DESIGN METHOD FOR SYNTHETIC GENES |
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| 申请号 | US14848535 | 申请日 | 2015-09-09 | 公开(公告)号 | US20160076052A1 | 公开(公告)日 | 2016-03-17 |
| 申请人 | JNC CORPORATION; | 发明人 | Satoshi INOUYE; | ||||
| 摘要 | The present invention provides a method of designing an optimized gene which comprises altering a nucleotide sequence of a target protein gene, so that only preferential codons with high frequency of use in human cells are selected and a GC content of not less than 60% is achieved. A gene design method which involves the feature “only preferential codons with high frequency of use are selected and a GC content of not less than 60% is achieved” can be established as a general rule for preparing proteins with high expression level, in order to obtain chemically synthesized genes for proteins capable of high-level expression in eukaryotes. | ||||||
| 权利要求 | |||||||
| 说明书全文 | The present invention relates to a design method for a gene suitable for achieving high-level expression in cells derived from eukaryotes, specifically in mammalian cells, and use thereof. Protein synthesis in living cells is defined by 61 codons (genetic code) encoding 20 amino acids with mRNA transcribed from DNA (gene) as a template. However, it is known that the frequencies of codon usage differ among organisms while amino acids are the same. Thus, all codons are not used equally. The frequencies of codon usage are strongly biased among organisms. Consequently, when a recombinant protein is expressed using a gene derived from other organisms, it has been attempted to choose the preferred codons for the amino acids used in host cells, chemically synthesize a target gene and optimize the expression level of the protein. For example, the gene that is termed a humanized gene was synthesized by considering codon composition used in human cells to express a heterologous protein in a mammalian cell culture system and gene expression has been studied. The frequency of codon usage has been analyzed in detail (http://www.kazusa.or.jp/codon/), and the data of codon usage frequency in human cells are disclosed to the public (Table 1). The frequency of codon usage for each amino acid is shown in Table 1, which reveals that codon bias exists in each amino acid. In general, a method for synthesis of humanized genes, which designs a target gene with a GC content of 40% to 50%, and codons with less frequence of use are avoided, has been used for closely match the distribution rate of amino acids and codons shown in Table 1. In addition, humanized genes are designed using various software tools, in which not only codon proportions are considered but also deletions of recognition sites for transcription factors, avoidance of palindrome structures, etc. in nucleic acid sequences, deletions of unnecessary restriction enzyme sites and the like are taken into account. However, a synthetic humanized gene could have many different nucleotide sequences depending on combinations even though the gene encodes for the same amino acid sequence. Consequently, it is not assured to provide an improved synthesis method for the production of a gene product, and not always to express it as high expression level when expressed in mammalian cells. It is the current state that humanized genes are thus synthesized. On the other hand, the genes for aequorin (189 amino acid residues: Patent Document 1) and clytin II (189 amino acid residues: Patent Document 2), which are heterologous proteins derived from coelenterates and low molecular weight photoproteins with molecular weight of about 20,000, were synthesized using a codon with high frequency of use in human cells and examined the expression in an animal cultured cell system derived from mammal. As a result, these genes showed a higher expression activity than wild-type genes, which are described in Patent Documents 1 and 2. However, “a preferred human codon-optimized gene method,” which involves synthesizing genes by selecting only preferential codons with high frequency of use, has not yet been recognized to date as a general rule. The reason is considered to be because an extreme codon bias for amino acids in a gene sequence will affect the efficiency of protein production in intracellular protein synthesis, judging from the amount of tRNA species for each amino acid in cells and the difference among biological species. Furthermore, the efficiency of protein expression using synthetic genes prepared by selecting and using only preferential codons with high frequency of use has not been verified either for the proteins with normal molecular weight of 30,000 to 60,000. The GC content of genes in eukaryotes including human is approximately 40%. It is unclear if, in general, synthetic genes with the GC content of not less than 60% and preferentially biased codons in usage frequency are efficiently expressed in eukaryotes. [Patent Document 1] International Publication WO 02/88168 [Patent Document 2] Japanese Patent Application Publication No. 2010-172260 The inventor has addressed the problem of investigating whether or not a gene design method which involves the feature “only preferential codons with high frequency of use are selected and a GC content of not less than 60% is achieved” can be established as a general rule for preparing proteins with high expression level, and has examined the problem in order to obtain chemically synthesized genes for proteins capable of high-level expression in eukaryotes. The inventor has also addressed the problem whether or not a synthetic gene for the target protein can be efficiently expressed in cells derived from eukaryotes, without considering recognition sites of transcription factors, palindrome structures in nucleic acid sequences, etc. by designing a target protein gene so that only preferential codons with high frequency of use are selected and a GC content of not less than 60% is achieved, and thus investigated the problem by comparing with protein expression using wild-type protein genes. In order to solve the foregoing problem, the inventor chemically synthesized target protein genes by designing a target protein gene so that only preferential codons for 20 amino acids with high frequency of use are selected from the codon usage frequency table (Table 1) in human cells and a GC content of not less than 60% is achieved. Evaluation of the codon-optimize method was performed by using the target protein genes chemically synthesized, expressing the genes in cells and comparing the expression to that using wild-type gene. The target protein genes were evaluated by determining luminescence activity using the model genes of photoproteins (aequorin and clytin II) and various photoenzymes (luciferases), which have lower homology in the primary structure and show different protein structures in high order structure. The results of the evaluation reveal that a gene synthesis method which involves selection of preferred codons with high frequency of use and a GC content over 60% is extremely effective. The present invention includes the following features. (1) A method of designing an optimized gene, which comprises altering a nucleotide sequence of a target protein gene, so that only a codon with high frequency of use in human cells is selected and a GC content of not less than 60% is achieved. (2) The method according to (1) above, wherein the target protein gene is a gene encoding a functional protein or a structural protein. (3) The method according to (2) above, wherein the target protein gene is a gene encoding a photoprotein or a photoenzyme. (4) The method according to (3) above, wherein the photoprotein or photoenzyme is selected from aequorin, clytin II, Gaussia luciferase, the mutated catalytic protein of Oplophorus (shrimp) luciferase, North American firefly luciferase, Japanese firefly Luciola cruciate luciferase or Renilla luciferase. (5) The optimized gene synthesized by the method according to (1) or (2) above. (6) The optimized gene synthesized by the method according to (3) above, encoding a photoprotein or a photoenzyme. (7) The optimized gene synthesized by the method according to (4) above, encoding aequorin. (8) The optimized gene synthesized by the method according to (4) above, encoding clytin II. (9) The optimized gene synthesized by the method according to (4) above, encoding Gaussia luciferase. (10) The optimized gene synthesized by the method according to (4) above, encoding the mutated catalytic protein of Oplophorus (shrimp) luciferase. (11) The optimized gene synthesized by the method according to (4) above, encoding North American firefly luciferase. (12) The optimized gene synthesized by the method according to (4) above, encoding Japanese firefly Luciola cruciate luciferase. (13) The optimized gene synthesized by the method according to (4) above, encoding Renilla luciferase. (14) An optimized gene comprising the optimized gene according to any one of (5) to (13) above fused with a polynucleotide encoding other protein. (15) A method of preparing a target protein, which comprises: preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (1) or (2) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (16) A method of producing a photoprotein or photoenzyme, which comprises: preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (3) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (17) A method of producing a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which any one of the optimized genes synthesized by the method according to (4) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (18) A method of producing a protein, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (14) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (19) The method according to any one of (15) to (18), wherein the mammalian cell is a human cell. (20) A target protein produced by the method according to (15) or (19) above. (21) A photoprotein or photoenzyme produced by the method according to (16) or (19) above. (22) A photoprotein or photoenzyme produced by the method according to (17) or (19) above. (23) A fused target protein produced by the method according to (18) or (19) above. (24) A recombinant expression vector wherein the optimized gene according to any one of (5) to (14) above is located under the control/regulation of a promoter in a mammalian cell. (25) A recombinant mammalian cell comprising the optimized gene according to any one of (5) to (14) above. (26) The recombinant mammalian cell of (25) above, wherein the mammalian cell is a human cell. (27) A method of increasing the expression level of a target protein, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (1) or (2) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (28) A method of increasing the expression level of a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (3) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (29) A method of increasing the expression level of a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which any one of the optimized genes synthesized by the method according to (4) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (30) A method of increasing the expression level of a fused target protein, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (14) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (31) A method of increasing the expression level according to any one of (27) to (30) above, wherein the mammalian cell is a human cell. (32) A method of increasing the detection sensitivity of a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized by the method according to (3) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (33) A method of increasing the detection sensitivity of a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which any one of the optimized genes synthesized by the method according to (4) above is used to be placed under the control/regulation of a promoter in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. (34) The method of increasing the detection sensitivity according to (32) or (33) above, wherein the mammalian cell is a human cell. (35) A method of determining a luminescence activity, which comprises contacting the photoprotein or photoenzyme according to (21) or (22) above, or the fused target protein according to (23) above, with luciferin or a luciferin analogue to determine an amount of light generated. (36) Use of the optimized gene according to any one of (5) to (14) above, the photoprotein or photoenzyme according to (21) or (22) above, or the fused target protein according to (23) above, to enhance the luminescence intensity of luciferin or a luciferin analogue. (37) A method of assaying the activity of a sequence associated with promoter control, which comprises using as a reporter gene the optimized gene according to any one of (5) to (14) above. (38) A method of determining changes in intracellular calcium concentration, which comprises expressing the optimized gene according to any one of (5) to (14) above in a mammalian cell to form a photoprotein, a photoenzyme or a fused target protein, contacting the mammalian cell with luciferin or a luciferin analogue, and determining an amount of light generated. (39) The method of determining changes in intracellular calcium concentration according to (38) above, wherein the mammalian cell is a human cell. (40) A kit comprising at least one of the optimized gene according to any one of (5) to (14), the recombinant expression vector according to (24) above and the recombinant mammalian cell according to (25) or (26) above, and further comprising luciferin and/or a luciferin analogue. The present invention provides synthetic genes prepared by designing a target protein gene, so that only preferential codons with high frequency of use in human cells are selected and the GC content of not less than 60% is achieved, as well as a method of designing the synthetic genes, thereby expressing the target protein at a high level. The present invention provides synthetic genes for photoproteins or photoenzymes prepared by designing a gene for a photoprotein or photoenzyme, so that only preferential codons with high frequency of use in human cells are selected and the GC content of not less than 60% is achieved, as well as the method of designing the synthetic gene, resulting in higher expression than wild-type genes to improve the detection sensitivity. In a specific embodiment of the present invention, photoproteins (aequorin, clytin II) and photoenzymes (Gaussia luciferase, the mutated 19 kDa protein of Oplophorus gracilirostris luciferase, firefly luciferases (from North American firefly, Japanese firefly Luciola cruciate), Renilla luciferase) are used for an evaluation system, which results are shown. This luminescence system is chosen as an evaluation system because the activity is assayed by luminescence to allow high sensitivity and it is simpler than other evaluation systems. By using the method of the present invention, an increased expression level of proteins has been confirmed in all of the photoproteins or photoenzymes that have low homology in amino acid sequences and have different high-order structure in proteins. Accordingly, the method of the present invention can be applied to general protein expression, but is not limited only to photoproteins or photoenzymes. In an embodiment, the present invention relates to a method of designing optimized genes, which comprises altering a nucleotide sequence of a target protein gene so that only a codon with high frequency of use in human cells is selected and a GC content of not less than 60% is achieved. In an embodiment of the present invention, the term “only a codon with high frequency of use in human cells is selected and a GC content of not less than 60% of total cells is achieved” is intended to mean that, based on Table 1, codon bases (cytosine, guanine, thymidine and adenine) are altered or mutated and a GC content of not less than 60% is achieved. In another embodiment, the GC content can be varied depending on kind of a target protein by appropriately selecting the content from 60% or more. The optimized gene of the present invention refers to cDNA in general, including genomic DNA. The optimized gene of the present invention can be chemically synthesized by standard techniques in the art of genetic engineering. Alterations or mutations of nucleotide sequences may be performed by novel nucleic acid synthesis, PCR, site-specific mutagenesis using primers properly designed, or methods known to those skilled in the art of genetic engineering. The terminus of the optimized gene of the present invention may be designed to have an appropriate restriction enzyme sequence(s), or a restriction enzyme sequence(s) may also be used for easier cloning to plasmid vectors, etc. In an embodiment of the present invention, the target protein gene is intended to mean a polynucleotide encoding a protein to be expressed. The target protein gene is appropriately chosen from, but not particularly limited to, polynucleotides encoding desired proteins, and provided for use. The polynucleotide encoding the target protein gene can be chemically synthesized by known techniques based on its nucleotide sequence information. In an embodiment of the present invention, the target protein gene includes a functional protein and a structural protein. As used herein, the functional protein refers to a protein having functions such as enzymes, antibodies, receptors, hormones, and the like. The functional protein further includes photoproteins or photoenzymes. The structural protein refers to cell constituent proteins including collagen, actin, etc. In a preferred embodiment of the present invention, the target protein gene is intended to mean a polynucleotide encoding a photoprotein or photoenzyme. The photoprotein or photoenzyme is intended to mean wild-type, recombinant or mutant proteins having a luminescence activity, which use a luminescence substrate (luciferin) including its analogue. Wild-type protein genes can be obtained by chemical synthesis using known techniques in the art of genetic engineering, or may also be chemically synthesized when their amino acid sequences are known. More preferably, the target protein of the present invention includes (i) aequorin, clytin II, clytin I, mitrocomin, obelin, mnemiopsin (Mnemiopsis photoprotein) and berovin, which are calcium-binding photoproteins derived from the coelenterata wherein coelenterazine serves as a luminophore, (ii) Gaussia luciferase, Metridia luciferase, mutated catalytic protein of Oplophorus luciferase, Renilla luciferase and Pleuromamma luciferase, in which coelenterazine serves as a luminescence substrate, (iii) a luciferase derived from beetles (North American firefly luciferase, Japanese firefly Luciola cruciate luciferase, Japanese firefly Luciola lateralis luciferase, click beetle luciferase, etc.), in which a firefly luciferin (beetle luciferin) serves as a luminescence substrate, (iv) Vargula luciferase in which Vargula luciferin serves as a luminescence substrate, (v) dinoflagellate luciferase in which dinoflagellate luciferin serves as a luminescence substrate; and the like. The optimized gene of the present invention may also be a fused type of the optimized gene encoding the target protein with a polynucleotide encoding other protein. The fused protein bearing the control sequence capable of protein expression and the fused sequence is thus expressed in mammalian cells. Other protein may be either an N-terminal fusion protein or a C-terminal fusion protein. The polynucleotide encoding other protein which is fused with the optimized gene of the present invention specifically includes, but not particularly limited to, secretory or other control sequences, label sequences (e.g., 6-his tag), target-directed sequences, etc. Proteins other than those include green fluorescent proteins, etc. which act as reporters or other markers. An embodiment of the present invention is a method of producing a target protein, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized is used to be placed under the control/regulation of a promoter operable in a mammalian cell, introducing the recombinant expression vector into mammalian cells to produce recombinant mammalian cells, and, culturing the recombinant mammalian cells to express the optimized gene. In another embodiment of the method of producing the target protein of the invention, the target protein may be a photoprotein or a photoenzyme. The photoenzyme includes wild-type, recombinant or mutant enzymes having a luminescence activity, which use a wild-type luminescence substrate (luciferin) or its analogue (luciferin analogue). More preferably, the target protein of the present invention includes (i) aequorin, clytin II, clytin I, mitrocomin, obelin, mnemiopsin (Mnemiopsis photoprotein) and berovin, which are calcium-binding photoproteins derived from the coelenterata wherein coelenterazine serves as a luminophore, (ii) Gaussia luciferase, Metridia luciferase, mutated catalytic protein of Oplophorus luciferase, Renilla luciferase and Pleuromamma luciferase, in which coelenterazine serves as a luminescence substrate, (iii) a luciferase derived from beetles (North American firefly luciferase, Japanese firefly (Luciola cruciate) luciferase, Japanese firefly (Luciola lateralis) luciferase, click beetle luciferase, etc.), in which a firefly luciferin (beetle luciferin) serves as a luminescence substrate, (iv) Vargula luciferase in which Vargula luciferin serves as a luminescence substrate, (v) dinoflagellate luciferase in which dinoflagellate luciferin serves as a luminescence substrate; and the like. In a further embodiment of the method of producing the target protein of the invention, the target protein may be a fused target protein. The fused target protein is a fusion protein of the target protein (e.g., a photoenzyme, etc.) with other protein (e.g., a tag, a reporter, a marker, etc.). Other protein may be located either at the N-terminus or at the C-terminus. The expression vector of the present invention may be any vector available for genetic engineering, and plasmid vectors, viral vectors, cosmid vectors, bacterial artificial chromosomes (BAC), yeast artificial chromosomes (YAC) or other non-plasmid vectors. The expression vector of the present invention is an expression vector for mammalian cells, which contains a promoter operable in mammalian cells and further contains a replication origin, a transcription initiation site, a protein coding site, a polyadenylation site, a transcription termination site, etc. The expression vector of the present invention also contains one or more antibiotic-resistant markers for selection. The promoter operable in mammalian cells includes, for example, cytomegalovirus (CMV) promoter, thymidine kinase (TK) promoter of herpes simplex virus (HSV), SV40 promoter, etc. The protein coding site in the expression vector of the present invention may also contain a signal peptide or a leader sequence for extracellular secretion of the target protein. A further embodiment of the present invention provides an expression vector suitable for expressing the optimized gene of the present invention. That is, the expression vector is a recombinant expression vector comprising the optimized gene of the present invention. The recombinant expression vector of the present invention is placed under the control/regulation of the promoter operable in mammalian cells. The host cell in the present invention may be mammalian cells and includes cells derived from mammalians, for example, CHO cells, NSO cells, BHK cells, HT1080 cells, COS cells, HEK293 cells, HeLa cells, MDCK cells, HepG2 cells, MIN6 cells, INS-E1 cells, and iPS cells, etc. More preferably, the mammalian cells of the invention are human cells, namely, cells that can be isolated from humans. The expression vector of the present invention can be introduced into mammalian cells by techniques known in the art of genetic engineering, which include, for example, the calcium phosphate method, electroporation, microinjection, the DEAE-dextran method, a method using liposome, lipofection using cationic lipids, etc. Where the vector is cyclic, the vector can be linearized by known techniques to introduce into cells. A further embodiment of the present invention provides mammalian cells suitable for expressing the optimized gene of the present invention. That is, the cells are mammalian cells containing the optimized gene of the present invention. The recombinant mammalian cells of the present invention are preferably human cells. In an embodiment of the method of producing the target protein of the present invention, incubation of the recombinant mammalian cells, expression of the target protein and purification of the target protein from the culture can be implemented by those skilled in the art using techniques known in the art of genetic engineering (e.g., Sambrook et al. “Molecular Cloning—A Laboratory Manual, second edition 1989”). A still further embodiment of the present invention provides the target protein, photoprotein, photoenzyme or fused target protein, which is produced by expressing the optimized gene of the present invention. The target protein, photoenzyme or fused target protein of the present invention is obtained by the recombinant mammalian cells with an enhanced expression efficiency. In particular, the photoprotein or photoenzyme has an effect of increasing the detection sensitivity because of an increased level of protein expression. Accordingly, the target protein, photoprotein, photoenzyme or fused target protein of the present invention has an unexpected effect of markedly increased expression level, as compared to the target protein, photoenzyme or fusion protein obtained by a production method using conventional wild-type gene sequences. An embodiment of the present invention is a method of increasing the expression level of a target protein, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized is used to be placed under the control/regulation of a promoter operable in mammalian cells, introducing the recombinant expression vector into mammalian cells to produce recombinant mammalian cells, and culturing the recombinant mammalian cells to express the optimized gene. In a further embodiment of the method of increasing the expression level of a target protein of the present invention, the target protein may be a photoprotein or photoenzyme or a fusion protein in which the photoprotein or photoenzyme is fused with other protein (e.g., a tag, a reporter, a marker, etc.). In general, recognition sites of transcription factors in mammalians often have a highly AT-rich sequence; when there is the AT-rich sequence in the sequence of a target protein gene, it is suggested that transcription factors will bind to the sequence to cause reduction in its transcription efficiency. Likewise, an increase in the GC content will result in rare presence of the polyA addition sequence AATAAA. The present invention provides an improved efficiency of expression because the GC content of not less than 60% reduces unwanted transcription factor-like binding sequences to make the expression of the optimized gene easier. An embodiment of the present invention is a method of increasing the detection sensitivity of a photoprotein or photoenzyme, which comprises preparing a recombinant expression vector, in which the optimized gene synthesized is used to be placed under the control/regulation of a promoter operable in a mammalian cell, introducing the recombinant expression vector into a mammalian cell to produce a recombinant mammalian cell, and, culturing the recombinant mammalian cell to express the optimized gene. In a further embodiment of the method of increasing the expression level of the target protein of the present invention, the protein may be a fusion protein in which the target protein (e.g., the photoprotein or photoenzyme, etc.) is fused with other protein (e.g., a tag, a reporter, a marker, etc.). The present invention provides an increased detection sensitivity of photoenzymes because the expression level of the protein is increased due to the improved transcription efficiency of the gene and improved stability of mRNA. An embodiment of the present invention is a method of assaying a luminescence activity, which comprises contacting a photoprotein, photoenzyme or fused target protein for the optimized gene of the present invention with wild-type luciferin or a luciferin analogue, and determining an amount of light generated. The amount of light generated can be determined by any known methods. An embodiment of the present invention is use of the optimized gene of the present invention, the photoprotein or photoenzyme of the present invention, or the fused target protein of the present invention, to enhance the luminescence intensity of luciferin or a luciferin analogue. Another embodiment of the present invention includes use of the optimized gene of the present invention as a reporter gene. An embodiment of the present invention is a method of assaying the activity of a sequence associated with promoter control, in which the optimized gene of the present invention is used as a reporter gene. Specifically, the activity of the target promoter or other expression control sequence is assayed by fusing the optimized gene of the present invention with a target promoter or other expression control sequence (e.g., an enhancer) to construct a recombinant expression vector, introducing the vector into mammalian cells and detecting luminescence in the presence of luciferin or luciferin analogues. An embodiment of the present invention is a method of determining changes in intracellular calcium concentration, which comprises expressing the optimized gene of the present invention in a mammalian cell to form a photoprotein, a photoenzyme or a fused target protein, contacting the mammalian cell with luciferin or a luciferin analogue, and determining an amount of light generated. A further embodiment of the present invention can be used as a method of determining the capability of a compound to activate, block, inhibit, or antagonize a receptor, such as G-protein coupled receptor or ion channel that, when activated, mediates the changes of intracellular calcium ions. For example, mammalian cells genetically engineered to express a receptor for regulating intracellular calcium are incubated with a test compound, and luciferin or a luciferin analogue is added thereto to assay the intensity of luminescence with a standard luminometer. As used herein, the intensity of luminescence is an indicator of the level of intracellular calcium that is released. The results of the luminescence intensity can be used to directly locate a receptor agonist, a receptor antagonist, etc. An embodiment of the present invention is a kit comprising at least one of the optimized gene of the present invention, the recombinant expression vector of the present invention and the recombinant mammalian cell of the present invention, and further comprising luciferin and/or a luciferin analogue. The kit of the present invention optionally further includes the photoprotein, photoenzyme or fused target protein of the present invention. The kit of the present invention can be prepared with conventional materials by conventional methods. The kit of the present invention may further contain, e.g., sample tubes, plates, instructions for the kit user, solutions, buffers, reagents, and samples suitable for standardization or control samples. The kit of the present invention may also be used in a variety of methods including measurements using reporter genes, detection markers using luminescence, etc. Regardless of their purposes, all of the documents and publications described in the specification are incorporated herein by reference, each in its entirety. Furthermore, the specification incorporates by reference disclosure in the claims, specification, abstract and drawings of Japanese Patent Application No. 2014-185629 (filed on Sep. 11, 2014), based on which the priority of the present application is claimed for. The SEQ ID Nos. in the sequence list of the specification represent the following sequences, respectively. [SEQ ID NO: 1] represents the nucleotide sequence of the wild-type aequorin gene. The GenBank Accession No. is L29571. [SEQ ID NO: 2] represents the nucleotide sequence of the humanized aequorin gene. [SEQ ID NO: 3] represents the nucleotide sequence of the optimized aequorin gene. [SEQ ID NO: 4] represents the nucleotide sequence of the wild-type clytin II gene. The GenBank Accession No. is AB360785. [SEQ ID NO: 5] represents the nucleotide sequence of the optimized clytin II gene. The GenBank Accession No. is HJ241347. [SEQ ID NO: 6] represents the nucleotide sequence of the wild-type Gaussia luciferase gene. The GenBank Accession No. is AY015993. [SEQ ID NO: 7] represents the nucleotide sequence of the humanized Gaussia luciferase gene. [SEQ ID NO: 8] represents the nucleotide sequence of the optimized Gaussia luciferase gene. [SEQ ID NO: 9] represents the nucleotide sequence of the humanized gene for the mutated catalytic protein of Oplophorus gracilirostris luciferase. The GenBank Accession No. is JQ437370. [SEQ ID NO: 10] represents the nucleotide sequence of the optimized gene for the mutated catalytic protein of Oplophorus gracilirostris luciferase. The GenBank Accession No. is AB823628. [SEQ ID NO: 11] represents the nucleotide sequence of the wild-type gene for North American firefly (Photinus pyralis) luciferase. The GenBank Accession No. is M15077. [SEQ ID NO: 12] represents the nucleotide sequence of the humanized North American firefly (Photinus pyralis) luciferase gene. The GenBank Accession No. is AY738225. [SEQ ID NO: 13] represents the nucleotide sequence of the optimized North American firefly (Photinus pyralis) luciferase gene. [SEQ ID NO: 14] represents the nucleotide sequence of the wild-type Japanese firefly (Luciola cruciate) luciferase gene. The GenBank Accession No. is M26194. [SEQ ID NO: 15] represents the nucleotide sequence of the humanized Japanese firefly (Luciola cruciate) luciferase gene. [SEQ ID NO: 16] represents the nucleotide sequence of the optimized Japanese firefly (Luciola cruciate) luciferase gene. [SEQ ID NO: 17] represents the nucleotide sequence of the wild-type Renilla luciferase gene. The GenBank Accession No. is M63501. [SEQ ID NO: 18] represents the nucleotide sequence of the humanized Renilla luciferase gene. The GenBank Accession No. is AY738226. [SEQ ID NO: 19] represents the nucleotide sequence of the optimized Renilla luciferase gene. [SEQ ID NO: 20] represents the nucleotide sequence of the DNA fragment (HindIII sequence—Kozak sequence—ATG sequence) used in EXAMPLE 2. [SEQ ID NO: 21] represents the nucleotide sequence of the DNA fragment (BamHI sequence—Kozak sequence) used in EXAMPLE 2. [SEQ ID NO: 22] represents the nucleotide sequence of the DNA fragment (HindIII sequence—Kozak sequence) used in EXAMPLE 2. [SEQ ID NO: 23] represents the nucleotide sequence of the DNA fragment (HindIII sequence—Kozak sequence) used in EXAMPLE 2. The present invention is specifically described with reference to EXAMPLES below but not limited thereto. Novel optimized genes (opAQ, opCLII, nanoKAZ, opGLuc, opPyLuc, opLcLuc, opRLuc) were chemically synthesized to design, without altering the wild-type amino acid sequences, so that only codons with high frequency of use in human cells are selected and its GC content became over 60% in photoprotein genes (aequorin: AQ, clytin II: CLII) and luciferase genes (Gaussia luciferase: GLuc, two firefly luciferases: PyLuc and LcLuc, mutated 19 kDa protein of Oplophorus gracilirostris luciferase: KAZ, Renilla luciferase: RLuc) as model proteins shown in Table 2; the synthesis was outsourced (to Operon Biotechnologies Inc.). Wild-type genes (wAQ, wCLII, wGLuc, wPyLuc and wLcLuc) and humanized genes (hAQ, nanoLuc, hGLuc, hPyLuc, hLcLuc and hRL), if necessary, and control genes for expression and activity comparisons were prepared by chemical synthesis or PCR. The frequencies of codons for photoproteins and photoenzymes in wild-type, humanized and optimized protein genes are summarized in Table 2. It was found that the amino acid compositions of the optimized genes of the invention used for evaluation are clearly different from those of wild-type and humanized genes. The GC contents of wild-type, humanized and optimized genes encoding photoproteins and photoenzymes were compared and summarized in Table 3. As a result, the GC contents of the wild-type genes showed approximately 36.4% to 44.8% in all of the photoproteins and photoenzymes; the GC contents of the humanized genes showed 44.9% to 58.8% in all of the photoproteins and photoenzymes, whereas the GC contents of the optimized genes showed over 60% in all of the photoproteins and photoenzymes. The HindIII-XbaI fragment of wild-type (SEQ ID NO: 1), humanized (SEQ ID NO: 2) or optimized (SEQ ID NO: 3) gene for aequorin with the restriction enzyme HindIII sequence-Kozak sequence-ATG sequence (AAGCTTGGTACCACCATG: SEQ ID NO: 20) at the 5′ end and with the restriction enzyme site XbaI sequence (TCTAGA) at the 3′ end was prepared and inserted into the restriction enzyme HindIII-XbaI site of animal cultured cell expression vector pcDNA3 (manufactured by Invitrogen) to construct pcDNA3-wAQ, pcDNA3-hAQ and pcDNA3-opAQ, respectively. The HindIII-XbaI fragment of wild-type (SEQ ID NO: 4) or optimized (SEQ ID NO: 5) clytin II gene with the restriction enzyme HindIII sequence-Kozak sequence-ATG sequence (AAGCTTGGTACCACCATG: SEQ ID NO: 20) at the 5′ end and with the restriction enzyme XbaI sequence (TCTAGA) at the 3′ end was prepared and inserted into the restriction enzyme HindIII-XbaI site of animal cultured cell expression vector pcDNA3 (manufactured by Invitrogen) to construct pcDNA3-wCLII and pcDNA3-opCLII, respectively. The BamHI-XbaI fragment of wild-type (SEQ ID NO: 6), humanized (SEQ ID NO: 7) or optimized (SEQ ID NO: 8) gene for Gaussia luciferase with the restriction enzyme BamHI sequence-Kozak sequence (GGATCCAACCGCC: SEQ ID NO: 21) at the 5′ end and with the restriction enzyme XbaI sequence (TCTAGA) at the 3′ end was prepared and inserted into the restriction enzyme BamHI-XbaI site of animal cultured cell expression vector pcDNA3 (manufactured by Invitrogen) to construct pcDNA3-wGluc and pcDNA3-opGLuc, respectively. (4) Mutated Catalytic Protein of Oplophorus gracilirostris Luciferase The fragment with restriction enzymes EcoRI and XbaI at the 5′ and 3′ ends of humanized (SEQ ID NO: 9) or optimized (SEQ ID NO: 10) gene for the mutated catalytic protein of Oplophorus gracilirostris luciferase was prepared and inserted into the restriction enzyme EcoRI-XbaI site of animal cultured cell secretion expression vector pcDNA3-GLsp (Biochem. Biopphys. Res. Commun. (2013) 437: 23-28) bearing the secretion signal sequence of Gaussia luciferase to construct pcDNA3-GLsp-nanoLuc and pcDNA3-GLsp-dnKAZ, respectively. (5) North American Firefly (Photinus pyralis) Luciferase The HindIII-XbaI fragments of the wild-type (SEQ ID NO: 11) and optimized (SEQ ID NO: 13) North American firefly (Photinus pyralis) luciferase genes with the restriction enzyme HindIII sequence-Kozak sequence (AAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACC: SEQ ID NO: 22) at the 5′ end and the restriction enzyme XbaI sequence (TCTAGA) at the 3′ end were prepared and replaced for the North American firefly (Photinus pyralis) luciferase gene, which was inserted into the restriction enzyme HindIII-XbaI site of the humanized (SEQ ID NO: 12) North American firefly (Photinus pyralis) luciferase expression vector pGL4.13[luc2/sv40] (manufactured by Promega Inc.) to construct pJN-wPyLuc-sv and pJN-opPyLuc-sv, respectively. (6) Japanese Firefly (Luciola cruciate) Luciferase The HindIII-XbaI fragments of the wild-type (SEQ ID NO: 14), humanized (SEQ ID NO: 15) and optimized (SEQ ID NO: 16) Japanese firefly (Luciola cruciate) luciferase genes with the restriction enzyme HindIII sequence-Kozak sequence (AAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACC, SEQ ID NO: 22) at the 5′ end and the restriction enzyme XbaI sequence (TCTAGA) at the 3′ end were prepared and replaced for the North American firefly (Photinus pyralis) luciferase gene inserted into the restriction enzyme HindIII-XbaI site of the humanized (SEQ ID NO: 12) North American firefly (Photinus pyralis) luciferase expression vector pGL4.13[luc2/sv40] (manufactured by Promega Inc.) to construct pJN-wLcLucsv, pJN-hLcLuc-sv and pJN-opLcLuc-sv, respectively. (7) Renilla luciferase The HindIII-XbaI fragment of wild-type (SEQ ID NO: 17), humanized (SEQ ID NO: 18) or optimized (SEQ ID NO: 19) Renilla luciferase gene with the restriction enzyme site HindIII-Kozak sequence (AAGCTTGGTACCACC: SEQ ID NO: 22) at the 5′ end and with the restriction enzyme site XbaI sequence (TCTAGA) at the 3′ end was prepared and inserted into the restriction enzyme HindIII-XbaI site of animal cultured cell expression vector pcDNA3 (manufactured by Invitrogen) to construct pcDNA3-RL, pcDNA3-hRL and pcDNA3-opRL. (1) Purification of expression plasmid The following experiment was performed using the recombinant plasmid obtained in EXAMPLE 2. The recombinant plasmid was purified from Escherichia coli JM83 or DH5a using a plasmid purification kit (manufactured by QIAGEN), dissolved in sterile water, which was used for transfection. Animal cultured cell line CHO-K1 cells were cultured in Ham's F-12 medium (manufactured by Wako Pure Chemicals) (hereinafter sometimes referred to as Ham's-F12) supplemented with 10% (v/v) fetal bovine serum (manufactured by HyClone or Biowest). CHO-K1 cells were seeded in a 6-well plate with 1×105 cells/well/2 mL medium (n=3), and cultured in an incubator at 37° C. in 5% (v/v) CO2. After 24 hours, the purified recombinant plasmid was transfected to CHO-K1 cells using a FuGene HD (manufactured by Promega) transfection kit. Specifically, 1 μg of the recombinant plasmid and 3 μL of FuGene HD were added to 100 μL of serum-free Ham's-F12 medium, which was allowed to stand at room temperature for 15 minutes. Where an internal standard vector is necessary, 0.1 μg of pGL4.13[luc2/sv40] (manufactured by Promega) was used. A solution of DNA-FuGene complex was added to cells in 6 wells. After incubation for 24 hours, luminescence activity was determined using cell extracts. (ii) Transfection of Expression Plasmid for Luciferases Including Gaussia Luciferase, Mutated Catalytic Protein of Oplophorus gracilirostris Luciferase, Firefly Luciferase and Renilla Luciferase: CHO-K1 cells were seeded in a 24-well plate with 1×105 cells/well/0.5 mL medium (n=4), and cultured in an incubator at 37° C. in 5% (v/v) CO2. After 24 hours, the purified recombinant plasmid was transfected to CHO-K1 cells using a FuGene HD (manufactured by Promega) transfection kit. Specifically, 0.5 μg of the recombinant plasmid and 1.5 μL of FuGene HD were added to 25 μL of serum-free Ham's-F12 medium, which was allowed to stand at room temperature for 15 minutes. Where an internal standard vector is necessary, 0.05 μg of pGL4.13[luc2/sv40] (manufactured by Promega) or pGL4.75 [hRLuc/CMV] (manufactured by Promega) was added. A solution of DNA-FuGene complex was added to cells in 24 wells. After incubation for 24 hours, luminescence activity was determined using the culture medium or cell extracts. The cells expressed apophotoprotein of the photoprotein obtained in EXAMPLE 3 was washed with 3 mL of PBS (manufactured by Wako Pure Chemicals), and 1 mL of PBS was added thereto. The cells were collected with a scraper. After 250 μL of 30 mM Tris-HCl (pH 7.6)-10 mM EDTA was added to 250 μL of the cell collected, the cells were disrupted on ice with an ultrasonic cell disruptor for 5 seconds. To the cell lysate were added 1 μg of coelenterazine (manufactured by JNC Corp.) and 1 μL, of 2-mercaptoethanol (manufactured by Wako Pure Chemicals). The mixture was allowed to stand at 4° C. for over 3 hours to regenerate photoprotein from apophotoprotein. The regenerated solution (10 μL) was injected with 100 μL of 50 mM CaCl2 dissolved in 50 mM Tris-HCl (pH 7.6) to start the luminescence reaction. Luminescence activity was determined using a luminometer (Berthold Technologies: LB960) in 0.1 second intervals for 5 seconds, and expressed as the mean values (n=3) of the maximum intensity of luminescence (Imax). Luminescence activity of secreted Gaussia luciferase from cells obtained in EXAMPLE 3 was determined using the culture medium and cell extracts. Cell extracts were prepared by washing the expressed cells 3 times with 0.5 mL of PBS, then adding 100 μL of Passive lysis buffer (manufactured by Promega) thereto and shaking the mixture at room temperature for 15 minutes. After diluting to 100-fold with Passive lysis buffer for determination of luminescence activity in the culture medium or cell extracts, 1 μL was added to 50 μL of PBS containing coelenterazine (0.25 μg) to start the luminescence reaction. Luminescence activity was determined using a luminometer (manufactured by Atto: AB2200) in 0.1 second intervals for 5 seconds, and expressed as the mean values (n=4) of the maximum intensity of luminescence (Imax). (3) Determination of Luminescence Activity of Mutated Catalytic Protein of Secretory Oplophorus gracilirostris Luciferase The culture medium (1 μL) of the mutated catalytic protein of Oplophorus gracilirostris luciferase obtained in EXAMPLE 3 was added to 50 μl of PBS containing coelenterazine (0.25 μg) to start the luminescence reaction. Luminescence activity was determined using a luminometer (manufactured by Atto: AB2200) in 0.1 second intervals for 5 seconds in the presence of a 1/100 attenuation filter, and expressed as the mean values (n=4) of the maximum intensity of luminescence (Imax). (4) Determination of Luminescence Activity of North American Firefly (Photinus pyralis) luciferase and Japanese firefly (Luciola cruciate) luciferase Cell extracts from firefly luciferase expressed cells obtained in EXAMPLE 3 were prepared by washing the expressed cells 3 times with 1 mL of PBS, then adding thereto 100 μL of Passive lysis buffer (manufactured by Promega) and shaking the mixture at room temperature for 15 minutes. The resulting cell extract (10 μL) was added to 50 μL of firefly luciferase assay solution (manufactured by Promega) to start the luminescence reaction. Luminescence activity was measured using a luminometer (manufactured by Atto: AB2200) in 0.1 second intervals for 10 seconds in the presence of a 1/100 attenuation filter, and expressed as the mean values (n=4) of the integrated intensity of luminescence (Int.) for 10 seconds. Cell extracts from Renilla luciferase expressed cells obtained in EXAMPLE 3 were prepared by washing the expressed cells 3 times with 1 mL of PBS, then adding 100 μL of Passive lysis buffer (manufactured by Promega) thereto and shaking the mixture at room temperature for 15 minutes. The resulting cell extract (10 μL) was added to 50 μL of PBS containing coelenterazine (0.25 μg) to start the luminescence reaction. Luminescence activity was measured using a luminometer (manufactured by Atto: AB2200) in 0.1 second intervals for 10 seconds in the presence of a 1/10 attenuation filter, and expressed as the mean values (n=4) of the integrated intensity of luminescence for 10 seconds. The activity of aequorin expressed in cells was determined by the assay method described in EXAMPLE 4 (Table 4). As a result, the luminescence activities of the humanized gene and the optimized gene were 2.7- and 7.9-fold higher, respectively, than that of the wild-type gene. The activity of clytin II expressed in cells was determined by the assay method described in EXAMPLE 4 (Table 5). As a result, the luminescence activity of the optimized gene was 11.8-fold higher than that of the wild-type gene. The activity of Gaussia luciferase expressed in cells was determined by the assay method described in EXAMPLE 4 (Table 6). As a result, the optimized gene showed 12.6- and 10.8-fold higher activity in the culture medium and in the cells, respectively, than the activity of the wild-type gene in the culture medium and in the cytoplasm. (4) Secretory Expression of the Mutated Catalytic Protein of Oplophorus gracilirostris Luciferase The activity of the mutated catalytic protein of Oplophorus gracilirostris luciferase secreted in the culture medium was determined by the assay method described in EXAMPLE 4 (Table 7). As a result, the humanized gene showed the activity of 89% compared to the optimized gene, which was almost the same activity. (5) Expression of North American Firefly (Photinus pyralis) Luciferase The activity of North American firefly (Photinus pyralis) luciferase in cells was determined by the assay method described in EXAMPLE 4 (Table 8). As a result, the activities of the humanized gene and the optimized gene were 5.2- and 3.4-fold higher, respectively, than that of the wild-type gene. (6) Expression of Japanese Firefly (Luciola cruciate) Luciferase The activity of Japanese firefly (Luciola cruciate) luciferase in cells was determined by the assay method described in EXAMPLE 4 (Table 9). As a result, the activities of the humanized gene and the optimized gene were 320- and 402-fold higher, respectively, than that of the wild-type gene. The activity of Renilla luciferase in cells was determined by the assay method described in EXAMPLE 4 (Table 10). As a result, the activities of the humanized gene and the optimized gene were 25.4- and 47.4-fold higher, respectively, than that of the wild-type gene. |
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