# Patent

## Title
Linker for unimolecular FRET biosensor based on principle of fluorescence resonance energy transfer

## Abstract

A linker for a unimolecular FRET biosensor based on a principle of fluorescence resonance energy transfer, the linker including: a polypeptide containing 52 to 400 amino acids residues, wherein at least 45% of a total number of the amino acid residues are glycine, alanine, or both thereof, and at least 10% of the total number of the amino acid residues are alanine.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This is a continuation application of PCT/JP2011/071891, filed on Sep. 26, 2011, which claims priority to Japanese Patent Application No. 2010-215738, filed on Sep. 27, 2010, all of which are hereby incorporated by reference in their entirety.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a linker for optimizing a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer; a biosensor containing the linker; a gene encoding for the linker or the unimolecular FRET biosensor; an expression vector containing the linker or the unimolecular FRET biosensor; a transformed cell and a transgenic non-human animal harboring the expression vector; and a measurement method using the biosensor.
2. Description of the Related Art
Biosensors utilizing the principle of fluorescence resonance energy transfer (hereinafter may be referred to as “FRET”) and fluorescent proteins have been increasingly used in the field of life science (see Aoki, K. and M. Matsuda. 2009. Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors. Nature Protocol 4:1623-1631, Giepmans, B. N., S. R. Adams, M. H. Ellisman, and R. Y. Tsien. 2006. The fluorescent toolbox for assessing protein location and function. Science 312:217-224, Jares-Erijman, E. A. and T. M. Jovin. Imaging molecular interactions in living cells by FRET microscopy. 2006. Curr. Opin. Chem. Biol. 10:409-416, and Kiyokawa, E., S. Hara, T. Nakamura, and M. Matsuda. 2006. Fluorescence (Forster) resonance energy transfer imaging of oncogene activity in living cells. Cancer Sci. 97:8-15).
The FRET is a phenomenon of excitation energy transfer from an excited fluorescent molecule (donor: energy donor) to a fluorescent molecules in the close vicinity of the donor (acceptor: energy acceptor). A development and improvement of Green fluorescent protein (GFP) mutants of different colors have greatly contributed to the spread of the biosensors utilizing the FRET. Nowadays, CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein), which both are GFP mutants, have often been used as donor and acceptor fluorescent proteins.
FRET biosensor systems utilizing the fluorescent proteins are classified into two types: bimolecular FRET biosensors (see FIG. 1) and unimolecular FRET biosensors (see FIG. 2). The bimolecular FRET biosensors detect intermolecular interactions, whereas the unimolecular FRET biosensors detect conformational changes in molecules (see Aoki, K. and M. Matsuda. 2009. Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors. Nature Protocol 4:1623-1631, Giepmans, B. N., S. R. Adams, M. H. Ellisman, and R. Y. Tsien. 2006. The fluorescent toolbox for assessing protein location and function. Science 312:217-224, Jares-Erijman, E. A. and T. M. Jovin. Imaging molecular interactions in living cells by FRET microscopy. 2006. Curr. Opin. Chem. Biol. 10:409-416, and Kiyokawa, E., S. Hara, T. Nakamura, and M. Matsuda. 2006. Fluorescence (Forster) resonance energy transfer imaging of oncogene activity in living cells. Cancer Sci. 97:8-15).
Among them, there have been developed the unimolecular biosensors (unimolecular FRET biosensors) for quantifying small molecules such as ions, saccharides and lipids or for measuring activities of low molecular weight GTP-binding proteins or kinases (see Kiyokawa, E., S. Hara, T. Nakamura, and M. Matsuda. 2006. Fluorescence (Forster) resonance energy transfer imaging of oncogene activity in living cells. Cancer Sci. 97:8-15).
However, in order to create the biosensors, at least 3, often 4 or more protein domains are required to be connected. Unimolecular FRET biosensors having a satisfactory sensitivity usually cannot be achieved simply by connecting the protein domains to each other. That is, in order to create such unimolecular FRET biosensors, the following three factors should be taken into account: (i) an overlap of emission spectra of donor fluorescent proteins and absorption spectra of acceptor fluorescent proteins, (ii) a distance between the donor fluorescent proteins and the acceptor fluorescent proteins, and (iii) an orientation of emission moments of the donor fluorescent proteins and the absorption moments of acceptor fluorescent proteins. The fluorescent proteins may be fused with other proteins, which may apply stress to the fluorescent proteins to thereby cause misfoldings in the fluorescent proteins. As a result, the fluorescent proteins may form fluorophores inefficiently to thereby be nonfluorescent, which also should be taken into account. As described above, the FRET between the donor fluorescent proteins and the acceptor fluorescent proteins can be excellently achieved only when strict conditions are met. However, no requirement regarding, for example, an arrangement of the donor fluorescent proteins and the acceptor fluorescent proteins has been established. Therefore, for each unimolecular FRET biosensor to be created, optimizations have been performed by varying lengths of the protein domains or sequences of linkers connecting the domains, which needs a lot of trial and error and complex and advanced experiments. Accordingly, unimolecular FRET biosensors having a satisfactory sensitivity have been very hard to be developed.
Some linkers for connecting the domains have been reported such as a 9-amino acid linker consisting of glycine, serine and threonine (see Itoh, R. E., K. Kurokawa, Y. Ohba, H. Yoshizaki, N. Mochizuki, and M. Matsuda. 2002. Activation of Rac and Cdc42 video-imaged by FRET-based single-molecule probes in the membrane of living cells. Mol. Cell. Biol. 22:6582-6591) and a 72-amino acid glycine linker (see Harvey, C. D., A. G. Ehrhardt, C. Cellurale, H. Zhong, R. Yasuda, R. J. Davis, and K. Svoboda. 2008. A genetically encoded fluorescent sensor of ERK activity. Proc. Natl. Acad. Sci. U.S.A. 105:19264-19269), which linkers have not been sufficiently optimized. Additionally, the above-described linkers could not be optimized in common with many types of unimolecular FRET biosensors.
SUMMARY OF THE INVENTION
The present invention aims to solve the above existing problems and achieve the following objects. That is, the present invention aims to provide a linker which is capable of being widely used for optimizing a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer to thereby achieve a high-sensitive unimolecular FRET biosensor (hereinafter, the linker of the present invention may be referred to as “EV (enhanced visualization) linker”); a biosensor containing the linker; a gene encoding for the linker or the biosensor; an expression vector containing the linker or the biosensor; a transformed cell and a transgenic non-human animal harboring the expression vector; and a measurement method using the unimolecular FRET biosensor suitable for measuring a serine-threonine kinase activity, a tyrosine kinase activity and a low molecular weight GTP-binding protein activity by means of the biosensor containing the linker.
The present inventors conducted extensive studies to achieve the above objects, and have found that a linker having a certain length or longer can solve the above objects and be a linker which is capable of being widely used for optimizing a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer to thereby achieve a high-sensitive unimolecular FRET biosensor. Additionally, the present inventors have also been found that a linker containing certain amino acids at a certain percentage or certain repeated amino acid sequences has an improved optimization effect.
That is, the present invention is based on a finding that a linker having a certain length or longer can significantly reduce a FRET at a basal state which is a cause of a decrease in a gain of a unimolecular FRET biosensor. The present invention can be widely used for creating unimolecular FRET biosensors. The linker of the present invention has been developed for the purpose of increasing a gain of a unimolecular FRET biosensor, which is very technically valuable.
Means for solving the above problems are as follows.
The present invention provides a linker for a unimolecular FRET biosensor based on a principle of fluorescence resonance energy transfer, the linker including: a polypeptide containing 52 to 400 amino acids residues, wherein at least 45% of a total number of the amino acid residues are glycine, alanine, or both thereof, and at least 10% of the total number of the amino acid residues are alanine.
In an object the present invention provides a linker according to the present invention wherein the polypeptide contains 84 or more amino acid residues.
In an object the present invention provides a linker according to the present invention wherein at least 10% of the total number of the amino acid residues are serine, threonine, or both thereof.
In an object the present invention provides a linker according to the present invention wherein at least 95% of the total number of the amino acid residues are glycine, serine, threonine and alanine, 35% to 65% of the total number of the amino acid residues are glycine, 10% to 40% of the total number of the amino acid residues are serine, threonine, or both thereof, and 10% to 40% of the total number of the amino acid residues are alanine.
In an object the present invention provides a linker according to the present invention wherein at least 95% of the total number of the amino acid residues are repeats of an amino acid sequence of SAGG or GGAS, and wherein the number of the repeats of the amino acid sequence of SAGG or GGAS is 13 to 100.
In an object the present invention provides a linker according to the present invention wherein at least 10% of the total number of the amino acid residues are arginine, glutamic acid, or both thereof.
In an object the present invention provides a linker according to the present invention wherein at least 95% of the total number of the amino acid residues are glycine, arginine, glutamic acid and alanine, 4% to 30% of the total number of the amino acid residues are glycine, 5% to 30% of the total number of the amino acid residues are arginine, 5% to 30% of the total number of the amino acid residues are glutamic acid, and 30% to 60% of the total number of the amino acid residues are alanine.
The present invention provides a gene, wherein the gene encodes the linker according to the present invention.
The present invention provides an expression vector, including a gene encoding the linker according to the present invention.
The present invention provides a transformed cell, including an expression vector according to the present invention.
The present invention provides a transgenic non-human animal, including an expression vector according to the present invention.
The present invention provides a unimolecular FRET biosensor based on a principle of fluorescence resonance energy transfer, the unimolecular FRET biosensor including: a fused protein, which includes a sensor domain, a ligand domain, an acceptor fluorescent protein domain, a donor fluorescent protein domain, and a linker domain which links the sensor domain with the ligand domain, wherein the linker domain includes the linker of the present invention.
An object of the present invention provides an unimolecular FRET biosensor according to the present invention, wherein the donor fluorescent protein is YPet.
An object of the present invention provides a gene, wherein the gene encodes the unimolecular FRET biosensor according to the present invention.
An object of the present invention provides an expression vector, including a gene according to the present invention.
An object of the present invention provides a transformed cell, including the expression vector according to the present invention.
An object of the present invention provides a transgenic non-human animal, including the expression vector according to the present invention.
The present invention provides a method for measuring a serine-threonine kinase activity, a tyrosine kinase activity, or a low molecular weight GTP-binding protein activity, the method including: detecting FRET with the unimolecular FRET biosensor according to the present invention.
The present invention provides a method for measuring a serine-threonine kinase activity, a tyrosine kinase activity, or a low molecular weight GTP-binding protein activity, the method including: detecting FRET with the transformed cell according to the present invention or the transgenic non-human animal according to the present invention.
The present invention provides a method for screening a regulator of a serine-threonine kinase activity, a tyrosine kinase activity, or a low molecular weight GTP-binding protein activity, the method including: (a) contacting a test substance with the transformed cell according to the present invention; and (b) detecting FRET to thereby detect a change in the serine-threonine kinase activity, the tyrosine kinase activity, or the low molecular weight GTP-binding protein activity.
The linker of the present invention can optimize a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer to thereby achieve a high-sensitive unimolecular FRET biosensor. In addition, the unimolecular FRET biosensor of the present invention enables non-invasive measurements of a serine-threonine kinase activity, a tyrosine kinase activity and a low molecular weight GTP-binding protein activity



BRIEF DESCRIPTION OF THE DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
FIG. 1 illustrates a basic structure and a mode of action of a bimolecular FRET biosensor. In order to detect an intermolecular interaction escent protein (in this figure, CFP), and the B has been fused with a FRET between molecules A and B, the A has been fused with a ceptor fluorescent protein. As a result, FRET occurs and fluorescence can beFRET donor fluor acceptor fluorescent protein (in this figure, YFP). When the A binds to the B, the FRET donor fluorescent protein approaches the FRET ac detected from the FRET acceptor fluorescent protein. In this figure, wavy arrows denote excitation light and fluorescence, respectively.
FIG. 2 illustrates a basic structure and a mode of action of a unimolecular FRET biosensor. When a molecule A is known to be conformationally changed, a FRET donor fluorescent protein (in this figure, CFP) and a FRET acceptor fluorescent protein (in this figure, YFP) are fused with the A at different sites. A conformational change of the molecule A changes FRET efficiency. In this figure, wavy arrows denote excitation light and fluorescence, respectively
FIG. 3 illustrates a principle of a unimolecular FRET biosensor containing a sensor domain and a ligand domain based on FRET. Between a FRET donor fluorescent protein (in this figure, CFP) and a FRET acceptor fluorescent protein (in this figure, YFP), the sensor domain and the ligand domain are connected via a linker sequence. The sensor domain contains a region of which conformation changes in response to various intracellular environmental changes such as activations of a kinase or a GTP exchange factor. The ligand domain is a domain to be bound to the sensor domain in response to the conformational change of the sensor domain. When the sensor domain conformationally changes, the ligand domain binds to the sensor domain. Thus, the FRET donor fluorescent protein approaches the FRET acceptor fluorescent protein. As a result, the FRET occurs and fluorescence can be detected from the FRET acceptor fluorescent protein.
FIG. 4 illustrates a role of a linker domain in a unimolecular FRET biosensor containing a sensor domain and a ligand domain based on FRET. In this figure, a biosensor for PKA, Eevee-PKA, is shown by way of example. The sensor domain contains a substrate sequence to be specifically phosphorylated by PKA. The ligand domain is a FHA1 domain of Rad1 protein which is known to bind to the phosphorylated peptide. When the substrate sequence in the sensor domain is phosphorylated by PKA, the ligand domain binds to the phosphorylated sensor domain. Thus, a FRET donor fluorescent protein (CFP) approaches a FRET acceptor fluorescent protein (YFP). As a result, FRET occurs and fluorescence can be detected from the FRET acceptor fluorescent protein.
FIG. 5 illustrates a relationship between lengths of EV linkers and gains. Eevee-PKAs having various lengths were expressed in HeLa cells. After 24 hours, PKAs were activated with 1 mM dibutyryl-cAMP. FRET/CFP fluorescence ratios were measured before and 30 min after stimulation. The “gain” is defined as a percentage of increase of the FRET/CFP fluorescence ratio relative to that of before stimulation.
FIG. 6 demonstrates that the EV linkers can exhibit more significant effect when a YPet mutant is used as the YFP acceptor protein. Eevee-PKAs having the YPets and varying lengths of EV linkers were constructed. Then, these Eevee-PKAs were expressed in HeLa cells. After 24 hours, PKAs were activated with 1 mM dibutyryl-cAMP. FRET/CFP fluorescence ratios were measured before and 30 min after stimulation. The “gain” is defined as a percentage of increase of the FRET/CFP fluorescence ratio relative to that of before stimulation.
FIG. 7A demonstrates that an effect of the EV linker results from a reduction of FRET at the basal state. FIG. 7A illustrates measurement results of fluorescence intensities at various wavelengths when Eevee-PKA-52-expressing HeLa cells were observed by a confocal laser scanning microscope FV1000 upon excitation at 438 nm.
FIG. 7B illustrates measurement results of Eevee-PKA-84 measured in the same manner as in FIG. 7A.
FIG. 7C illustrates measurement results of Eevee-PKA-116 measured in the same manner as in FIG. 7A. As can be seen from these figures, as the EV linkers become longer, then fluorescence intensities at 530 nm, which indicate FRET at the basal state, are significantly reduced.
FIG. 8A demonstrates that a reduction of FRET efficiency at the basal state by the EV linker results from a reduction of phosphorylations. The Eevee-PKAs were expressed in HeLa cells in the same manner as in FIG. 7A. Untreated cells, cells treated with 1 mM dibutyryl-cAMP for 15 min, and cells treated with 1 mM dibutyryl-cAMP and 50 nM Calyculin for 15 min were separated with a 6% SDS polyacrylamide gels containing 50 μM Phos-tag. Then, the samples were subjected to an immunoblotting analysis with anti-GFP antibodies and mouse monoclonal antibodies. As can be seen from this figure, as the EV linkers become shorter, then phosphorylation levels at the basal state are reduced.
FIG. 8B illustrates a graph representing phosphorylation levels in FIG. 8A.
FIG. 9A illustrates a structure of an Akt biosensor (Eevee-Akt-84) having a PIP3-binding domain. Here, “84 a.a.” denotes an EV84 linker, “AktPH” denotes a PH domain of Akt protein, and “NES” denotes a nuclear export signal.
FIG. 9B illustrates a structure of an Akt biosensor (Eevee-Akt-116) having a PIPS-binding domain in the same manner as in FIG. 9A. Here, “116 a.a.” denotes an EV116 linker.
FIG. 10 demonstrates that a reduction of FRET at the basal state by the EV linker is also observed in the Akt biosensors. Eevee-Akt was expressed in COS7 cells and measured for FRET/CFP fluorescence ratio. Five or more cells were measured and their measurement results are shown with average values. It has been found that, the EV116 linker has lower FRET at the basal state than that of a 72-Gly linker.
FIG. 11A illustrates measurement results of ERK activities when using Eevee-ERK compared with that of a glycine linker. FIG. 11A illustrates a graph in which FRET/CFP fluorescence ratios (measured values) are plotted on Y-axis when Eevee-ERK (3560 NES) containing the EV116 linker was expressed in HeLa cells and stimulated with 10 ng/mL EGF.
FIG. 11B illustrates a graph of the FRET/CFP fluorescence ratios normalized against that of at pre-stimulation.
FIG. 11C illustrates measurement results of EKAR-1667 nes (72-Gly linker) (1667 NES) containing a glycine linker in the same manner as FIG. 11A.
FIG. 11D illustrates a graph of the FRET/CFP fluorescence ratios normalized against that of pre-stimulation. An upper limit of the measured FRET/CFP is about 2.2, indicating that a lower basal FRET efficiency results in a higher gain of the Eevee-ERK containing the EV116 linker (see FIGS. 11A and 11B) than that of EKAR-1667 nes containing the glycine linker.
FIG. 12 illustrates a reactivity of Picchu-734 which is a biosensor of EGFR/Abl containing the EV linker. The Picch-734 was expressed in HeLa cells and stimulated with 10 ng/mL EGF. Picchu-734 is found to have a higher gain than Picchu-730 containing no EV linker.
FIG. 13A illustrates measurement results of Rac1 activities with Raichu-Rac1 (2246X) containing the EV linker. HeLa cells were transfected with pRaichu-Rac1 (2241X) containing no EV linker and pRaichu-Rac1 (2246X) containing the EV linker. After 48 hours, the cells imaged according to the method described in Example 2. Fluorescence intensities at various wavelengths were measured by the confocal laser scanning microscope FV-1000 upon excitation at 438 nm. It has been found that as the EV linkers become longer, then fluorescence intensities at 530 nm, which indicate FRET at the basal state, are significantly reduced.
FIG. 13B illustrates a graph of normalized FRET/CFP when, in the imaging in FIG. 13A, epidermal growth factor (EGF) was added to a concentration of 25 ng/mL at 10 min after the onset of the imaging, and then the imaging proceeded. It has been found that Raichu-Rac1 (2246X) containing the EV linker has higher activities.
FIG. 14A illustrates measured data of FRET/CFP efficiency (described as Rac1 activity) when rat C6 cells stably expressing Raichu-2246X were time lapse-imaged for 24 hours. An arrow denotes a cell division. This figure suggests that FRET can be stably measured for a long time in EV linker expressing cells.
FIG. 14B illustrates results of another cell imaged under the same conditions as described above.
FIG. 14C illustrates results of another cell imaged under the same conditions as described above.
FIG. 14D illustrates results of another cell imaged under the same conditions as described above.
FIG. 15A illustrates FRET efficiencies at the basal state in CO7 cells expressing Raichu-Cdc42 containing the EV linker. It is found that the EV linker significantly reduces the FRET efficiency at the basal state.
FIG. 15B illustrates a graph of normalized FRET/CFP for the Raichu-Cdc42 containing the EV linker when epidermal growth factor (EGF) was added to a concentration of 25 ng/mL at 10 min after the onset of the imaging, and then the imaging proceeded.
FIG. 15C illustrates a graph of normalized FRET/CFP for the Raichu-Cdc42 containing no EV linker as the same manner as in FIG. 15B. It is found that Raichu-Cdc42 containing the EV linker has higher reactivity than the Raichu-Cdc42 containing no EV linker.
FIG. 16A illustrates a time-lapse image acquired every 1 min when HeLa cells expressing Raichu-Ras (3705X) containing the EV linker were stimulated with 10 ng/mL EGF. It has been found that Raichu-HRas containing the EV linker can detect more rapidly and sensitively activations compared with Raichu-HRas containing no EV linker (FIG. 16B).
FIG. 16B illustrates a time-lapse image acquired in the same manner as in FIG. 16A for Raichu-HRas containing no EV linker.
FIG. 17 illustrates a FRET image of a sagittal section in a transgenic mouse fetus expressing Eevee-ERK acquired by a fluorescence microscope. Values which are higher and lower by 40% than the basal FRET are shown in pseudo colors (the warmer color denotes higher FRET). An activity distribution in an individual can be visualized.
FIG. 18A illustrates results when HeLa cells stably expressing Eevee-ERK were seeded onto a 96-well plate, were added thereto serial-diluted inhibitors and stimulated with 25 ng/mL EGF. ERK activities were automatically measured for 30 or more cells, averaged, and plotted. FIG. 18A illustrates results of DMSO controls.
FIG. 18B illustrates results when, as the inhibitors, EGF receptor inhibitors (AG1478) were used.
FIG. 18C illustrates results when, as the inhibitors, MEK inhibitors (PD15035) were used.
FIG. 18D illustrates results when, as the inhibitors, BRAF inhibitors (PLX4720) were used.
FIG. 18E illustrates results when, as the inhibitors, MEK inhibitors (PD184351) were used.
FIG. 18F illustrates results when, as the inhibitors, phosphatidylinositol 3-phosphate kinase inhibitors (LY294002) were used.
FIG. 18G illustrates results when, as the inhibitors, RSK inhibitors (BI-D1870) were used.
FIG. 18H illustrates results when, as the inhibitors, JNK inhibitors (JNK inhibitor VIII) were used. It has been found that EGF dependent-ERK activation is effectively inhibited by the EGF receptor inhibitors and the MEK inhibitors in HeLa cells.
FIG. 19 illustrates results when the transgenic mouse expressing Eevee-PKA (3536 NES) was intravenously injected with theophylline, which is a phosphodiesterase inhibitor, and actosin, which is a cyclic adenosine triphosphate analog, and measured for PKA activities. Changes in PKA activities can be real-time visualized in an intermuscular nerve cell, an intestinal smooth muscle and a vascular smooth muscle.
FIG. 20 illustrates a graph of images of FIG. 19.
FIG. 21 demonstrates that biosensors containing EV3x8 or EV6x4 linker having low content of glycine have a comparable effect to biosensors containing EV116 linker. Fluorescence intensities at various wavelengths were measured for HeLa cells expressing Eevee-PKA-3x8, Eevee-PKA-4x6 or Eevee-PKA-116 by the confocal laser scanning microscope FV-1000 upon excitation at 438 nm in the same manner as in FIG. 7A. It has been found that the EV3x8 linker and the EV4x6 linker have a comparable effect to the EV116 linker.



DETAILED DESCRIPTION OF THE INVENTION
There will be explained embodiments of the present invention.
A linker of the present invention (referred to as “EV linker”) is a linker for a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer (FRET). The linker is a polypeptide containing 52 to 400 amino acids residues in which at least 45% of the total number of amino acid residues are glycine and/or alanine and which contains alanine in a percentage of at least 10% of the total number of amino acid residues.
The linker of the present invention is an element of the unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer (FRET), i.e., the unimolecular FRET biosensor, and is used by connecting with other elements. The FRET is a phenomenon of excitation energy transfer from an excited fluorescent molecule (donor: energy donor) to a fluorescent molecules in the close vicinity of the donor (acceptor: energy acceptor). The unimolecular FRET biosensor generally contains the following four domains: a donor fluorescent protein, an acceptor fluorescent protein, a sensor domain, and a ligand domain. The linker connects two domains of the above domains.
FIG. 3 exemplifies the linker of the present invention used in the unimolecular FRET biosensor. The present invention will be specifically explained using CFP as an example of the donor fluorescent protein and YFP as an example of the acceptor fluorescent protein. However, as described below, the donor fluorescent protein and the acceptor fluorescent protein are not limited thereto. The sensor domain and the ligand domain are spatially spaced apart from each other in a basal state. In this state, the donor fluorescent protein and the acceptor fluorescent protein are also spatially spaced apart from each other. Therefore, FRET efficiency is low in the basal state. In the activated state, the ligand domain “B” consisting of a conformation recognition domain recognizes a conformational change of the sensor domain “A” induced by various signals such as a phosphorylation or a GTP-binding. As a result, the ligand domain “B” binds to the sensor domain “A,” so that the donor approaches the acceptor, which increases the FRET efficiency.
The FRET efficiency is defined as a decrease rate of the fluorescent intensity resulting from the excited donor fluorescent protein in the presence of the acceptor fluorescent protein. However, for convenience, the FRET efficiency as used herein refers to a ratio of the fluorescent intensity of the donor fluorescent protein and the fluorescent intensity of the acceptor fluorescent protein (fluorescent intensity ratio) when the unimolecular FRET biosensor are irradiated at an excitation wavelength of the donor fluorescent protein (see Aoki, K. and M. Matsuda. 2009. Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors. Nature Protocol 4:1623-1631, Giepmans, B. N., S. R. Adams, M. H. Ellisman, and R. Y. Tsien. 2006. The fluorescent toolbox for assessing protein location and function. Science 312:217-224, Jares-Erijman, E. A. and T. M. Jovin. Imaging molecular interactions in living cells by FRET microscopy. 2006. Curr. Opin. Chem. Biol. 10:409-416). All references described herein are incorporated by reference in their entirety.
The EV linker according to the present invention has at least 52 to 400 amino acids in length and is a polypeptide which does not form a stable tertiary structure. When the EV linker has less than 52 amino acids, the FRET efficiency in the basal state increases, leading to a decreased gain. When the EV linker has more than 400 amino acids, the FRET biosensor is increased in molecular weight, leading to a low expression level. From the viewpoint of increasing the gain, the EV linker has more preferably 84 or more amino acids, particularly preferably 116 or more amino acids. From the viewpoint of decreasing the molecular weight, the EV linker has more preferably 244 or less amino acids. Therefore, the EV linker has particularly preferably 84 to 244 amino acids in length.
The EV linker of the present invention is a polypeptide which does not form the stable tertiary structure. The EV linker is a linker in which at least 45% of the total number of amino acid residues are glycine and/or alanine (i.e., the sum of the number of glycine residues and the number of alanine residues accounts for at least 45% of the total number of amino acid residues), and which contains alanine in a percentage of at least 10% of the total number of amino acid residues. It is important from the viewpoint of flexibility of the polypeptide that at least 45% of the total number of amino acid residues are glycine and/or alanine. The presence of alanine in a percentage of at least 10% of the total number of amino acid residues enables to achieve a higher gain than that of a linker containing only glycine residues. The EV linker may contain amino acids other than glycine and alanine as long as it does not form the stable tertiary structure. From the viewpoint of obtaining the polypeptide which does not form the stable tertiary structure, for example, serine, threonine, arginine and glutamic acid are particularly preferably contained.
For example, preferred is a polypeptide which contains, besides alanine and glycine, serine and/or threonine in a percentage of at least 10% of the total number of amino acid residues. Example of such polypeptide includes a polypeptide in which at least 95% of the total number of amino acid residues are Gly, Ser, Thr and Ala, and which contains 35% to 65% of Gly, 10% to 40% of Ser and/or Thr, and 10% to 40% of Ala. These amino acid residues are preferably uniformly distributed over a full-length. In particular, preferred is a sequence repeatedly containing Ser-Ala-Gly-Gly, an inverted sequence thereof (i.e., Gly-Gly-Ala-Ser), or Gly-Ala-Gly-Ser. Preferred example thereof includes a sequence which contains repeated units such as Ser-Ala-Gly-Gly, Gly-Gly-Ala-Ser or Gly-Ala-Gly-Ser in a percentage of 95% or more of the total number of amino acid residues, and in which, besides the above described basic sequences (i.e., repeated units), for example, Gly, Ser, Ala or Thr are inserted between the basic sequences in a percentage of less than 5%. Also preferred is a sequence in which Ser is replaced by Thr, which is an amino acid having very similar properties as Ser, in the above described sequence. In the sequence, 13 to 100 repeated units are preferably contained. Specific examples of such linkers include the followings:







EV52 linker


(SEQ ID NO: 12)


SAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGS


 


AGG


 


EV84 linker


(SEQ ID NO: 15)


SAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGS


 


AGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGG


 


EV116 linker


(SEQ ID NO: 18)


SAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGS


 


AGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSA


 


GGSAGGSAGGSAGGSAGG


 


EV180 linker


(SEQ ID NO: 23)


SAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGS


 


AGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSA


 


GGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAG


 


GSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGG


 


EV244 linker


(SEQ ID NO: 26)


SAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGS


 


AGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSA


 


GGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAG


 


GSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGG


 


SAGGSAGGSAGGSAGGSGSAGGSAGGSTSAGGSAGGSAGGSAGGSAGG






Also preferred is a polypeptide which contains, besides alanine and glycine, arginine and/or glutamic acid in a percentage of at least 10% of the total number of amino acid residues. Example of such polypeptide includes a polypeptide in which at least 95% of the total number of amino acid residues are glycine, arginine, glutamic acid and alanine, and which contains 4% to 30% of glycine, 5% to 30% of arginine, 5% to 30% of glutamic acid and 30% to 60% of alanine. These amino acid residues are preferably uniformly distributed over a full-length. Examples thereof include the followings:







EV3x8 linker


(SEQ ID NO: 45)


EAAAREAAAREAAARGGEAAAREAAAREAAARGGEAAAREAAAREAAAR


 


GGEAAAREAAAREAAARGGEAAAREAAAREAAARGGEAAAREAAAREAA


 


ARGGEAAAREAAAREAAARGGEAAAREAAAREAAAR


 


EV6x4 linker


(SEQ ID NO: 46)


EAAAREAAAREAAAREAAAREAAAREAAARGGEAAAREAAAREAAAREA


 


AAREAAAREAAARGGEAAAREAAAREAAAREAAAREAAAREAAARGGEA


 


AAREAAAREAAARAAREAAAREAAAR






The EV3x8 linker is a polypeptide of 134 amino acid residues in which 8 sequence units of 15 amino acid residues (3 repeats of a sequence EAAAR) are connected via GG sequences. Of the total 134 amino acid residues, there are 72 alanine residues (53.7%), 14 glycine residues (10.4%), 24 glutamic acid residues (17.9%), and 24 arginine residues (17.9%). The sum of the percentage of alanine and glycine is 64.1%. The EV6x4 linker is a polypeptide of 124 amino acid residues. Of the total 124 amino acid residues, there are 71 alanine residues (57.3%), 6 glycine residues (4.8%), 23 glutamic acid residues (18.5%) and 24 arginine residues (19.4%). The sum of the percentage of alanine and glycine is 62.1%.
The EV linker of the present invention increases the gain of the unimolecular FRET biosensor. An insertion site of the EV linker in the unimolecular FRET biosensor may be appropriately selected depending on an increase of a difference in the FRET efficiency between the basal state and the activated state, i.e., the gain. That is, the EV linker may connect any two domains selected from the donor fluorescent protein, the acceptor fluorescent protein, the sensor domain and the ligand domain in the unimolecular FRET biosensor. The EV linker may be inserted between any domains described above. For example, as shown in FIG. 3, the EV linker may be used for connecting between the sensor domain and the ligand domain.
The unimolecular FRET biosensor according to the present invention is a unimolecular FRET biosensor based on the principle of fluorescence resonance energy transfer and is a fused protein containing a sensor domain, a ligand domain, an acceptor fluorescent protein domain, a donor fluorescent protein, and a linker domain which links the sensor domain with the ligand domain. The linker domain consists of the linker of the present invention. Preferred aspects of the unimolecular FRET biosensor according to the present invention includes (1) a biosensor which contains at least one each of the following 5 domains: the donor fluorescent protein domain, the acceptor fluorescent protein domain, the sensor domain, the ligand domain and the linker, and which contains, from the amino-terminus, the donor (or acceptor) fluorescent protein, the sensor (or ligand) domain, the EV linker, the ligand (or sensor) domain and the acceptor (or donor) fluorescent protein; (2) a biosensor which contains at least one each of the following 5 domains: the donor fluorescent protein domain, the acceptor fluorescent protein domain, the sensor domain, the ligand domain and the linker, and which contains, from the amino-terminus, the sensor (or ligand) domain, the donor (or acceptor) fluorescent protein, the EV linker, the acceptor (or donor) fluorescent protein and the ligand (or sensor) domain; (3) a biosensor which contains at least one each of the following 5 domains: the donor fluorescent protein domain, the acceptor fluorescent protein domain, the sensor domain, the ligand domain and the linker, and which contains, from the amino-terminus, the donor (or acceptor) fluorescent protein, the sensor (or ligand) domain, the EV linker, the acceptor (or donor) fluorescent protein and the ligand (or sensor) domain; and (4) a biosensor which contains at least one each of the following 5 domains: the donor fluorescent protein domain, the acceptor fluorescent protein domain, the sensor domain, the ligand domain and the linker, and which contains, from the amino-terminus, the sensor (or ligand) domain, the donor (or acceptor) fluorescent protein, the EV linker, the acceptor (or donor) fluorescent protein and the ligand (or sensor) domain.
When the sensor domain contains a low molecular weight GTP-binding protein or a peptide to be phosphorylated, the aspect (1) is preferred. Thus, the EV linker is preferably present between the ligand domain and the sensor domain in the unimolecular FRET biosensor. Notably, the unimolecular FRET biosensor may not necessarily contain each one of the donor fluorescent protein, the acceptor fluorescent protein, the ligand domain, the acceptor domain and the EV linker, and may contain a plurality of each of the above domains.
The donor fluorescent protein contained in the donor fluorescent protein domain is not particularly limited as long as it can retain the ability to form a FRET pair. From the viewpoint of its function, preferred is CFP or TFP (Teal Fluorescence Protein). On the other hand, the acceptor fluorescent protein contained in the acceptor fluorescent protein domain is also not particularly limited as long as it can retain the ability to form a FRET pair. From the viewpoint of its function, YFP is preferred. The ability to form a FRET pair as used herein means that excitation energy can transfer from an excited donor fluorescent protein to an acceptor fluorescent protein in the close vicinity of the donor fluorescent protein, and the excitation energy transfer can be detected.
The donor fluorescent protein and/or the acceptor fluorescent protein may be a partial protein, that is, may not necessarily be a whole (full-length) protein as long as they can retain the ability to form a FRET pair. When the carboxyl-terminus of an amino acid sequence thereof is shortened, the difference in the FRET efficiency is often increased. Examples of a partial donor fluorescent protein and/or a partial acceptor fluorescent protein include those having preferably at least one, more preferably 1 to 11 deletions at the carboxyl-terminal region in amino acid sequences thereof. Notably, any amino acids in the carboxyl-terminal region region may be deleted. In the case of YFP, preferred are those having preferably at least one, more preferably 1 to 11, further preferably 11 amino acid deletions at the carboxyl-terminal region in amino acid sequences thereof. In the case of CFP, preferred are those having preferably at least one, more preferably 1 to 11, further preferably 11 amino acid deletions at the carboxyl-terminal region in amino acid sequences thereof.
The carboxyl-terminal region as used herein refers to a region consisting of, from the carboxyl-terminus, preferably 1 to 20 amino acids, more preferably 11 or less amino acids in amino acid sequences of GFP-related proteins used in the present invention. Whether the ability to form a FRET pair is retained can be examined as follows. A pair of protein molecules expected to form a FRET pair is co-produced in E. coli according to known methods. Cell extract containing the pair of protein molecules is measured for fluorescence intensities at expected excitation wavelengths of each of the pair of protein molecules.
The acceptor fluorescent protein and/or the donor fluorescent protein may have a mutation. The mutation may be introduced into any positions in amino acid sequences of the acceptor fluorescent protein and/or the donor fluorescent protein as long as the ability to form a FRET pair can be retained. Example of the mutation includes a multiple amino acid substitution. Specific examples of the amino acid substitution include Leu65Phe, Phe47Leu or Thr66Ser in a GFP mutant. Such mutations are preferred from the viewpoint of increasing the efficiency in fluorophore formation and increasing the FRET efficiency. The mutations can be introduced according to known methods such as a method using a PCR (polymerase chain reaction). Examples of YFP mutants include Ypet (yellow fluorescent protein for energy transfer) [Nguyen A. W., and P. S. Daugherty. Evolutionary optimization of fluorescent proteins for intracellular FRET. 2005. Nat. Biotechnol. 23:355-360], EYFP (product of Clontech Laboratories, Inc.), and Venus [Nagai, T., K. Ibata, E. S. Park, M. Kubota, K. Mikoshiba, and A. Miyawaki. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. 2002. Nat. Biotechnol. 20:87-90.] Examples of CFP mutants include CyPet [Nguyen A. W., and P. S. Daugherty. Evolutionary optimization of fluorescent proteins for intracellular FRET. 2005. Nat. Biotechnol. 23:355-360], ECFP (product of Clontech Laboratories, Inc.), SECFP (see PNL 5), and Turquoise (Goedhart, J., L. an Weeren, M. A. Hink, N. 0. Vischer, K. Jalink, and T. W. Gadella, Jr. Bright cyan fluorescent protein variants identified by fluorescence lifetime screening. 2010. Nat. Methods 7:137-139.) Suitable examples of a combination of the acceptor fluorescent protein with the donor fluorescent protein include Venus and ECFP, YPet and ECFP, Venus and Turquoise, and YPet and Turquoise.
A combination of a sensor protein contained in the sensor domain with a ligand contained in the ligand domain is not particularly limited. However, suitable examples thereof include a combination which enables a measurement of a serine-threonine kinase activity, a tyrosine kinase activity, and a low molecular weight GTP-binding protein activity. Examples of the combination for measuring the serine-threonine kinase activity include a combination of a Forkhead-associated (hereinafter referred to as FHA1) domain, a WW (Trp-Trp) domain or a BRCT (BRCA1-C terminal) domain with a peptide sequence containing serine or threonine. Examples of the combination for measuring the tyrosine kinase activity include a combination of a SH2 (Src homology 2) domain or a PTB (phosphotyrosine-binding) domain with a peptide sequence containing tyrosine. Examples of the combination for measuring the low molecular weight GTP-binding protein activity include a combination of a low molecular weight GTP-binding protein belonging to a Ras-family, a Rho-family, a Rab-family, an Arf-family or a Ran-family with a target protein thereof.
From the viewpoint of effectivity, specificity and sensitivity, examples of an elements in the unimolecular FRET biosensor of the present invention and a particularly preferably combination thereof include the followings: a combination in which the sensor domain is the low molecular weight GTP-binding protein Ras, the ligand domain is Raf which is a target protein of the Ras, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP; or a combination in which the sensor domain is the low molecular weight GTP-binding protein Rac1, the ligand domain is Pak which is a target protein of the Rac1, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP; or a combination in which the sensor domain is the low molecular weight GTP-binding protein Cdc42, the ligand domain is Pak which is a target protein of the Cdc42, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP; or a combination in which the sensor domain is a peptide to be phosphorylated by Protein kinase A (A kinase, hereinafter referred to as PKA), the ligand domain is the FHA1 domain, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP; or a combination in which the sensor domain is a peptide to be phosphorylated by Extracellular Signal-regulated Kinase (hereinafter referred to as ERK), the ligand domain is the WW domain, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP; or a combination in which the sensor domain is a peptide to be phosphorylated by the tyrosine kinase, the ligand domain is the SH2 domain in Crk protein, the donor fluorescent protein is CFP and the acceptor fluorescent protein is YFP.
From the viewpoint a increase in the gain, the acceptor (or donor) fluorescent protein, the ligand (or sensor) domain, the low molecular weight GTP-binding protein and the target protein are, in the unimolecular FRET biosensor containing the EV linker of the present invention, preferably connected in the following orders from the amino-terminus: YFP-FHA1-EV linker-PKA substrate peptide-CFP, YFP-FHA1-EV linker-ERK substrate peptide-CFP, YFP-Raf-EV linker-Ras-CFP, YFP-Rac1-EV linker-Pak-CFP, YFP-Cdc42-EV linker-Pak-CFP, or YFP-CRK SH2 domain-EV linker-tyrosine kinase substrate peptide-CFP. Also, positions of YFP and CFP may be exchanged with each other. Alternatively, various YFP and CFP mutants may be suitably used such as Ypet, CyPet, EYFP (product of Clontech Laboratories, Inc.), ECFP (product of Clontech Laboratories, Inc.), SECFP and Venus.
The unimolecular FRET biosensor of the present invention suitably usable contains, for example, a peptide tag, other fluorescent proteins, an intracellular localization signal, or a protein-protein interaction regulating domain at the N-terminus, the C-terminus or internally as long as it contains the above-described five domains in order to alter an intracellular distribution depending on the intended purpose or to allow the unimolecular FRET biosensor to be easily purified.
Notably, whether the EV linker of the present invention exhibits a desired effect can be evaluated according to the method of Example 1 described below.
The present invention also provides a gene (DNA) encoding the EV linker according to the present invention and a gene (DNA) encoding the unimolecular FRET biosensor according to the present invention. The gene of the EV linker can be chemically synthesized. Component proteins other than the EV linker in the unimolecular FRET biosensor can be each produced according to conventional methods. For example, their gene sequences can be available from, for example, GenBank. Based on thus obtained gene sequences, known PCR amplifications, restriction enzyme cleavages, and ligations are performed.
The present invention also provides an expression vector containing the gene. Such vector can be constructed by inserting the gene encoding the EV linker or the unimolecular FRET biosensor of the present invention into a known prokaryotic expression vector (e.g., pGEX-2T; product of GE Healthcare), a known eukaryotic expression vector (e.g., pCAGGS [Niwa, H., K. Yamamura, and J. Miyazaki. 1991. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene 108:193-200.]) or a known viral vector (e.g., pCX4 [Iwahara, T., T. Akagi, Y. Fujitsuka, and H. Hanafusa. 2004. CrkII regulates focal adhesion kinase activation by making a complex with Crk-associated substrate, p 130 Cas. Proc. Natl. Acad. Sci. U.S. A 101:17693-17698]) according to known methods.
The present invention also provides a transformed cell and a transgenic non-human animal harboring the expression vector. Such transformed cell can be obtained by introducing the expression vector into an intended cell. A method for introducing the expression vector into the cell is not particularly limited, and may be any known transfection methods or viral infection methods. Examples thereof include a calcium phosphate method, a lipofection method, an electroporation method or a transposon-based method. The cell is not particularly limited, and may be any prokaryotic or eukaryotic cells. Examples of the eukaryotic cell include HeLa cells derived from human cancer, HEK293T cells derived from human embryonic kidney, MDCK cells derived from canine kidney, COS7 cells derived from monkey kidney, rat C6 glioma cells and yeast. Example of the prokaryotic cell includes E. coli. Additionally, other various cells may be used.
Meanwhile, the transgenic non-human animal can be generated by directly introducing the expression vector into an individual (e.g., mouse) using known methods such as a method for microinjecting a plasmid DNA into a nucleus of a fertilized mouse egg or a Tol2 transposase-mediated method [Sumiyama, K., K. Kawakami, and K. Yagita. 2010. A simple and highly efficient transgenesis method in mice with the Tol2 transposon system and cytoplasmic microinjection. Genomics 95:306-311.]. The transgenic non-human animal is not particularly limited as long as it is not human. Examples thereof include mouse, rat, pig, zebrafish and C. elegans. Preferred is mouse from the viewpoint of an application in the pharmaceutical industry.
The present invention also provides a method for measuring a serine-threonine kinase activity, a tyrosine kinase activity, or a low molecular weight GTP-binding protein activity, the method including detecting FRET with the unimolecular FRET biosensor of the present invention. Examples of a method for detecting FRET with the unimolecular FRET biosensor of the present invention include a method in which a unimolecular FRET biosensor-expressing cell line is observed under a fluorescence microscope, followed by a time-lapse imaging and a method in which a unimolecular FRET biosensor-expressing cell line is analyzed with a flow cytometer. Such methods enable the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity to be measured by detecting FRET occurred with the unimolecular FRET biosensor according to the present invention.
The present invention also provides a measurement method for measuring a serine-threonine kinase activity, a tyrosine kinase activity, or a low molecular weight GTP-binding protein activity including detecting FRET using the transformed cell and the transgenic non-human animal according to the present invention. The serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity can be measured using the unimolecular FRET biosensor containing a sensor domain and a ligand domain which domains may be used for measuring the serine-threonine kinase activity, the tyrosine kinase activity, or the low molecular weight GTP-binding protein activity. A method for detecting FRET is not particularly limited as long as it can detect excitation energy transfer due to FRET. For example, a microscope, a flow cytometer, a spectrophotometer or a fluorescent ELISA reader can be used for the FRET. Using the measurement method, the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity can be directly measured in the cell or animal by detecting FRET. In such a case, a calibration curve may be separately generated as follows: a phosphorylation rate is calculated using a phosphorylation-specific antibody, and thus the corresponding FRET efficiency is determined; or a GTP/GDP ratio (or GTP/(GDP+GTP) ratio) (both in molar ratio) is calculated by measuring a GTP-bound form of the low molecular weight GTP-binding protein and a GDP-bound form of the low molecular weight GTP-binding protein resulting from a release of an inorganic phosphate from GTP, and thus the corresponding FRET efficiency is determined. Such calibration curve enables the phosphorylation rate or the GTP/GDP ratio to be calculated based on the FRET efficiency in the cell or animal.
For example, the following method is specifically exemplified.
The unimolecular FRET biosensor-expressing transformed cell or transgenic non-human animal of the present invention is observed under a fluorescence microscope to thereby directly detect a change in the FRET efficiency before and after a conformational change of the sensor domain, which can be performed according to Aoki, K. and M. Matsuda. 2009. Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors. Nature Protocol 4:1623-1631. In the case of the transgenic non-human animal, a body part which can be easily fixed (e.g., external ear) is preferably observed.
The fluorescence microscope to be used is not particularly limited. However, an inverted fluorescence microscope (IX81, product of Olympus Corporation) equipped with a known xenon light source, a fluorescence excitation filter wheel, a fluorescence emission filter wheel, and a high sensitive cooled CCD camera. The filters and camera images can desirably be controlled and analyzed with Meta Morph image analysis software (product of Molecular Devices, LLC).
The cell or animal is irradiated with excitation light of the donor fluorescent protein. At a fluorescence wavelength of the donor fluorescent protein, an image is taken by the CCD camera. Then, a fluorescence wavelength of the acceptor fluorescent protein, an image is taken by the CCD camera. A ratio of fluorescence intensities in both images is determined to thereby calculate the FRET efficiency at each measuring points.
According to the present invention, there are provided a unimolecular FRET biosensor containing the EV linker according to the present invention and allowing the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity to be non-invasively measured; and a gene encoding the unimolecular FRET biosensor. The biosensor is excited with light in a visible light region, which is a reason why the activities can be non-invasively measured. There are also provided a transformed cell and a transgenic non-human animal harboring the expression vector which is useful to express the unimolecular FRET biosensor and to non-invasively measure the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity; and a measurement method for measuring the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity by means of the unimolecular FRET biosensor containing the EV linker (hereinafter may be referred to as “EV linker containing-unimolecular FRET biosensor”). Thus, the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity can be non-invasively determined in cells or individuals, which can provide great advantages in understanding of biological phenomena as well as in drug developments (e.g., therapeutic agents or prophylactic agents for cancers, autoimmune diseases and allergic diseases).
A further aspect of the present invention is a method for screening a regulator of the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity. That is, the above method is a method for screening a regulator of the serine-threonine kinase activity, the tyrosine kinase activity, or the low molecular weight GTP-binding protein activity including (a) contacting a test substance with the transformed cell of the present invention; and (b) detecting FRET to thereby detect a change in the serine-threonine kinase activity, the tyrosine kinase activity, or the low molecular weight GTP-binding protein activity. The transformed cell of the present invention is a transformed cell harboring expression vector which contains a gene of the EV linker containing-unimolecular FRET biosensor and which expresses the unimolecular FRET biosensor of the present invention. According to the screening method of the present invention, substances and salt thereof can be efficiently screened which regulate the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity (i.e., regulators of the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity) by constructing a cell which expresses the EV linker containing-unimolecular FRET biosensor of the present invention and using a bioassay system. The test substance used in the method is not particularly limited. Examples thereof include a peptide, a protein, a non-peptidic substance, a synthetic substance and a fermentation product.
EXAMPLES
The present invention will be explained with reference to the following Examples. However, a scope of the present invention is not limited thereto.
Example 1
Measurement of Serine-Threonine Kinase A (PKA) Enzyme Activity with Eevee-PKAs
(1) Construction of Gene Encoding EV Linker Containing-Unimolecular FRET Biosensor for Measurement of PKA Enzyme Activity
(i) Construction of Platform Eevee-PKA-G72 (3520 NES) Gene for Insertion of EV Linker Gene
A unimolecular FRET biosensor Eevee-PKA-G72 (3520 NES) gene was constructed using known methods (e.g., PCR) (see FIG. 3). The unimolecular FRET biosensor contains, from the amino-terminus, YFP, a linker, a ligand domain (herein, FHA1 domain which specifically binds to a phosphorylated threonine), a linker, a substrate sequence to be phosphorylated by PKA, a linker, and a CFP donor fluorescent protein. There will be described a nucleotide sequence (SEQ ID NO: 1) of the resultant Eevee-PKA-G72 and a predicted amino acid sequence thereof (SEQ ID NO: 2).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1392: glycine linker
nt 1393-1437: PKA substrate sequence
nt 1438-1446: linker (Gly-Gly-Arg)
nt 1447-2163: Aequorea CFP (ECFP)
nt 2164-2169: linker (Ser-Arg)
nt 2170-2205: nuclear export signal (NES)
nt 2206-2208: stop codon
(ii) Synthesis of EV20 Linker and Construction of Eevee-PKA-20 Gene (3532 NES)
A sense-primer F—20 a.a_linker (SEQ ID NO: 3) was annealed with an antisense-primer R—20 a.a_linker (SEQ ID NO: 4). The resultant annealed product was inserted into a restriction enzyme Asp718I/Aor13HI cleavage site in 3520 NES. A 20 a.a. linker encoded by the inserted nucleotides is referred to as “EV20 linker” (SEQ ID NO: 5). Then, YPet was replaced by Venus in the above unimolecular FRET biosensor. The resultant unimolecular FRET biosensor was designated as “Eevee-PKA-20 (3532 NES)”. There will be described a nucleotide sequence (SEQ ID NO: 6) of the Eevee-PKA-20 and a predicted amino acid sequence thereof (SEQ ID NO: 7).
nt 1-714: Aequorea YFP (Venus)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1143-1149: linker (Gly-Thr)
nt 1150-1209: EV20linker (SEQ ID NO: 5)
nt 1210-1215: linker (Ser-Gly)
nt 1216-1239: PKA substrate sequence
nt 1239-1248: linker (Gly-Gly-Arg)
nt 1249-1965: Aequorea CFP (ECFP)
nt 1966-1971: linker (Ser-Arg)
nt 1972-2007: nuclear export signal (NES)
nt 2008-2010: stop codon
(iii) Construction of Eevee-PKA-52 (3535 NES)
A pEevee-PKA-20, which was a mammalian cell expression vector of the Eevee-PKA-20, was cleaved with restriction enzymes EcoRI and Asp718I. The resultant larger cleavage product was used to prepare a vector. The pEevee-PKA-20 fragment was ligated with a linker-containing fragment which is a cleavage product with EcoRI/Aor13HI and a DNA fragment which was obtained by annealing a sense-primer F—10 a.a_linker (SEQ ID NO: 8) with an antisense-primer R—10 a.a_linker (SEQ ID NO: 9), resulting in a pEevee-PKA-52. There will be described a nucleotide sequence (SEQ ID NO: 10) of the Eevee-PKA-52 and a predicted amino acid sequence thereof (SEQ ID NO: 11).
nt 1-714: Aequorea YFP (Venus)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1305: EV52 linker (SEQ ID NO: 12)
nt 1306-1311: linker (Ser-Gly)
nt 1312-1335: PKA substrate sequence
nt 1336-1344: linker (Gly-Gly-Arg)
nt 1345-2061: Aequorea CFP (ECFP)
nt 2062-2067: linker (Ser-Arg)
nt 2068-2103: nuclear export signal (NES)
nt 2104-2106: stop codon
(iv) Construction of pEevee-PKA-84 (3537 NES)
The pEevee-PKA-20, which was a mammalian cell expression vector of the Eevee-PKA-20, was cleaved with restriction enzymes EcoRI and Asp718I. The resultant larger cleavage product was used to prepare a vector. The pEevee-PKA-20 fragment was ligated with a linker-containing fragment which is a cleavage product with EcoRI/Aor13HI and a DNA fragment which was obtained by annealing a sense-primer F—10 a.a_linker (SEQ ID NO: 8) with an antisense-primer R—10 a.a_linker (SEQ ID NO: 9), resulting in an Eevee-PKA-84. There will be described a nucleotide sequence (SEQ ID NO: 13) of the Eevee-PKA-84 and a predicted amino acid sequence thereof (SEQ ID NO: 14).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1401: EV84 linker (SEQ ID NO: 15)
nt 1402-1407: linker (Ser-Gly)
nt 1408-1431: PKA substrate sequence
nt 1432-1440: linker (Gly-Gly-Arg)
nt 1441-2157: Aequorea CFP (ECFP)
nt 2158-2163: linker (Ser-Arg)
nt 2164-2199: nuclear export signal (NES)
nt 2200-2202: stop codon
(v) Construction of Eevee-PKA-116 (3536 NES)
The pEevee-PKA-20, which was a mammalian cell expression vector of the Eevee-PKA-52, was cleaved with restriction enzymes EcoRI and Asp718I. The resultant larger cleavage product was used to prepare a vector. The pEevee-PKA-52 fragment was ligated with a linker-containing fragment which is a cleavage product with EcoRI/Aor13HI and a DNA fragment which was obtained by annealing a sense-primer F—10 a.a_linker (SEQ ID NO: 8) with an antisense-primer R—10 a.a_linker (SEQ ID NO: 9), resulting in an Eevee-PKA-116. There will be described a nucleotide sequence (SEQ ID NO: 16) of the Eevee-PKA-116 and a predicted amino acid sequence thereof (SEQ ID NO: 17).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1497: EV116 linker (SEQ ID NO: 18)
nt 1498-1503: linker (Ser-Gly)
nt 1504-1527: PKA substrate sequence
nt 1528-1536: linker (Gly-Gly-Arg)
nt 1537-2247: Aequorea CFP (ECFP)
nt 2248-2253: linker (Ser-Arg)
nt 2254-2289: nuclear export signal (NES)
nt 2290-2292: stop codon
(vi) Construction of pEevee-PKA-5 (3522 NES)
A unimolecular FRET biosensor pEevee-PKA-5 was constructed using known methods (e.g., PCR). There will be described a nucleotide sequence (SEQ ID NO: 19) of the pEevee-PKA-5 and a predicted amino acid sequence thereof (SEQ ID NO: 20).
nt 1-714: Aequorea YFP (Venus)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1170: linker (Gly-Thr-Gly-Gly-Ser-Gly-Gly-Ser-Gly)
nt 1171-1194: PKA substrate sequence
nt 1195-1203: linker (Gly-Gly-Arg)
nt 1204-1920: Aequorea CFP (ECFP)
nt 1921-1926: linker (Ser-Arg)
nt 1927-1962: nuclear export signal (NES)
nt 1963-1965: stop codon
(vii) Construction of pEevee-PKA-180 (3597 NES)
The pEevee-PKA-116, was cleaved with restriction enzymes EcoRI and Asp718I. The resultant larger cleavage product was used to prepare a vector. The pEevee-PKA-116 fragment was ligated with a linker-containing fragment which is a cleavage product with EcoRI/Aor13HI and a DNA fragment which was obtained by annealing a sense-primer F—10 a.a_linker (SEQ ID NO: 8) with an antisense-primer R—10 a.a_linker (SEQ ID NO: 9), resulting in an Eevee-PKA-180. Then, Venus was replaced by YPet in the above unimolecular FRET biosensor. There will be described a nucleotide sequence (SEQ ID NO: 21) of the Eevee-PKA-180 and a predicted amino acid sequence thereof (SEQ ID NO: 22).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1689: EV180 linker (SEQ ID NO: 23)
nt 1690-1695: linker (Ser-Gly)
nt 1696-1719: PKA substrate sequence
nt 1720-1728: linker (Gly-Gly-Arg)
nt 1729-2439: Aequorea CFP (ECFP)
nt 2440-2445: linker (Ser-Arg)
nt 2446-2481: nuclear export signal (NES)
nt 2482-2484: stop codon
(vii) Construction of pEevee-PKA-244 (3598 NES)
The pEevee-PKA-116 was cleaved with restriction enzymes EcoRI and Asp718I. The resultant larger cleavage product was used to prepare a vector. The pEevee-PKA-116 fragment was ligated with a linker-containing fragment which is a cleavage product with EcoRI/Aor13HI and a DNA fragment which was obtained by annealing a sense-primer F—10 a.a_linker (SEQ ID NO: 8) with an antisense-primer R—10 a.a_linker (SEQ ID NO: 9), resulting in a pEevee-PKA-244. There will be described a nucleotide sequence (SEQ ID NO: 24) of the pEevee-PKA-244 and a predicted amino acid sequence thereof (SEQ ID NO: 25).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1881: EV244 linker (SEQ ID NO: 26)
nt 1882-1887: linker (Ser-Gly)
nt 1888-1911: PKA substrate sequence
nt 1912-1920: linker (Gly-Gly-Arg)
nt 1921-2631: Aequorea CFP (ECFP)
nt 2632-2637: linker (Ser-Arg)
nt 2638-2673: nuclear export signal (NES)
nt 2674-2676: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor (EeVee-PKA) in Mammalian Cell and Time-Lapse Fluorescence Microscopy Analysis
Here, PKA-biosensors containing various lengths of the EV-linkers and mammalian cell expression vectors thereof are collectively referred to as “EeVee-PKAs” and “pEevee-PKAs”, respectively. As the mammalian cell expression vectors, pCAGGS [Niwa, H., K. Yamamura, and J. Miyazaki. 1991. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene 108:193-200.] may be optimally used. HeLa cells derived from cervical cancer were cultured in a DMEM medium (product of INVITROGEN) supplemented with 10% fetal bovine serum. The pEeVee-PKAs obtained in the step (1) were transfected into the HeLa cells by 293 fectin (product of INVITROGEN) according to the protocol supplied with the reagent. Post-transfected HeLa cells were cultured in the DMEM medium (product of INVITROGEN) supplemented with 10% fetal bovine serum to thereby express Eevee-PKA proteins. Twenty-four hours after transfection, the cultured cells were observed under a time-lapse fluorescence microscope.
The microscope was the inverted fluorescence microscope (IX81, product of Olympus Corporation) equipped with a xenon light source, a fluorescence excitation filter wheel device and a fluorescence emission filter wheel device (product of Ludl Electronic Products Ltd.), and a high sensitive cooled CCD camera (CoolSNAP-HQ, product of NIPPON ROPER K.K.) Upon observation, Meta Morph image analysis software (product of Molecular Devices, LLC) was used to control the microscope and to analyse observation results. A fluorescence excitation filter, a fluorescence emission filter and a dichroic mirror were purchased from Omega SA.
The cultured cells were irradiated with excitation light at 440 nm. An image was taken by the CCD camera at a fluorescence wavelength of the CFP donor, i.e., 480 nm. Then, an image was taken by the CCD camera at a fluorescence wavelength of the YFP acceptor, i.e., 530 nm. Based on the both image data, a ratio between fluorescence intensities in both images was determined to thereby use as an index of the FRET efficiency at each measuring points.
The gain of the Eevee-PKAs can be determined by comparing the FRET efficiencies before and after stimulation with 1 mM dibutyryl cAMP which is an activating agent of PKA. As can be seen from FIG. 4, the EV linkers having 52 a.a. or more have markedly increased gains due to the activation of PKA.
Additionally, when the YFP donor protein was replaced by, for example, YPet, which has been optimized for the FRET, the gains were more significantly increased (see FIG. 6). However, the increasing effect reached a zenith at 116 a.a, and the gain cannot be significantly increased even when having longer linkers.
In order to examine a cause of the increase in the gain, fluorescent profiles at the basal state were determined (see FIGS. 7A, 7B and 7C). It has been found that the longer the EV linker is, the lower fluorescence of the YFP donor protein at the basal state is. That is, it has been found that the EV linker increases the gain by reducing the FRET at the basal state. This effect could be achieved with linkers having up to 244 a.a.
(3) Immunoblotting Analysis of Phosphorylation Levels of Eevee-PKAs
As described above, the Eevee-PKAs were expressed in HeLa cells. After 24 hours, the cells were treated with 1 mM dibutyryl-cAMP and 50 nM Calyculin. Thereafter, the cells were solubilized according to known methods, followed by separation with SDS-PAGE. Proteins were separated using a 6% polyacrylamide gel containing 50 μM Phos-tag (product of Phos-tag Consortium). The gel was transferred to a PVDF membrane (product of Millipore) and sequentially reacted with anti-GFP antibodies (in-house) and IR Dye 800 CW-labeled anti-rabbit antibodies (product of LI-COR Biosciences) to thereby detect the Eevee-PKA proteins. Fluorescence labeled antibodies bound to the Eevee-PKA proteins were quantified by Odyssey Fluorescence Analyzer (product of LI-COR Biosciences). As can be seen from FIGS. 8A and 8B, the EV linkers significantly reduce phosphorylation levels at the basal state. That is, the ligand domain generally binds to the sensor domain to thereby inhibit the activated sensor domain from returning to the basal state. The EV linkers suppress the inhibitory effect to thereby reduce FRET at the basal state, which increases the gain.
Example 2
Measurement of Enzyme Activity of Serine-Threonine Kinase Akt with Eevee-PKAs
(1) Construction of Gene Encoding EV Linker Containing-Unimolecular FRET Biosensor for Measurement of Serine-Threonine Kinase Akt Enzyme Activity
There were constructed sequences in which PKA substrate sequences in Eevee-Akt-84 (3547 NES) and Eevee-Akt-116 (3548 NES) were replaced by amino acid sequences suitable for phosphorylation of Akt by means of, for example, synthetic primers. The above sequences were inserted into the Eevee-PKAs and PH domains of Akt were added to the amino-termini. There will be described nucleotide sequences (SEQ ID NOs: 27 and 29) of the resultant Eevee-Akt-84 and Eevee-Akt-116, and predicted amino acid sequences thereof (SEQ ID NOs: 28 and 30). Structures thereof are shown in FIGS. 9A and 9B.
Eevee-Akt-84 (3547 NES)
nt 1-453: AH domain of Akt protein
nt 454-462: linker (Glu-Phe-Gly)
nt 463-1176: Aequorea YFP (YPet)
nt 1177-1182: linker (Leu-Glu)
nt 1183-1605: FHA1 domain of yeast Rad53 gene
nt 1606-1611: linker (Gly-Thr)
nt 1612-1863: EV84 linker
nt 1864-1869: linker (Ser-Gly)
nt 1870-1902: PKA substrate sequence
nt 1903-1911: linker (Gly-Gly-Arg)
nt 1912-2622: Aequorea CFP (ECFP)
nt 2623-2628: linker (Ser-Arg)
nt 2629-2664: nuclear export signal (NES)
nt 2665-2667: stop codon
Eevee-Akt-116 (3548 NES)
nt 1-453: AH domain of Akt protein
nt 454-462: linker (Glu-Phe-Gly)
nt 463-1176: Aequorea YFP (YPet)
nt 1177-1182: linker (Leu-Glu)
nt 1183-1605: FHA1 domain of yeast Rad53 gene
nt 1606-1611: linker (Gly-Thr)
nt 1612-1959: EV116 linker
nt 1864-1965: linker (Ser-Gly)
nt 1870-1998: PKA substrate sequence
nt 1903-2007: linker (Gly-Gly-Arg)
nt 1912-2718: Aequorea CFP (ECFP)
nt 2623-2724: linker (Ser-Arg)
nt 2629-2760: nuclear export signal (NES)
nt 2665-2763: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensors (EeVee-Akts) in Mammalian Cell and Time-Lapse Fluorescence Microscopy Analysis
An analysis was performed in the same manner as in Example 1-(2), except that COS7 cells were used. As shown in FIG. 10, a 116 a.a. EV linker significantly reduces the basal state.
Example 3
Measurement of ERK Enzyme Activity with Eevee-ERK
(1) Construction of Gene Encoding EV Linker Containing-Unimolecular FRET Biosensor Eevee-ERK (3550 NES) for Measurement of ERK Enzyme Activity
(i) There was produced a sequence in which a substrate sequence and a phosphorylated peptide recognition sequence in the Eevee-PKA-116 were replaced by an ERK substrate sequence by means of a PCR method using synthetic primers. The resultant plasmid was designated as “Eevee-ERK”. There will be described a nucleotide sequence (SEQ ID NO: 31) of the Eevee-ERK, and a predicted amino acid sequence thereof (SEQ ID NO: 32).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-882: WW domain of Pin1 gene
nt 1144-888: linker (Gly-Thr)
nt 1150-1236: EV116 linker
nt 1498-1242: linker (Ser-Gly)
nt 1504-1272: ERK substrate sequence
nt 1528-1281: linker (Gly-Gly-Arg)
nt 1537-1992: Aequorea CFP (ECFP)
nt 2248-2004: linker (Gly-Arg-Ser-Arg)
nt 2254-2040: nuclear export signal (NES)
nt 2290-2043: stop codon
(ii) There was also constructed a vector in which a docking sequence unique to the ERK substrate was added, which was designated as “Eevee-ERK-DS (3560 NES)”. There will be described a nucleotide sequence (SEQ ID NO: 33) of the Eevee-ERK-DS (3560 NES), and a predicted amino acid sequence thereof (SEQ ID NO: 34).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-882: WW domain of Pin1 gene
nt 883-888: linker (Gly-Thr)
nt 889-1236: EV116 linker
nt 1237-1242: linker (Ser-Gly)
nt 1243-1272: ERK substrate sequence
nt 1273-1284: linker (Ala-Lys-Leu-Ser)
nt 1285-1296: docking sequence (Phe-Gln-Phe-Pro)
nt 1297-1305: linker (Gly-Gly-Arg)
nt 1306-2016: Aequorea CFP (ECFP)
nt 2017-2028: linker (Gly-Arg-Ser-Arg)
nt 2029-2064: nuclear export signal (NES)
nt 2065-2067: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor (EeVee-ERK) in Mammalian Cell and Time-Lapse Fluorescence Microscopy Analysis
An analysis was performed in the same manner as in Example 1-(2). That is, the Eevee-ERK was expressed in HeLa cells and stimulated with EGF. As shown in FIGS. 11A, 11B, 11C and 11D, the EV linker containing-biosensor (3560 NES) had more increased gain than that of a Gly linker containing-biosensor (EKAR-1667 nes), which is partially caused by low FRET at the basal state.
Example 4
Measurement of Tyrosine Kinase Enzyme Activity with EV Linker Containing-Unimolecular FRET Biosensor Picchu-734
(1) Construction of EV Linker Containing-Unimolecular FRET Biosensor Picchu-734 for Measurement of Tyrosine Kinase Enzyme Activity
(i) A region containing a SH2 domain of CrkII protein was amplified by PCR, and inserted into a cleavage product of Eevee-PKA-116 (3536 NES) with XhoI/Asp718I. A substrate sequence site in the resultant product was replaced, resulting in a gene of Picchu-734. There will be described a nucleotide sequence (SEQ ID NO: 35) of the Picchu-734, and a predicted amino acid sequence thereof (SEQ ID NO: 36).

    
    
        nt 1-714: Aequorea YFP (YPet)
        nt 715-720: linker (Leu-Glu)
        nt 721-1332: SH2 domain of CRKII gene
        nt 883-1338: linker (Gly-Thr)
        nt 889-1686: EV116linker
        nt 1237-1692: linker (Ser-Gly)
        nt 1243-1719: tyrosine-phosphorylated substrate sequence of CRKII
        nt 1273-1728: linker (Ala-Lys-Leu-Ser)
        nt 1306-2439: Aequorea CFP (ECFP)
        nt 2017-2451: linker (Gly-Arg-Ser-Arg)
        nt 2029-2487: nuclear export signal (NES)
        nt 2065-2490: stop codon

(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor Picchu-734 and Time-Lapse Fluorescence Microscopy Analysis for Measurement of Tyrosine Kinase Activity in Mammalian Cell

    
    


An analysis was performed in the same manner as in Example 3-(2). As can be seen from FIG. 12, the EV linker containing-Picchu biosensor (Picchu-734) had more increased gain than that of the non-EV linker containing-biosensor (Picchu-730) [Kurokawa, K., N. Mochizuki, Y. Ohba, H. Mizuno, A. Miyawaki, and M. Matsuda. 2001. A pair of FRET-based probes for tyrosine phosphorylation of the CrkII adaptor protein in vivo. J. Biol. Chem. 276:31305-31310.].
Example 5
Measurement of Rac1 Activity with Raichu-Rac1
(1) Construction of EV linker Containing-Unimolecular FRET Biosensor Raichu-Rac1 (2246X) for Measurement of Rac1 Activity
(i) A unimolecular FRET biosensor Raichu-Rac1 (2241X) for measuring Rac1 activity was constructed by means of, for example, a PCR based on a known Raichu-Rac1 (1011X) (see Itoh, R. E., K. Kurokawa, Y. Ohba, H. Yoshizaki, N. Mochizuki, and M. Matsuda. 2002. Activation of Rac and Cdc42 video-imaged by FRET-based single-molecule probes in the membrane of living cells. Mol. Cell. Biol. 22:6582-6591). There will be described a nucleotide sequence (SEQ ID NO: 37) of the Raichu-Rac1 (2241X), and a predicted amino acid sequence thereof (SEQ ID NO: 38).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-969: CRIB domain of Pak protein
nt 883-996: glycine linker
nt 1237-1527: Rac1
nt 1273-1536: linker (Arg-Gly-Arg)
nt 1306-2247: Aequorea CFP (Turquoise)
nt 1273-2253: linker (Ser-Arg)
nt 2017-2313: C-terminal domain of KRas protein
nt 2065-2316: stop codon
(ii) An EV linker containing-mmolecular FRET biosensor Raichu-Rac1 (2246X) for measuring Rac1 activity was constructed based on the Raichu-Rac1 (2241X) by exchanging a linker. There will be described a nucleotide sequence (SEQ ID NO: 39) of the Raichu-Rac1 (2246X), and a predicted amino acid sequence thereof (SEQ ID NO: 40).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-969: CRIB domain of Pak protein
nt 970-1332: EV116 linker
nt 1333-1860: Rac1
nt 1861-1869: linker (Arg-Gly-Arg)
nt 1870-2580: Aequorea CFP (Turquoise)
nt 2581-2586: linker (Ser-Arg)
nt 2587-2646: C-terminal domain of KRas protein
nt 2647-2649: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor Raichu-Rac1 and Time-Lapse Fluorescence Microscopy Analysis for Measurement of Rac1 Activity in Mammalian Cell
An analysis was performed in the same manner as in Example 3-(2). As can be seen from FIGS. 13A and 13B, the EV linker containing-Raichu biosensor (Raichu-2246X) had lower FRET at the basal state and significantly increased FRET in the presence of EGF-stimulation, i.e., had significantly higher sensitivity than the Raichu biosensor containing a conventional linker (Raichu-2241X).
(3) Establishment of Cell Line Stably Expressing Raichu-Rac1 (2246X)
The gene of Raichu-Rac1 (2246X) was inserted into pPB plasmid. This plasmid and a transposase expression vector (pCMV-mPBase) [Yusa, K., R. Rad, J. Takeda, and A. Bradley. 2009. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat. Methods 6:363-369.] were co-transfected into C6 cells. Two days after the co-transfection, blasticidine was added thereto to a concentration of 10 ng/mL and cultured for additional 2 weeks. Thereafter, cloning was performed in a 96-well culture plate. As a result, a cultured cell line stably expressing the biosensor was successfully established. This cell line enabled Rac1 activity to be monitored for a long period (see FIGS. 14A, 14B, 14C and 14D).
Example 6
Measurement of Cdc42 Activity with Raichu-Cdc42 (2253X)
(1) Construction of EV Linker Containing-Unimolecular FRET Biosensor Raichu-Cdc42 (2253X) for Measurement of Cdc42 Activity
(i) A unimolecular FRET biosensor Raichu-Cdc42 (2253X) for measuring Cdc42 activity was constructed by means of, for example, PCR based on a known Raichu-Cdc42 (1054X). There will be described a nucleotide sequence (SEQ ID NO: 41) of the Raichu-Cdc42 (2253X), and a predicted amino acid sequence thereof (SEQ ID NO: 42).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-969: CRIB domain of Pak protein
nt 970-1332: EV116 linker
nt 1333-1857: Cdc42
nt 1858-1866: linker (Arg-Gly-Arg)
nt 1867-2577: Aequorea CFP (Turquoise)
nt 2578-2583: linker (Ser-Arg)
nt 2584-2643: C-terminal domain of KRas protein
nt 2644-2646: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor Raichu-Cdc42 and Time-Lapse Fluorescence Microscopy Analysis for Measurement of Cdc42 Activity in Mammalian Cell
An analysis was performed in the same manner as in Example 3-(2). As can be seen from FIGS. 15A to 15C, this biosensor had also low FRET at the basal state. Therefore, an EGF-stimulus dependent activation of Cdc42, which had been hard to be detected, was enabled to be high-sensitively detected.
Example 8
Measurement of HRas Activity with Raichu-HRas (3705X)
(1) Construction of EV linker Containing-Unimolecular FRET Biosensor Raichu-HRas (3705X) for Measurement of HRas Activity
(i) A unimolecular FRET biosensor Raichu-HRas (3705X) for measuring HRas activity was constructed by means of, for example, PCR based on a known Raichu-HRas [Mochizuki, N., S. Yamashita, K. Kurokawa, Y. Ohba, T. Nagai, A. Miyawaki, and M. Matsuda. 2001. Spacio-temporal images of growth factor-induced activation of Ras and Rap1. Nature 411:1065-1068.]. There will be described a nucleotide sequence (SEQ ID NO: 43) of the Raichu-HRas (3705X), and a predicted amino acid sequence thereof (SEQ ID NO: 44).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1236: HRas protein
nt 1237-1602: EV116 linker
nt 1603-1845: PBD domain of Raf protein
nt 1846-1854: linker (Gly-Gly-Arg)
nt 1855-2565: Aequorea CFP (Turquoise)
nt 2566-2571: linker (Ser-Arg)
nt 2584-2631: C-terminal domain of KRas protein
nt 2632-2634: stop codon
(2) Expression of EV Linker Containing-Unimolecular FRET Biosensor Raichu-HRas and Time-Lapse Fluorescence Microscopy Analysis for Measurement of HRas Activity in Mammalian Cell
An analysis was performed in the same manner as in Example 3-(2). Thus obtained time-lapse FRET imaging data are shown in FIGS. 16A and 16B. It has been found that the Raichu-HRas could detect activation more rapidly and sensitively than a prototype HRas [Mochizuki, N., S. Yamashita, K. Kurokawa, Y. Ohba, T. Nagai, A. Miyawaki, and M. Matsuda. 2001. Spacio-temporal images of growth factor-induced activation of Ras and Rap1. Nature 411:1065-1068.].
Example 10
Generation of Transgenic Mouse Expressing Eevee-ERK (3560 NES) and Eevee-PKA (3536 NES)
(1) Microinjection of Gene Encoding EV Linker Containing-Unimolecular FRET biosensor Eevee-ERK (3560 NES) and Eevee-PKA (3536 NES) into Fertilized Egg for Measurement of ERK and PKA Enzyme Activities
A mammalian cell expression plasmid containing a gene of Eevee-PKA (3536 NES) described in Example 1 or Eevee-ERK (3560 NES) described in Example 3 was inserted into a plasmid pT2A having a transposon recognition sequence. This plasmid and To12 transposon were microinjected as previously reported [Sumiyama, K., K. Kawakami, and K. Yagita. 2010. A simple and highly efficient transgenesis method in mice with the To12 transposon system and cytoplasmic microinjection. Genomics 95:306-311.]
(2) Screening of Transgenic Mouse Expressing Biosensor
The resultant mouse was irradiated with LED at 420 nm and imaged by a color digital camera with 470 nm short wavelength cut filter to thereby confirm the presence or absence of green fluorescence. Thus, transgenic mice could be easily identified. Also, a FRET image of a sagittal section in the transgenic mouse fetus was acquired by the fluorescence microscope described in Example 1. Based on the image, a spatial distribution of ERK or PKA activity could be examined (see FIG. 17).
Example 11
Drug Sensitivity Test with Cell Line Expressing Eevee-ERK (3560 NES)
(1) Establishment of Cell Line Stably Expressing Gene Encoding EV linker containing-unimolecular FRET biosensor Eevee-ERK (3560 NES) for Measurement of ERK Enzyme Activity
A mammalian cell expression plasmid containing the gene of Eevee-ERK (3560 NES) described in Example 3 was inserted into a plasmid having a transposon recognition sequence. This plasmid and a transposon expression vector was co-transfected as previously reported and screened for biosensor-expressing cell lines by blasticidin [Yusa, K., R. Rad, J. Takeda, and A. Bradley. 2009. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat. Methods 6 (5)363-369].
(2) FRET measurement in Cell Line Stably Expressing Biosensor
Cultured cell lines were seeded onto a 96-well culture plate. Serial-diluted inhibitors were added thereto. The cell lines were stimulated with 25 ng/mL EGF. After 30 min, ERK activities were measured as described in Example 3 (see FIGS. 18A to 18H). The average ERK activities of 30 or more cells were plotted. The following inhibitors were used: EGF receptor inhibitors (AG1478), MEK inhibitors (PD15035, PD184351), BRAF inhibitors (PLX4720), phosphatidylinositol 3-phosphate kinase inhibitors (LY294002), RSK inhibitors (BI-D1870) and JNK inhibitors (JNK inhibitor VIII). The results indicate that the EGF dependent-activation of ERK is effectively inhibited by EGF receptors (AG1478) and MEK inhibitors (PD153035, PD184352) for HeLa cells. It could be very easily measured in living cells that the EGF dependent-activation of ERK were concentration-dependently inhibited by the above inhibitors.
Example 12
Drug Sensitivity Test with Transgenic Mouse Expressing Eevee-PKA (3536 NES)
(1) Imaging of Small Intestine in Transgenic Mouse Expressing Eevee-PKA (3536 NES)
The transgenic mouse expressing Eevee-PKA (3536 NES) generated in Example 10 was anesthetized with isoflurane. A small intestine of the mouse was time-lapse imaged by an inverted two-photon microscope IX81/FV1000 (product of Olympus Corporation). Cells were excited at 840 nm with a titanium-sapphire laser system (Mai Tai Deep See HP; product of Spectra-Physics, Inc.). CFP fluorescence and YFP fluorescence were acquired using BA 460-500 fluorescence filter (product of Olympus Corporation) and BA 520-560 fluorescence filter (product of Olympus Corporation), respectively. FRET images were obtained in the same manner as in Example 3.
(2) Visualization of Drug Effect in Living Mouse
The transgenic mouse was intravenously injected with theophylline, which is a phosphodiesterase inhibitor, and actosin, which is a cyclic adenosine triphosphate analog, and measured for PKA activities. As shown in FIGS. 19 and 20, changes in PKA activities can be real-time visualized in an intermuscular nerve cell, an intestinal smooth muscle and a vascular smooth muscle.
Example 13
There is high possibility that long linkers are susceptible to degradation by proteases. Therefore, linkers EV3x8 and EV6x4, which have increased number of alanines which easily form α-helix and decreased number of glycines, were constructed and determined for the gain.
(1) (i) Construction of Eevee-PKA-3x8 (3676 NES)
In the same manner as in Example (1) (iii), the pEevee-PKA-20, which was a mammalian cell expression vector of the Eevee-PKA-20, was cleaved with restriction enzymes Asp718I and Aor13HI. The resultant larger cleavage product was used to prepare a vector. DNA in which restriction enzyme cleavage sites of Asp718I and Aor13HI were added at each termini of DNA encoding an EV3x8 linker (SEQ ID NO: 45) was synthesized. The above DNA cleaved with Asp718I/Aor13HI and the resultant cleavage product was used as an insert. The insert was ligated with the vector, resulting in a pEevee-PKA-3x8. There will be described a nucleotide sequence (SEQ ID NO: 47) of the pEevee-PKA-3x8 and a predicted amino acid sequence thereof (SEQ ID NO: 48).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1551: EV3x8 linker (SEQ ID NO: 45)
nt 1552-1557: linker (Ser-Gly)
nt 1558-1581: PKA substrate sequence
nt 1582-1590: linker (Gly-Gly-Arg)
nt 1591-2307: Aequorea ECFP
nt 2308-2313: linker (Ser-Arg)
nt 2314-2349: nuclear export signal (NES)
nt 2350-2352: stop codon
(1) (ii) Construction of Eevee-PKA-6x4 (3677 NES)
The pEevee-PKA-20, which was a mammalian cell expression vector of the Eevee-PKA-20, was cleaved with restriction enzymes Asp718I and Aor13HI. The resultant larger cleavage product was used to prepare a vector. DNA in which restriction enzyme cleavage sites of Asp718I and Aor13HI were added at each termini of DNA encoding EV6x4 linker (SEQ ID NO: 46) was synthesized. The DNA cleaved with Asp718I/Aor13HI and the resultant cleavage product was used as an insert. The insert was ligated with the vector, resulting in a pEevee-PKA-6x4. There will be described a nucleotide sequence (SEQ ID NO: 49) of the pEevee-PKA-6x4 and a predicted amino acid sequence thereof (SEQ ID NO: 50).
nt 1-714: Aequorea YFP (YPet)
nt 715-720: linker (Leu-Glu)
nt 721-1143: FHA1 domain of yeast Rad53 gene
nt 1144-1149: linker (Gly-Thr)
nt 1150-1521: EV6x4linker (SEQ ID NO: 46)
nt 1522-1527: linker (Ser-Gly)
nt 1528-1551: PKA substrate sequence
nt 1552-1560: linker (Gly-Gly-Arg)
nt 1561-2277: Aequorea ECFP
nt 2278-2283: linker (Ser-Arg)
nt 2284-2319: nuclear export signal (NES)
nt 2320-2322: stop codon
(2) The EV3x8 and the EC6x4 were determined for gains in the same manner as in Example 1, which revealed that both have comparable gains to the 116 a.a. linker (see FIG. 21).
INDUSTRIAL APPLICABILITY
The present invention provides an EV linker and a unimolecular FRET biosensor containing the EV linker which allow the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity to be non-invasively measured; a gene encoding the EV linker or the biosensor; an expression vevtor containing the gene; a transformed cell and a transgenic non-human animal harboring the expression vector which is useful to express the biosensor and to non-invasively measure the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity; a measurement method for measuring the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity by means of the biosensor; and a method for screening a regulator of the serine-threonine kinase activity, the tyrosine kinase activity and the low molecular weight GTP-binding protein activity.

## Claims

1. A linker for a unimolecular fluorescence resonance energy transfer (FRET) biosensor based on a principle of fluorescence resonance energy transfer, the linker comprising:
a polypeptide comprising 84 to 244 amino acids residues,
wherein the polypeptide consists of (i) glycine, (ii) alanine, and (iii) serine, threonine or both thereof,
wherein 35% to 65% of a total number of the amino acid residues are glycine, 10% to 40% of the total number of the amino acid residues are alanine, and 10% to 40% of the total number the amino acid residues are serine, threonine or both thereof, and
wherein the polypeptide has repeats of an amino acid sequence of SAGG, and wherein the number of the repeats of the amino acid sequence of SAGG is 19 to 54, and
wherein the polypeptide is selected from a sequence consisting of SEQ ID NO: 15, SEQ ID NO: 18, SEQ ID NO: 23 and SEQ ID NO: 26.

2. A unimolecular fluorescence resonance energy transfer (FRET) biosensor based on a principle of fluorescence resonance energy transfer, the unimolecular FRET biosensor comprising:
a fused protein, which comprises a sensor domain, a ligand domain, an acceptor fluorescent protein domain, a donor fluorescent protein domain, and a linker domain which links the sensor domain with the ligand domain,
wherein the linker domain comprises a polypeptide comprising 84 to 244 amino acids residues,
wherein the polypeptide consists of (i) glycine, (ii) alanine, and (iii) serine, threonine, or both thereof,
wherein 35% to 65% of a total number of the amino acid residues are glycine, 10% to 40% of the total number of amino acid residues are alanine, and 10% to 40% of the total number of the amino acid residues are serine, threonine, or both thereof,
wherein the polypeptide has repeats of an amino acid sequence of SAGG, and wherein the number of the repeats of the amino acid sequence of SAGG is 19 to 54, and
wherein the polypeptide is selected from a sequence consisting of SEQ ID NO: 15, SEQ ID NO: 18, SEQ ID NO: 23 and SEQ ID NO: 26.

3. The unimolecular FRET biosensor according to claim 2, wherein the donor fluorescent protein is a yellow fluorescent protein for energy transfer (YPet).