAMP binding domain includes a protein fold from a native protein that binds cAMP which protein fold has substantially the same three-dimensional structure as the cAMP binding site of RIIβB and an amino acid residue that is different than the residue at a position corresponding to residue 266, 282, 284, 286, 296, 316, 333, 338, 382, 389, 404 or 407 of RIIβB having SEQ ID NO:4, which results in an altered affinity for cAMP, e.g., an increase in the EC50 for activation, and/or results in an enhanced response in live cells, for instance, as a result of decreased binding under basal conditions.
In one embodiment, the mutant cAMP binding site has one or more substitutions that enhance the bioluminescence signal of the modified luciferase, enhance the response of the modified luciferase to an agent that alters the amount of cAMP in a cell, or both, relative to a corresponding luciferase with a cAMP binding site that lacks the one or more substitutions. In one embodiment, the one or more substitutions are at a position corresponding to residue 266, 282, 284, 286, 296, 316, 333, 338, 382, 389, 404 or 407 of RIIβB having SEQ ID NO:4. In one embodiment, the residue in the mutant cAMP binding site corresponding to residue 266 is not M, the residue in the mutant cAMP binding site corresponding to residue 282 is not F, the residue in the mutant cAMP binding site corresponding to residue 286 is not L, the residue in the mutant cAMP binding site corresponding to residue 296 is not V, the residue in the mutant cAMP binding site corresponding to residue 333 is not V, or the residue in the mutant cAMP binding site corresponding to residue 404 is not V. In one embodiment, the one or more substitutions are at a position corresponding to residue 266, 282, 284, 286, 296, 316, 333, 338, 382, 389, 404 or 407 of RIIβB having SEQ ID NO:4. For example, the residue in the mutant cAMP binding site corresponding to residue 389 is not M, the residue in the mutant cAMP binding site corresponding to residue 284 is not E, the residue in the mutant cAMP binding site corresponding to residue 308 is not D, or residue in the mutant cAMP binding site corresponding to residue 286 is not L. In one embodiment, the mutant cAMP binding site has at least about 80%, 85%, 90%, 95%, or 99%, but not 100%, amino acid sequence identity to the cAMP binding site in SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, e.g., residues 266 to 414 in SEQ ID NO:4, residues 284 to 381 in SEQ ID NO:5 or residues 241 to 375 in SEQ ID NO:6.
In one embodiment, the modified luciferase has a detectable activity and includes an insertion of one or more amino acids relative to a corresponding unmodified luciferase at a site or in a region which is tolerant to modification, which insertion includes an amino acid sequence which directly interacts with cAMP, e.g., an insertion which includes a recognition sequence for cAMP, or indirectly interacts with cAMP, e.g., via another molecule. In one embodiment, a modified luciferase comprises an insertion of 10 or more, e.g., 20, 50, 100, 200, 300 or more, but less than about 1000, or any integer in between, amino acid residues. In one embodiment, the modified luciferase with an insertion further comprises a deletion of luciferase sequences, e.g., a deletion of 1 or more, but less than about 100, for instance less than 50, 40, 30, 20, 10 or 5, or any integer in between, residues.
Hence, in one embodiment, a modified luciferase of the invention comprises an amino acid sequence which is circularly permuted relative to the amino acid sequence of a corresponding luciferase, such as an unmodified wild type luciferase, resulting in a new N- and C-terminus in the circularly permuted luciferase, at least one of which is at a site or in a region which is tolerant to modification, and is engineered to have functionality by introducing a heterologous amino acid sequence which directly or indirectly interacts with cAMP. In another embodiment, the circularly permuted luciferase includes other modifications, including but not limited to insertions and/or deletions internal to the N- or C-terminus of the circularly permuted luciferase, for instance, another insertion and/or a deletion, e.g., at or near the N- and C-terminus of the corresponding unmodified luciferase such as at residues corresponding to residues 1 to about 10 or about 30, or any integer in between, of the N-terminus and/or corresponding to the last residue or about the last 30, e.g., last 15, or any integer in between 1 and 30, residues of the C-terminus of the corresponding unmodified luciferase. In one embodiment, the amino acid sequence that interacts with cAMP is flanked by at least one linker, e.g., flanked at each end, such as a peptide linker, which linkers may be the same or different, which optionally improve luminescence and/or response, e.g., to forskolin or isoproterenol. In one embodiment, the amino acid sequence that interacts with cAMP is flanked by at least one linker at the N-terminus, which optionally improves luminescence and/or response to forskolin or isoproterenol, or foskolin and dopamine. In one embodiment, the linker has at least one of the following sequences: GSSGGSGGSGGG, GSSSDSDSSAGS, GSNDSSGGSEGG, GSNGGFDSSEGG, GSIRWSGLSGGD, GSRGGSVYSEGG, GSSEGSSDFGGD, GSIVVSCSSEGG, GSNWDSGCSREG, GSNWDSGCSREC, GSSGCTGDAGGS, GSNWDSGCSRQC, GSS/NS/D/GD/S/GS/FD/GS/GSA/EGS/G, GSI/R/SR/G/EW/GSGN/SL/Y/DS/FG/EGD/G, GSI/N/SV/W/GV/D/CS/TC/GS/C/DS/AE/R/GG/EG/S, GSI/SV/G/AV/GS/CG/DG/D/SS/AG/EG/EG/N, GSI/N/SV/W/G/AV/D/C/GS/T/CC/GS/C/DS/AE/R/GG/EG/S, GSIAGCGDAGEG, GSNWDSGCSRE, GSIAGCGDAGEG, GSNWDSGCSREG, NWDSGCSREG, or IAGCGDAGEG (SEQ ID Nos. 41-57 and 126-131 respectively). A linker employed in the biosensor of the invention is an amino acid sequence, the presence of which in the biosensor does not substantially decrease the activity of that biosensor, e.g., does not decrease the activity by more than 10-fold, such as by no more that 4-fold, or no more than 2-fold, relative to a corresponding biosensor that lacks the linker(s), and/or the presence of the linker employed in the biosensor of the invention increases luminescence or response to agents such as forskolin or isoproterenol, or both, relative to a corresponding biosensor that lacks the linker(s) or a corresponding biosensor having the linker(s) GSSGGSGGSGGG (SEQ ID NO:41), or relative to both corresponding biosensors. In one embodiment, a linker containing biosensor has one of SEQ ID Nos. 42-57 or 126-131 flanking a mutant amino acid sequence that interacts with cAMP and has increased luminescence or an increased response to forskolin or isoproterenol, or both, relative to a corresponding biosensor having the linker(s) GSSGGSGGSGGG (SEQ ID NO:41).
The peptide linker of the invention may be employed to separate two polypeptides, each of which has an activity, or two polypeptide fragments, which individually have little or no activity but together have activity or increased activity corresponding to an activity of one of the full length polypeptides relative to the individual fragments. In one embodiment, the invention provides a polynucleotide comprising a nucleic acid sequence comprising an open reading frame for a first protein or a fragment of a first protein fused to a peptide linker fused to a second protein or a fragment of a second protein. In one embodiment, the fragment of a first protein is a fragment of a luciferase and the fragment of a second protein is a different fragment of the luciferase, e.g., the first fragment has residues 234 to 544 of a firefly luciferase and the second fragment has residues 4 to 233 of a firefly luciferase or the first fragment has residues 359 to 544 of a firefly luciferase and the second fragment has residues 4 to 355 of a firefly luciferase, e.g., the luciferase sequences are circularly permuted. In one embodiment, the fragment of a first protein is a fragment of a luciferase and the fragment of a second protein is a fragment of a protein that is not a luciferase, e.g., it is a hydrolase such as a dehalogenase. In another embodiment, the fragment of a first protein is a fragment of a luciferase and the fragment of a second protein is a fragment of a different luciferase. In another embodiment, the first protein is a luciferase and the second protein is a different luciferase. In yet another embodiment, the first protein is a luciferase and the second protein is a protein that is not a luciferase.
The peptide linker of the invention may also be employed to separate three polypeptide fragments or two polypeptide fragments and another polypeptide, where the fragments have little or no activity but together have activity or increased activity corresponding to an activity of one of the full length polypeptides relative to the individual fragments. Thus, in one embodiment, the invention provides a polynucleotide comprising a nucleic acid sequence comprising an open reading frame for a first protein or a fragment of a first protein fused to a first peptide linker fused to a second protein or a fragment of a second protein, e.g. a domain of a protein with binding or catalytic activity, fused to a second peptide linker fused to a third protein or a fragment of a third protein. In one embodiment, the fragment of a first protein is a fragment of a luciferase, the fragment of a third protein is a different fragment of the luciferase, and the second protein or the fragment thereof is not a luciferase. In another embodiment, the fragment of the first protein is a fragment of a luciferase, the second protein or the fragment thereof is not a luciferase, and the fragment of a third protein is a fragment that restores or increases the luciferase activity of the first fragment. In another embodiment, the second protein or the fragment thereof is not a luciferase, the fragment of a third protein is a fragment of a luciferase, and the fragment of the first protein is a fragment of the luciferase that restores or increases the luciferase activity of the first fragment. In one embodiment, the second fragment has a cAMP binding site.
In one embodiment, a peptide linker of the invention is positioned N-terminal to a cAMP binding site in a cAMP biosensor of the invention, e.g., one having firefly luciferase or click beetle luciferase sequences. In one embodiment, a peptide linker of the invention is positioned C-terminal to a cAMP binding site in a cAMP biosensor of the invention. In one embodiment, a peptide linker of the invention is positioned N-terminal and C-terminal to a cAMP binding site in a cAMP biosensor of the invention, and optionally the peptide linkers have different sequences and/or different lengths. The use of peptide linkers of the invention may result in biosensors with improved properties, e.g., in assays with endogenous or exogenous Gs- or Gi-coupled 7 transmembrane receptors, relative to the linker GSSGGSGSGGG (SEQ ID NO:41).
In one embodiment, a peptide linker of the invention is positioned N-terminal to a peptide sequence which is capable of directly or indirectly interacting with a molecule of interest, e.g., a molecule to be detected. In one embodiment, a peptide linker of the invention is positioned C-terminal to that peptide sequence in a biosensor of the invention. In one embodiment, a peptide linker of the invention is positioned N-terminal and C-terminal to peptide sequence which is capable of directly or indirectly interacting with a molecule to be detected.
In one embodiment, in the absence of cAMP, the activity of a modified luciferase of the invention is less than the activity of a corresponding unmodified luciferase, e.g., the reporter activity of the modified luciferase is about 0.001%, 0.01%, 0.1%, 1%, 10%, 20%, 50%, 70% or more, but less than 100% that of a corresponding unmodified luciferase, the activity of which modified luciferase is optionally detectable. In another embodiment, in the absence of cAMP, the activity of a modified luciferase of the invention is substantially the same or greater than the activity of a corresponding unmodified luciferase, e.g., the reporter activity of the modified luciferase of the invention is about 1.5-fold, e.g., at least 2-, 3- or 5-fold or more, that of a corresponding unmodified luciferase. In the presence of cAMP, the activity of the modified luciferase of the invention is detectably altered. For instance, a detectable alteration in activity of a modified luciferase in the presence of cAMP is an alteration of at least 0.001%, 0.01%, 0.1%, 1%, 10%, or 100%, and up to 2-fold, 4-fold, 10-fold, 100-fold, 1,000-fold, 10,000-fold or more, relative to the activity of the modified luciferase in the absence of cAMP. Thus, the physical proximity of cAMP which interacts with a modification present in the modified luciferase but not the corresponding unmodified luciferase, alters, e.g., decreases, eliminates or increases, the activity of the modified luciferase. In one embodiment, the luminescent signal of a modified luciferase of the invention in the presence of cAMP is increased relative to the luminescent signal of a corresponding luciferase with a heterologous native cAMP binding domain in the presence of cAMP.
The amino acid sequence of the modified luciferase is different than the amino acid sequence of a corresponding unmodified luciferase (native, wild-type or parental), e.g., a mutant luciferase with one or more substitutions in the luciferase sequences as a result of an insertion of heterologous amino acid sequences at a site (residue) or in a region in the luciferase which is tolerant to modification, e.g., tolerant to an insertion, a deletion, circular permutation, or any combination thereof. In one embodiment, in addition to the insertion of heterologous amino acid sequences, the luciferase sequences of the modified luciferase are circularly permuted relative to the amino acid sequence of a corresponding unmodified luciferase (native, wild-type luciferase) wherein the permutation is at a site (residue) or in a region that is tolerant to modification. In one embodiment, the regions which are tolerant to modification include surface loops between secondary structures, such as beta sheets or alpha helices, found on the native, wild-type luciferase. The heterologous amino acid sequences may be internal relative to the N- or C-terminus of a wild-type or circularly permuted luciferase, or may be at the N- and/or C-terminus of a wild-type or circularly permuted luciferase, and may include a deletion of luciferase sequences at the modification sites. In one embodiment, the one or more heterologous amino acid sequences which directly or indirectly interact with cAMP are at or near the N-terminal and/or C-terminal residues of a circularly permuted or a noncircularly permuted luciferase. In one embodiment, the one or more heterologous amino acid sequences which directly or indirectly interact with cAMP are not at or near the N-terminal and/or C-terminal residues of a circularly permuted luciferase or a nonpermuted luciferase, i.e., the heterologous sequences are internal to the N- and C-termini. In one embodiment, the modified luciferase may be circularly permuted, have one or more discreet (isolated) heterologous amino acid sequences, at least one of which directly or indirectly interacts with cAMP, and optionally may include the deletion of one or more amino acids, e.g., at a site(s) or in a region(s) tolerant to modification including the N- and/or C-terminus of the unmodified luciferase, so long as the resulting modified luciferase has bioluminescent activity before and/or after the interaction with cAMP, e.g., bioluminescent activity is altered after interaction with cAMP, such as an alteration in light intensity, color or kinetic profile.
A deletion within the scope of the invention includes a deletion of one or more amino acid residues at a site or in a region of a luciferase sequence that is tolerant to a deletion. The modified luciferase may include deletions at the N- and C-terminus of 1 to about 10 or about 30, residues, or any integer in between, e.g., 15 residues, corresponding to the N- or C-terminus of the unmodified luciferase. The length of the deletion may be greater than 30 residues depending on the particular luciferase and the length of a desirable deletion may be determined by routine deletion analysis.
A beetle luciferase may be modified at a residue, for instance, residue 21, 25, 117, 358, 376, 379, 398, 399, 400, 401, 402, 403, 405, 406, 407, 409 or 490, or in a region corresponding to residue 15 to 30, e.g., residue 21 or 25, residue 112 to 122, e.g., residue 117, residue 352 to 362, for instance, residue 358, residue 371 to 384, e.g., residue 379, residue 393 to 414, or residue 485 to 495, of a click beetle luciferase, e.g., one having SEQ ID NO:9, or at residue 7, 37, 47, 75, 83, 107, 121, 144, 160, 174, 188, 198, 205, 225, 233, 242, 255, 268, 308, 316, 358, 377, 403, 435, 490 or 540, or in a region corresponding to residue 2 to 12, residue 32 to 53, e.g., residue 32 to 43 or residue 42 to 52, residue 70 to 88, e.g., residue 70 to 80 or residue 78 to 88, residue 102 to 126, e.g., residue 102 to 112 or residue 116 to 126, residue 139 to 165, residue 183 to 203, residue 220 to 247, e.g., residue 228 to 238, residue 262 to 273, residue 303 to 313, residue 353 to 408, residue 485 to 495, or residue 535 to 546 of a firefly luciferase, e.g., one having SEQ ID NO:106, 118, or 120. The residue numbering is based on that in an unmodified (native) click beetle or firefly luciferase sequence. Corresponding positions may be identified by aligning luciferase sequences using, for instance, sequence alignment programs. Residues or regions in a luciferase tolerant to modification may be employed as sites to circularly permute the luciferase or for an insertion.
The invention further includes a modified anthozoan luciferase having at least one modification at a site or in a region which is tolerant to modification, including but not limited to at a residue corresponding to residue 2, 30, 31, 42, 45, 46, 68, 69, 90, 91, 92, 110, 111, 150, 151, 168, 169, 193, 207, 208, 223, 224, 251, 259, 274, or 311 or in a region corresponding to residue 2 to 12, residue 26 to 36, residue 37 to 47, residue 64 to 74, residue 86 to 97, e.g., residue 90 or 91, residue 96 to 116, residue 147 to 157, residue 218 to 234, e.g., residue 223, 234, 228, 229 or 230, or residue 301 to 311 of a Renilla luciferase (Genbank ID AF025843), e.g., one having SEQ ID NO:116. The residue numbering is based on that in an unmodified (native) Renilla luciferase sequence. Corresponding positions may be identified by aligning luciferase sequences using, for instance, sequence alignment programs. Residues or regions in a luciferase tolerant to modification may be employed as sites to circularly permute the luciferase or for an insertion.
Further included is a modified crustacean luciferase, e.g., a copepod luciferase, having at least one modification at a site or in a region which is tolerant to modification, including but not limited to in a region corresponding to residue 43 to 53, residue 63 to 73, residue 79 to 89, residue 95 to 105, residue 105 to 115, residue 109 to 119, residue 121 to 131 or residue 157 to 168 of a Gaussia luciferase, e.g., one having SEQ ID NO:121, or in a region corresponding to residue 45 to 55 or residue 79 to 89 of a mature Oplophorus luciferase, e.g., one having SEQ ID NO:122. The residue numbering is based on that in an unmodified (native) Gaussia luciferase sequence or the Oplophorus luciferase sequence with a molecular weight of 19 kDa. Corresponding positions may be identified by aligning luciferase sequences using, for instance, sequence alignment programs. Residues or regions in a luciferase tolerant to modification may be employed as sites to circularly permute the luciferase or for an insertion.
Accordingly, a modified luciferase of the invention may be employed as a biosensor.
The invention also provides an isolated nucleic acid molecule (polynucleotide) comprising a nucleic acid sequence encoding a modified luciferase of the invention. Further provided is an isolated nucleic acid molecule comprising a nucleic acid sequence encoding fusion protein comprising a modified luciferase and one or more amino acid residues at the N-terminus (a N-terminal fusion partner) and/or C-terminus (a C-terminal fusion partner) of the modified luciferase. Thus, as used herein, a “fusion protein” is a polypeptide which includes one or more amino acids at the N-terminus and/or C-terminus of a modified luciferase of the invention. In one embodiment, the presence of one or more fusion partners in the fusion protein does not substantially alter the detectable activity of the fusion protein relative to a corresponding modified luciferase. The N- or C-terminal fusion partner may be a sequence used for purification, e.g., a glutathione S-transferase (GST) or a polyHis sequence, a sequence intended to alter a property of the modified luciferase, e.g., a protein destabilization sequence, a protein or nucleic acid interaction sequence (e.g., a binding sequence), a subcellular localization sequence, or a sequence which has a property which is distinguishable from one or more properties of the luciferase in the fusion protein. In one embodiment, the fusion protein comprises a modified luciferase and a fusion partner which is a reporter protein that is different than the luciferase, which reporter protein is useful as an intramolecular control, e.g., a fluorescent protein or another luciferase. In another embodiment, the invention includes a vector comprising a nucleic acid sequence encoding a fusion protein comprising a modified luciferase of the invention and a nucleic acid fragment which encodes a reporter protein that is different than the luciferase in the modified luciferase. In one embodiment, the mutant cAMP binding domain containing luciferase of the invention further includes a subcellular localization signal, which is useful to detect subcellular localization and/or concentration of cAMP.
Optionally, optimized nucleic acid sequences, e.g., human codon optimized sequences, encoding at least the luciferase, and in one embodiment the modified luciferase or a fusion protein comprising a modified luciferase, are employed in the nucleic acid molecules of the invention, as those optimized sequences can increase the strength of the signal for luciferase. The optimization of nucleic acid sequences is known to the art, see, for example, WO 02/16944.
The invention also includes a stable cell line that expresses a modified luciferase, or fusion protein of the invention, as well as an expression cassette comprising a nucleic acid molecule encoding the modified luciferase or fusion protein of the invention, and a vector (e.g., a plasmid, virus, or defective viral particles) capable of expressing the nucleic acid molecule of the invention in a host cell. In one embodiment, the expression cassette comprises a promoter, e.g., a constitutive or regulatable promoter, operably linked to the nucleic acid sequence. In one embodiment, the expression cassette contains an inducible promoter. Also provided is a host cell, e.g., a prokaryotic cell or an eukaryotic cell such as a plant or vertebrate cell, e.g., a mammalian cell, including but not limited to a human, non-human primate, canine, feline, bovine, equine, ovine or rodent (e.g., rabbit, rat, ferret or mouse) cell, which comprises the expression cassette or vector of the invention, and a kit which comprises the nucleic acid molecule, expression cassette, vector, host cell or modified luciferase or fusion protein of the invention.
For instance, a vector encoding a modified luciferase comprising an insertion of a cAMP binding site of the invention, or a modified luciferase comprising an insertion of a cAMP binding site of the invention, is mixed with a sample, e.g., a cell, cell lysate, in vitro transcription/translation mixture, or supernatant, and the activity of the modified luciferase in the sample detected or determined, e.g., optionally at one or more time points, or relative to a control sample without cAMP or having a differing amount of cAMP. An alteration in luminescent activity in the sample, for instance, over time, and/or relative to a control, e.g., a cell having a specified amount of cAMP, indicates the presence or amount of cAMP in the sample, or change in amount of cAMP related to experimental condition. In one embodiment, a cell is contacted with a vector comprising a promoter, e.g., a regulatable or constitutive promoter, and a nucleic acid sequence encoding a modified luciferase of the invention which comprises an insertion which interacts with the cyclic nucleotide. In one embodiment, a transfected cell is cultured under conditions in which the promoter induces transient expression of the modified luciferase, and the presence or amount of luminescence determined. In another embodiment, a modified luciferase of the invention which comprises an insertion which interacts with the cAMP and a sample suspected of having a cAMP are mixed. Then the amount of luminescence is determined. The invention thus provides a method of detecting the amount of cAMP.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. PKA regulatory subunit type IIβ (RIIβB). X-ray crystal structure of rat RIIβB amino acids 264-412 (PDB 1CX4). RIIβB is rendered as a red ribbon; cAMP is rendered as ball and stick. The primary sequence similarity between rat (amino acids 264-412) and human RIIβB (amino acids 266-414) is 96.6% (program Megalign, DNAStar).
FIG. 2. Fold induction over time for circularly-permuted firefly luciferase (CPM-FF Luc/mutant RIIβB cAMP biosensors treated with isoproterenol.
FIG. 3. Fold induction over time for CPM-FF Luc/mutant RIIβB cAMP biosensors treated with isoproterenol.
FIG. 4. Fold induction over time for CPM-FF Luc/mutant RIIβB cAMP biosensors treated with isoproterenol.
FIG. 5. Fold induction over time for CPM-FF Luc/mutant RIIβB cAMP biosensors treated with isoproterenol.
FIG. 6. Fold induction over time for CPM-FF Luc/mutant RIIβB cAMP biosensors treated with isoproterenol.
FIGS. 7A-C. FIG. 7A) Basal activity of various cAMP biosensors with linkers over time. FIG. 7B) Activity of various cAMP biosensors with linkers after isoproterenol induction. FIG. 7C) Response of various cAMP biosensors with linkers.
FIGS. 8A-B. FIG. 8A) Fold response over time in 293 cells expressing a CPM-FF Luc/mutant RIIβB cAMP biosensor with a modified linker (L9) and treated with isoproterenol relative to 293 cells expressing a CPM-FF Luc/mutant RIIβB cAMP biosensor with a GSSGGSGGSGGG (SEQ ID NO: 41) linker. FIG. 8B) Fold change in RLU versus t=0 in the presence or absence of forskolin for HEK293/D2 cells expressing the CPM-FF Luc/mutant RIIβB cAMP biosensor L9 or a CPM-FF Luc/mutant RIIβB cAMP biosensor with GSSGGSGGSGGG (SEQ ID NO:41) linker.
FIG. 9A, FIG. 9B, and FIG. 9C. Fold response for clones treated with various compounds and with FSK.
FIG. 10A, FIG. 10B, and FIG. 10C. Graph of the absolute RLUs for clones at 30 minutes with each compound and with or without FSK.



DETAILED DESCRIPTION OF THE INVENTION
Definitions
All amino acid residues identified herein are in the natural L configuration. In keeping with standard polypeptide nomenclature, abbreviations for amino acid residues are as shown in the following Table of Correspondence.










TABLE OF CORRESPONDENCE











1 Letter
3 Letter
AMINO ACID







Y
Tyr
L tyrosine



G
Gly
L-glycine



F
Phe
L phenylalanine



M
Met
L methionine



A
Ala
L alanine



S
Ser
L serine



I
Ile
L isoleucine



L
Leu
L leucine



T
Thr
L threonine



V
Val
L valine



P
Pro
L proline



K
Lys
L lysine



H
His
L histidine



Q
Gln
L glutamine



E
Glu
L glutamic acid



W
Trp
L tryptophan



R
Arg
L arginine



D
Asp
L aspartic acid



N
Asn
L asparagine



C
Cys
L cysteine










The terms “cell,” “cell line,” “host cell,” as used herein, are used interchangeably, and all such designations include progeny or potential progeny of these designations. By “transformed cell” is meant a cell into which (or into an ancestor of which) has been introduced a nucleic acid molecule of the invention. Optionally, a nucleic acid molecule of the invention may be introduced into a suitable cell line so as to create a stably-transfected cell line capable of producing the protein or polypeptide encoded by the gene. Vectors, cells, and methods for constructing such cell lines are well known in the art. The words “transformants” or “transformed cells” include the primary transformed cells derived from the originally transformed cell without regard to the number of transfers. All progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Nonetheless, mutant progeny that have the same functionality as screened for in the originally transformed cell are included in the definition of transformants.
As used herein, the term “heterologous” nucleic acid sequence or protein refers to a sequence that relative to a reference sequence has a different source, e.g., originates from a foreign species, or, if from the same species, it may be substantially modified from the original form. The term “homology” refers to a degree of complementarity between two or more sequences. There may be partial homology or complete homology (i.e., identity). Homology is often measured using sequence analysis. Such software matches similar sequences by assigning degrees of homology to various substitutions, deletions, insertions, and other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
The term “in vitro” refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments include, but are not limited to, test tubes and cell lysates. The term “in vivo” refers to the natural environment (e.g., an animal or a cell) and to processes or reaction that occur within a natural environment.
The term “isolated” when used in relation to a nucleic acid or polypeptide, as in “isolated oligonucleotide”, “isolated polynucleotide”, “isolated protein” or “isolated polypeptide” refers to a nucleic acid or amino acid sequence that is identified and separated from at least one contaminant with which it is ordinarily associated in its source. Thus, an isolated nucleic acid or isolated polypeptide is present in a form or setting that is different from that in which it is found in nature. In contrast, non isolated nucleic acids (e.g., DNA and RNA) or non-isolated polypeptides (e.g., proteins and enzymes) are found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) is found on the host cell chromosome in proximity to neighboring genes; RNA sequences (e.g., a specific mRNA sequence encoding a specific protein), are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid includes, by way of example, such nucleic acid in cells ordinarily expressing that nucleic acid where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid or oligonucleotide may be present in single stranded or double stranded form. When an isolated nucleic acid or oligonucleotide is to be utilized to express a protein, the oligonucleotide contains at a minimum, the sense or coding strand (i.e., the oligonucleotide may single stranded), but may contain both the sense and anti sense strands (i.e., the oligonucleotide may be double stranded).
The term “nucleic acid molecule’, “polynucleotide”, or “nucleic acid sequence” as used herein, refers to nucleic acid, DNA or RNA, that comprises coding sequences necessary for the production of a polypeptide or protein precursor. The encoded polypeptide may be a full-length polypeptide, a fragment thereof (less than full-length), or a fusion of either the full-length polypeptide or fragment thereof with another polypeptide, yielding a fusion polypeptide.
A polynucleotide having a nucleotide sequence encoding a protein or polypeptide means a nucleic acid sequence comprising the coding region of a gene, or in other words the nucleic acid sequence encodes a gene product. The coding region may be present in either a cDNA, genomic DNA or RNA form. When present in a DNA form, the oligonucleotide may be single stranded (i.e., the sense strand) or double stranded. Suitable control elements such as enhancers/promoters, splice junctions, polyadenylation signals, etc. may be placed in close proximity to the coding region of the gene if needed to permit proper initiation of transcription and/or correct processing of the primary RNA transcript. Alternatively, the coding region. Other regulatory elements include, but are not limited to, transcription factor binding sites, splicing signals, polyadenylation signals, termination signals and enhancer elements.
By “peptide,” “protein” and “polypeptide” is meant any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). The nucleic acid molecules of the invention may also encode a variant of a naturally-occurring protein or polypeptide fragment thereof, which has an amino acid sequence that is at least 60%, 70%, 80%, 85%, 90%, 95% or 99% identical to the amino acid sequence of the naturally-occurring (native or wild-type) protein from which it is derived. For example, a coleopteran luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to one of SEQ ID Nos. 9, 106, 118 or 120; a firefly luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to one of 106, 118 or 120; a click beetle luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to SEQ ID NO:9; an anthozoan luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to SEQ ID NO:116; a copepod luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to SEQ ID NO:121; and decapod luciferase has at least 60%, 70%, 80%, 85%, 90%, 95% or 99% amino acid sequence identity to SEQ ID NO: 122. The term “fusion polypeptide” or “fusion protein” refers to a chimeric protein containing a reference protein (e.g., luciferase) joined at the N- and/or C-terminus to one or more heterologous sequences (e.g., a non luciferase polypeptide). In some embodiments, a modified polypeptide, fusion polypeptide or a portion of a full-length polypeptide of the invention, may retain at least some of the activity of a corresponding full-length functional (nonchimeric) polypeptide. In other embodiments, in the absence of an exogenous agent or molecule of interest, a modified polypeptide, fusion polypeptide or portion of a full-length functional polypeptide of the invention, may lack activity relative to a corresponding full-length functional polypeptide. In other embodiments, a modified polypeptide, fusion polypeptide or portion of a full-length functional polypeptide of the invention in the presence of an exogenous agent may retain at least some or have substantially the same activity, or alternatively lack activity, relative to a corresponding full-length functional polypeptide.
As used herein, “pure” means an object species is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition), and in one embodiment a substantially purified fraction is a composition wherein the object species comprises at least about 50 percent (on a molar basis) of all macromolecular species present. Generally, a “substantially pure” composition will comprise more than about 80 percent of all macromolecular species present in the composition, more in one embodiment more than about 85%, about 90%, about 95%, or about 99%. For instance, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
Nucleic acids are known to contain different types of mutations. A “point” mutation refers to an alteration in the sequence of a nucleotide at a single base position from the wild-type sequence. Mutations may also refer to insertion or deletion of one or more bases, so that the nucleic acid sequence differs from a reference, e.g., a wild-type, sequence.
The terms “recombinant vector” and “expression vector” as used herein refer to DNA or RNA sequences containing a desired coding sequence and appropriate DNA or RNA sequences necessary for the expression of the operably linked coding sequence in a particular host organism. Prokaryotic expression vectors include a promoter, a ribosome binding site, an origin of replication for autonomous replication in a host cell and possibly other sequences, e.g. an optional operator sequence, optional restriction enzyme sites. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and to initiate RNA synthesis. Eukaryotic expression vectors include a promoter, optionally a polyadenlyation signal and optionally an enhancer sequence.
The term “vector” is used in reference to nucleic acid molecules into which fragments of DNA may be inserted or cloned and can be used to transfer DNA segment(s) into a cell and capable of replication in a cell. Vectors may be derived from plasmids, bacteriophages, viruses, cosmids, and the like.
The term “wild-type” as used herein, refers to a gene or gene product that has the characteristics of that gene or gene product isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “wild-type” form of the gene. In contrast, the term “mutant” refers to a gene or gene product that displays modifications in sequence and/or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.
Exemplary Polynucleotides and Proteins for cAMP Biosensors
The invention includes cAMP luciferase biosensors including circularly permuted cAMP luciferase biosensors, which luciferase sequence may include deletions of residues at the original (wild type) N- or C-termini, or both, e.g., deletion of 1 to 3 or more residues at the N-terminus and 1 to 6 or more residues at the C-terminus, as well as sequences that directly or indirectly interact with cAMP. The luciferase sequences of a modified luciferase are the same or are substantially the same as the amino acid sequence of a corresponding unmodified luciferase. A polypeptide or peptide having substantially the same sequence means that an amino acid sequence is largely, but may not entirely be, the same and retains a functional activity of the sequence to which it is related. In general, two amino acid sequences are substantially the same or substantially homologous if they are at least 80% identical, e.g., have at least 85%, 90%, 95%, 99% or more identity.
Homology or identity is often measured using sequence analysis software. Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions and other modifications. The terms “homology” and “identity” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection.
For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
Methods of alignment of sequence for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted by the local homology algorithm of Smith et al. (Adv. Appl. Math. 2: 482 (1981)), by the homology alignment algorithm of Needleman et al. (J. Mol. Biol. 48: 443 (1970)), by the search for similarity method of Person et al. (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA), or by manual alignment and visual inspection.
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA. Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (Gene 73: 237 (1988)); Higgins et al. (CABIOS 5: 157 (1989)); Corpet et al. NAR 16: 1088 (1988); Huang et al. (CABIOS 8: 155 (1992)); and Pearson et al. (Methods Mol. Biol. 24: 307 (1994)). The ALIGN program is based on the algorithm of Myers and Miller (LABIOS 4: 11 (1988)). The BLAST programs of Altschul et al. (J. Mol. Biol. 215: 403 (1990)), are based on the algorithm of Karlin and Altschul (PNAS USA 90: 5873 (1993)).
Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al. J. Mol. Biol. 215: 403 (1990)). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached.
In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul PNAS USA 90: 5873 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, e.g., less than about 0.01, for instance, less than about 0.001.
To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (NAR 25: 3389 (1997)). Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al., supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g. BLASTN for nucleotide sequences, BLASTX for proteins) can be used. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff. PNAS USA 89: 10915(1989)). See http://www.ncbi.nlm.nih.gov.
In particular, a polypeptide may be substantially related but for a conservative variation. A conservative variation denotes the replacement of an amino acid residue by another, biologically similar residue. Examples of conservative variations include the substitution of one hydrophobic residue such as isoleucine, valine, leucine or methionine for another, or the substitution of one polar residue for another such as the substitution of arginine for lysine, glutamic for aspartic acids, or glutamine for asparagine, and the like. Other illustrative examples of conservative substitutions include the changes of: alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine, glutamine, or glutamate; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; valine to isoleucine to leucine.
In one embodiment, a polynucleotide of the invention is optimized for expression in a particular host. As used herein, optimization includes codon optimization as well as, in eukaryotic cells, introduction of a Kozak sequence, and/or one or more introns. Thus, a nucleic acid molecule may have a codon composition that differs from that of a wild-type nucleic acid sequence encoding an unmodified luciferase at more than 30%, 35%, 40% or more than 45%, e.g., 50%, 55%, 60% or more of the codons. Preferred codons for use in the invention are those which are employed more frequently than at least one other codon for the same amino acid in a particular organism and, optionally, are also not low-usage codons in that organism and are not low-usage codons in the organism used to clone or screen for the expression of the nucleic acid molecule. Moreover, preferred codons for certain amino acids (i.e., those amino acids that have three or more codons,), may include two or more codons that are employed more frequently than the other (non-preferred) codon(s). The presence of codons in the nucleic acid molecule that are employed more frequently in one organism than in another organism results in a nucleic acid molecule which, when introduced into the cells of the organism that employs those codons more frequently, is expressed in those cells at a level that is greater than the expression of the wild-type or parent nucleic acid sequence in those cells.
In one embodiment of the invention, the codons that are different are those employed more frequently in a mammal, while in another embodiment the codons that are different are those employed more frequently in a plant. A particular type of mammal, e.g., human, may have a different set of preferred codons than another type of mammal. Likewise, a particular type of plant may have a different set of preferred codons than another type of plant. In one embodiment of the invention, the majority of the codons which differ are ones that are preferred codons in a desired host cell. Preferred codons for mammals (e.g., humans) and plants are known to the art (e.g., Wada et al. NAR 18: 2367(1990); Murray et al. NAR 17: 477 (1989))
The modified luciferase proteins or fusion proteins of the invention may be prepared by recombinant methods or by solid phase chemical peptide synthesis methods. Such methods have been known in the art since the early 1960's (Merrifield. J. Am. Chem. Soc. 2149(1963); Stewart et al., Solid Phase Peptide Synthesis, 2nd ed., Pierce Chemical Co., Rockford, Ill., pp. 11-12)) and have recently been employed in commercially available laboratory peptide design and synthesis kits (Cambridge Research Biochemicals).
II. Fusion Partners Useful with the Modified Luciferase of the Invention
The polynucleotide of the invention which encodes a modified luciferase may be employed with other nucleic acid sequences, e.g., a native sequence such as a cDNA or one which has been manipulated in vitro, e.g., to prepare N-terminal, C-terminal, or N- and C-terminal fusion proteins, e.g., a fusion with a protein encoded by a different reporter gene including a selectable marker. Many examples of suitable fusion partners are known to the art and can be employed in the practice of the invention.
Fusion partners include but are not limited to affinity domains or other functional protein sequences, such as those having an enzymatic activity. For example, a functional protein sequence may encode a kinase catalytic domain (Hanks and Hunter. FASEB J. 9: 576(1995)), producing a fusion protein that can enzymatically add phosphate moieties to particular amino acids, or may encode a Src Homology 2 (SH2) domain (Sadowski et al. Mol. Cell. Bio. 6: 4396(1986); Mayer and Baltimore. Trends Cell. Biol. 3: 8(1993)), producing a fusion protein that specifically binds to phosphorylated tyrosines.
Affinity domains are generally peptide sequences that can interact with a binding partner, e.g., such as one immobilized on a solid support. DNA sequences encoding multiple consecutive single amino acids, such as histidine, when fused to the expressed protein, may be used for one-step purification of the recombinant protein by high affinity binding to a resin column, such as nickel sepharose. Sequences encoding peptides, such as the chitin binding domain (which binds to chitin), glutathione-S-transferase (which binds to glutathione), biotin (which binds to avidin and strepavidin), and the like, can also be used for facilitating purification of the protein of interest. The affinity domain can be separated from the protein of interest by methods well known in the art, including the use of inteins (protein self-splicing elements (Chong et al. Gene 192: 271(1997)). Exemplary affinity domains include HisV5 (HHHHH) (SEQ ID NO:15), HisX6 (HHHHHH) (SEQ ID NO:16), C-myc (EQKLISEEDL) (SEQ ID NO:17), Flag (DYKDDDDK) (SEQ ID NO:14), Step-Tag (WSHPQFEK) (SEQ ID NO:18), hemagluttinin, e.g., HA Tag (YPYDVPDYA) (SEQ ID NO:19), GST, thioredoxin, cellulose binding domain, RYIRS (SEQ ID NO:20), Phe-His-His-Thr (SEQ ID NO:21), chitin binding domain, S-peptide, T7 peptide, SH2 domain, C-end RNA tag, WEAAAREACCRECCARA (SEQ ID NO:22), metal binding domains, e.g., zinc binding domains or calcium binding domains such as those from calcium-binding proteins, e.g., calmodulin, troponin C, calcineurin B, myosin light chain, recoverin, S-modulin, visinin, VILIP, neurocalcin, hippocalcin, frequenin, caltractin, calpain large-subunit, 5100 proteins, parvalbumin, calbindin D9K, calbindin D28K, and calretinin, inteins, biotin, streptavidin, MyoD, Id, leucine zipper sequences, and maltose binding protein. In one embodiment, the fusion partner is a sequence useful to purify a fusion protein, e.g., a His or GST tag, and in one embodiment the purification tag is fused to the N- or C-terminus of a circularly permuted luciferase.
III. Vectors and Host Cells Encoding the Modified Luciferase or Fusions Thereof
Once a desirable nucleic acid molecule encoding a modified luciferase or a fusion thereof is prepared, an expression cassette encoding the modified luciferase or a fusion protein comprising the modified luciferase is prepared. For example, a nucleic acid molecule comprising a nucleic acid sequence encoding a modified luciferase is optionally operably linked to transcription regulatory sequences, e.g., one or more enhancers, a promoter, a transcription termination sequence or a combination thereof, to form an expression cassette. The nucleic acid molecule or expression cassette may be introduced to a vector, e.g., a plasmid or viral vector, which optionally includes a selectable marker gene, and the vector introduced to a cell of interest, for example, a prokaryotic cell such as E. coli, Streptomyces spp., Bacillus spp., Staphylococcus spp. and the like, as well as eukaryotic cells including a plant (dicot or monocot), fungus, yeast, e.g., Pichia, Saccharomyces or Schizosaccharomyces, or a mammalian cell. Exemplary mammalian cells include bovine, caprine, ovine, canine, feline, non-human primate, e.g., simian, and human cells. Exemplary mammalian cell lines include, but are not limited to, CHO, COS, 293, Hela, CV-1, SH-SY5Y, HEK293, and NIH3T3 cells.
The expression of an encoded modified luciferase may be controlled by any promoter capable of expression in prokaryotic cells or eukaryotic cells. Exemplary prokaryotic promoters include, but are not limited to, SP6, T7, T5, tac, bla, trp, gal, lac or maltose promoters. Exemplary eukaryotic promoters include, but are not limited to, constitutive promoters, e.g., viral promoters such as CMV, SV40 and RSV promoters, as well as regulatable promoters, e.g., an inducible or repressible promoter such as the tet promoter, the hsp70 promoter and a synthetic promoter regulated by CRE. The nucleic acid molecule, expression cassette and/or vector of the invention may be introduced to a cell by any method including, but not limited to, calcium-mediated transformation, electroporation, microinjection, lipofection and the like.
IV. Exemplary Uses
The modified luciferases or fusions thereof are useful for any purpose including, but not limited to, detecting the amount or presence of cAMP (a biosensor), isolating a particular molecule, detecting conformational changes in a particular molecule, e.g., due to binding, facilitating high or low throughput screening, detecting protein-protein, protein-DNA or other protein-based interactions, or selecting or evolving biosensors. For instance, a modified luciferase or a fusion thereof, is useful to detect, e.g., in an in vitro or cell-based assay, the amount, presence or activity of cAMP (for example, by inserting a cAMP binding site into a luciferase protein); to identify recognition sites or to detect substrate specificity, e.g., using a modified luciferase with a selected recognition sequence or a library of modified luciferases having a plurality of different sequences with a single molecule of interest or a plurality (for instance, a library) of molecules; to select or evolve biosensors or molecules of interest; or to detect protein-protein interactions via complementation or binding, e.g., in an in vitro or cell-based approach. In one embodiment, a modified luciferase which includes a cAMP binding site is contacted with a random library or mutated library of molecules, and molecules identified which interact with the site. In another embodiment, a library of modified luciferases having a plurality cAMP binding sites is contacted with a molecule, and modified luciferases which interact with the molecule identified. In one embodiment, a modified luciferase or fusion thereof, is useful to detect, e.g., in an in vitro or cell-based assay, the amount or presence of cAMP (for example, by inserting a cAMP binding site into a circularly permuted luciferase), to screen for inhibitors or activators, e.g., inhibitors or activators of cAMP, inhibitors or activators of cAMP binding to a cAMP binding site or inhibitors or activators of G protein coupled receptors (GPCR), to identify recognition sites or to detect substrate specificity, e.g., using a modified luciferase with a selected recognition sequence or a library of modified luciferases having a plurality of different sequences with a single molecule of interest or a plurality (for instance, a library) of molecules, to select or evolve cAMP binding sites, or in whole animal imaging.
The invention also provides methods of screening for agents (“test” agents) capable of modulating the amount of cAMP. “Modulation” refers to an alteration of a property; such enhancement or inhibition of a biological or chemical activity, where the alteration may be contingent on the occurrence of a specific event, such as activation of a signal transduction pathway, and/or may be manifest only in particular cell types. A “modulator” refers to an agent (naturally occurring or non-naturally occurring), such as, for example, a biological macromolecule (e.g., nucleic acid, protein, non-peptide, or organic molecule), small molecules, an extract made from biological materials such as bacteria, plants, fungi, or animal (particularly mammalian) cells or tissues, or any other agent. Modulators are evaluated for potential activity as inhibitors or activators (directly or indirectly) of a biological process or processes (e.g., agonist, partial antagonist, partial agonist, or antagonist) by inclusion in the screening assays described herein. The activities (or activity) of a modulator may be known, unknown or partially known. Such modulators can be screened using the methods of the invention. The term “test agent” refers to an agent to be tested by one or more screening method(s) of the invention as a putative modulator. Usually, various predetermined concentrations are used for screening such as 0.01 μM, 0.1 μM, 1.0 μM, and 10.0 μM. Controls can include the measurement of a signal in the absence of the test agent, comparison to an agent known to modulate the target, or comparison to a sample (e. a cell, tissue or organism) before, during and/or after contacting with the test agent.
In one embodiment, a modified luciferase of the invention is useful as a substrate to study agents or conditions that modulate an interaction between a cAMP binding site in the modified luciferase and a molecule of interest such as a cyclic nucleotide, agents or conditions that modulate the presence or amount of a cyclic nucleotide, or agents or conditions that modulate molecules such as receptors that are associated with intracellular cyclic nucleotide concentrations. In particular, the invention contemplates modified luciferase proteins in which the insertion includes a cAMP binding site. Thus, when the molecule of interest is cAMP, the invention provides a method to determine the presence or the amount of cAMP in a sample by contacting the sample with a modified luciferase polypeptide of the invention and measuring changes in luciferase activity. The modified luciferase protein of the invention can be used for, among other things, monitoring the amount or presence of cAMP or molecules that alter the amount or presence of cAMP inside a cell that has the modified luciferase.
The assays of the invention can be used to screen drugs to identify compounds that alter the amount, for example, of cyclic nucleotide or alter the binding of a cyclic nucleotide to a cyclic nucleotide binding site. In one embodiment, the assay is performed on a sample in vitro containing cAMP. A sample containing a known amount of cAMP is mixed with a modified luciferase of the invention and with a test agent. The amount of the luciferase activity in the sample is then determined. Then the amount of activity per mole of cAMP in the presence of the test agent may be compared with the activity per mole of cAMP in the absence of the test agent. A difference indicates that the test agent alters the amount of cAMP or binding of cAMP to the cAMP binding site.
In one embodiment, cells are conditioned or contacted with an agent suspected of directly or indirectly modulating, for instance, cAMP amount or binding. The cells or cells in culture are lysed and the amount of cAMP measured. For example, a lysed cell sample containing a known or unknown amount of cAMP is mixed with a modified luciferase of the invention. The amount of cAMP in the sample is then determined as above by determining the degree of modified luciferase activity in a control or non-treated sample and the treated lysed cellular sample. The activity or inhibition can be calculated based on a per microgram or milligram protein in the sample. Typically, the difference is calibrated against standard measurements to yield an absolute amount of cAMP.
The materials and composition for use in the assay of the invention are ideally suited for the preparation of a kit. Such a kit may comprise a carrier means containing one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method. One of the containers comprises a modified luciferase or polynucleotide (e.g., in the form of a vector) of the invention. A second container may contain a substrate for the modified luciferase.
The invention will be further described by the following non-limiting examples.
Example I
Exemplary Sites Tolerant to Modification in Luciferases
To prepare cAMP luciferase biosensors, a cAMP binding site is fused to a luciferase that is tolerant to modification. Positions in click beetle and firefly luciferases that are tolerant to modification, e.g., for circular permutation or insertion of heterologous sequences, are disclosed in U.S. published application 20050153310, U.S. Ser. No. 11/732,105, PCT/US2004/032705 and PCT/US2007/008176, the disclosures of which are incorporated by reference herein.
Example II
Generation of Mutations in the Human RIIβB Site
To identify improved biosensors for cAMP, constructs were prepared with substitutions in a human cAMP binding domain (subsite B from the human PKA regulatory subunit type IIβ (RIIβB; Genbank Accession No. BC075800, residues 266-414). Substitutions in RIIβB were generated using the oligo-based site-directed mutatagenesis kit (Kunkel, PNAS USA 82(2):488 (1985)), Quik Change (Stratagene) on the human RIIβB site or the error-prone, mutagenic PCR-based system (Daugherty, PNAS USA 97(5):2029 (2000)), GeneMorph II (Stratagene) on the circularly-permuted firefly luciferase construct (Met-(FF luc 359-544)-(RIIβB)-(FF luc 4-355)-Val) according to the manufacture's instructions.
Example III
Screening of Human RIIβB Mutants
Biosensor constructs containing mutations to RIIβB (Example 2) were inserted into a circularly permuted firefly luciferase (CP-FF) construct (Met-(FF luc 359-544)-(RIIβB)-(FFluc4-355)-Val). These constructs were first screened in E. coli to identify mutant RIIβB sites which provided improved luminescence, improved response or both. Briefly, the constructs were overexpressed in E. coli in the presence or absence of 50 μM cAMP. Those constructs which demonstrated improved luminescence were screened for enhanced signal or enhanced response to agents that increase cAMP in HEK293 cells. The performance of these mutant biosensors was compared to that of the parent construct (GS358) with primary sequence Met-(FF luc 359-544)-GSSGGSGGSGGG (SEQ ID NO:41)-(RIIβB)-(FFluc4-355)-Val.
Methods and Results
On day 1, 15,000 HEK293 cells were plated to the individual wells of a 96-well plate. On day 2, cells were transiently transfected with plasmid DNAs encoding various biosensor mutants (with mutations in the RIIβB cAMP binding domain) using the TransIT-LT1 reagent from Mirus Bio. Plasmids also carried a gene for constitutive expression of Renilla luciferase to act as a transfection control. Cells were equilibrated for 2 hours at room temperature using 2 mM endotoxin-free luciferin (EF-luc). Isoproterenol or foskolin (FSK) were added to 10 μM final concentration to the individual wells, and luminescence was monitored continuously in time (Mithras luminometer; 1 second integration time). Once measurements were complete (>30 minutes), cells were lysed, and Renilla luciferase activity was measured.
Biosensor luminescence (FF RLU) was normalized using the Renilla luminescence signal (RL norm), and fold-induction (response) was calculated by dividing the normalized biosensor luminescence from isoproterenol- or forskolin-treated wells by the normalized luminescence from control wells that received no compound addition (FIGS. 2-6).
As indicated in Table 1, some of the substitutions were found to improve only luminescent signal or response. Other substitutions, e.g., residues 389 and 333, were found to improve either luminescent signal or response depending on the amino acid substituted at that residue. Some substitutions, e.g., V333N, provided improvement in both the luminescent signal and response. Combinations of substitutions were also screened to determine if the substitutions had a cumulative effect on the improvement of the luminescent signal or response.










TABLE 1







Agonist Signal
Agonist Response



Improvements
Improvements









M266Q
E284A



F282S
V291S



L286N
V296T



V296T
D308E



V333N, V333G
V316I



M389K
V333P, V333N



V404S
M389Y, M289S, M289C, M389V,




M389L




E284A + V316I




E284A + V316I + V333P + M289Y










Example IV
Generation of Mutated Linker Sequences
To identify if changes in the linker sequence of a cAMP biosensor could also improve luminescence, response to agents, or both, linker variants were prepared with substitutions in the parent linker sequence GS358, GSSGGSGGSGGG (SEQ ID NO:41). Linker variants were generated using a cassette-based cloning approach or by directly synthesizing annealed, duplex oligo linkers. The cassette based approach comprises the direct ligation of duplex library fragments or individual fragments into the sequence/gene. Briefly, linker variants were generated by amplification of single-stranded random sequences representing the linker region. The resulting duplex cassettes containing the appropriate restrication sites were ligated into the appropriate region of the sequence to create a plasmid-based library of linker variants. For linker variants synthesized directly, both strands of the linker cassette were synthesized (IDT), annealed, and cloned as in the cassette-based approach. Linker variants were screened for improved luminescence, improved response, or both in E. coli. The best linker variants were then used to rationally design linker composites (n=48) from the amino acid sequences of these best linker variants. These composites were synthesized (IDT), annealed and cloned into CP-FF Luc construct.
Table 2 identifies the variant linker sequences generated.











TABLE 2







Variant ID
Sequence
SEQ ID NO




















Parent-GS358
GSSGGSGGSGGG
41



 



5A7
GSSSDSDSSAGS
42



 



9H9
GSNDSSGGSEGG
43



 



9F1
GSNGGFDSSEGG
44



 



64C1
GSRGGSVYSEGG
46



 



36D1
GSRGGSVYSEGG
46



 



54B8
GSSEGSSDFGGD
47



 



72E8
GSIVVSCSSEGG
48



 



7A1
GSNWDSGCSREG
49



 



7A2
GSSGCTGDAGGS
51



 



L9
GSIAGCGDAGEG
126










Example V
Screening of Mutated Linker Sequences
The linker variants of Example III were inserted into a CP-FF construct as in Example II. The construct further comprised a mutant RIIβb cAMP binding site containing the substitutions at E284A and V316I. As in Example II, the constructs were first screened in E. coli to identify linker sequences which provided improved luminescence, improved response or both. The linker variants were then screened for improved luminescence signal, response to isoproterenol, or both in HEK293 cells.
Methods and Results
On day 1, 15,000 HEK293 cells were plated to the individual wells of a 96-well plate. On day 2, cells were transiently transfected with plasmid DNAs encoding a cAMP biosensor variant comprising a variant linker sequence using the LT1 reagent from Mirus Bio. Plasmids also carried a gene for constitutive expression of Renilla luciferase to act as a transfection control. Cells were equilibrated for 2 hours at room temperature using 5 mM luciferin EF (EF-luc). Isoproterenol was added to 10 μM final concentration to the individual wells, and luminescence was monitored continuously in time (Mithras luminometer; 1 second integration time). Once measurements were complete (>30 minutes), cells were lysed, and Renilla luciferase activity was measured.
Biosensor luminescence (FF RLU) was normalized using the Renilla luminescence signal (RL norm), and fold-induction (response) was calculated by dividing the normalized biosensor luminescence from isoproterenol-treated wells by the normalized luminescence from control wells that received no compound addition (Figure). Table 3 provides a summary of the linker improvements. The data in Table 8 comprises fold improvement values in luminescent signal, response to Isoproterenol, or both over the parental GS358 construct (GS358 with E284A and V316I substitutions in RIIβB).











TABLE 3








Signal
Response



Linker Variant ID
Improvement
Improvement









5A7
4.8
0.9



9H9
3.2
1.2



9F1
3.1
1.1



64C1
0.9
1.8



36D1
1.5
1.7



54B8
2.0
1.6



72E8
2.4
1.3



7A1
2.4
1.4



7A2
2.7
1.5










Example VI
In Vitro Detection of cAMP with CPM-FF Luc/Mutant RIIβB cAMP Biosensors
Plasmid DNA encoding cAMP biosensor variants were expressed in vitro using TnT® T7 Coupled Rabbit Reticulocyte Lysate System (Promega) according to the manufacturer's instructions for 1 hour at 30° C. cAMP biosensor variants expressed included: a double variant comprising substitutions V316I and E284I in RIIβB, clone 7A1 (SEQ ID NO: 113; SEQ ID NO:114) comprising V316I and E284 substitutions in RIIβB and the modified linker sequence GSNWDSGCSRE (SEQ ID NO: 127), clone L9 (SEQ ID NO:104; SEQ ID NO: 105) comprising substitutions E284A and V316I in RIIβB and the modified linker sequence GSIAGCGDAGEG (SEQ ID NO:56; SEQ ID NO: 128), and parental clone GS358 (SEQ ID NO:111; SEQ ID NO:112). Following expression, 20 μL of the TnT® reaction was combined with 2 μL of a 10× stock solution of cAMP diluted in H2O. The mixture was incubated at room temperature for 15 minutes, and luminescence was measured from 5 μL of sample following injection of 90 μL of Luciferase Assay Reagent using a Glomax luminometer (0.5 second integration time). The three cAMP variants all right shifted which is indicative of reduced affinity for cAMP (FIG. 9).
Example VII
Increased Stimulatory Response to Isoproterenol by a CPM-FF Luc/Mutant RIIβB cAMP Biosensor with a Modified Linker Region
A mutant cAMP biosensor (termed L9; SEQ ID NO: 104; SEQ ID NO: 105) having a mutant RIIβB binding site (substitutions E284A and V316I) and a modified linker sequence (GSIAGCGDAGEG, SEQ ID NO: 57; SEQ ID NO: 128) was screened for increased light output and increased fold response when expressed in mammalian cells (primary sequence Met-(Photinus pyralis luciferase residues 359-544)-(GSIAGCGDAGEG (SEQ ID NO: 57; SEQ ID NO: SEQ ID NO: 128))-(RIIβB E284A, V316I)-(Photinus pyralis luciferase residues 4-355)-Val). For a stimulatory response, transient expression in HEK293 cells was followed by treatment with 10 μM isoproterenol (agonist of the endogenous beta2-adrenergic receptor). For an inhibitory response, transient expression in HEK293 cells that stably express the dopamine D2 receptor was followed by simultaneous treatment with dopamine in the presence or absence of forskolin
L9 transfected cells provide an improved fold response to isoproterenol induction of the Gs pathway (FIG. 8A) and also an improved fold response for the Gi pathway (FIG. 8B).
B. HEK293 cells were transiently transfected with plasmid DNAs encoding various biosensor mutants as above. These biosensor mutants contained the E284A and V316I mutation in the RIIbetaB cAMP binding domain and the modified linker sequence 7A1 (GSNWDSGCSREG; SEQ ID NO: 129). The clones also contained the additional mutations outlined in Table 5. Cells were equilibrated for 2 hours at room temperature with 2 mM EF-Luc. Luminescence was measured 5 and 15 minutes after addition of the isoproterenol and 15 minutes after addition of FSK. Fold response (response; Resp.) was calculated by dividing relative light units (RLUs) from induced cells by the RLUs from uninduced cells. As a control, the biosensor GS358 and 7A1 were included.










TABLE 4








Isoproterenol-
Isoproterenol-




5 minutes
15 minutes
Forskolin (FSK)

















Un-


Un-


Un-




Clone
induced
Induced
Resp
induced
Induced
Resp 
induced
Induced
Resp



















4H7
493
42467
86
2665
207210
78
2665
88555
33


9G4
553
27930
50
5760
264500
46
5760
263020 
46


1B3
1673
59767
36
6460
344375
53
6460
305500 
47


15C6
560
47663
85
1970
141250
72
1970
162400 
82


16A2
527
44890
85
2025
141135
70
2025
153670
76


15H6
1073
91567
85
4040
244700
61
4040
29500
57


16B3
2063
72003
35
6555
248415
38
6555
257605 
39


7A1
1231
73287
60
3415
173340
51
3415
161755 
47


GS358
4943
41610
8
14895
184150
12
14895
195335
13




















TABLE 5







Clone
Substitution
SEQ ID NO









15C6
F369I, K541Q-substitutions in
23, 24




Luc2.0 (SEQ ID NO: 106)



16A2
F518L-substitution in Luc2.0
60, 61



15H6
F433Y, M493V-substitutions in
107, 108




Luc2.0; modified linker sequence:




GSNWDSGCSRGC



4H7
F407Y-substitution in RIIβb
35, 36



16B3
S440N-substitution in Luc2.0
72, 73



9G4
E382K-substitution in RIIβb
37, 38



1B3
A338E-substitution in RIIβb
33, 34










Example VIII
To measure changes in the intracellular concentration of cAMP, HEK293 cells are transiently transfected with mutant cAMP biosensors followed by treatment with compounds known to increase or decrease the intracellular cAMP concentration through GPCR activation of Gs- or Gi-coupled receptors, respectively. FSK (direct activator of endogenous adenylate cyclase) is used to elevate cAMP, dopamine is used to reduce cAMP (agonist of the Gi-coupled dopamine D2 receptor), and Haloperidol (dopamine D2 receptor antagonist) is used demonstrate the use of the assay in screens for Gi-coupled receptor antagonists.
Materials and Results
HEK293 cells stably expressing the dopamine D2 receptor were transiently transfected with the mutant cAMP biosensors from Example VIIB. Cells were also transfected with either 7A1 (Example III) or GS358 (parent biosensor) as controls. Cells were equilibrated for 2 hours at room temperature using 2 mM EF-luc. Antagonist assay wells were pre-treated for 10-15 minutes at room temperature with 10 μM Haloperidol (Halo). Next, the following reagents were added to their respective wells: media alone to “untreated” samples; 3 μM forskolin (FSK) to “forskolin-treated” samples; 3 μM FSK+0.3 μM dopamine to “agonist-treated” samples; and 3 μM FSK+0.3 μM dopamine to the aforementioned wells pre-treated with Halo. The cells were then incubated at room temperature for 10 minutes and luminescence was measured. Fold response for FSK was calculated by dividing the RLU from “forskolin-treated” cells by the RLU from the “untreated” cells. Fold response for dopamine treatment was calculated by dividing the RLU from the “agonist-treated” cells by the RLU from the “forskolin-treated” cells. Fold response for Haloperidol treatment was calculated by dividing the RLU from the cells treated with haloperidol then forskolin plus dopamine by the RLU of cells treated with forskolin plus dopamine alone.










TABLE 6








Forskolin (FSK)
Dopamine
Halo















Un-

Re-

Re-

Re-


Clone
induced
Induced
sponse
Induced 
sponse
Induced
sponse

















15C6
117
3520
30
1463
0.42
2918
2.0


16A2
147
4117
28
95
0.33
223
2.3


15H6
283
7177
25
30
0.56
65
2.2


4H7
230
3180
14
583
0.18
2778
4.8


16B3
370
6400
17
3050
0.48
6188
2.0


9G4
293
4133
14
1735
0.42
4370
2.5


1B3
460
8410
18
1898
0.23
5228
2.8


7A1
307
4709
15
1860
0.38
5429
2.9


GS358
1704
9166
5
5153
0.56
9218
1.9









Example IX
cAMP mutant biosensor variants were generated which contained combinations of amino acid substitutions which seemed to provide the most improved response in Example VII. These amino acid substitutions included substitutions in Luc2.0: F369I (I), K541Q (Q), F518L (L) and/or RIIβB: F407Y (Y). The cAMP biosensor variants were generated in either the 7A1 or L9 background. Naming of the variants is provided as the background clone (7A1 or L9) plus the amino acid substitution(s) (I, Q, L and/or Y). These variants were screened for improved luminescence and/or response.
HEK293 cells stably expressing GPCR receptors GPR41 (Multispan, Inc.), GPR44 (Multispan), or dopamine D2 receptor were plated at 15,000 cells/well in individual wells of 96-well plates. After 24 hours, the cells were transiently transfected with one of the cAMP biosensor variants (Tables 7A and 7B). After another 24 hours, the cells were equilibrated for 2 hours at room temperature using 5 mM EF-luc in CO2 independent media with 10% FBS. Prior to the addition of the compounds, luminescence was measured. The compounds (12× stock in CO2 independent media without FBS) were then added to the cells. For GPR41 expressing cells, sodium proprionate CRC was added. For GPR44 expressing cells, 15(R)-prostaglandin D2 (PGD2) CRC was added. For dopamine D2 expressing cells, dopamine CRC was added. After a 5 minute incubation with the compounds, FSK was added to all cells. The cells were allowed to incubate another 30 minutes and luminescence read on a Varioskan Flash. EC50 values and fold responses were calculated for each of the clones with each of the compounds with or without FSK. In addition, variants L9, 15C6 (Example VIIIB), 4H7 (Example VIIB), 16A2 (Example VIIB) and GS358 were also screened.
Tables 7A and 7B provide fold response (ratio of induced signal to uninduced signal) and fold signal change (ratio of RLU of FSK treated well to untreated well) for Na proprionate treated GPR41 cells. Tables 8A and 8B provide the EC50 values obtained for each of the clones with each of the compounds with or without FSK. FIG. 9 (A=GPR44, B=GPR41, C=D2) provides the fold response seen in each clone with each of the compounds with FSK (versus without). Fold response is calculated by dividing the RLU at 30 minutes by the RLU prior to compound addition. FIG. 10 (A=GPR44, B=GRP41, C=D2) provides a graph of the absolute RLUs for each of the clones at 30 minutes with each compound with or without FSK.










TABLE 7A







Fold Response




Fold Response
Na proprionate +
Fold Signal


Clone
Na proprionate
FSK(1 μM)
Change


















L9
2.73
2.60
40.9


L9-IY
2.53
NA
86.4


L9-IQY
3.82
NA
96.0


L9-ILQY
NA
NA
152.7


L9-ILY
3.34
4.91
161.2


L9-L
3.04
5.72
72.2


L9-I
3.61
3.83
83.5


L9-Q
2.57
5.24
42.0


L9-IL
3.67
7.43
96.7


L9-IQ
3.41
5.17
64.0


L9-ILQ
4.13
10.21
140.4


L9-Y
2.17
3.88
55.8


L9-LY
2.07
5.57
126.7


L9-LQ
2.83
7.20
98.6


L9-QY
2.01
10.02
61.3


L9-LQY
1.95
13.78
136.0


GS358
2.56 (n = 8)
3.19 (n = 7)
9.48 (n = 8)


15C6
3.42
3.55
104.5


4H7
1.94
2.98
93.6


16A2
2.73
3.76
89.7



















TABLE 7B







Fold Response




Fold Response
Na proprionate +
Fold Signal


Clone
Na proprionate
FSK(1 μM)
Change


















7A1-LQ
2.70
6.6
85.2


7A1-IY
2.81
8.66
165.7


7A1-ILQY
2.57
8.13
220.1


7A1-ILY
2.49
8.96
194.6


7A1-IQY
2.42
NA
128.0


7A1-ILQ
4.09
5.68
181.8


7A1-IQ
3.66
3.42
128.0


7A1-IL
4.66
4.36
200.0


7A1-Q
2.26
4.26
71.6


7A1-I
3.07
6.60
133.9


7A1-LY
2.15
62.19
141.7


7A1-LQY
1.94
NA
153.1


7A1-QY
1.68
161.29
87.6


GS358
2.56 (n = 8)
3.19 (n = 7)
9.48 (n = 8)


15C6
3.42
3.55
104.5


4H7
1.94
2.98
93.6


16A2
2.73
3.76
89.7

















TABLE 8A








EC50(nM)















Na

Dopamine +





Na
proprionate +

FSK

PGD2 +


Clone
proprionate 
FSK(1 μM)
Dopamine
(1 μM)
PGD2
FSK(1 μM)
















L9
13.7
20.4
110.33
5723.3
5.34
10.4


L9-IY
18.6
NA
66.65
88.4
3.40
13.3


L9-IQY
9.8
NA
59.24
77.2
5.39
11.4


L9-ILQY
NA
NA
86.89
75.4
4.52
8.6


L9-ILY
14.6
16.8
70.91
73.6
3.34
9.8


L9-L
16.1
29.7
80.36
66.4
5.59
10.2


L9-I
20.8
60.9
79.71
58.3
3.33
11.3


L9-Q
19.4
78.8
90.37
66.2
4.25
16.3


L9-IL
17.9
21.2
93.62
104.7
4.21
3.3


L9-IQ
18.7
36.7
77.66
105.3
6.43
10.3


L9-ILQ
19.3
57.7
89.54
108.4
5.51
9.1


L9-Y
13.1
45.4
91.29
262.4
3.26
6.5


L9-LY
21.4
11.6
91.06
103.6
4.80
0.1


L9-LQ
18.9
7.4
78.89
107.3
5.61
24.2


L9-QY
22.8
4.3
97.23
100.7
6.35
0.0


L9-LQY
24.7
6.8
NA
113.6
4.65
13.4


GS358
20.0 (n = 8)
55.4 (n = 8)
88.6 (n = 8)
1404.6 (n = 7)
12.2 (n = 7)
33.2 (n = 8)


15C6
16.5
21.7
137.45
58016.0
5.72
10.1


4H7
13.4
28.8
106.15
59296.0
2.43
4.1


16A2
14.3
21.8
142.88
77197.0
5.00
7.6

















TABLE 8B








EC50(nM)















Na

Dopamine +





Na
proprionate +

FSK (1

PGD2 +


Clone
proprionate 
FSK(1 μM)
Dopamine
μM)
PGD2
FSK(1 μM)
















7A1-LQ
13.6
17.0
65.41
69.0
4.16
1.5


7A1-IY
8.7
4.6
65.66
94.0
2.10
15.4


7A1-ILQY
21.9
8.9
61.98
70.8
2.89
3.5


7A1-ILY
17.5
7.3
76.51
92.0
1.89
5.3


7A1-IQY
17.4

81.64
98.4
5.40
0.0


7A1-ILQ
16.3
24.4
94.35
108.6
5.09
4.1


7A1-IQ
17.4
28.3
96.40
111.9
2.65
19.8


7A1-IL
8.3
40.3
93.04
76.9
4.46
10.4


7A1-Q
16.7
53.6
98.27
98.6
3.02
9.5


7A1-I
19.9
25.1
125.31
18066.0
4.20
11.4


7A1-LY
19.7
0.1
0.00
119.4
3.61
9.0


7A1-LQY
14.0
NA
108.71
331.1
3.99
8.8


7A1-QY
17.6
NA
102.88
177.4
3.0
8.2


GS358
20.0 (n = 8)
63.3 (n = 7)
88.6 (n = 8)
1404.6 (n = 7)
12.2 (n = 7)
33.2 (n = 8)


15C6
16.5
21.7
137.45
58016.0
5.72
10.1


4H7
13.4
28.8
106.15
59296.0
2.43
4.1


16A2
14.3
21.8
142.88
77197.0
5.00
7.6









Exemplary cAMP biosensor clones include, but are not limited to, 15H6 (SEQ ID NO:107; SEQ ID NO:108); 7A1-QY (SEQ ID NO:109; SEQ ID NO:110); GS358 (SEQ ID NO:111; SEQ ID NO:112); 7A1 (SEQ ID NO:113; SEQ ID NO:114); 7A1-IQ (SEQ ID NO:23; SEQ ID NO:24); 7A1-LY (SEQ ID NO:25; SEQ ID NO:26); 7A1-ILY (SEQ ID NO:27; SEQ ID NO:28); 7A1-IQY (SEQ ID NO:29; SEQ ID NO:30); 7A1-ILQY (SEQ ID NO:31; SEQ ID NO:32); 1B3 (SEQ ID NO:33; SEQ ID NO:34); 4H7 (SEQ ID NO:35; SEQ ID NO:36); 9G4 (SEQ ID NO:37; SEQ ID NO:38); 7A1-IY (SEQ ID NO:39; SEQ ID NO:40); 7A1-LQY (SEQ ID NO:58; SEQ ID NO:59); 16A2 (SEQ ID NO:60; SEQ ID NO:61); 7A1-Q (SEQ ID NO:62; SEQ ID NO:63); 7A1-LQ (SEQ ID NO:64; SEQ ID NO:65); 7A1-I (SEQ ID NO:66; SEQ ID NO:67); 7A1-ILQ (SEQ ID NO:68; SEQ ID NO:69); 7A1-IL (SEQ ID NO:70; SEQ ID NO:71); 16B3 (SEQ ID NO:72; SEQ ID NO:73); L9-IQ (SEQ ID NO:74; SEQ ID NO:75); L9-IY (SEQ ID NO:76; SEQ ID NO:77); L9-IQY (SEQ ID NO:78; SEQ ID NO:79); L9-ILQY (SEQ ID NO:80; SEQ ID NO:81); L9-ILY (SEQ ID NO:82; SEQ ID NO:83); L9-IL (SEQ ID NO:84; SEQ ID NO:85); L9-ILQ (SEQ ID NO:86; SEQ ID NO:87); L9-LQY (SEQ ID NO:88; SEQ ID NO:89); L9-QY (SEQ ID NO:90; SEQ ID NO:91); L9-I (SEQ ID NO:92; SEQ ID NO:93); L9-L (SEQ ID NO:94; SEQ ID NO:95); L9-Q (SEQ ID NO:96; SEQ ID NO:97); L9-Y (SEQ ID NO:98; SEQ ID NO:99); L9-LY (SEQ ID NO:100; SEQ ID NO:101); L9-LQ (SEQ ID NO:102; SEQ ID NO:103); and L9 (SEQ ID NO:104; SEQ ID NO:105).
D7A1-ILY (SEQ ID NO:12) is a cAMP biosensor with three substitutions in the cAMP binding site, the 7AI linker (including NWDSGCSREG; SEQ ID NO: 130) and two substitutions in the luciferase sequence (Met-FF Luc2.0 (359-544)-7AI-cAMP binding site-FF Luc2.0 (4-355)-Val). DL9-IL (SEQ ID NO:13) is a cAMP biosensor with two substitutions in the cAMP binding site, the L9 linker (including IAGCGDAGEG; SEQ ID NO: 131), and two substitutions in the luciferase sequence (Met-FF Luc2.0 (359-544)-L9-cAMP binding site-FF Luc2.0 (4-355)-Val). These clones included mutant cAMP binding sites, linkers obtained by random cassette mutagenesis, and whole gene random mutageneis/error prone PCR/recombination. D7A1-ILY and DL9-IL have improved properties including enhanced luminescence and an enhanced response relative to GS358.
All publications, patents and patent applications are incorporated herein by reference. While in the foregoing specification, this invention has been described in relation to certain embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details herein may be varied considerably without departing from the basic principles of the invention.

## Claims

1. A method to detect one or more modulators of a G protein coupled receptor, comprising:
a) contacting a sample with one or more test agents and reagents for a luminescence reaction, wherein the sample comprises a cell expressing a G-protein coupled receptor and a polynucleotide, wherein the G-protein coupled receptor is a Gs or Gi coupled receptor; and
b) detecting or determining luminescence in the sample, wherein an increase or decrease in luminescence detected in the sample compared to a control sample indicates that the test agent is a modulator of the G protein coupled receptor,
wherein the polynucleotide encodes a modified luciferase comprising luciferase sequences and a heterologous amino acid sequence for a mutant RIIβB cAMP binding site inserted at a site or region in the luciferase that is tolerant to modification, wherein the luciferase sequences in the modified luciferase are circularly permuted relative to a wild-type luciferase and are firefly luciferase sequences, wherein the permutation is in a region corresponding to residue 2 to 12, residue 32 to 53, residue 70 to 88, residue 102 to 126, residue 139 to 165, residue 183 to 203, residue 220 to 247, residue 262 to 273, residue 303 to 313, residue 353 to 408, residue 485 to 495, or residue 535 to 546 of SEQ ID NO: 106, 118, or 120, wherein the mutant RIIβB cAMP binding site has at least 80% amino acid sequence identity to the cAMP binding site of residue 266-414 of SEQ ID NO: 4, wherein the cAMP binding site is in a region corresponding to residue 2 to 12, residue 32 to 53, residue 70 to 88, residue 102 to 126, residue 139 to 165, residue 183 to 203, residue 220 to 247, residue 262 to 273, residue 303 to 313, residue 353 to 408, residue 485 to 495, or residue 535 to 546 of SEQ ID NO: 106, 118, or 120, wherein binding of cAMP to the mutant RIIβB cAMP binding site produces a response from the modified luciferase, wherein the mutant RIIβB cAMP binding site has one or more substitutions that enhance the luminescence signal of the modified luciferase, enhance the response of the modified luciferase to a change in the amount of cAMP in a cell, reduce affinity of wild-type cAMP binding, or a combination thereof, relative to a corresponding luciferase with a RIIβB cAMP binding site that lacks the one or more substitutions, wherein one or more of the substitutions are at a position corresponding to residue 266, 282, 284, 286, 296, 316, 333, 338, 382, 389, 404, or 407 of RIIβB having SEQ ID NO: 4.

2. The method of claim 1, wherein the mutant cAMP binding site is flanked by a peptide linker.

3. The method of claim 2, wherein the peptide linker comprises GSSGGSGGSGGG (SEQ ID NO:41), GSSSDSDSSAGS (SEQ ID NO:42), GSNDSSGGSEGG (SEQ ID NO:43), GSNGGFDSSEGG (SEQ ID NO:44), GSIRWSGLSGGD (SEQ ID NO:45), GSRGGSVYSEGG (SEQ ID NO:46), GSSEGSSDFGGD (SEQ ID NO:47), GSIVVSCSSEGG (SEQ ID NO:48), GSNWDSGCSREG (SEQ ID NO:49), GSNWDSGCSREC (SEQ ID NO:50), GSSGCTGDAGGS (SEQ ID NO:51), GSNWDSGCSRQC (SEQ ID NO:52), GSS/NS/D/GD/S/GS/FD/GS/GSA/EGS/G (SEQ ID NO:53), GSI/R/SR/G/EW/GSG/V/SL/Y/DS/FG/EGD/G (SEQ ID NO:54), GSI/N/SV/W/GV/D/CS/TC/GS/C/DS/AE/R/GG/EG/S (SEQ ID NO:55), GSI/SV/G/AV/GS/CG/DG/D/SS/AG/EG/EG/N (SEQ ID NO:56), GSI/N/SV/W/G/AV/D/C/GS/T/CC/GS/C/DS/AE/R/GG/EG/S (SEQ ID NO:57), GSIAGCGDAGEG (SEQ ID NO:126), GSNWDSGCSRE (SEQ ID NO: 127), GSNWDSGCSREG (SEQ ID NO:129), NWDSGCSREG (SEQ ID NO: 130), or IAGCGDAGEG (SEQ ID NO: 131).