# Patent

## Title
Light-switchable gene expression system

## Abstract

Provided is a light-switchable gene expression system, comprising: a) a recombinant light-switchable transcription factor-encoding gene, said recombinant light-switchable transcription factor comprising a first polypeptide as the DNA bonding domain, a second polypeptide as the photosensitive domain, and a third polypeptide as the transcription regulatory domain; b) a target transcription unit comprising at least one reaction element recognized and bound by the first polypeptide, a promoter regulated by the third polypeptide and a nucleotide sequence to be transcribed. Also provided is an eukaryotic expression vector comprising said light-switchable gene expression system, and a method for regulating gene expression in a host cell by using the light-switchable gene expression system. Also provided is a reagent kit containing different elements of the light-switchable gene expression system. The light-switchable gene expression system has a quick, effective and powerful induction with little or no toxicity. It is safer than other inducers, and can spatiotemporally control gene expression.

## Background
CROSS REFERENCE TO RELATED PATENT APPLICATION
The present application is the US national stage of PCT/CN2012/071679 filed on Feb. 27, 2012, which claims the priority of the Chinese patent application No. 201110048142.1 filed on Feb. 28, 2011, which application is incorporated herein by reference.
FIELD OF INVENTION
The invention relates to the fields of genetic engineering and synthetic biology, especially, relates to gene expression, and more especially, relates to an inducible gene expression system based on light-switchable proteins and a method of regulating the gene expression in host cells by using this expression system.
BACKGROUND OF INVENTION
In the field of genetic engineering, precise controlling gene expression provides a valuable tool for studying and manipulating development and other physiological processes. Gene expression is a complex biological progress in which many specific protein-protein interactions are involved. The first step is the transcription of DNA into RNA, which needs the delivery of transcription factors to the promoter of gene. Transcription factor, also known as a sequence-specific DNA binding protein, is a kind of protein or protein complex which is capable of binding specific DNA sequence of promoter to initiate or prevent the transcription of downstream gene into RNA by recognizing/binding to the promoter. There are two kinds of transcription factors, termed as transcriptional activator and transcriptional repressor. In general, a transcription factor contains at least a DNA binding domain which can recruit cofactor(s), also named as co-activators, to bind proper locus of the promoter together so as to initiate the gene transcription. Besides, a transcription factor also contains a transcriptional activation domain or a transcriptional repression domain; the transcriptional activation domain may be in a certain distance from the DNA binding domain. Conventional transgenic method for heterologous gene expression usually uses universal promoter or cell type-specific promoter. The construct with a target gene and a corresponding promoter is transfected into host cells or integrated into the genome, and the target gene is transcribed and further translated into the corresponding protein in specific cell type when binding the transcription factor to the promoter.
An alternative way to regulate heterologous gene expression in host cells is using inducible promoters, which includes two categories: 1) Chemical substance inducible promoter and gene expression systems, and 2) physical methods inducible promoter and gene expression systems. Chemical substance inducers include small molecule drugs, a typical example is antibiotics such as tetracycline [Gossen, M. and H. Bujard, Proc Natl Acad Sci USA, 1992, 89 (12): 5547-5551—Gossen, M., etc., Science, 1995, 268 (5218): 1766-1769], and streptomycin [M. etc., Nat Biotechnology, 2000, 18 (11): 1203-1208]; hormone [Wang, Y, Proc Natl Acad Sci USA, 1994. 91 (17): 8180-8184] and its analogues and other inducers such as acetaldehyde [Weber, W., etc. NAT Biotechnol, 2004, 22 (11): 1440-1444]. Physical methods inducible promoters and gene expression system include ultraviolet (UV)-regulated “cage” (Caged) technology [Keyes, W M and A A Mills, Trends Biotechnology, 2003, 21 (2): 53-55]; and far-infrared light controlled heat shock effect mediated gene expression system [Kamei, Y., etc., Nat Methods, 2009, 6 (1): 79-81].
Although many of those methods have been widely used, there exist some potential problems, such as (1) pleiotropic effect of the inducers may interfere with endogenous gene expression, which may lead to a complicated result. For example, in heavy metal ions-induced gene expression systems, heavy metal ions are not only able to induce target gene expression but also cause other heavy metal ion-induced endogenous gene expression; (2) some inducers have potential toxicity which can affect the functions of other genes, e.g., the cytotoxicity of heavy metal ions impedes their use in animals or humans; (3) Many promoter systems have a high leakage expression in the absence of inducers, thus the gene expression cannot be in a completely off state and the ratio of gene expression level before and after adding the inducers (also termed as induction ratio) is low, such as hormone-induced gene expression system [Wang, Y., and so on. Proc Natl Acad Sci USA, 1994, 91 (17): 8180-8184]. Those promoter systems are not suitable for expressing toxic genes or genes for that low expression level can cause significant biological effects; (4) Some chemical-induced gene expression systems consist of two or more proteins, such as the gene expression system based on FKBP-FRAP, and they have lower transfection efficiency than the single transcription factor [Rivem, V M, etc., Nat Med, 1996 2 (9): 1028-1032]. (5) Chemicals can temporally but not spatially regulate gene expression in specific cells and tissues. (6) Most physical methods have a strong toxicity to cells, e.g., the UV-induced cage technology may cause irreversible damage to cells, the inducible expression system based on far-infrared laser-controlled heat shock may activate endogenous gene expression, and the device is complex and expensive [Kamei, Y., etc., Nat Methods, 2009, 6 (1): 79-81].
However, light is a non-toxic inducer, which can be spatiotemporally controlled. One feasible way is introducing heterogenous light-regulated proteins (also known as photosensitive protein) into eukaryotic cells and reconstructing them to be light-regulated transcription factors which can regulate gene expression via light irradiation. These proteins are expected not to interfere with the physiological processes of eukaryotic cells, and they would not cause pleiotropic effects or non-specific effects in eukaryotic cells. However, studies on light-regulated transcription factors have been rarely reported. Shimizu-Sato et al. reported a light-switchable gene expression system in yeast cells [Shimizu-Sato S. et al, NAT Biotechnology, 2002 20 (10): 1041-1044]. U.S. Pat. No. 6,858,429 described using genetic engineering techniques to combine plant protein phytochrome (abbreviated as Phy) and Phytochrome interacting factor 3 (abbreviated as PIF3) with yeast Gal4 DNA binding domain and Gal4 transactivation domain of the yeast two-hybridization system to obtain fusion proteins Gal4-Phy and PIF3-GAD, respectively. Gal4-Phy interacts with PIF3-GAD and recruits PIF3-GAD to the target promoter to initiate gene transcription by red light illumination; while far-red light irradiation causes dissociation of the conjugate of Gal4-Phy and PIF3-GAD thus the AD domain of Gal4 cannot bind to the promoter and the transcription of target gene is terminated. This light-induced promoter system is reversible and has a high expression lever. However, the interaction of phytochrome Phy and PIF3 needs the existence of phycocyanobilin, the chromophore of PIF3, which needs to be added exogenously into yeast and mammalian cells since it does not exist in these cells. In addition, this system is based on yeast two-hybridization system in which the transcription factor consists of two proteins, and the resulting big construct is difficult to be introduced into host cells, thus limiting the wide usage of this system.
There are some other known photosensitive proteins: the photosensitive proteins using flavin as the chromophore (also called flavin-containing protein family blue light receptor), which can be divided into three groups: First is photoreceptors with light-oxygen-voltage (LOV) domain, such as phytochrome; the second is photolyase-like cryptochromes; the third is blue light using FAD (BLUF) family that is found in recent years. Phytochrome is the most common photoreceptor containing LOV domain, such as phototropin 1, white collar-1 (WC-1), white collar-2 (WC-2), photoactive yellow protein (PYP), Phy3, VVD, etc. Phytochrome is usually a membrane-coupled kinase which can autophosphorylate and alter its activity to regulate specific physiological processes upon blue light exposure. Most phytochromes have Serine/Threonine kinase domain at the C-terminal and two LOV domains with flavin at the N-terminal. With the illumination of blue light, the LOV domain and flavin bind covalently to form a cysteinyl-flavin adduct which can cause the conformation change of flavin-binding pocket and then enable the kinase domain at the C-terminal to alter the kinase activity. This process is reversible. In addition, LOV2 domain is more sensitive than LOV1. Based on the interaction of Arabidopsis FKF1 (flavin-binding, kelch repeat, f box 1) and GI (GIGANTEA) protein upon blue light irradiation, Masayuki Yazaw et al. fused FKF1 and GI to DNA binding domain of Gal4 and the transactivation domain AD of herpes simplex virus VP16 to form transcription factors Gal4-FKF1 and VP16-GI, respectively [Yazawa, M., et al., Nat Biotechnology, 2009. 27(10):941-945]. Upon blue light illumination, VP16-GI can interact with Gal4-FKF1 (specifically, the interaction happens between FKF1 and GI) which has bound to the promoter region, and initiate the transcription of target gene. The drawbacks of this system are that the large constructs containing FKF1 or GI gene are difficult to be transfected into cells, and the induction ratio is very low (the highest one is only 5-fold). Cryptochromes from Arabidopsis thaliana are the first separated blue light photosensitive plant proteins, of which some have been well studied, such as cryptochrome1 (CRY1), cryptochrome 2 (CRY2), phytochrome A (phyA) and phytochrome B (phyB). Based on the interaction of Arabidopsis CRY2 and CIB1 (CRY-interacting bHLH1) protein upon blue light illumination, researchers fused CRY2 and CIB1 to Gal4 DNA binding domain and Gal4 transactivation domain of the yeast two hybridization system to construct transcription factors Gal4-CRY2 and CIB1-GAD, respectively. CIB1-GAD interacts with Gal4-CRY2 which has bound to the promoter, and initiate the expression of target gene [Kennedy, M J. et al. Nat Methods 2010.7 (12):973-975]. Although it is unnecessary for this system to add an exogenous chromophore, it is still difficult to manipulate since the system contains two fusion proteins on the basis of the two-hybridization system. Furthermore, there is some leaky expression in the absence of light. All these drawbacks limit the wide application of this system. Difference between blue light photoreceptor proteins with BLUF domain and photo-receptor proteins with LOV domain is that no adduct is generated between BLUF and flavin after light irradiation, but it will lead to 10 nm red-shift absorbance due to the conformation change of chromophore. The most well studied BLUF domain containing photoreceptor is AppA, which is a repressor of anti-transcription from Rhodobacter sphaeroides. AppA and transcription factor PpsR combine to form AppA-PpsR2 complex and enable PpsR not to bind with DNA in darkness; bright blue light irradiation may enable AppA to dissociate from the complex, and the released PpsR forms a tetramer and bind to a specific DNA sequence to repress the gene transcription.
In previous studies, hormone receptors or receptor mutants can be used to regulate gene functions and activities of transcription factors. For example, in Cre/LoxP system, we can reconstruct Cre recombinase to regulate its nucleus localization by fusing ER, PR or GR to it; thus the reconstructed Cre recombinase can play its function roles in the nucleus with the existence of corresponding ligand. Fusing a hormone receptor to a transcription factor can enable the transcription factor to function under the regulation of hormone, for example, a hormone-tetracycline co-regulated gene expression system in which tetracycline-regulated transcription factor is fused with EcR or GR, thus the gene expression is regulated by both the hormone and tetracycline.
As described above, the most widely used gene expression systems today utilize chemical substances as the inducers, which have reasonable desirable induction performance, low leakage expression and high expression levels. However, many of gene expression systems have side-effect and potential toxicity due to their pleiotropic effect. Besides, the chemical inducers cannot precisely control gene expression at high spatial resolution. Up to now, there are only a few of gene expression systems controlled by physical methods although they have the capability of spatial regulating gene expression in specific cells and tissues, their toxicity to host cells may cause irreversible damage or hard manipulation. Few photosensitive protein based gene expression systems have been developed, but the poor induction capacity, the requirement for exogenous chemicals, the difficulty for the transcription factor containing more than one protein to be introduced into host cells may limit their wide application. The applicants consider that a more excellent gene expression system can be created using a novel method to overcome the shortcomings of previous studies, and it can be widely used in biomedical sciences and technology researches. After painstaking studies, the applicant has invented a novel light-controllable gene expression system, which consists of two parts: a recombinant light-switchable transcription factor and a target transcription unit. It has excellent capacity to control gene expression and it can spatiotemporally regulate gene expression. Furthermore, in order to satisfy more complex synthetic biology research, we have modified the recombinant light-switchable transcription factor into a recombinant light-hormone dual regulated transcription factor which can regulate gene expression by both light and hormone.
Accordingly, the first object of the present invention is to provide a novel light-controllable gene expression system.
A second object of the present invention is to provide a light and hormone dual-regulated gene expression system.
A third object of the present invention is to provide a eukaryotic expression vector containing said light-controllable gene expression system.
A fourth object of the present invention is to provide a method of the regulation of gene expression by said light-controllable gene expression system in the host cell.
A fifth object of the present invention is to provide a kit containing components of the light controllable gene expression system.
A sixth object of the present invention is to provide a gene therapy method using the light-controllable gene expression system.
SUMMARY OF INVENTION
The present invention relates to a light-switchable gene expression system, comprising two parts: a) a gene encoding a recombinant light-switchable transcription factor, said recombinant light-switchable transcription factor including the first polypeptide as DNA-binding domain, the second polypeptide as light-switchable domain and the third polypeptide as transcriptional regulatory domain; b) a target transcription unit, including at least one reaction element recognized/bound by the first polypeptide, promoter connected thereto and the nucleic acid sequence to be transcribed.
In the first part of the light-switchable gene expression system according to the invention, the first polypeptide in the recombinant light-switchable transcription factor is a DNA-binding domain which is able to specifically recognize said reaction element, but unable to bind the reaction element or only have a weak binding affinity. The binding to the reaction element needs the assistance of the second polypeptide. The first polypeptide can be selected from the helix-turn-helix DNA-binding domain, zinc finger motif or zinc cluster DNA-binding domain, leucine zipper DNA-binding domain, winged helix DNA-binding domain, winged helix-turn-helix DNA-binding domain, helix-loop-helix DNA-binding domain, high mobility family DNA-binding domain and B3 DNA-binding domain. The second polypeptide is a light-switchable domain usually derived from the class of the photosensitive proteins containing flavin chromophore. The third polypeptide is a transcriptional regulatory domain including the transcriptional activation domain and the transcriptional repression domain.
The first polypeptide, the second polypeptide and the third polypeptide can be linked directly or operatively via a linker peptide. The amino acid number of the linker peptide is variable, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
The first polypeptide and the second polypeptide can constitute a fusion protein of the light-switchable DNA-binding-protein (abbreviated as a light-switchable DNA binding protein), and can be used for in vitro researches for DNA binding characteristics of the recombinant light-switchable transcription factor. In the second portion (i.e. target transcription unit) of the light-switchable gene expression system, the reaction element, the promoter and the nucleic acid sequence to be transcribed can also be linked each other directly or operatively.
In the first portion of the light-switchable gene expression system, the recombinant light-switchable transcription factor can further comprise additional polypeptides, such as the fourth polypeptide (i.e. nuclear localization signal peptide) which can promote the transportation of the recombinant light-switchable transcription factor fusion protein into the nucleus; and/or the fifth polypeptide regulated by hormones. The fourth or the fifth polypeptide can be linked directly or via a linker peptide, with the first, the second, or the third polypeptides.
The present invention also relates to a eukaryotic expression vector containing the light-switchable gene expression system. The eukaryotic expression vector can only contain the gene encoding the recombinant light-switchable transcriptional factor, or only contain the target transcription unit containing the reaction element-promoter but leaving a vacancy for the nucleic acid sequence to be transcribed. Otherwise, the eukaryotic expression vectors can contain both the gene encoding the recombinant light-switchable transcriptional factor and the reaction element-promoter in the target transcription unit.
The present invention also relates to a method for the regulation of gene expression in the host cells by using the light-switchable gene expression system, comprising the following steps:
a) constructing the light-switchable gene expression system in the eukaryotic plasmid expression vectors;
b) introducing the construct into the host cells containing said gene being regulated; and
c) inducing the host cells via illumination to express said gene being regulated.
In the above method, the illumination comprises the selection and the control of the light sources. The light sources include, but are not limited to, LED lamp, incandescent lamp, fluorescent lamp and laser; and the illumination method includes the selection of the quantity, time, intensity and frequency of the illumination. The spatial expression control of the target gene, using scan, projection, optical molds, etc., also falls into the range of the invention.
The present invention further relates to a kit containing the eukaryotic expression vector comprising the light-switchable gene expression system and/or the mammalian cells transfected by the eukaryotic expression vectors containing the transcription factor, as well as the directions, The kit can also contain the eukaryotic expression vector comprising the target transcription unit composed of the reaction element-promoter but leaving a vacancy for the nucleic acid sequence to be transcribed
The present invention further relates to a method for the gene therapy using the light-switchable gene expression system.
DETAILED DESCRIPTION OF INVENTION
The invention provides a photosensitive polypeptide-based light-switchable gene expression system useful for the regulation of target gene expression with high spatiotemporal resolution in eukaryotic host cells. The light-switchable gene expression system of the invention relates to at least two portions. The first portion is a nucleotide sequence (encoding the recombinant light-switchable transcription factor fusion protein) being able to express in the host cells. This fusion protein is composed of three or four or five polypeptides, wherein the first polypeptide is its DNA-binding domain, the second polypeptide is a light-switchable domain, the third polypeptide is a transcriptional regulatory domain, the fourth polypeptide is a nuclear localization signal peptide, and the fifth polypeptide is a polypeptide regulated by hormone. The second portion is a nucleotide sequence of the target transcription unit composed of a reaction element-promoter-nucleotide sequence to be transcribed, wherein the reaction element is a DNA nucleotide motif recognized/bound by the first polypeptide in the above-mentioned recombinant light-switchable transcription factor fusion protein; and the promoter is usually minimal promoter or other complete promoter. The three or four or five polypeptide in the first portion is preferred to be a truncated functional active fragment (i.e. Domain) of the proteins involved. The first and second portions of the light-switchable gene expression system can be constructed in one or two eukaryotic expression vectors, respectively. These vector(s) will be introduced into host cells, by using different conventional methods for particular host cells, to express the recombinant light-switchable transcription factor fusion protein. The illumination of appropriate wavelength light can result in the change of dimerization ability of the light-switchable second polypeptide, then the change of dimerization ability of the whole recombinant light-switchable transcription factor. The dimerized transcription factor can bind to the reaction element in the second portion, i.e., target transcription unit nucleotide sequence, to regulate (initiate/repress) the transcription and expression of the target gene via the synergistic effect on the promoter in the target transcription unit by the transcriptional activation/repression domain of the third polypeptide in this fusion protein and other transcriptional co-factors derived from the recruitment host cells. The light-switchable gene expression system of the invention can utilize the illumination which is hardly damaging cells or the body, to regulate the target gene expression in eukaryotic host cells at high spatiotemporal resolution.
The light-switchable gene expression system can utilize different light sources and illumination conditions to regulate the target gene expression in eukaryotic host cells in the space. The used light is cheap, easy to be obtained and non-toxic to cells.
Definition and Explanation of Terms Used Herein
“light-switchable”, “photosensitive” and “light-switchable” proteins have the same meaning and can be used interchangeably herein, refers these proteins which are sensitive to illumination and their activities (including activation, enhancement or repression) can be influenced by adjusting their conformations or configurations through being applied corresponding wavelength light in different intensities or different frequencies
“Host” refers to the eukaryotes, including unicellular eukaryotes such as yeast and multicellular eukaryotes such as plants and animals, especially mammals, including humans.
“Host cells” refer to the cells of the constituted eukaryote tissues or the established eukaryotic cell lines and, as long as these cells or cell lines are compatible with the target protein to be expressed, the used screening system or the fermentation and culture system; comprising: unicellular eukaryotic cells such as cultured BY4741 and AH109 Saccharomyces cerevisiae yeast, fission yeast, P. pastoris yeast, klebsiella lactate, H. polymorpha yeast cells (for its review, see Fleer et al., Curr Opin Biotechnol, 1992, 3(5):486-489) and fungal cells. The nonrestrictive examples of the established subculturing in vitro immortal mammalian cell lines comprising: human embryonic kidney epithelial cells (HEK293), African green monkey kidney fibroblast COS-7, human cervix carcinoma cells (Hela), mouse fibroblasts (NIH3T3), etc. The host cells also include normal cells such as ex vivo transgenic or homologous recombinant animal embryo cells for the purpose of gene therapy. The particular value cell types for the purpose of gene therapy comprising: hematopoietic stem cells, osteoplasts, hepatocytes, leukocytes, neuronal cells, skin epithelium and airway epithelium cells; ex vivo transgenic or homologous recombinant animal embryo stem cells and fertilized egg cells. The host cells also comprising non-mammalian eukaryotic cells such as bacterial, fungal, yeast, plant, drosophila, inset, zebra fish, nematode, animal and mammalian cells. The above-mentioned transgenic cells include these cells transferred thereto by the inventive recombinant light-switchable transcription factor gene and/or the target transcription unit containing target protein gene. The inventive recombinant light-switchable transcription factor can well regulate the target gene expression in these cells via controllable light irradiation. The expression in insect cells can be performed with baculovirus expression vectors (see, for example, O'Reilly et al. (1992) “Baculovirus expression vectors: A laboratory manual”, Stockton Press), available baculovirus vectors include pAc series (Smith, G. E., M. D. Summers, and M. J. Fraser, Mol Cell Biol, 1983. 3(12): 2156-2165) and pVL series ((Luckow, V. A. and M. D. Summers, Virology, 1989. 170(1): 31-39).
“Target protein” is also known as “interested protein” and refers to any useful protein, for example, useful eukaryotic protein, including natural or artificial modification or mutation proteins in need of expression in eukaryotic host cells for the preventive or therapeutic or other purposes, in particular, these proteins which must be modified after translation (such as glycosylation, amidation modification etc.) to obtain their activities, and they will be expressed in eukaryotic cells to obtain such modifications.
“Report protein”, one of target proteins, refers to a useful protein which expression is easy to be detected. In order to facilitate the detection for effect of the inventive photosensitive polypeptide-based light-switchable target gene expression system, the known widely used report proteins can be selected as following: firefly luciferase (Fluc), green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), β-galactosidase (LacZ), etc. However, the light-switchable target protein gene expression system is not limited to express a report protein, but may be used for the expression of any useful target protein.
“Gene”, “encoding nucleotide sequence” and “sequence to be transcribed” of a protein, as used herein, have the same meaning. They can be used interchangeably and refer to the natural or recombinant codon DNA sequence carrying the amino acid sequence information, and also refers to the DNA sequence encoding a functional RNA such as antisense RNA.
“Gene of a target protein”, “encoding nucleotide sequence of a target protein”, “nucleotide sequence encoding target protein” and its abbreviation “target gene”, as used herein, have the same meaning. They can be used interchangeably and refer to the gene encoding target protein, generally double-strands DNA sequence. This gene can be contained in the chromosomal DNA sequence of the host cells or in artificial expression vectors, such as the target transcription unit sequence of the invention. Similarly, “report gene” means a gene encoding a report protein.
“Transcription” as used herein specifically refers to a process wherein a target gene is transcribed by RNA polymerase to produce RNA carrying this gene information in the eukaryote host cells. The transcription of the eukaryote gene is much more complex than that of the prokaryote gene. In eukaryotes, there are three RNA polymerases, I, II and III, respectively for the transcription of three eukaryotic genes, resulting in three RNAs (rRNA, mRNA, tRNA) and antisense RNA. The transcription process, from DNA into mRNA, regulated by the transcription factor is the transcription started by RNA polymerase II.
“Transcriptional regulation” used herein refers to the regulation of eukaryotic gene transcription, including the transcriptional start or repression, enhancement or inhibition, upward or downward regulation.
“Expression”, “gene expression of a target protein” and “gene expression”, as used herein, have the same meaning. They can be used interchangeably and refer to both a target gene DNA sequence being transcribed to RNA (mRNA or antisense RNA) carrying this gene information and the information carried by this RNA being translated to produce the target protein, that is, both the messenger RNA production via transcription and the target protein production via translation are called as expression. As herein, these two meanings are included, mainly referring to produce the target protein.
“Transcription factor” and “transcription factor fusion protein” as herein have the same meaning. They can be used interchangeably, and refer to the eukaryote transcription factor. It is not a protein, but a general term for several interacting proteins or polypeptides. It may be natural or artificially modified or fused proteins composed of the polypeptide able to recognize/bind to the reaction element nucleotide sequence in the target transcription unit and the polypeptide able to recruit other transcriptional activation/repression cofactors. It can start and regulate the gene transcription of protein by binding to and interacting with the reaction element in the target transcription unit, as well as its acting on upstream promoter of the nucleic acid sequence together with other recruitment transcriptional activation or repression cofactors. Depending on the different composition, the transcription factors can be divided into “transcriptional activation factor” and “transcriptional repression factor”.
“Target transcription unit” refers to a artificial DNA sequence composed of a reaction element, a promoter and a nucleic acid sequence to be transcribed (not a protein), wherein the reaction element is usually located upstream of the promoter, sometime may also be located downstream of the promoter; and the nucleic acid sequence to be transcribed is located downstream of the reaction element and the promoter. The reaction element, promoter and nucleic acid sequence to be transcribed can be connected directly or operatively, i.e., separated by several nucleotides.
“Reaction element” refers to one or more cis-DNA motifs recognized/bound specifically by a transcription factor. Different transcription factors have their corresponding different reaction elements; and the binding domain contained in the transcription factor can bind to this DNA motif. When a transcription factor has bound specifically to its corresponding reaction element, the third polypeptide in the transcription factor can recruit co-factors to effect synergically on the promoter for activation or repression of downstream target gene transcription in order to produce the corresponding RNA. According to the invention, the reaction refers to a DNA motif able to be recognized/bound specifically by the first polypeptide in the recombinant light-switchable transcription factor, for example, a Gal4 reaction element is the long 17 bp DNA motif (Sequence 67).
“Promoter” refers to a DNA sequence which can start and lead to its downstream gene transcription to produce RNA. Promoter may be a naturally or artificially modified promoter. The different promoter may guide the gene transcription in different developmental stages of different tissues or cells, or the gene expression in response to different environmental or physiological conditions. Promoters are usually divided into “constitutive promoter”, “inducible promoter and “regulatory promoter”; or divided into “cell-specific promoter”, “tissue-specific promoter”, “developmental-specific promoter” and “cell-differentiation-specific promoter” based on tissues and cells. The upstream gene of the expressible natural cellular structure protein has its matching promoter; and DNA fragment of different genes may have the same promoter. The non-restrictive examples of the common constitutive promoters available for the expression of the recombinant light-switchable transcription factor are the promoters derived from polyoma virus, adenovirus 2, cytomegalovirus (CMV) and simian virus 40 (SV40). The non-restrictive examples of tissue-specific promoters available for the expression of the recombinant light-switchable transcription factor also include: the albumin promoter (liver-specific, Pinkert, C. A. et al, Genes Dev, 1987. 1(3): 268-276), lymphoid-specific promoter (Calame, K. and S. Eaton, Adv Immunol, 1988. 43: 235-275), in particular, T-cell receptor promoter (Winoto, A. and D. Baltimore, EMBO J, 1989. 8(3): 729-733), immune-globulin promoter (Banerji, J., L. Olson and W. Schaffner, Cell, 1983. 33(3): 729-740; Queen, C. and D. Baltimore, Cell, 1983. 33(3): 741-748), neuron-specific promoter (for example, nerve fibers promoter, Talbott, R. L., et al., Proc Natl Acad Sci USA, 1989. 86(15): 5743-5747), pancreas-specific promoter (Edlund, T. et al., Science, 1985. 230(4728): 912-916) and mammalian gland-specific promoter (such as milk whey promoter, U.S. Pat. No. 4,873,316). The developmental regulatory promoters are also included, such as murine hox promoters (Kessel, M. and P. Gruss, Science, 1990. 249(4967): 374-379) and α-fetoprotein promoter (Camper, S. A. and S. M. Tilghman, Genes Dev, 1989. 3(4): 537-546). AT-rich region located in about −25 to −30 nucleotide upstream of the transcription initiation point in most eukaryotic genes is called as TATA box, as herein known as “minimal promoter” which determines the transcription start site, but itself is not sufficient to effectively start gene transcription. In upstream of TATA box, there are other necessary nucleotide motifs for transcription, i.e., the reaction element recognized/bound specifically by the transcription factor described herein. When this reaction element is bound by its corresponding transcription factor, the reactivity is communicated to the minimal promoter, and the minimal promoter is activated in the synergistic assistant of the transcription factor-recruitment co-factors, finally resulting in the transcription of downstream gene to produce corresponding RNA.
“Vector”, “expression vector”, “gene expression vector” and “recombinant gene expression vector” have the same meaning. They can be used interchangeably and refer to a vector able to express recombinant target proteins in eukaryotic cells. This vector may be an artificial plasmid or a recombinant virus vector.
“Transfection” refers to a process that the host cells uptake the exogenous gene-carrying expression vector through physical or chemical methods such as electroporation, calcium phosphate co-precipitation, lipofection amine or DEAE-dextran mediated transfection, DNA particle bombardment and microinjection, etc., or the gene-carrying expression vectors delivery into the host cells through a biological medium, such as retrovirus vector, adenovirus vector and receptor-mediated DNA uptake. These vectors entered into host cells can reside in the cytoplasm as episomes, or be integrated into the chromosome of the cells. These cells can transiently or long-termly express the protein or functional RNA encoded by the vector-carried gene. Such host cells are called as vector-transfected cells. The methods for the host cells transfected with the expression vectors can be found in Sambrooka et al (Molecular Cloning, A laboratory Manual, Second Edition, Cold Spring Harbor Press (1989) and other related textbooks.
The recombinant light-switchable transcription factor in the first portion of the photosensitive polypeptide-based light-switchable gene expression system of the invention is a fusion protein formed by tandem connection of three or four or five functional polypeptide fragments via direct peptide bonds or via a linker peptide. Under illumination of an appropriate wavelength light, such fusion protein can bind to the reaction element in the second portion, i.e., target transcription unit nucleotide sequence of the system, so as to initiate or repress the expression of the target protein gene in the transcription unit via the synergistic effect on the promoter in the target transcription unit by its transcriptional activation/repression domain and the transcriptional co-factors derived from the recruitment host cells themselves.
As used herein, “recombinant light-switchable transcription factor fusion protein” and “recombinant light-switchable transcription factor” have the same meaning and can be used interchangeably.
The recombinant light-switchable transcription factor of the invention comprises the first polypeptide which is able to specifically recognize said reaction element in the target transcription unit nucleotide sequence, but unable to bind the reaction component or only have a weak binding affinity. The first polypeptide can only bind to the reaction component after homogenous dimerization of the transcription factor occurring with the assistance of the second polypeptide. The first polypeptide can be selected from: the helix-turn-helix DNA-binding domain, zinc finger motif or zinc cluster DNA-binding domain, leucine zipper DNA-binding domain, winged helix DNA-binding domain, winged helix-turn-helix DNA-binding domain, helix-loop-helix DNA-binding domain, high mobility family DNA-binding domain and B3 DNA-binding domain. Based on the related literature analysis, the useful first polypeptide of the invention includes, but not limited to DNA-binding domain of Gal4 protein, DNA-binding domain of LexA protein, DNA-binding domain of Lac repression protein (Lac1), DNA-binding domain of λphage cl repression protein, DNA-binding domain of tetracycline repression protein (TetR), DNA-binding domain of tryptophan repression protein (TrpR) etc., more preferably DNA-binding domains of Gal4 protein and LexA protein. Gal4 is a transcriptional activation domain of Saccharomyces cerevisiae, and it is able to recognize/bind to the upstream reaction element-UASG motif (SEQ. ID. NO:67). 1-94 Amino acids of the N-terminal of Gal4 protein is its DNA-binding domain (a zinc cluster DNA-binding domain), wherein 1-65 amino acid are useful for specific recognition of DNA, and 66-94 amino acids, useful for dimerization. Gal4 plays its role to bind to the reaction element in need of the formation of a homogeneous dimer [Marmorstein, R. et al., Nature, 1992. 356 (6368): 408-411]. Gal4/UAS-based double hybrid system is an effective tool for researching the gene expression. For example, this Gal4/UAS system has been used in CheckMateTM Mammalian Two-Hybrid System (Promega). LexA protein is a transcriptional repression protein present in E. Coli cells, and it can regulate the transcription of more than 20 genes and recognize/bind to palindromic structure of upstream reaction element (SEQ. ID. NO:68) of gene promoter to prevent the downstream gene transcription by RNA polymerase. LexA contains 202 amino acids with a winged helix-turn-helix DNA-binding domain, wherein the 1-87 amino acids are useful for specific recognition of DNA and the 88-202 amino acids, useful for dimerization. Only dimerized LexA can specifically bind to the corresponding reaction element. LexA exists in the dimeric form in normal cells. When the cells are stimulated by an internal or external SOS signal, the dimerized LexA is cut by certain enzymes in vivo and dissociated from the DNA, resulting in the activation of the gene previously repressed by LexA [Fogh, R. H. et al., EMBO J, 1994. 13 (17), 3936-3944]. LexA-based double hybrid system has also been used for researching the interaction of gene expression and proteins. For example, MATCHMAKERTM yeast LexA Two-Hybrid System (Clontech) is based on this system. LacI repression protein can recognize/bind to the operon of lactose system to regulate the transcription of the corresponding genes. Lac protein has a helix-turn-helix DNA-binding domain with 1-62 amino acids for the specific recognition of DNA, and its specifically recognizing/binding conserved sequence is shown as SEQ. ID. NO:69. Only dimerized or tetromerized LacI can bind to the DNA, but monomer LacI almost can not [Lewis, M. et al., Science, 1996. 271 (5253), 1247-1254]. The cI protein is a transcription repression protein encoded by λ phage cI gene, and it can prevent the transcription activity of λ left and right early promoters, resulting in the production of protein unable to perform cell duplication and cell division. The cI protein contains 236 amino acids with a helix-turn-helix DNA-binding domain, wherein 1-102 amino acids are useful for specific recognition of DNA and 132-236 amino acids, useful for dimerization. Only dimerized cI can specifically bind to the corresponding reaction element. The homogenous dimer of cI protein can recognize/bind to two operon sequences, PL and PR, each contains three recognization/binding sites, OL1, OL2 and OL3 for PL, and OR1, OR2 and OR3 for PR, respectively. The cI protein has stronger ability to bind to OR1. The conserved DNA sequence is showed as SEQ. ID. NO:71. The monomer cI protein almost has no such binding ability [Burz, D. S., Beckett, D., Benson, N. and Ackers, G. K., Biochemistry, 1994. 33(28), 8399-8405, Hu, J. C., O'Shea, E. K., Kim, P. S. and Sauer, R. T., Science, 1990. 250 (4986), 1400-1403]. Tetracycline repression protein (TetR), a transcription factor resided in many Gram-negative bacteria, represses the transcription of corresponding genes via the bind to specific DNA motifs. TetR protein has a helix-turn-helix DNA-binding domain. The monomer of TetR protein can form the homogenous dimer for recognition/binding to the operon containing a specific DNA sequence (SEQ. ID. NO:70), but the monomer of TetR protein itself almost has no such binding ability [Wissmann, A. et al., EMBO J, 1991.10 (13), 4145-4152, Ramos, J. L. and, Microbiol Mol Biol Rev, 2005. 69(2), 326-356].
In a preferred embodiment of the invention, the first polypeptide is the 1-65 amino acid sequence of DNA-binding domain of Gal4 protein (its nucleic acid and protein sequences are SEQ. ID. NO:1 and SEQ. ID. NO:2, respectively), i.e., truncated DNA-binding domain which can not bind to the reaction element alone. In another preferred embodiment of the invention, the first polypeptide is the 1-87 amino acid sequence of DNA-binding domain of LexA protein (its nucleic acid and protein sequences are SEQ. ID. NO:5 and SEQ. ID. NO:6, respectively), i.e., truncated DNA-binding domain which can not bind to the reaction element alone. In another preferred embodiment of the invention, the first polypeptide is the 1-62 amino acid sequence of DNA-binding domain of LacI protein (its nucleic acid and protein sequences are SEQ. ID. NO:9 and SEQ. ID. NO:10, respectively), i.e., truncated DNA-binding domain which can not bind to the reaction element alone. In another preferred embodiment of the invention, the first polypeptide is the 1-63 amino acid sequence of DNA-binding domain of TetR protein (its nucleic acid and protein sequences are SEQ. ID. NO:13 and SEQ. ID. NO:14, respectively), i.e., truncated DNA-binding domain which can not bind to the reaction element alone. In another preferred embodiment of the invention, the first polypeptide is the 1-102 amino acid sequence of DNA-binding domain of cI protein (its nucleic acid and protein sequences are SEQ. ID. NO:17 and SEQ. ID. NO:18, respectively), i.e., truncated DNA-binding domain which also can not bind to the reaction element alone.
The second polypeptide in the recombinant light-switchable transcription factor fusion protein is a photosensitive polypeptide derived from the photosensitive domain containing flavin chromophore (FMN or FAD). For example, the photosensitive protein contains light-O-voltage (LOV) domain, the photolyase-like cryptochromes and the blue light protein using FAD (BLUF), preferably, the photosensitive protein contains LOV domain. After the illumination with the appropriate wavelength light, the dimerization ability of the second polypeptide has been changed to alter the dimerization ability of the transcription factor, then the dimer of the transcription factor can bind to the corresponding reaction element, thereby to regulate the expression level of the target genes. The invention includes, but is not limited to, several preferred photosensitive proteins or their functionally active truncated fragments described below.
The most preferred second polypeptide of the invention is the light-switchable domain of Neurospora crassa VIVID protein and its mutants. VIVID exists in the cells of Neurospora crassa and it is a photosensitive protein involved in cellular signaling pathway regulated by blue-light. Under the illumination of blue light, it can form a dimer with flavin adenine dinucleotide (FAD) in an intermolecular reaction. Full-length VIVID protein contains 186 amino acids with only one photosensitive LOV domain. Studies have showed that VIVID-36, the truncated protein of VIVID protein (missing 36 amino acid sequence in the N-terminal), were more stable than the full-length VIVID protein, Meanwhile, without illumination, the half-life of VIVID-36 dimer formed by illumination with blue light for regaining its monomeric form is 180000 s; the VIVID-36 containing point mutation C71V has more strong dimerization ability. In a preferred embodiment of the invention, the second polypeptide is selected from one point-mutation-containing and 1-36 amino acid sequence deleted VIVID (C71V), VIVID (N56K) and VIVID (Y50W) mutants (their nucleic acid sequences are SEQ. ID. NO:23, 25 and 29, respectively; their amino acid sequences are SEQ. ID. NO:24, 26 and 30, respectively). In a more preferred embodiment of the invention, the second polypeptide is two point-mutation-containing and 1-36 amino acid sequence deleted VIVID (N56K+C71V) mutants (The nucleic acid and protein sequences are SEQ. ID. NO:27 and SEQ. ID. NO:28, respectively).
The secondly preferred second polypeptide of the invention is LOV2 domain of Avena sativa phytochrome 1 (abbreviated as AsLOV2) [Peter, E., B. Dick, and S. A. Baeurle, Nat Commun, 2010. 1(8): 122]. The N-terminal of phytochrome 1 of Avena sativa is light-O-voltage (LOV) domain, LOV1 or LOV2, which can bind to flavin mononucleotide (FMN) to produce an additional compound under illumination of blue light. In the invention, LOV2 domain is linked to the first polypeptide, thus successfully resulting in the ability to bind to the corresponding reaction element for the first polypeptide in the transcription factor. The second polypeptide in the transcription factor GALP containing AsLOV2 domain (its nucleic acid and protein sequences are SEQ. ID. NO:41 and SEQ. ID. NO:42, respectively) can bind to its corresponding reaction element in dark, resulting in the expression of target gene, whereas this binding is weakening under illumination, resulting in the down-regulation of target gene expression level.
The thirdly preferred second polypeptide of the invention is LOV domain (abbreviated as AuLOV, its nucleic acid and protein sequences are SEQ. ID. NO:45 and SEQ. ID. NO:46 respectively) in the C-terminal of aureochrome1 of Stramenopile algae Vaucheria frigida [Takahashi, F. et al, Proc Natl Acad Sci USA, 2007. 104(49): 19625-19630]. The dimerization ability of the second polypeptide in the transcription factor GAAP containing AuLOV domain has been enhanced after illumination, thus resulting in the up-regulation of target gene expression level.
The dimerization of the recombinant light-switchable transcription factor constituted from VIVID or AuLOV is enhanced by the illumination of a light with an appropriate wavelength thus resulting in the bind of the second polypeptide to the reaction element to start or up-regulate the transcription. However, the light-switchable transcription factor containing AsLOV2 is dimerized in the dark, and binds to the reaction element, but the illumination depolymerizes the dimer to be monomer, thus weakening the bind or make it no more, thus repressing or down-regulating the transcription.
The homology of six different LOV domains derived from photosensitive proteins was analysed by using Accelry Discovery Studio 2.1. These LOV domains are derived from VIVID (Nc_VVD), White-collar-1 (Nc_Wc1), FKF1 (At_FKF1), aureochrome1 (Vf_Aureo1_LOV), oat phototropin 1 (As_phot_LOV1 and As_phot_LOV2). Results showed that these proteins have about 15% identical amino acids and about 36% similar sequences (FIG. 1).
The first polypeptide and the second polypeptide can constitute a light-switchable DNA-binding fusion protein (abbreviated as DNA-binding protein). Light-switchable DNA-binding proteins can be used to research DNA-binding abilities of various recombinant light-switchable transcription factors of the invention, especially, in vitro researches of DNA-binding ability of the complete DNA-binding domain constructed by the first polypeptide and the second polypeptide and its binding properties such as binding constants, the kinetics of the recovery of dimer to monomer, etc. The selected DNA-binding proteins are used to connect to the third polypeptide to constitute the transcription factors. In a particular embodiment, the first polypeptide in the light-switchable DNA-binding protein is Gal4 (1-65), the second polypeptide is wild type VIVID-36, Gal4-VIVID (WT) fusion protein (abbreviated as GAV (WT) (its nucleic acid and amino acid sequences are SEQ. ID. NO:84 and SEQ. ID. NO:85, respectively) has spectral properties similar to those of VIVID protein, and its DNA-binding ability is regulated by illumination. Its DNA-binding levels before and after illumination are significantly different, that is, the fusion protein in a high concentration can bind to the probe with a weak binding affinity in the dark, but it shows binding ability to the probe in all used protein concentration range after illumination.
The recombinant light-switchable transcription factor can contain the third polypeptide which is a transcriptional regulatory domain, a transcriptional activation domain (abbreviated as AD) or a transcriptional repression domain. The third polypeptide of the invention is used as a transcriptional activation domain or a transcriptional repression domain including, but not limited to, acidic amino acid-rich transcriptional activation domain (such as AD of VP16 and Gal4), proline-rich transcriptional activation domain (such as 399-499 amino acid residues of CTF/NF1), serine/threonine-rich transcriptional activation domain (such as 1-427 amino acid residues of ITF1) and glutamine-rich transcriptional activation domain (175-269 amino acid residues of Oct1), of which amino acid sequences and other useful transcriptional activation domains was described by Seipei et al [Seipel, K., Georgiev, O. and Schaffner, W., EMBO J, 1992. 11(13), 4961-4968 (1992)]. In addition, the sequence of Kruppel related box (KRAB) transcriptional repression domain has been reported [Peng, H. et al, J Biol Chem, 2000. 275(24): 18000-18010].
In embodiments of the invention, the third polypeptide is selected from VP16 transcriptional activation domain (abbreviated as VP16AD, its nucleic acid and protein sequence are SEQ. ID. NO:51 and SEQ. ID. NO:52, respectively), Gal4 transcriptional activation domain (abbreviated as Gal4AD, its nucleic acid and protein sequence are SEQ. ID. NO:53 and SEQ. ID. NO:54, respectively), the transcriptional activation domain of the general control protein (Gcn4AD, its nucleic acid and protein sequence are SEQ. ID. NO:95 and SEQ. ID. NO:96, respectively), the transcriptional activation domain of NF-κB p65 protein (abbreviated as p65AD, its nucleic acid and protein sequence are SEQ. ID. NO:49 and SEQ. ID. NO:50, respectively) and KRAB transcriptional repression domain of zinc finger protein 354A (its nucleic acid and protein sequence are SEQ. ID. NO:55 and SEQ. ID. NO:56, respectively). The two subunits of NF-κB protein often form homogeneous or heterogeneous dimer, most commonly, p65/p50 dimer or p65/p65 dimer; and the transcriptional activation domain of p65 subunit has been widely used to constitute various systems to induce gene expression with good effect [Wang, Y. et al., Gene Ther 1997.4(5), 432-441]. The transcriptional activation domain (AD) of Gal4 protein is mainly located in 768-881 amino acids of the C-terminal, among which many acidic amino acids can recruit other transcription accessory proteins in Saccharomyces cerevisiae cells to co-active the promoter, thus resulting in the transcription of the related gene [Shimizu-Sato, S., Huq, E., Tepperman, J. M., and Quail, P. H., Nat Biotechnol, 2002.20 (10), 1041-1044]. The transcriptional activation domain of yeast Gcn4 is mainly located in 1-144 amino acids of the N-terminal of Gcn4 protein, and it recruits other transcription accessory proteins in Saccharomyces cerevisiae cells to co-active the promoter, thus resulting in the transcription of the related gene [Drysdale, C. M. et al., Mol Cell Biol, 1995. 15(3):1220-1233]. VP16 is a viral intermediate layer protein composed of 490 amino acid residues expressed by UL48 structural gene in herpes simplex virus HSV-1. The acidic amino acid-rich C-terminal of VP16 is a transcriptional activation domain which has been successfully used in a variety of gene expression systems [Gossen, M. and H. Bujard et al., Proc Natl Acad Sci USA, 1992. 89(12): 5547-5551]. In preferred embodiments of the invention, transcriptional activation domains of VP16, NF-κB p65, Gal4 and Gcn4, and KBAB transcriptional repression domain of zinc finger protein 254A are used as the third polypeptide, respectively.
The recombinant light-switchable transcription factor fusion protein can also contain the fourth polypeptide, which is a nuclear localization signal peptide useful for promoting the transportation of the fusion protein into the nucleus. If all the first, second and third polypeptides contain no nuclear localization signal (NLS), the fourth polypeptide can be added. The nuclear localization signal peptide typically comprises a basic amino acid segment. The preferable nuclear localization signal peptide is that of Simian vacuoles virus 40 (SV40 NLS) [Fanara, P. et al., J Biol Chem, 2000. 275 (28): 21218-21223]. In one specific embodiment, the first polypeptide of the recombinant light-switchable transcription factor comprises Gal4 protein as a nuclear localization signal peptide, thus the fusion protein contains no the fourth polypeptide. In another specific embodiment, the fourth polypeptide link, directly or via a linker, with the first, the second, or the third polypeptides.
The recombinant light-switchable transcription factor fusion protein can further contain the fifth polypeptide, and the fifth polypeptide-containing recombinant light-switchable transcription factor fusion protein is also known as recombinant light-hormone double regulating transcription factor. In most cases, the fifth polypeptide is used to regulate the ability entering into nucleus, thus regulating the target gene expression in combination with illumination. The fifth polypeptide links, directly or via a linker, to the first, the second, or the third polypeptides. The fifth polypeptide includes, but not limited to, ecdysone receptor and its mutants, glucocorticoid receptor and its mutants, estrogen receptor and its mutants, and progesterone receptor and its mutants; preferably, drosophila ecdysone receptor and its mutants, bombyx mori ecdysone receptor and its mutants, human glucocorticoid receptor and its mutants, human estrogen receptor and its mutants, and human progesterone receptor and its mutants; more preferably, bombyx mori ecdysone receptor (V454I/Y474E) mutant, and human estrogen receptor (G400V/M543A/L544A) mutant. In one specific embodiment, the fifth polypeptide in the recombinant light-switchable transcription factor is the 272-606 amino acid sequence of bombyx mori ecdysone receptor (V454I/Y474E) mutant. In another specific embodiment, the fifth polypeptide is the 282-594 amino acid sequence of human estrogen receptor. In another specific embodiment, the fifth polypeptide is the 640-914 amino acid sequence of progesterone receptor.
As described above, there are various options for each of the third, fourth and fifth polypeptides contained in the recombinant light-switchable transcription factor and various combination options for the third, fourth and fifth polypeptides to be connected to become a fusion protein. The fragments of the functional domain of each polypeptide with good activity are preferably used for the preparation of the recombinant light-switchable transcription factor fusion protein. Recombinant light-switchable transcription factor with strong regulatory ability (i.e. large differences of its gene expression level during the illumination and in the dark), selected by the expression in mammalian cells or yeast cells, are used to regulate the expression of the nucleic acid sequence to be transcribed. Whatever choices and combinations are, they fall into the range of the invention provided the gene expression regulated by illumination is achieved.
The second portion of the photosensitive polypeptide-based light-switchable gene expression system is a target transcription unit (nucleotide sequence) composed of the reaction element (specifically recognized/bound by the transcription factor)-promoter-nucleotide sequence to be transcribed. Specifically, the reaction element, a nucleotide motif, is dependent on the first polypeptide selected to be used in the recombinant light-switchable transcription factor fusion protein. In other words, the reaction element, specific to the first polypeptide, must be selected based on the first polypeptide. For example, when the first polypeptide is the DNA recognition/binding domain of Gal4, LexA, LacI, TetR or cI proteins, the corresponding reaction element should be a motif of SEQ. ID. NO:67, 68, 69, 70 or 71. Target transcription unit contains one or more reaction elements, e.g., 1, 2, 3, 4 or 5 reaction elements, in specific embodiments. If the effect of more reaction elements is better, more reaction elements are selected.
The reaction element is usually linked operatively with a minimal promoter which is not enough to initiate gene transcription effectively. The minimal promoter, together with its upstream reaction element, must interact with members of transcription factors, so as to activate or up-regulate the transcription of the downstream target gene. Based on the analysis of related literatures, the available minimal promoters include, but not be limited to, the major late promoter of adenovirus (its nucleic acid sequence is SEQ. ID. NO:72), the minimal promoter of cytomegalovirus (CMV) (SEQ. ID. NO:75), GaL1 gene promoter of yeast (its nucleic acid sequence is SEQ. ID. NO:74). In specific embodiments of the invention, the minimal promoter is the major late promoter of adenovirus and GaL1 gene promoter of yeast, but other minimal promoters may also be used. The promoter linked operatively with the reaction element can also be a complete promoter, such promoter itself has the ability to initiate gene transcription, binding of transcription factor to the reaction element can enhance or repress the expression of downstream nucleic acid sequence to be transcribed. In another specific embodiment, the promoter is SV40 promoter (its nucleic acid sequence is SEQ. ID. NO:73). The person skilled in the art knows that so-called “operatively link” refers the connection between the reaction element and the promoter or among reaction elements is not a direct connection, but spaced by several nucleotides, provided the synergistic effect still exists.
In the target transcription unit of the invention, the downstream nucleotide sequence is a nucleotide sequence to be transcribed, a nucleotide sequence encoding the target protein or functional RNA. As above-mentioned, the target protein can be any useful protein. In order to verify the effects of the present system and to facilitate the detection, following exemplary report proteins have been used as target protein in the examples: firefly luciferase (Fluc, its nuclei acid and amino acid sequence are SEQ. ID. NO:76 and SEQ. ID. NO:77, respectively), Gaussian luciferase (Gluc, its nuclei acid and protein sequence are SEQ. ID. NO:78 and SEQ. ID. NO:79, respectively), Red fluorescent protein mCherry (its nuclei acid and protein sequence are SEQ. ID. NO:80 and SEQ. ID. NO:81, respectively), Green fluorescent protein (hrGFP, its nuclei acid and protein sequence are SEQ. ID. NO:82 and SEQ. ID. NO:83, respectively), yellow fluorescent protein (EYFP, its nuclei acid and protein sequence are SEQ. ID. NO:91 and SEQ. ID. NO:92, respectively), β-galactosidase (LacZ, its nuclei acid and protein sequence are SEQ. ID. NO:93 and SEQ. ID. NO:94, respectively). However, the target protein of the invention is not limited to these report proteins. The nucleotide sequence to be transcribed can also encode functional RNA molecules, such as antisense RNA molecule. Functional RNA molecules expressed in host or animal cells can regulate some activities within the host cells, for example, inhibit the mRNA translation, thus preventing the expression of target protein.
The first portion and the second portion of the light-switchable target protein gene expression system of the invention can be constituted in one eukaryotic expression vector or in two eukaryotic expression vectors, respectively, by using standard recombinant DNA technique. Such expression vectors can be introduced into various eukaryotic host cell population to express the interested target proteins, or introduced into various eukaryotic host cell population such as animal embryonic germ cells or plant germ cells to further selectively produce useful transgenic organisms such as transgenic goats, sheep, pigs, cattle or other livestock, or transgenic plants.
The expression system of the invention may be used for the expression of the endogenous or foreign proteins in the eukaryotic cells, for gene therapy and gene expression in transgenic or homologous recombinant organisms (e.g., animal or plant).
The present invention provides recombinant light-switchable transcription factor fusion proteins composed of three or four or five polypeptides, the encoding nucleic acids and the eukaryotic expression vectors containing same. In one embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:3), amino acid sequence (SEQ. ID. NO:4) and mammalian cell expression vector pGAVV (WT) of the recombinant light-switchable transcription factor Gal4-VIVID-VP16 (abbreviated as GAVV (WT). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:31), amino acid sequence (SEQ. ID. NO:32) and mammalian cell expression vector pGAVP (WT) of the recombinant light-switchable transcription factor Gal4-VIVID-p65 (abbreviated as GAVP). In a preferable embodiment of the invention, provided are the encoding nucleic acid sequences (SEQ. ID. NO:33, 35, 39), amino acid sequences (SEQ. ID. NO:34, 36, 40) and mammalian cell expression vectors pGAVP(C71V), pGAVP (N56K) and pGAVP(Y50W) of three recombinant light-switchable transcription factors Gal4-VIVID-p65 wherein brackets are the mutation sites in VIVID. In another preferable embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:37), amino acid sequence (SEQ. ID. NO:38) and mammalian cell expression vector pGAVP (N56K+C71V) of the recombinant light-switchable transcription factor Gal4-VIVD-p65 containing double mutants in VIVID. In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:43), amino acid sequence (SEQ. ID. NO:44) and mammalian cell expression vector pGALP of the recombinant light-switchable transcription factor Gal4-AsLOV2-p65 (abbreviated as GALP). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:47), amino acid sequence (SEQ. ID. NO:48) and mammalian cell expression vector pGAAP of the recombinant light-switchable transcription factor Gal4-AuLOV-p65 (abbreviated as GAAP). In another preferable embodiment of the invention, provided are the encoding nucleic acid sequences (SEQ. ID. NO:59, 61, 63), amino acid sequences (SEQ. ID. NO:60, 62, 64) and mammalian cell expression vectors pGAVP-9, pGAVP-11 and pGAVP-12 (wherein 9, 11, 12 represent different linker peptides) of three recombinant light-switchable transcription factors Gal4-VIVID-p65, wherein the connection between the first polypeptide and the second polypeptide is via different linker peptides. In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:57), amino acid sequence (SEQ. ID. NO:58) and mammalian cell expression vector pGAVK (C71V) of the recombinant light-switchable transcription factor Gal4-VIVID-KRAB (C71V) (abbreviated as GAVK(C71V)). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:97, 99, 101, 103, 105 and 107, respectively), amino acid sequence (SEQ. ID. NO:98, 100, 102, 104, 106 and 108, respectively) and mammalian cell expression vector pGPMA-GVG-Ln (N56KC71V) of a group of the recombinant light-switchable transcription factor Gal4-VIVID-Gal4AD-Ln (N56K+C71V), wherein n is 1, 2, 3, 4, 5 or 6. In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:109), amino acid sequence (SEQ. ID. NO:110) and Saccharomyces cerevisiae expression vector pGPMA-GVVP(N56K+C71V) of the recombinant light-switchable transcription factor Gal4-VIVID-VP16 (N56K+C71V) (abbreviated as GVVP (N56K+C71V)). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:111), amino acid sequence (SEQ. ID. NO:112) and Saccharomyces cerevisiae expression vector pGPMA-GVGc (N56K+C71V) of the recombinant light-switchable transcription factor Gal4-VIVID-Gcn4 (N56K+C71V) (abbreviated as GVGc (N56K+C71V)). In another embodiment of the invention, provided are encoding nucleic acid sequences (SEQ. ID. NO:113, 115, 117, respectively), amino acid sequence (SEQ. ID. NO:114, 116, 118, respectively) and Saccharomyces cerevisiae expression vector pGPMA-GVG (WT), pGPMA-GVG (C71V) and pGPMA-GVG (Y50W) of a group of the recombinant light-switchable transcription factor Gal4-VIVID-Gal4AD containing a point mutation in VIVID. In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:119), amino acid sequence (SEQ. ID. NO:120) and Saccharomyces cerevisiae expression vector pGPMA-GLG of the recombinant light-switchable transcription factor Gal4-AsLOV2-Gal4AD (abbreviated as GLG). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:7), amino acid sequence (SEQ. ID. NO:8) and Saccharomyces cerevisiae expression vector pGPMA-NLVG (N56K+C71V) of the recombinant light-switchable transcription factor NLS-LexA-VIVID-Gal4AD (N56K+C71V) containing the fourth polypeptide (abbreviated as NLVG (N56K+C71V)). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:19), amino acid sequence (SEQ. ID. NO:20) and Saccharomyces cerevisiae expression vector pGPMA-NCVG (N56K+C71V) of the recombinant light-switchable transcription factor NLS-cI-VIVID-Gal4AD (N56K+C71V) containing the fourth polypeptide (abbreviated as NCVG (N56K+C71V)). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:11), amino acid sequence (SEQ. ID. NO:12) and Saccharomyces cerevisiae expression vector pGPMA-NLcVG (N56K+C71V) of the recombinant light-switchable transcription factor NLS-LacI-VIVID-Gal4AD (N56K+C71V) containing the fourth polypeptide (abbreviated as NLcVG (N56K+C71V)). In another embodiment of the invention, provided are the encoding nucleic acid sequence (SEQ. ID. NO:15), amino acid sequence (SEQ. ID. NO:16) and Saccharomyces cerevisiae expression vector pGPMA-NTVG (N56K+C71V) of the recombinant light-switchable transcription factor NLS-TetR-VIVID-Gal4AD (N56K+C71V) containing the fourth polypeptide (abbreviated as NTVG (N56K+C71V)). It is known in the art that the codons of amino acid, nucleotides, have degeneracy, i.e. certain amino acids have two or three or four codons which are known as degenerate codons of amino acid. The present invention includes all the respective degenerate nucleotide sequences. In the case of the amino acid sequences of above-mentioned various recombinant light-switchable transcription factors, the present invention includes all their respective amino acid sequence analogs containing conserved deletions, additions, substitutions modified but still retains their original function and activation.
The invention also provides the eukaryotic expression vector containing the reaction element-promoter but leaving a vacancy for the nucleic acid sequence to be transcribed. This vacant location for the nucleic acid sequence can be replaced with the interested nucleotide sequence selected by the user himself, such as the gene encoding the target protein which is inserted into the expression vector of the invention by using standard recombinant DNA techniques, then this expression vector and above-mentioned expression vector containing the gene of the recombinant light-switchable transcription factor are used to co-transfect host cells for the regulation of the expression of the nucleotide sequence (gene) to be transcribed.
The invention also provides mammalian cells transfected with eukaryotic expression vectors containing genes encoding various recombinant light-switchable transcription factors, and provides eukaryotic expression vectors containing the target transcription unit composed of the reaction component-promoter, but leaving an vacancy for the nucleotide sequence to be transcribed. The nucleotide sequence to be transcribed (target protein gene) selected by the user himself can be inserted into said vector by using standard recombinant DNA techniques, then this re-constructed vector can be used to transfect mammalian cells already transfected by the eukaryotic expression vector containing the recombinant light-switchable transcription factor. These mammalian cells can be cultured to express the interested gene or to study how to regulate the expression of the target gene.
The present invention further provides a kit containing the expression vectors comprising two portions of the gene expression regulation system of the invention or the mammalian cells already transfected by these vectors. In one embodiment, some containers in the kit are filled, respectively, with the eukaryotic expression vector(s) containing one or more recombinant light-switchable transcription factor genes. In another embodiment, some containers in the kit are filled, respectively, with the eukaryotic expression vector(s) containing one or more recombinant light-switchable transcription factor genes, other containers are filled with the eukaryotic expression vector(s) containing the target transcription unit composed of the corresponding reaction component-promoter but leaving a vacancy for the nucleotide sequence to be transcribed. In a further embodiment, some containers in the kit are filled with mammalian cells already transfected with eukaryotic expression vectors containing the recombinant light-switchable transcription factor genes, other containers are filled with eukaryotic expression vectors containing the target transcription unit composed of the corresponding reaction component-promoter but leaving a vacancy for the nucleotide sequence to be transcribed.
The kit of the invention can also contain appropriate illumination control devices, such as LED lamp and its control devices. All kits of the invention will be equipped with a direction for the description of each component, its intended use and methods of application and provide relevant reference catalog.
The invention further provides a method for the regulation of gene expression in host cells using the light-switchable gene expression system, comprising following steps:
a) constructing the light-switchable gene expression system in eukaryotic plasmid expression vectors;
b) introducing the construct into host cells containing the gene being regulated; and
c) inducing host cells via illumination to express the nucleotide being regulated.
The illumination method for inducing the gene expression in host cells comprising: selection and application of light sources. The light sources include, but not are limited to, LED lamp, incandescent lamp, fluorescent lamp and laser. In one embodiment of the invention, blue LED (460-470 nm) is selected as the light source. The illumination methods include illumination quantity, time, intensity and frequency as well as the spatial expression control of the target gene via scan, projection, optical molds, etc. They are also comprised in the range of the invention. In one embodiment of the invention, the illumination intensities are varying within 0-0.8 W/m2. In another embodiment of the invention, the total illumination quantity are different, i.e., when the illumination intensity and total illumination time are identical, illumination induction are carried out for 1 s illumination every 30 s, is illumination every 60 s and 1 s every 120 s, respectively. In another embodiment of the invention, the cellular target gene expression in different locations is regulated in the space using the printing projection film as a light mold. In another embodiment of the invention, the cellular target gene expression in different locations is regulated in the space using the neutral gray film as a light mold.
The invention further provides a method for the gene therapy of type I diabetes, comprising treating a mammal (including a human) in need of treatment with the light-switchable gene expression system of the invention.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 shows homology analysis of LOV domains derived from six photosensitive proteins, wherein the black color represents 100% homologous amino acid sequence, the dark grey represents the higher homologous sequences and french gray represents the medium homologous Sequences.
FIG. 2 is a schematic diagram of homologous recombination ligation.
FIG. 3 shows the principle of reverse PCR.
FIG. 4 is a schematic diagram of construction of mammalian cell expression vectors containing the light-switchable transcription factor. Top panel is schematic diagram of the light-switchable transcription factor fusion protein. Bottom panel is schematic diagram of orbicular expression vectors, wherein the backbone of these vectors is pGFP-N1, and the intrinsic EGFP gene was replaced with the light-switchable transcription factor gene. * represents the different linker peptides for two polypeptides.
FIG. 5 is a schematic diagram of construction of mammalian cell expression vectors containing the target transcription unit. Top panel is a schematic diagram of respective target transcription units, and the bottom panel is a schematic diagram of orbicular expression vectors. The backbone of these vectors is pcDNA3.1 (+)-hygro, and the intrinsic CMV promoter and multiple clone sites were replaced with the target transcription units.
FIG. 6 is a schematic diagram of construction of yeast expression vectors containing the light-switchable transcription factor. Top panel is a schematic diagram of the light-switchable transcription factor fusion protein Bottom panel is a schematic diagram of orbicular expression vectors. The backbone of these vectors is pGADT7, and the intrinsic Gal4AD gene and multiple clone sites were replaced with the light-switchable transcription factor fusion protein gene. * represents the different linker peptide for two polypeptides.
FIG. 7 is a schematic diagram of construction of yeast expression vectors containing the target transcription unit. Top panel is a schematic diagram of respective target transcription units, and the bottom panel is a schematic diagram of orbicular expression vectors. The backbone of these vectors is pYES2.1 TOPO.
FIG. 8 is the agrose gel electrophoresis result of the overlap PCR product of Gal4, VIVID (WT) or VP16. Left arrow points to the target band of overlap PCR product, and the right bands are the DNA maker.
FIG. 9 is the agrose gel electrophoresis result of the p65AD amplified by PCR. The left arrow points to the target band of PCR product, and the right bands are the DNA maker.
FIG. 10 is the agrose electrophoresis result of the AsLOV2 amplified by PCR. The right arrow points to the target band of PCR product and the left bands are the DNA maker.
FIG. 11 is the agrose electrophoresis result of the AuLOV amplified by PCR. The right arrow points to the target band of PCR product, the left bands are the DNA maker.
FIG. 12 is the agrose gel electrophoresis result of the LexA (1-87) amplified by PCR. The right arrow points to the target band of PCR product, and the left bands are the DNA maker.
FIG. 13 is the agrose gel electrophoresis result of the LacI (1-62) amplified by PCR. The right arrow points to the target band of PCR product and the left bands are the DNA maker.
FIG. 14 is the agrose gel electrophoresis result of the cI (1-102) amplified by PCR. The right arrow points to the target band of PCR product, and the left bands are the DNA maker.
FIG. 15 is the agrose gel electrophoresis result of the TetR (1-63) amplified by PCR. The right arrow points to the target band of PCR product, left band is the DNA maker.
FIG. 16 is the agrose gel electrophoresis result of the Gcn4 (1-144) amplified by PCR. The right arrow points to the target band of PCR product; and the left bands are the DNA makers.
FIG. 17 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the transcription factors containing several different transcriptional activation domains as the third polypeptide respectively.
FIG. 18 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the transcription factors containing several VIVID mutants as the second polypeptide respectively.
FIG. 19 shows Fluc expression levels regulated by illuminating NIH3T3 cells transfected by the light-switchable transcription factor GAVP (N56K+C71V).
FIG. 20 shows Fluc expression levels regulated by illuminating COS-7 cells transfected by the light-switchable transcription factor GAVP (N56K+C71V).
FIG. 21 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the recombinant light-switchable transcription factor GAVP(WT) containing different linkers between the first polypeptide and the second polypeptide.
FIG. 22 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the transcription factor containing AsLOV2 as the second polypeptide.
FIG. 23 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the transcription factor containing AuLOV as the second polypeptide.
FIG. 24 shows the Fluc expression levels regulated by illuminating mammalian cells transfected by the transcription factor containing KRAB as the third polypeptide.
FIG. 25 shows the clone screening of HEK293 cells expressing the recombinant light-switchable transcription factor GAVP (C71V).
FIG. 26 shows the EYFP expression level regulated by illuminating Saccharomyces cerevisiae AH109 cells transfected by the recombinant light-switchable transcription factor GVG (N56K+C71V).
FIG. 27 shows the EYFP expression level regulated by illuminating Saccharomyces cerevisiae AH109 cells transfected by the recombinant light-switchable transcription factor GVVP (N56K+C71V).
FIG. 28 shows the LacZ expression level regulated by illuminating Saccharomyces cerevisiae AH109 cells transfected by the recombinant light-switchable transcription factor GVGc (N56K+C71V).
FIG. 29 shows the LacZ expression level regulated by illuminating Saccharomyces cerevisiae AH109 cells transfected by the recombinant light-switchable transcription factor GVG (N56K+C71V) containing different linkers between the second polypeptide and the third polypeptide.
FIG. 30 shows the detection of the target gene expression regulated by different expression level of the recombinant light-switchable transcription factor Gal4-VIVID-Gal4AD in Saccharomyces cerevisiae cells.
FIG. 31 shows the EYFP expression levels regulated by illuminating Saccharomyces cerevisiae AH109 cells transfected by the transcription factors containing several different VIVID mutants as the second polypeptide respectively.
FIG. 32 shows the EYFP expression level regulated by illuminating saccharomyces cerevisiae AH109 cells transfected by the transcription factor containing AsLOV2 as the second polypeptide upon blue light exposure.
FIG. 33 shows the EYFP expression difference of the target transcription units containing different numbers of Gal4 reaction elements regulated by the recombinant light-switchable transcription factor.
FIG. 34 shows the EYFP expression levels regulated by illuminating saccharomyces cerevisiae AH109 cells transfected by the recombinant light-switchable transcription factors containing LexA, LacI, cI or TetR as first polypeptide respectively.
FIG. 35 shows the kinetics and reversible process of light-induced target gene expression in mammalian cells transfected by the recombinant light-switchable transcription factor GAVP (N56K+C71V).
FIG. 36 shows the target gene expression levels regulated by illuminating with different intensities in cells expressing the recombinant light-switchable transcription factor GAVP (N56K+C71V).
FIG. 37 shows the target gene expression levels regulated by the different total illumination dose (illumination frequency) in cells expressing the recombinant light-switchable transcription factor GAVP (N56K+C71V).
FIG. 38 is the microscopic image of mCherry fluorescence (red fluorescent protein) expression regulated by illuminating cells expressing the recombinant light-switchable transcription factor GAVP (N56K+C71V). Top panel is a phase contrast image, and bottom panel is a fluorescence image.
FIG. 39 is the microscopic image of hrGFP fluorescence (green fluorescent protein) expression regulated by illuminating cells expressing the recombinant light-switchable transcription factor GAVP (N56K+C71V). Top panel is a phase contrast image, and bottom panel is a fluorescence image.
FIG. 40 shows the determination of the fluorescent protein expression using non-reducing polyacrylamide gel electrophoresis. The target band in top panel is hrGFP (green fluorescent protein), and the target band in bottom panel is mCherry (red fluorescent protein).
FIG. 41 shows Fluc expression identification under blue light illumination or darkness using RT-PCR.
FIG. 42 shows the Gluc expression level regulated by illuminating mammalian cells transfected by the recombinant light-hormone co-regulated light-switchable transcription factor.
FIG. 43 shows the spatial fluorescent protein expression regulated by illuminating cells transfected with the recombinant light-switchable transcription factor GAVP (N56K+C71V) cultured in 96 well microplate with neutral gray filter.
FIG. 44 is the ECUST pattern obtained from “taking photograph” of the cells expressing the recombinant light-switchable transcription factor GAVP (N56K+C71V) using a printed patterns projection film. The left panel is the photograph of culture dish affixed with projection film, and the right panel is the image of fluorescent cells.
FIG. 45 is the purity of purified DNA-binding protein GAV (WT). The arrow points to the target protein band.
FIG. 46 shows the spectrum characteristics of the light-switchable DNA-binding protein GAV (WT).
FIG. 47 shows the result of the electrophoresis mobility shift assay for the light-switchable DNA-binding protein GAV (WT). Each GAV (WT) protein concentration is 5.5 μM, 2.8 μM, 1.4 μM, 0.7 μM, 0.35 μM, respectively from the left to the right; and all probe concentrations are 125 nM.
FIG. 48 shows the result of gene therapy in type I diabetic mice using the light-switchable gene expression system.



PREFERABLE EMBODIMENTS
The invention will be described in detail by using following examples. These examples are only used for the illustration of the invention without any restriction on the scope of protection. It is not difficult for those skilled in the art to successfully implement the invention on the basis of the examples with some modifications or alternatives. All these modifications or alternatives are within the scope of the attached claims.
Methods, Equipment and Regents Used in the Examples
The methods used in the samples were the routine methods of molecular biology cloning in genetic engineering and cell biology field, such as: Lab Ref: A handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench written by Roskams, J. et al, Molecular Cloning: A Laboratory Manual (the third edition, August in 2002, Science press, Beijing) written by Sambrook J and Russell D W, and translated by Peitang Huang et al.; Chapters in book Short protocols in Protein Science (Science press, background) written by Coligan J. E. et al, and translated by Shentao Li et al.
Eukaryotic expression vectors pEGFP-N1, pGADT7 and pGBKT7 were purchased from Clontech; pcDNA3.1 (+)-hygro and pYES2.1 TOPO were purchased from Invitrogen; and pG5luc, pBIND and pACT were purchased from Promega. pcDNA3.1 (+)-hygro and pEGFP-N1, both containing CMV promoter, were used to construct eukaryotic expression vectors that could express target gene in mammalian cells, pcDNA3.1 (+)-hygro had hygromycin resistance while pEGFP-N1 had neomycin resistance. pGADT7 contained the gene of Gal4 transcriptional activation domain, pBIND contained the gene of DNA binding domain of Gal4 from yeast, and pACT contained the gene of VP16 transcriptional activation domain. pG5luc contained Gal4 operon, TATA minimal promoter and firefly luciferase Fluc gene. pIRES-hrGFP (purchased from Stratagene) contained hrGFP gene, pGluc-basic from NEB contained Gluc gene, pTRIPZ from Openbiosystem contained the sequence of SV40 promoter and pCDFDuet1 from Novagen contained LacI gene.
All the primers were synthesized, purified and identified via mass spectrometry by Shanghai Generay Biotech Co. Ltd. All the vectors obtained in the examples were verified via sequencing by BGI Company. Taq DNA polymerase used in the examples was purchased from DongSheng Biotech Company; pfu DNA polymerase was purchased from TianGen Biotech (Beijing) Co. LtD., and PrimeStar DNA polymerase was purchased from TaKaRa. All the three polymerases contained corresponding buffer and dNTP when purchased. Restriction enzyme such as BsrGI, Eco47III, BglII, PstI, HindIII, BamHI, et al., T4 ligase and T4 phosphatase (T4 PNK) were purchased, together with 10×TangoTM buffer, from Fermentas. CloneEZ PCR clone kit was purchased from GenScript (Nanjing). Unless otherwise mentioned, inorganic salt chemical reagents were purchased from Sinopharm Chemical Reagent Co.; Kanamycin, Ampicillin, PNPG, Streptozotocin (STZ) and Dithiothreitol (DTT) were purchased from Ameresco; Flavin adenosine dinucleotide (FAD), ATP and Imidazole were purchased from Alfa; Gluc-detecting kit was purchased from NEB. Potassium Salt of D-Luciferin was purchased from Synchem; EGTA was purchased from BBI; Trizol regent, Trpsin-EDTA, FBS, Lipofectamine2000, L-glutamine, sodium pyruvate, Opti-mem medium, Penicillin/Streptomycin-resistant antibiotics were purchased from Invitrogen; and amino acids was purchased from Sinopharm Chemical Reagent Co. unless mentioned, disposable equipments for cell culture were purchased from Corning. 20 mm diameter dishes for cell culture with glass bottom were purchased from NEST; 384 well white plates for luminescence detection and 384 well black plates for fluorescene detection were purchased from Grenier; and 96 well quadrate plates for cell culture was purchased from GE.
The kit for DNA purification was purchased from BBI (Canada); common plasmid kit was purchased from TianGen Biotech (Beijing) Co. LtD.; transfection grade plasmid kit was purchased from Omega; RNA extraction kit was purchased from TianGen Biotech (Beijing) Co. LtD.; ImpromIIreverse transcription kit was purchased from Promega company; DC protein assay kit was purchased from Bio-rad; E. coli strain Mach1 was purchased from Invitrogen; E. coli strain JM109 was purchased from Promega; E. coli strain BL21(DE3) was purchased from Novagen; and HEK293, COS-7 and NIH3T3 cell lines were purchased from American Type Culture Collection (ATCC). Neurospora crassa was a gift of Bin Chen from School of Resources and Environment Science in Guangxi Normal University. AH109 strain was purchased from Clontech; BY4741 strain was purchased from Openbiosystem Company; Tebufenozide and 4-OHTamxoifen was purchased from Sigma and Mifepristone was purchased from Cayman.
Main equipments: Biotek Synergy 2 multi-mode microplate reader (BioTek, US), X-15Rhigh speed refriger (Beckman, US), Microfuge22Rhigh speed refriger (Beckman, US), PCR Amplifier (Biometra, Germany), In-Vivo Multispectral System FX (Kodak, US), Luminometer (Sanwa, Japan), electrophoresis apparatus (shanghai Biocolor BioScience & Technology Co.), Eclipse Ti inverted microscope system (Nikon, Japan), four-use ultraviolet analyzer (Shanghai Jiapeng Co.), ACCU-CHEK Integra Glucose Meter (Roche).
The meaning of abbreviations: h=hour, min=minute, s=second, μL=microliter, mL=milliliter, L=liter, bp=base pair, mM=millimole, μM=Micromolar.
Some sequences used in the examples were obtained from NCBI (National Center for Biotechnology Information) or official websites or websites of companies selling commercial vectors with corresponding genes. Websites for searching gene sequences are as follows:
Gluc (Gaussia luciferase): (http://www.ncbi.nlm.nih.gov/protein/AAG54095.1);
hrGFP (humanized Renilla Green Fluorescent Protein):
(http://www.ncbi.nlm.nih.gov/nuccore/AY613996.1);
Fluc (firefly luciferase): (http://www.promega.com/vectors/pG5luc.txt);
Gal4: (http://www.ncbi.nlm.nih.gov/nuccore/NC_001148?report=genbank&from=79711&to=82356&strand=true)
VP16 (herpes simplex virus VP16 protein): (http://www.promega.com/vectors/pACT.txt);
NF-κB p65: (http://www.ncbi.nlm.nih.gov/nuccore/23958349?report=GenBank);
VIVID: (http://www.ncbi.nlm.nih.gov/nuccore/AF338412.1);
Phototropin1: (http://www.ncbi.nlm.nih.gov/nucleotide/2754822?report=genbank&log$=nucltop&blast_rank=1&RID=P49RPCAR01S);
Aureochrome1: (http://www.ncbi.nlm.nih.gov/nuccore/AB252504.1);
Gcn4: (http://www.ncbi.nlm.nih.gov/nuccore/NC_001137?report=genbank&from=138918&to=139763&strand=true);
LacI (repressor from Lac operon): (http://www.ncbi.nlm.nih.gov/nuccore/NC000913?report=genbank&from=365652&to=366734&strand=true);
LexA: (http://biocyc.org/ecoli/sequence?type=GENE&object=EG10533);
EYFP (enhanced yellow fluorescent protein): (http://www.ncbi.nlm.nih.gov/protein/37551795);
BmEcR (Bombyx mori ecdysone receptor):
http://www.ncbi.nlm.nih.gov/nucleotide/290560663?report=genbank&log$=nuchop&blast_rank=2&RID=K3Z8WXTW01R;
hPR (human progesterone receptor):
http://www.ncbi.nlm.nih.gov/nucleotide/321117149?report=genbank&log$=nucltop&blast_rank=1&RID=K3ZDKTB901R; and
ER (estrogen receptor):
http://www.ncbi.nlm.nih.gov/nucleotide/170295798?report=genbank&log$=nuchop&blast_rank=1&RID=K3ZPW1MT01R.
Other gene sequences used in the examples were obtained from NCBI (National Center for Biotechnology Information) or Uniprot (Universal Protein Resource), and then were transferred to nucleotide sequences according to the codon preference of each species using software DNA design 2.0. Websites of searching gene sequences are:
cI (repressor of λ operon) (http://www.uniprot.org/uniprot/P03034);
TetR (Tn10 B class) (http://www.uniprot.org/uniprot/P04483); and
mCherry (http://www.ncbi.nlm.nih.gov/nuccore/AY678264.1).
Example 1: Construction of Mammalian Cell Expression Vectors Containing the Recombinant Light-Switchable Transcription Factors Using VP16, p65 or KRAB as the Third Polypeptide
Plasmids construction of this example is shown in FIG. 4. The Gal4 (1-65 amino acid) gene was amplified from pBIND (Promega) by PCR using primer P1, P2; The VP16 gene was amplified from pACT (Promega) by PCR using primer P3, P4. After extracting the genomic DNA of Neurospora crassa by using Trizol Kit (Invitrogen), the intact VIVID gene was amplified by using primers P5 and P6. The resulted VIVID gene contained two introns. Then introns were removed by reverse PCR (see FIG. 3) using primer P7, P8, P9 and P10 as primers to obtain cDNA (SEQ ID NO: 21). Gal4, VIVID-36 and VP16 genes were fused by overlap PCR (see FIG. 8), and inserted into pEGFP-N1 vector (Clontech) by Eco47III and BsrGI digestion, the resulted mammalian cell expression vectors was named pGAVV(WT), which contains the fusion protein gene of recombinant light-switchable transcription factor Gal4-VIVID-VP16 (GAVV(WT)) (SEQ. ID. No:3 (polynucleotide) and 4 (polypeptide)), of which VIVID was 1-36 amino acid truncation form VIVID-36, and the other place mentioned is truncation form VIVID-36 as well. There is a BglII site between Gal4 and VIVID, and an EcoRI site between VIVID and VP16.
Primers for the amplification of Gal4 gene:







Forward primer (P1):


5′-CTTTTGGATCCAAGCGCTATGAAGCTACTGTCTTCTATCGAACA-3′


 


Reverse primer (P2):


5′-AGATCTGGTGGCGATGGATCTTTCCAGTCTTTCTAGCCTTGATT


 


C-3′






Primers for the amplification of VP16 gene:







Forward primer (P3):


5′-CAGTACCCATACGATGTTCCAGATTACGCTGAATTCCCGGGGATCTC


 


GAC-3′


 


Reverse primer (P4):


5′-AGAAATTCGAATGTACATGGCGATCCCGGACCC-3′






Primers for the amplification of VIVID gene:







Forward primer (P5):


5′-AGATCCATCGCCACCAGATCTCATACGCTCTACGCTCCCG-3′


 


Reverse primer (P6):


5′-TCTGGAACATCGTATGGGTACTGCAGTTCCGTTTCGCACTGGAAA


 


C-3′






Primers for removing introns of VIVID gene:
Removing the first intron:









Forward primer (P7)



5′-CAATACCACTATGACCCTCGAACCGCGCCC-3′



 



Reverse primer (P8):



5′-CTGATACGCCTCAACCTCCCATGGGTTCAT-3′






Removing the second intron:









Forward primer (P9)



5′-ATTCAGATTATGAACAGGCCAAACCCCC-3′



 



Reverse primer (P10):



5′-CAGATAGCCCATAATGTCATAACCGCCG-3′






For subcloning the recombinant light-switchable transcription factor with p65 transcriptional activation domain as the third polypeptide, total mRNA was extracted from HEK293 cells by using Trizol reagent (Invitrogen) and converted into cDNA by using ImpromII reverse transcriptase (Promega). P65AD of NF-κB P65 gene was amplified by using primers P11 and P12 (see FIG. 9), and the plasmid pGAVV(WT) constructed in this sample was double digested by using EcoRI and BsrGI. Then the VP16 gene was replaced with p65AD gene, and the resulting mammalian cell expression vector was named pGAVP(WT), which contains the fusion protein gene of Gal4-VIVID-p65 (GAVP(WT)) (SEQ. ID. No:31 (polynucleotide) and 32 (polypeptide)).
Primers for the amplification of p65 gene:









Forward primer (P11):



5′-GAATTCCAGTACCTGCCAGATACAG-3′



 



Reverse primer (P12):



5'-TGTACATTAGGAGCTGATCTGACTCAGCAG-3′






The artificial KRAB gene with EcoRI and BsrGI sites was synthesized by Generay Company (Shanghai) for subcloning recombinant light-switchable transcription factor with KRAB transcription repression domain as the third polypeptide. P65AD of pGAVP(C71V) described in example 2 was substituted with KRAB gene by double digestion, resulting mammalian cell expression vector named pGAVK(C71V), which contains the fusion protein gene of recombinant light-switchable transcription factor Gal4-VIVID-KRAB (C71V) (GAVK(C71V)) (SEQ. ID. No:57 (polynucleotide) and 58 (polypeptide)).
All the constructs were verified by DNA sequencing. Plasmids were prepared in transfection grade.
Example 2: Construction of Mammalian Cell Expression Vectors Containing the Recombinant Light-Switchable Transcription Factors Using VIVID Mutants or AsLOV2 or AuLOV as the Second Polypeptide
Refer to FIG. 4 for the plasmid construction of this example. VIVID of pGAVP (WT) described in example 1 was mutated into C71V or Y50W or N56K by reverse PCR using primers 13, 14, 15, 16, 17 and 18, the resulting mammalian cell expression vectors were named as pGAVP (C71V) (SEQ. ID. No:33 (polynucleotide) and 34 (polypeptide)), pGAVP (Y50W) (SEQ. ID. No:35 (polynucleotide) and 36 (polypeptide)) and pGAVP (N56K) (SEQ. ID. No:37 (polynucleotide) and 38 (polypeptide)), respectively.
Primer sequences was as follows:









pGAVP (C71V):



Forward primer (P13):



5′-GTTGCTCTGATTCTGTGCG-3′



 



Reverse primer (P14):



5′-TGACGTGTCAACAGGTCCC-3′



 



pGAVP (Y50W):



Forward primer (P15):



5′-GCTGATTCAGATTATGAACAGGC-3′



 



Reverse primer (P16):



5′-CAGCCCATAATGTCATAACCGC-3′



 



pGAVP (N56K):



Forward primer (P17):



5′-GAGGCCAAACCCCCAAGTAG-3′



 



Reverse primer (P18):



5′-TTCATAATCTGAATCAGATAGCCC-3′






GAVP (C71V) was constructed firstly and N56K mutation was introduced into VIVID (C71V) of GAVP (C71V) to obtain a double mutant-containing plasmid pGAVP (N56K+C71V) Recombinant light-switchable transcription factor GAVP (C71V), GAVP (N56K), GAVP (N56K+C71V) and GAVP (Y50W) fusion proteins have sequences of polypeptide, SEQ. ID. No: 34, 36, 38, 40, respectively, and the corresponding sequences of polynucleotide are SEQ. ID. No: 33, 35, 37, 39, respectively.
For subcloning the recombinant light-switchable transcription factor with LOV2 domain of phototropin 1 (AsLOV2, a kind gift from Gardner lab, The University of Texas at Dallas) as the second polypeptide, AsLOV2 was PCR amplified using primers 19 and 20 (see FIG. 10). VIVID of pGAVP(WT) was replaced with AsLOV2 by using BglII and EcoRI digestion, and the resulting mammalian cell expression vector containing Gal4-AsLOV2-p65 fusion protein gene was named as pGALP (SEQ. ID. No:43 (polynucleotide) and 44 (polypeptide)).
Primers for the amplification of AsLOV2:







Forward primer (P19):


5′-CTTTAGATCTTTCTTGGCTACTACACTTGAAC-3′


 


Reverse primer (P20):


5′-CTTTGAATTCACCTGATCCGCCACCAAGTTCTTTTGCCGCCTC-3′






For subcloning the recombinant light-switchable transcription factor with LOV domain of Aureochrome (AuLOV, a kind gift from Hironao Kataoka lab, Ritsumeikan University) as the second polypeptide, AuLOV was PCR amplified by using primers 21 and 22 (see FIG. 11). VIVID of pGAVP (WT) was replaced by AuLOV by BglII and EcoRI digestion, the resulting mammalian cell expression vector was named as pGAAP, and the fusion protein was GAAP (SEQ. ID. No:47 (polynucleotide) and 48 (polypeptide)).
Primers for the amplification of AuLOV:









Forward primer (P21):



5′-CTTTAGATCTCAGAATTTTGTGATAACTGAT-3′



 



Reverse primer (P22):



5′-CTTTGAATTCCACTAGCAACTTGGCGTAATC-3′






Example 3: Construction of Mammalian Cell Expression Vectors Containing the Recombinant Light-Switchable Transcription Factors Using Different Linkers Between the First Polypeptide and Second Polypeptide
Refer to FIG. 4 for the plasmid construction of this example. Linker between the first polypeptide and the second polypeptide of pGAVP (WT) described in Example 2 was optimized. pGAVP(WT) was amplified by reverse PCR using primers 23-28 to add different linkers between the first peptide and the second peptide, the resulting mammalian cell expression vectors were named as pGAVP(WT)-9, pGAVP(WT)-11 and pGAVP(WT)-12 containing recombinant light-switchable transcription factor GAVP(WT)-9 (SEQ. ID. No:59 (polynucleotide) and 60 (polypeptide)), pGAVP(WT)-11 (SEQ. ID. No:61 (polynucleotide) and 62(polypeptide)), pGAVP(WT)-12 (SEQ. ID. No:63 (polynucleotide) and 64 (polypeptide)), respectively.
Primer sequences were as follows:









pGAVP (WT)-9



Forward primer (P23):



5′-AGATCCATCGCCACCAGATCTCATACGCTCTACGCTCCCG-3′



 



Reverse primer (P24):



5′-CTTCCAGTCTTTCTAGCCTTGATTC-3′



 



pGAVP (WT)-11



Forward primer (P25):



5′-AGATCCATCGCCACCAGATCTCATACGCTCTACGCTCCCG-3′



 



Reverse primer (P26):



5′-GGATCCTCCACCACCTTCCAGTCTTTCTAGCCTTGATTC-3′



 



pGAVP (WT)-12



Forward primer (P27):



5′-TCATGAACCACAGATCTCATACGCTCTACGCTCCCGGCG-3′



 



Reverse primer(P28):



5′-CTTTCTGTTTCAGGTCGTTTTCCAGTCTTTCTAGCCTTG-3′






All the constructs were verified by DNA sequencing. Plasmids were prepared in transfection grade.
Example 4: Construction of Mammalian Cell Expression Vectors Containing Transcription Units (with Different Target Gene)
Refer to FIG. 5 for the plasmid construction of this example. For constructing expression vector containing the transcription unit with Gluc reporter gene, 5×UASG-TATA was amplified from pG5luc vector (Promega) (TATA is short for adenoviral E1b promoter) and Gluc gene was amplified from pGluc-basic (NEB), these two segment were fused by overlap PCR and ligated into NruI/BamHI site of pcDNA3.1(+)-hygro by homologous recombination. At the meanwhile, the CMV promoter of pcDNA3.1(+)-hygro was removed, the resulting vector pU5Gluc contains the transcription unit 5×UASG-TATA-Gluc (SEQ. ID. No:89 (polynucleotide)).
Expression vectors containing transcription units having Fluc, green fluorescent protein hrGFP or red fluorescent protein mCherry reporter gene were constructed as follows:
Gluc gene of pU5Gluc vector has HindIII/BamHI restriction site at its two ends. Fluc gene of pG5luc was double digested by HindIII/BamHI and then ligated into pU5Gluc to obtain reporter vector pU5Fluc containing the transcription unit 5×UASG-TATA-Fluc with Fluc reporter gene (SEQ. ID. No:86 (polynucleotide)).
Similarly, hrGFP and mCherry genes were amplified from pIRES-hrGFP (Stratagene) and synthesized mCherry gene using primers P29-30 and P31-32, respectively, and inserted into pU5Gluc by HindIII/BamHI double digestion to obtain vectors pU5hrGFP and pU5mCherry, which contain transcription units 5×UASG-TATA-hrGFP and 5×UASG-TATA-mCherry (SEQ. ID. No:87 (polynucleotide) and SEQ. ID. No:88 (polynucleotide)), respectively.
Primers for the amplification of hrGFP:









Forward primer (P29):



5′-CTTAAGCTTGCCACCATGGTGAGCAAGCAGATCCTG-3′



 



Reverse primer (P30):



5′-CAAGGATCCTTACACCCACTCGTGCAGGC-3′






Primers for the amplification of mCherry:









Forward primer (P31):



5′-CTTAAGCTTGCCACCATGGTGAGCAAGGGCGAG-3′



 



Reverse primer (P32):



5′-CAAGGATCCCTACTTGTACAGCTCGTCCATG-3′






For constructing expression vector containing the transcription unit with Simian virus 40 (SV40) promoter, SV40 promoter was amplified from pTRIPZ vector (Openbiosystem) using primers 33 and 34, and the obtained SV40 promoter fragment was inserted into pG5luc vector, which was digested with KpnI, by homologous recombination. The resulting vector pSU5Fluc contains the transcription unit with SV40 promoter (SEQ. ID. No:90 (polynucleotide)).







Forward primer (P33):


5′-TCGATAGGTACCCTGTGGAATGTGTGTCAGTTAGGGT-3′


 


Reverse primer (P34):


5′-TCCGTCTAGAAACTCGGTACCAGCTTTTTGCAAAAGCCTAGGC-3′






For constructing the expression vector containing the transcription unit with Insulin gene, Insulin gene containing HindIII and BamHI sites at its two ends was synthesized by Shanghai Generay Biotech Co. Ltd. pU5GLuc constructed in this sample was double digested by HindIII/BamHI sites and then the Gluc gene was replaced with Insulin gene, resulting the vector named pU5-Insulin (SEQ. ID. No:137 (polynucleotide), SEQ. ID. No:138 (polypeptide)).
All the constructs were verified by DNA sequencing. Plasmids were prepared in transfection grade.
Example 5: Construction of Saccharomyces cerevisrae Expression Vector Containing the Recombinant Light-Switchable Transcription Factor with Gal4, LexA, cI, TetR or Gcn4 as the First Polypeptide
Plasmids construction of this example is shown in FIG. 6. To construct the vector containing the recombinant light-switchable transcription factor Gal4-VIVID-Gal4AD (N56K+C71V) with Gal4 as the first polypeptide, pGADT7 from the yeast hybrid system (Clontech company) was amplified by PCR using primers P35 and P36 to remove its multiple clone site (MCS region) and Gal4AD sequence. Gal4-VIVID (N56K+C71V) was amplified from pGAVP (N56K+C71V) described in sample 2 by PCR using primers P37 and P38 and inserted into the linearized pGADT7 to create pGAD-GV(N56K+C71V) vector by recombination. pGAD-GV (N56K+C71V) is a transitional vector that can be used to obtain yeast expression vectors containing recombinant light-switchable transcription factors with the third polypeptide (such as Gal4AD).
In the experiment of recombination, primers for removing the multiple clone site and Gal4AD sequence of pGADT7:









Forward primer (P35):



5′-AGGATCCTGAGCTCGAGCTGCAGATGAATC-3′



 



Reverse primer (P36):



5′-CATCTTTGCAAAGCTTGGAGTTGATTG-3′






Primers for amplifying Gal4-VIVID (N56K+C71V):









Forward primer (P37):



5′-AGCTTTGCAAAGATGAAGCTACTGTCTTC-3′



 



Reverse primer (P38):



5′-CGAGCTCAGGATCCTTCCGTTTCGCACTGG-3′






Gal4AD gene was amplified from pGADT7 (Clontech company) by PCR using primers P39, P40 (containing nucleotide sequences encoding two different lengths of linkers) and P41, the obtained Gal4AD sequences contained two linkers with different lengths and were ligated into pGAD-GV(N56K+C71V) by BamHI/XhoI double digestion, the resulting vectors were named pGAD-GVG-L1(N56K+C71V) and pGAD-GVG-L2(N56K+C71V) containing Gal4-VIVID-Gal4AD-L1 (N56K+C71V) (SEQ. ID. No: 97 (polynucleotide), SEQ. ID. No:98 (polynucleotide)) and Gal4-VIVID-Gal4AD-L2(N56K+C71V) fusion protein genes (SEQ. ID. No:99 (polynucleotide), SEQ. ID. No:100 (polynucleotide)) with two different lengths of linkers, respectively (L1 and L2).
The forward primers for amplifying two Gal4AD sequences with different length of linkers:







Linker L1 (P39):


5′-CCCGGATCCGGTGGAGGTGGCTCCAATTTTAATCAAAGTGG-3′


 


Linker L2 (P40):


5′-CCCGGATCCGGTGGAGGTGGCTCCAATTTTAATCAAAGTGG-3′






The common reverse primer (P41):









5′-GGGCTCGAGTTACTCTTTTTTTGGGTTTGGTG-3′






To obtain pGPMA vector with a stronger promoter PMA1 that can increase the expression level of recombinant transcription factor, pGADT7 was amplified by PCR using primers P42 and P43 to generate the linearized fragment that lost PADH1 promoter sequence. At the meanwhile, PMA1 promoter fragment was amplified from pZF1/2-FRET (a gift from David J. Eide laboratory, University of Wisconsin-Madison, USA) by PCR using primers P44 and P45 and cloned into the linearized pGADT7 vector by recombination to obtain pGPMA. Construction of the following plasmids was based on pGPMA: pGPMA vector was amplified by PCR using primers P46 and P47, and then similarly to construction of pGAD-GV (N56K+C71V), Gal4-VIVID (N56K+C71V) gene fragment was cloned into the linearized pGPMA by recombination, the obtained pGPMA-GV (N56K+C71V) contains fusion protein gene Gal4-VIVID (N56K+C71V), which could be used to construct following yeast expression vectors.
To screen effective linkers for the following experiments, the effects of recombinant light-switchable factors with different linkers were determined. In detailed, Gal4AD was amplified from pGAD-GV (N56K+C71V) by PCR using primers P48-P54 that contain the nucleotide sequences encoding six kinds of linkers with different lengths, and then were ligated into pGPMA-GV(N56K+C71V) vector by BamHI/XhoI double digestion, the resulting vectors that contain fusion proteins Gal4-VIVID-Gal4AD-Ln(N56K+C71V) encoding genes with six kinds of linkers (L1, L2, L3, L4, L5 and L6) were named as pGPMA-GVG-L1 (N56K+C71V), pGPMA-GVG-L2 (N56K+C71V), pGPMA-GVG-L3 (N56K+C71V), pGPMA-GVG-L4 (N56K+C71V), pGPMA-GVG-L5 (N56K+C71V), pGPMA-GVG-L6 (N56K+C71V), respectively. Nucleotide sequences of these recombinant proteins are SEQ. ID. No:97, SEQ. ID. No:99, SEQ. ID. No:101, SEQ. ID. No:103, SEQ. ID. No:105 and SEQ. ID. No:107; Amino acid sequences were SEQ. ID. No:98, SEQ. ID. No:100, SEQ. ID. No:102, SEQ. ID. No:104, SEQ. ID. No:106 and SEQ. ID. No:108.
Primers for linearizing pGADT7 by PCR amplification:









Forward primer (P42):



5′-AGCTTTGCAAAGATGGCCATGGAGGCCAGTGA-3′



 



Reverse primer (P43):



5′-CATGCAAGCAACGAAGCATCTGTGCTTCATTTTG-3′






Primers for amplifying PMA1 promoter:









Forward primer (P44):



5′-TTCGTTGCTTGCATGGCCAAGCTTCCTGAAAC-3′



 



Reverse primer (P45):



5′-CATCTTTGCAAAGCTGCTGGGGTATATTTTTTTTC-3′






Primers for linearizing pGPMA by PCR amplification:









Forward primer (P46):



5′-AGGATCCTGAGCTCGAGCTGCAGATGAATC-3′



 



Reverse primer (P47):



5′-CATCTTTGCAAAGCTGCTGGGGT-3′






Forward primers for amplifying Gal4AD with six kinds of length of linkers:







Linker L1 (P48):


5′-CCCGGATCCGGTGGAGGTGGCTCCAATTTTAATCAAAGTGG-3′


 


Linker L2 (P49):


5′-CCCGGATCCGGCGGTGGTGGATCAGGTGGAGGTGGCTCCAAT-3′


 


Linker L3 (P50):


5′-CCCGGATCCGGTGGATCAGGTGGAGG-3′


 


Linker L4 (P51):


5′-CCCGGATCCGGAAGCGGCGGTGGTGGATCAGG-3′


 


Linker L5 (P52):


5′-CCCGGATCCGGTGGCGGCGGAAGCGGCGGTGGTG-3′


 


Linker L6 (P53):


5′-CCCGGATCCGGCGGAGGTGGGGGCTCCGGTGGCGGCGGAAG-3′






The common reverse primer (P54) is:









5′-GGGCTCGAGTTACTCTTTTTTTGGGTTTGGTG-3′






To construct yeast expression vector that contains recombinant light-switchable transcription factor NLS-LexA-VIVID-Gal4AD (N56K+C71V) (abbreviated to NLVG (N56K+C71V)) with LexA as the first peptide, LexA (1-87) was amplified from the genome of E. coli strain BL21 by PCR using primers P55 and P56 (see FIG. 12), VIVID (N56K+C71V) was amplified from pGAVP (N56K+C71V) described in example 2 using primers P57 and P58. LexA (1-87) and VIVID (N56K+C71V) were overlapped by overlapping PCR to obtain LexA-VIVID (N56K+C71V) gene fragment. SV40 nuclear localization signal gene fragment was amplified from pGADT7 vector (Clontech company) by PCR using primers P59 and P60 and overlapped with LexA-VIVID (N56K+C71V) resulting in NLS-LexA-VIVID (N56K+C71V) gene fragment. pGPMA-GVG-L2 (N56K+C71V) described in this example was amplified by PCR using primers P61 and P62, the linearized vector was ligated with NLS-LexA-VIVID (N56K+C71V) by EcoRI/BamHI double digestion, the resulting vector was named as pGPMA-NLVG (N56K+C71V) which contains recombinant protein gene NLVG (N56K+C71V) (SEQ. ID. No:7(polynucleotide) and SEQ. ID. No:8 (polypeptide)).
Primers for amplifying LexA (1-87):









Forward primer (P55):



5′-GGTGGCTCTGGAGGCATGAAAGCGTTAACGGCCAGGC-3′



 



Reverse primer (P56):



5′-AGATCTCGGTTCACCGGCAGCCACACG-3′






Primers for amplifying VIVID (N56K+C71V):









Forward primer (P57):



5′-GGTGAACCGAGATCTCATACGCTCTACGCTCCC-3′



 



Reverse primer (P58):



5′-CGAGCTCAGGATCCTTCCGTTTCGCACTGG-3′






Primers for amplifying NLS:









Forward primer (P59):



5′-CCCGAATTCTGCAAAGATGGATAAAGCGGAATTAATTCC-3′



 



Reverse primer (P60):



5′-GCCTCCAGAGCCACCACCGGCGGCGGTACCC-3′






Primers for linearizing pGPMA-GVG-L2 (N56K+C71V) by PCR amplification:









Forward primer (P61):



5′-CCCGGATCCGGCGGTGGTGGATCAGG-3′



 



Reverse primer (P62):



5′-CCCGAATTCGCTGGGGTATATTTTTTTTC-3′






To construct yeast expression vector that contains recombinant light-switchable transcription factor NLS-LacI-VIVID-Gal4AD (N56K+C71V) (abbreviated to NLcVG (N56K+C71V)) with LacI as the first polypeptide, DNA binding domain of LacI (1-62 amino acid) was amplified from commercial vector pCDFDuet1 (Novagen) by PCR using primers P63 and P64 (see FIG. 13), NLS gene fragment was amplified from commercial pGADT7 vector by PCR using primers P65 and P66, then LacI and NLS gene fragments were ligated by overlapping PCR, the obtained NLS-LacI gene fragment was inserted into pGPMA-NLVG (N56K+C71V) described in this example by EcoRI/BglII double digestion. The resulting vector was named as pGPMA-NLcVG (N56K+C71V) containing the gene of recombinant light-switchable transcription factor NLcVG (N56K+C71V) (SEQ. ID. No:11 (polynucleotide) and 12 (polypeptide)).
Primers for amplifying the DNA binding domain of LacI:









Forward primer (P63):



5′-GGCTCTGGAGGCATGAAACCAGTAACGTTATAC-3′



 



Reverse primer (P64):



5′-CCCAGATCTCAACGACTGTTTGCCCGCC-3′






Primers for amplifying NLS:









Forward primer (P65):



5′-CCCGAATTCATGGATAAAGCGGAATTAATTCC-3′



 



Reverse primer (P66):



5′-CCTCCAGAGCCACCGAACCGGCGGCGGTACCC-3′






To construct yeast expression vector that contains recombinant light-switchable transcription factor NLS-cI-VIVID-Gal4AD(N56K+C71V) with cI as the first peptide, DNA binding domain of cI(1-102 amino acid) was synthesized by Shanghai Generay Biotech Co. Ltd. and amplified by PCR using primers P67 and P68 (see FIG. 14), NLS gene fragment was amplified from commercial pGADT7 vector by PCR using primers P69 and P70, cI and NLS gene fragments were ligated by overlapping PCR, the obtained NLS-cI fragment was inserted into pGPMA-NLVG(N56K+C71V) vector described in this example by EcoRI/BglII double digestion. The resulting vector was named as pGPMA-NCVG (N56K+C71V) containing the gene of recombinant light-switchable transcription factor NCVG (N56K+C71V) (SEQ. ID. No:19 (polynucleotide) and 20 (polypeptide)).
Primers for amplifying the DNA binding domain of cI:









Forward primer (P67):



5′-GGTGGCTCTGGAGGCATGTCTACCAAGAAGAAAC-3′



 



Reverse primer (P68):



5′-CCCAGATCTATATTCTGACCTCAAAGACG-3′






Primers for amplifying NLS:









Forward primer (P69):



5′-CCCGAATTCTGCAAAGATGGATAAAGCGGAATTAATTCC-3′



 



Reverse primer (P70):



5′-GCCTCCAGAGCCACCACCGGCGGCGGTACCC-3′






To construct yeast expression vector containing the recombinant light-switchable transcription factor NLS-TetR-VIVID-Gal4AD (N56K+C71V) (abbreviated to NTVG (N56K+C71V)) with TetR as the first peptide, DNA binding domain of TetR (1-63 amino acid) synthesized by Shanghai Generay Biotech Co. Ltd. was amplified by PCR using primers P71 and P72 (see FIG. 15), NLS gene fragment was amplified from commercial pGADT7 vector by PCR using primers P73 and P74, TetR and NLS gene fragments were ligated by overlapping PCR, the obtained NLS-TetR gene fragment was cloned into pGPMA-NLVG (N56K+C71V) described in this example by EcoRI/BglII double digestion. The resulting vector was named as pGPMA-NCVG (N56K+C71V) containing the gene of recombinant light-switchable transcription factor NTVG (N56K+C71V) (SEQ. ID. No:15 (polynucleotide) and 16 (polypeptide)).
Primers for amplifying the DNA binding domain of TetR:









Forward primer (P71):



5′-GGTGGCTCTGGAGGCATGTCTAGGCTAGATAAG-3′



 



Reverse primer (P72):



5′-CCCAGATCTGGTGCCGTGTCTATCCAGCATCTC-3′






Primers for amplifying NLS:









Forward primer (P73):



5′-CCCGAATTCTGCAAAGATGGATAAAGCGGAATTAATTCC-3′



 



Reverse primer (P74):



5′-GCCTCCAGAGCCACCACCGGCGGCGGTACCC-3′






All the constructs were verified by DNA sequencing. Plasmids were prepared for the following yeast transformation.
Example 6: Construction of Saccharomyces cerevisiae Expression Vectors Containing the Genes of Recombinant Light-Switchable Transcription Factors with VIVID Mutants or AsLOV2 as the Second Polypeptides
Refer to FIG. 6 for the plasmid construction of this example. To construct vectors containing the genes of recombinant light-switchable transcription factors with VIVID mutants as the second polypeptide, pGPMA-GVG-L2(N56K+C71V) vector described in example 5 was double digested by BglII/BamHI sites to remove VIVID(N56K+C71V) sequence, VIVID(WT), VIVID(C71V) and VIVID(Y50W) gene fragments were amplified from pGAVP(WT), pGAVP(C71V) and pGAVP(Y50W) described in example 3 by PCR using primers P75 and P76, and then were ligated with pGPMA-GVG-L2(N56K+C71V) vector whose VIVID(N56K+C71V) gene fragment has been removed, the resulting vectors were named as pGPMA-GVG(WT), pGPMA-GVG(C71V) or pGPMA-GVG(Y50W) containing the genes of recombinant protein Gal4-VIVID-Gal4AD(WT) (abbreviated to GVG(WT), (SEQ. ID. No:113 (polynucleotide) and 114 (polypeptide)), Gal4-VIVID-Gal4AD (C71V) (abbreviated to GVG(C71V), (SEQ. ID. No:115 (polynucleotide) and 116 (polypeptide))) or Gal4-VIVID-Gal4AD(Y50W) (abbreviated to GVG(Y50W), SEQ. ID. No:117 (polynucleotide) and 118 (polypeptide)), respectively.
Primers for amplifying VIVID or its mutants:









Forward primer (P75):



5′-GGGAGATCTCATACGCTCTACGCTCCCG-3′



 



Reverse primer (P76):



5′-CGAGCTCAGGATCCTTCCGTTTCGCACTGG-3′






To construct yeast expression vector containing the gene of recombinant light-switchable transcription factor Gal4-AsLOV2-Gal4AD (abbreviated to GLG) with AsLOV2 as the second polypeptide, pGPMA-GVG-L2(N56K+C71V) vector described in example 6 was double digested by BglII/BamHI to remove the VIVID(N56K+C71V) gene fragment, AsLOV2 gene was amplified from pGALP described in example 2 by PCR using primers P77 and P78 and ligated with pGPMA-GVG-L2(N56K+C71V) whose VIVID(N56K+C71V) gene fragment has been removed, the obtained expression vector was named as pGPMA-GLG containing the gene of recombinant light-switchable transcription factor GLG (SEQ. ID. No:119 (polynucleotide) and 120 (polypeptide)).
Primers for amplifying AsLOV2:









Forward primer (P77):



5′-CCCAGATCTTTCTTGGCTACTACACTT-3′



 



Reverse primer (P78):



5′-CCCGGATCCAAGTTCTTTTGCCGCCTC-3′






All the constructs were verified by DNA sequencing. Plasmids were prepared for the following yeast transformation.
Example 7: Construction of Saccharomyces cerevisiae Expression Vectors Containing the Gene of Recombinant Light-Switchable Transcription Factor with VP16 or Gcn4 as the Third Polypeptide
Plasmids construction of this example is shown in FIG. 6. To construct yeast expression vector containing the gene of recombinant light-switchable transcription factor Gal4-VIVID-VP16 (N56K+C71V) (abbreviated to GVVP (N56K+C71V)) with VP16 as the third polypeptide, VIVID-VP16 (N56K+C71V) gene fragment was amplified from pGAVV (WT) constructed in sample 2 by PCR using primers P79 and P80, and then was ligated with pGPMA-GVG-L2 (N56K+C71V) described in example 5 by BglII/XhoI double digestion. The obtained vector was named as pGPMA-GVG-L2 (N56K+C71V) containing the gene of recombinant light-switchable transcription factor GAVE (N56K+C71V) (SEQ. ID. No:109 (polynucleotide) and 110 (polypeptide)).
Primers for amplifying VIVID-VP16 (N56K+C71V):









Forward primer (P79):



5′-GGGAGATCTCATACGCTCTACGCTCCCG-3′



 



Reverse primer (P80):



5′-GGGCTCGAGTGGCGATCCCGGACCCGGG-3′






To construct yeast expression vector containing the gene of recombinant light-switchable transcription factor Gal4-VIVID-Gcn4 (N56K+C71V) (abbreviated to GVGc(N56K+C71V)) with Gcn4 as the third polypeptide, the gene fragment of Gcn4 transcriptional activation domain was amplified from the genome of yeast strain BY4741 by PCR using primers P81 and P82 (see FIG. 16), pGPMA-GVG-L2(N56K+C71V) vector was amplified by PCR using primers P83 and P84, the obtained linearized vector contained EcoRI and XhoI sites at the two ends, then Gcn4 gene fragment was ligated into the linearized pGPMA-GVG-L2(N56K+C71V) by EcoRI/XhoI double digestion. The obtained vector was named as pMPMA-GVGc (N56K+C71V) that contains the gene encoding recombinant light-switchable transcription factor GVGc (N56K+C71V) (SEQ. ID. No:111 (polynucleotide) and 112 (polypeptide)).
Primers for amplifying Gcn4:









Forward primer (P81):



5′-CCCGAATTCATGTCCGAATATCAGCCAAGT-3′



 



Reverse primer (P82):



5′-GGGCTCGAGTTAGGATTCAATTGCCTTATC-3′






Primers for amplifying pGPMA-GVG-L2 (N56K+C71V):









Forward primer (P83):



5′-AGGATCCTGAGCTCGAGCTGCAGATGAATC-3′



 



Reverse primer (P84):



5′-CCCGAATTCGGAGCCACCTCCACCTGATCCAC-3′






All the constructs were verified by DNA sequencing. Plasmids were prepared for the following yeast transformation.
Example 8: Construction of Saccharomyces cerevisiae Expression Vectors Containing Target Transcription Units with the Reaction Elements of Gal4, LexA, CI, TetR or Gcn4
Plasmid construction of this example is shown in FIG. 7. To detect the effect of recombinant light-switchable transcription factor with Gal4 as the first peptide on the transcriptional regulation of EYFP gene, Saccharomyces cerevisiae expression vector containing the target transcription unit with Gal4 reaction element and fluorescent protein reporter gene was constructed. PYES2.1 TOPO (Invitrogen) was amplified by PCR using primers P85 and P86, the obtained linearized vector backbone contained BamHI and EcoRI sites. EYFP gene was amplified from pZF1/2-FRET (a gift from David J. Eide lab, Wisconsin university in Madison in USA) by PCR using primers P87 and P88 and ligated with the linearized pYES2.1 TOPO by BamHI/EcoRI double digestion. The obtained vector pYE-EYFP contains the target transcription unit 5×UASG-Gal1-EYFP (SEQ. ID. No:121 (polynucleotide))
Primers for linearizing pYES2.1 TOPO by PCR amplification:









Forward primer (P85):



5′-CCCGAATTCAGGGCGAGCTTCGAGGTCACC-3′



 



Reverse primer (P86):



5′-CCCGGATCCGGGCGAGCTTAATATTCCCTATAG-3′






Primers for amplifying EYFP:









Forward primer (P87):



5′-CCCGGATCCAAAAAAATGGTGAGTAAAGGAG-3′



 



Reverse primer (P88):



5′-GGGGAATTCTTATTTGTATAGTTCATC-3′






To detect the effects of target transcription units with different number of Gal4 reaction elements on the recombinant light-switchable transcription factor regulated EYFP gene transcription, yeast expression vectors containing target transcription units with different number of Gal4 reaction elements were constructed. pYE-EYFP constructed in this example contains five Gal4 reaction elements, i.e. 5×UASG. pYE-EYFP was amplified by PCR using primers P89-P92, the obtained three pYE-EYFP vectors lacked one, two or four Gal4 recognition/binding sites in the target transcription unit, and were named as pYE-EYFP(1×UASG), pYE-EYFP(3×UASG) or pYE-EYFP(4×UASG) containing the transcription unit 1×UASG-Gal1-EYFP (SEQ. ID. No:122 (polynucleotide)), 3×UASG-Gal1-EYFP (SEQ. ID. No: 123 (polynucleotide)) and 4×UASG-Gal1-EYFP (SEQ. ID. No:124 (polynucleotide)), respectively. The forward primers for amplification are different, while the reverse primers are the same, their sequences are as following:









Common reverse primer (P89):



5′-TACTAGTGGATCATCCCCACGCGCC-3′



 



Forward primer 1(90):



5′-CCCGAATTCAGGGCGAGCTTCGAGGTCACC-3′



 



Forward primer 2(P91):



5′-CCCGAATTCAGGGCGAGCTTCGAGGTCACC-3′



 



Forward primer 3(P92):



5′-CCCGAATTCAGGGCGAGCTTCGAGGTCACC-3′






To detect the effect of recombinant light-switchable transcription factor with LexA as the first polypeptide, Saccharomyces cerevisiae expression vector containing target transcription unit with the LexA reaction element was constructed. pYE-EYFP in this example was amplified by PCR using primers P93 and P94 to remove the 5×UASG sequence, the linearized vector was double digested by XhoI/HindIII sites and ligated with the fragment from the annealing product of primers P95 and P96. The resulting vector was named as pYEL4-EYFP containing the target transcription unit 4×LexA UAS-Gal1-EYFP (SEQ. ID. No:125 (polynucleotide)).
Primers for linearizing pYE-EYFP by PCR amplification:









Forward primer (P93):



5′-CCCAAGCTTTAATGCGATTAGTTTTTTAG-3′



 



Reverse primer (P94):



5′-TAGGCTCGAGCCCACGCGCCCTGTAGCGC-3′






Primers for annealing:







Forward primer (P95):


5′-TCGAGGGCGTTCGTCCTCACTGTATGATCATACAGTCTGTATATAT


 


ATACAGTACTGTATGATCATACAGGTTCCTGAAACGCAGATGTGCCTAC


 


TGTATATATATACAGTAACAATAAAGATTCA-3′


 


Reverse primer (P96):


5′-AGCTTGAATCTTTATTGTTACTGTATATATATACAGTAGGCACATC


 


TGCGTTTCAGGAACCTGTATGATCATACAGTACTGTATATATATACAGA


 


CTGTATGATCATACAGTGAGGACGAACGCCC-3′






To detect the effect of recombinant light-switchable transcription factor with LacI as the first polypeptide, Saccharomyces cerevisiae expression vector containing target transcription unit with the LacI reaction element was constructed. pYEL4-EYFP in this example was double digested by XhoI/HindIII sites and ligated with the fragment from the annealing product of primers P97 and P98, the resulting vector was named as pYELc4-EYFP that contains the target transcription unit 4×LacI UAS-Gal1-EYFP (SEQ. ID. No: 126 (polynucleotide)).
Primers for annealing:







Forward primer (P97):


5′-TCGAGAATTGTGAGCGGATAACAATTGTAATTGTGAGCGGATAACA


 


ATTATTTGAATTGTGAGCGGATAACAATTGTAATTGTGAGCGGATAACA


 


ATTA-3′


 


Reverse primer (P98):


5′-AGCTTAATTGTTATCCGCTCACAATTACAATTGTTATCCGCTCACA


 


ATTCAAATAATTGTTATCCGCTCACAATTACAATTGTTATCCGCTCACA


 


ATTC-3′






To detect the effect of recombinant light-switchable transcription factor with cI as the first polypeptide of cI, Saccharomyces cerevisiae expression vector containing target transcription unit with the cI reaction element was constructed. pYEL4-EYFP in this example was double digested by XhoI/HindIII sites and ligated with the fragment from the annealing product of primers P99 and P100, the resulting vector was named as pYEPR-EYFP that contains the target transcription unit PRUAS-Gal1-EYFP (SEQ. ID. No:127 (polynucleotide)).
Primers for annealing:







Forward primer (P99):


5′-TCGAGTAAATCTATCACCGCAAGGGATAAATATCTAACACCGTGCG


 


TGTTGACTATTTTACCTCTGGCGGTGATAATGGTTGA-3′


 


Reverse primer (P100):


5′-AGCTTCAACCATTATCACCGCCAGAGGTAAAATAGTCAACACGC


 


ACGGTGTTAGATATTTATCCCTTGCGGTGATAGATTTAC-3′






To detect the effect of recombinant light-switchable transcription factor with TetR as the first polypeptide, Saccharomyces cerevisiae expression vector containing target transcription unit with the TetR reaction element was constructed. pYEL4-EYFP in this example was double digested by XhoI/HindIII sites and ligated with the fragment from the annealing product of primers P101 and P102, the resulting vector was named as pYET4-EYFP that contains the transcription unit 4×TetR UAS-Gal1-EYFP (SEQ. ID. No:128 (polynucleotide)).
Primers for annealing:







Forward primer (P101):


5′-TCGAGCCACTCCCTATCAGTGATAGAGAAAAGTCCACTCCCTATCA


 


GTGATAGAGAAAAGTCCACTCCCTATCAGTGATAGAGAAAAGTCCACTC


 


CCTATCAGTGATAGAGAAAAGTA-3′


 


Reverse primer (P102):


5′-AGCTTACTTTTCTCTATCACTGATAGGGAGTGGACTTTTCTCTATC


 


ACTGATAGGGAGTGGACTTTTCTCTATCACTGATAGGGAGTGGACTTTT


 


CTCTATCACTGATAGGGAGTGGC-3′






Example 9: Construction of Mammalian Cell Expression Vectors Containing Recombinant Hormone and Light Dual-Regulated Transcription Factors with Different Fifth Polypeptides
Refer to FIG. 4 for the plasmid construction of this example. The 272-606 amino acid ligand-binding domain of EcR (Bombyx mori ecdysone receptor) gene was amplified from pCS2-GVVEcR F′ (a kind gift from James K Chen lab, Stanford University School of Medicine in California) by PCR using primers 103 and 104; ER (estrogen receptor, ligand-binding domain 282-595 amino acid) gene was amplified from ER-CRE vector (a kind gift from Zhiqi Xiong lab, Shanghai Institutes for Biological Sciences) by PCR using primer 105 and 106; hPR (human progesterone receptor 640-891 amino acid) gene was amplified from pSwitch (Invitrogen) by PCR using primer 107 and 108. EcR, ER or hPR gene was ligated into pGAVP (N56K+C71V) by MluI/SpeI double digestion to obtain recombinant hormone and light dual-regulated transcription factor GAVPEcR (SEQ. ID. No:131 (polynucleotide) and 132 (polypeptide), GAVPER (SEQ. ID. No:133 (polynucleotide) and 134 (polypeptide) or GAVPhPR (SEQ. ID. No:135 (polynucleotide) and 136 (polypeptide), the resulting mammalian cell expression vectors were named as pGAVPEcR, pGAVPER and pGAVPhPR, respectively.
Primer sequences were as following:









pGAVPEcR:



Forward primer (P103):



GACTACGCGTATGAGGCCTGAATGTGTCATACAG



 



Reverse primer (P104):



GACTACTAGTTAGCACCACCGGGTTGGTG



 



pGAVPER:



Forward primer (P105):



GACTACGCGTTCTGCTGGAGACATGAGAGCTG



 



Reverse primer (P106):



GACTACTAGTAGCTGTGGCAGGGAAACCC



 



pGAVPhPR:



Forward primer (P107):



GACTACGCGTAAAAAGTTCAATAAAGTCAGAGTTGTG



 



Reverse primer (P108):



GACTACTAGTAGCAATAACTTCAGACATCATTTCTG






Example 10: Regulation of Gene Expression by Recombinant Light-Switchable Transcription Factor in Mammalian Cells
All of cell lines used in this example were cultured in CO2 incubator in DMEM containing 10% fetal bovine serum (FBS) and penicillin-streptomycin, and subcultured when cell density reach 80-90% confluence. Transfection was carried out by following the Lipofectamine 2000 manual. Fluc assay was carried out refer to “Molecular biology experiment reference manual” (Jane Roskams); Gluc activity was determined by using BioLux® Gaussia Luciferase Assay Kit (NEB) according to the manufacturer's instruction. Sample 11, 13, 14 and 15 also utilized the same experiment methods.
Fluc was used as the reporter gene to test light-regulated gene expression by recombinant light-switchable transcription factor with VIVID and its mutants as the second polypeptide. HEK293 cells with 90-95% density were seeded into two identical 48 well plates 16 h before transfection, pU5Fluc described in sample 4 with pGAVV(WT) or pGAVP(WT) or pGAVP(C71V) or pGAVP(Y50W) or pGAVP(N56K) or pGAVP(C71V+N56K) or pEGFP-N1 described in sample 2 was co-transfected into HEK293 cells, manipulation of the two plates was the same. Then one plate was cultured in darkness, while the other was illuminated for 1 s every 30 s 6 h after transfection, the light source was blue LED above mentioned, Fluc activity was determined 22 h after illumination. The result showed that Fluc activity of cells without recombinant light-switchable transcription factor and dark group cells with light-switchable transcription factor almost equaled to untransfected cells, while light group cells expressing these recombinant light-switchable transcription factors showed higher Fluc expression than dark group, which indicated that these light-switchable transcription factors could regulate the target gene expression level in cells. In detailed, the target gene expression in cells expressing GAVP(WT) after illumination was 13-fold greater than the dark group; light-regulated Fluc expression level mediated by GAVP(WT) was dozen of times than GAVV(WT), indicating GAVP(WT) transcription factor with p65AD as the third polypeptide had stronger induction capacity (FIG. 17). Induction ratios of recombinant light-switchable transcription factors GAVP(C71V), GAVP(N56K), GAVP(Y50W), GAVP(N56K+C71V), containing different mutants of VIVID, were higher than GAVP(WT) with wild type VIVID in different degree; the recombinant light-switchable transcription factor GAVP(N56K+C71V) with double mutations had the highest induction ratio which could achieve 200-fold (FIG. 18). We concluded that all of light-switchable transcription factors with VIVID or its mutants as the second polypeptide may activate gene expression after blue light illumination.
The system in the invention can be applied to a variety of mammalian cells. Fluc was used as the reporter gene, pGAVP(N56K+C71V) and pU5Fluc vectors were co-transfected into NIH3T3 or COS-7 cell lines, cells culture, transfection, blue light induction, cell manipulation and determination of the expressed Fluc were the same as the description in the first paragraph of this example. The result indicated that the cell expressing GAVP (N56K+C71V) could activate the target gene (Flue) expression after light irradiation in NIH3T3 or COS-7 cell lines (FIG. 19, 20). Fluc was used as the reporter gene to detect the regulation of recombinant light-switchable transcription factor with different linkers between the first peptide and second peptide on the target gene expression after light illumination, pU5Fluc with pGAVP(WT)-9 or pGAVP(WT)-11 or pGAVP(WT)-12 described in sample 2 were co-transfected into HEK293 cells, cells culture, transfection, blue light induction, cell manipulation and determination of the expressed Fluc were the same as the description in the first paragraph of this example. The result showed that light-switchable transcription factors GAVP(WT)-9, GAVP(WT)-11 and GAVP(WT)-12 could activate Fluc expression after light illumination, but the induction ratios were different, GAVP(WT)-12 had the highest induction ratio (FIG. 21).
To detect the regulation of gene expression by recombinant light-switchable transcription factor with AsLOV2 as the second polypeptide in mammalian cells, Fluc was used as the reporter gene to detect the regulation of gene expression by the recombinant light-switchable transcription factor Gal4-AsLOV2-p65 (abbreviated to GALP). pU5Fluc with pGALP constructed in sample 2 were co-transfect into HEK293, cells culture, transfection, blue light induction, cell manipulation and determination of the expressed Fluc were the same as the description in the first paragraph of this example. The result showed that Fluc expression of light group was lower that dark group, which was approximately half of the dark group, indicating that the recombinant light-switchable transcription factor GALP could decrease the target gene expression after light illumination (FIG. 22).
To detect the regulation of gene expression by recombinant light-switchable transcription factor with AuLOV as the second polypeptide in mammalian cells, Fluc was used as the reporter gene to detect the regulation of gene expression by the recombinant light-switchable transcription factor Gal4-AuLOV-p65 (abbreviated to GAAP). pU5Fluc with pGAAP constructed in sample 2 were co-transfect into HEK293, cells culture, transfection, blue light induction, cell manipulation and determination of the expressed Fluc were the same as the description in the first paragraph of this example. The result showed that Fluc gene expression of light group was higher that dark group, indicating that the recombinant light-switchable transcription factor GAAP could increase the target gene expression after light illumination (FIG. 23).
To detect the regulation of gene expression by recombinant light-switchable transcription factor with KRAB as the third polypeptide in mammalian cells, the effect of recombinant light-switchable transcription factor GAVK (C71V) on gene expression upon light exposure was detected. pU5Fluc vector constructed in sample 4 and pGAVK (C71V) vector constructed in sample 1 were co-transfected into HEK293 cells, cells culture, transfection, blue light induction, cell manipulation and determination of the expressed Fluc were the same as the description in the first paragraph of this example. The result indicated that the recombinant light-switchable transcription factor GAVK (C71V) could decrease Fluc expression level after light illumination (FIG. 24).
Example 11: Regulation of Gene Expression by Recombinant Light-Switchable Transactivation Factor in Stable Cell Line
To establish stable cell line expressing light-switchable transcription factor GAVP (C71V), pGAVP(C71V) vector described in example 2 was transfected into HEK293 cells, cells were and seeded into 100 mm dish 48 h after transfection. 24 h later, media was refreshed using medium with additional 600 μg/mL G418 and repeated every two days in the following 3 weeks. After that, 10 monoclonal cell lines were selected by serial dilution in the survival cells. These monoclonal cell lines were seeded into 48 well plate, and transfected with pU5Fluc vector constructed in sample 4 to detect whether these cell lines expressed the recombinant light-switchable transcription factor, if yes, cells could express Fluc gene after light illumination. Blue light induction, cell manipulation and determination of the expressed Fluc were the same as sample 10. The result showed that, clone 2, 4, 5, 6, 9 contained the recombinant light-switchable transcription factor; clone 2 showed the highest Fluc expression level after illumination, the induction ratio was approximate 30-fold which was similar to transient transfection of the recombinant light-switchable transcription factor. These results indicated that the recombinant light-switchable transcription factor gene integrated into the genome could regulate the expression level of target gene (FIG. 25).
Example 12: Regulation of Gene Expression by Recombinant Light-Switchable Transcription Factors in Saccharomyces cerevisiae Cells
Protocol for the detection of fluorescent protein EYFP expressed by yeast cells: clones on the transformed plate were picked and incubated at 240 rpm and 30° C. in incubator shakers under darkness. 500 μl of the overnight cultured cells was diluted into two tubes with 4.5 mL fresh YPDA medium, one was illuminated by blue light exposure while the other was kept in darkness, the cells were kept at 240 rpm and 30° C. until the OD600 reached 0.8-1.0. 500 μl of the cultured cells was harvested in 1.5 mL tube and centrifuged at 4000 rpm for 5 min, then the supernatant was discarded and cells were washed with 1 mL PBS for twice. The cells were suspended to the OD600 around 0.5 using PBS. (Ensure the accuracy of the fluorescence determination). 100 μl of the supernatant was added to the 96-well black plate, the fluorescence was measured by Synergy 2 multi-mode microplate reader (BioTek) with excitation wavelength of 485±20 nm and emission wavelength of 528±20 nm. Each data point represents the average of 3 replicates. To detect the effect of recombinant light-switchable transcription factor GVG-L2 (N56K+C71V) constructed in sample 5 on regulation of gene expression in yeast cells, the effect of GVG-L2 (N56K+C71V) on the expression of EYFP upon blue light exposure was measured. pGPMA-GVG-L2(N56K+C71V) constructed in example 5 and pYE-EYFP constructed in example 8 were co-transformed into AH109 strain, co-transformation of empty pGPMA vector and pYE-EYFP into AH109 cell was used as the control. The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured; the result indicated that the recombinant light-switchable transcription factor GVG-L2 (N56K+C71V) could increase the expression level of EYFP in AH109 cells upon blue light exposure (FIG. 26).
To detect the effect of recombinant light-switchable transcription factor GVVP (N56K+C71V) on the regulation of gene expression in yeast cells, the effect of GVVP (N56K+C71V) described in example 7 on the expression of EYFP upon blue light exposure was measured. pGPMA-GVVP (N56K+C71V) described in example 7 and pYE-EYFP described in example 8 were co-transformed into AH109 strain, co-transformation of empty pGPMA vector and pYE-EYFP into AH109 cell was used as the control. The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured. The result showed that the recombinant light-switchable transcription factor GVVP (N56K+C71V could effectively increase the expression level of EYFP in AH109 cells upon blue light exposure (FIG. 27).
To detect the effect of recombinant light-switchable transcription factor GVGc (N56K+C71V) on the regulation of gene expression in yeast cells, the effect of GVGc (N56K+C71V) described in example 7 on the expression of LacZ upon blue light exposure was measured. pGPMA-GVGc (N56K+C71V) described in example 7 was transformed into AH109 strain, transformation of empty pGPMA vector into AH109 cell was used as the control. The expression level of LacZ of the cells upon blue light exposure or under darkness was measured according to the Yeast protocols handbook from Clontech Company. The result indicated that the recombinant light-switchable transcription factor GVGc (N56K+C71V) effectively increased the expression level of LacZ in AH109 cells, the induction ratio could reach nearly 10 folds (FIG. 28).
To detect the effects of recombinant light-switchable transcription factor GVG(N56K+C17V) containing different linkers on the regulation of gene expression in yeast cells, pGPMA-GVG-L1 (N56K+C71V), pGPMA-GVG-L2 (N56K+C71V), pGPMA-GVG-L3 (N56K+C71V), pGPMA-GVG-L4 (N56K+C71V), pGPMA-GVG-L5 (N56K+C71V) or pGPMA-GVG-L6 (N56K+C71V) was transformed into AH109 strain, transformation of empty pGPMA vector into AH109 cell was used as the control. The expression level of LacZ of the cells upon blue light exposure or under darkness was measured. The results showed that all the recombinant light-switchable factor GVG(N56K+C17V) with different linkers could regulate the LacZ expression but had different expression level of LacZ, recombinant light-switchable factors with linker L1, L3 and L6 had the higher expression level of LacZ, i.e. they had the highest activation capacity after light illumination. (FIG. 29).
To detect the effects of different expression levels of recombinant light-switchable transcription factor Gal4-VIVID-Gal4AD on the regulation of gene expression in yeast cells, pGAD-GVG-L1 (N56K+C71V), pGAD-GVG-L2 (N56K+C71V), pGPMA-GVG-L1 (N56K+C71V) or pGPMA-GVG-L2 (N56K+C71V) was co-transformed with pYE-EYFP described in example 8 into AH109 strain, The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured. The EYFP expression level regulated by Gal4-VIVID-Gal4AD under PMA1 promoter was higher than ADH1 promoter probably due to that PMA promoter had stronger initiation capacity than ADH1 promoter. The result indicated more Gal4-VIVID-Gal4AD resulted in higher expression level of EYFP in AH109 cells at the same conditions (FIG. 30).
To detect the effects of the recombinant light-switchable transcription factors Gal4-VIVID-Gal4AD with VIVID mutants on the regulation of gene expression in yeast cells, pGPMA-GVG (WT), pGPMA-GVG(C71V) or pGPMA-GVG(Y50W) was co-transformed with pYE-EYFP described in example 8 into AH109 cells, co-transformation of empty pGPMA vector and pYE-EYFP into AH109 cell was used as the control. The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured. The results showed that all the recombinant light-switchable transcription factors Gal4-VIVID-Gal4AD with different VIVID mutants we tested could increase the expression level of EYFP (FIG. 31).
To detect the effect of the recombinant light-switchable transcription factor GLG on the regulation of gene expression in yeast cells, pGPMA-GLG described in example 6 was transformed into AH109 strain, transformation of empty pGPMA vector into AH109 cell was used as the control. The expression level of LacZ of the cells upon blue light exposure or under darkness was measured. The result demonstrated that GLG could decrease the expression level of LacZ in AH109 cells; the induction ratio was about 0.8 fold (FIG. 32).
To detect the effects of recombinant light-switchable transcription factor on the regulation of EYFP expression when the target transcription unit contained different number of Gal4 reaction element, pYE-EYFP(1×UASG), pYE-EYFP(3×UASG), pYE-EYFP(4×UASG) or pYE-EYFP were co-transformed with pGPMA-GVG(N56K+C71V) described in example 5 into BY4741 strain. The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured. The result indicated that the EYFP expression level decreased along with the reduced number of Gal4 recognition elements at the same conditions, but the induction ratio remained almost the same (FIG. 33).
To detect the effects of recombinant light-switchable transcription factors NLVG(N56K+C71V), NLcVG(N56K+C71V), NCVG(N56K+C71V) or NTVG(N56K+C71V) on the regulation of gene expression in yeast cells, pGPMA-NLVG(N56K+C71V), pGPMA-NLcVG(N56K+C71V), pGPMA-NCVG(N56K+C71V) or pGPMA-NTVG(N56K+C71V) were co-transformed with pYEL4-EYFP, pYELc4-EYFP, pYEPR-EYFP or pYET4-EYFP into AH109 cells, respectively. The EYFP fluorescence of the cells upon blue light exposure or under darkness was measured. The result showed that all the four recombinant light-switchable transcription factors could increase the expression level of EYFP after blue light illumination while NLVG (N56K+C71V) had the highest induction ratio (FIG. 34).
Example 13: Characteristics of Gene Expression Regulation by the Recombinant Light-Switchable Transcription Factor Upon Light Illumination
Time course and reversibility of light-switchable transcription factor regulated gene expression were tested by co-transfection of pGAVP (N56K+C71V) constructed in sample 2 and pU5Gluc constructed in sample 4 into HEK293 cells, cells were seeded into 3 plates and their culture and transfection were the same. Two of the three plates were given illumination 10 h after transfection for 1 s every 30 s, and one of the two plates was transferred to darkness 15 h after illumination for reversibility study. The last one was kept in dark all the time as dark group sample. Samples were collected for Gluc assay at indicated time under red LED light according to sample 11. The result showed that Gluc expression level increased significantly after light illumination in recombinant light-switchable transcription factor GAVP (N56K+C71V) expressing cells. The induction ratio could achieve 30-fold, 100-fold after 3 h, 12 h illumination, respectively. For the reversibility sample (light-dark), Gluc expression gradually decreased and stopped 15 h after turning the light off (FIG. 35). These results indicated that the expression level of target gene induced by the light-switchable transcription factor in this invention increased along with the raising time, gene expression gradually stopped after removal of light, demonstrating this process is reversible.
To evaluate the gene expression regulated by light-switchable transcription factor in different light irradiance, pGAVP (N56K+C71V) constructed in sample 3 and pU5Fluc vector were co-transfected into HEK293 cells, the cells were divided into two plates, cell sample at the same conditions had three replicates, one plate was illuminated 6 h after transfection for 1 s every 30 s, neutral density filters were used to adjust the light intensity (Light intensity determine by a laminator (Sanwa)). 22 h after illumination, the cells were lysed and Fluc activity was determined. The result showed that recombinant light-switchable transcription factor GAVP(N56K+C71V) induced Fluc expression level depended on light intensity, demonstrating that gene expression level regulated by the recombinant light-switchable transcription factor in this invention depended on light intensity (FIG. 36).
To evaluate the gene expression regulated by light-switchable transcription factor in different illumination frequencies, pGAVP (N56K+C71V) vector and pU5Fluc vector were co-transfected into HEK293 cells, the cells were divided into three plates, cell sample at the same conditions had three replicates. Cells were illuminated 6 h after transfection for 1 s every 30 s, 1 s every 60 s, 1 s every 120 s, respectively. 22 h after illumination, the cells were lysed and Fluc activity was determined. The result showed that Fluc activity was the highest when illuminated is every 30 s and was the lowest when illuminated 1 s every 120 s, indicating that higher frequency of light illumination could result in higher gene expression level when the light intensity was the same (FIG. 37).
To observe recombinant light-switchable transcription factor regulated gene expression, mCherry and hrGFP were used as the reporter genes, pGAVP (N56K+C71V) and pU5mCherry or pU5hrGFP were co-transfected into HEK293 cells. 10 h after transfection, cells were illuminated for 20 s every 10 min. 24 h later, images were taken using an Eclipse Ti inverted microscope system (Nikon). The results were shown in FIG. 38 and FIG. 39, cells expressing mCherry or hrGFP reporter gene were in normal morphology before and after light illumination. Cells expressing fluorescent protein mCherry increased after light illumination which could reach more than 50% of the total cells, and its fluorescence intensity was higher than background. To directly observe fluorescent protein expression regulated by recombinant light-switchable transcription factor GAVP (N56K+C71V), the cells used for imaging were lysed by adding 280 μl cell lysis buffer, then the protein concentration of each sample was determined using DC protein assay kit; after that, equal amounts of cell lysate (10 mg) were loaded on 15% native PAGE and ran for 2 h in 20 mA constant current. The gel was imaged with 4×4 binning in Kodak In-Vivo Multispectral System FX (for mCherry, ex 550 nm/em 600 nm; for hrGFP, ex 480 nm/em 535 nm). The method of native PAGE can be seen in Short protocols in Protein Science written by Coligan J. E. et al, and translated by Shentao Li et al, page 303-307. The result was shown in FIG. 40, “+” referred to “yes”, i.e. using corresponding condition or eukaryotic expression vector, “−” referred to “no”. The result showed nearly no fluorescent protein expressed in cells only containing target transcription unit but without recombinant light-switchable transcription factor both in darkness and upon light exposure, while the cells expressing both target transcription unit and recombinant light-switchable transcription factor showed higher fluorescent protein (mCherry or hrGFP) expression upon light illumination than in the darkness, nearly no fluorescence was observed in cells kept in darkness, indicating the recombinant light-switchable transcription factor GAVP(N56K+C71V) had low leak expression and high induction capacity.
Transcription level of recombinant light-switchable transcription factor induced gene transcription was evaluated by RT-PCR (reverse transcriptional PCR). pGAVP (N56K+C71V) constructed in sample 2 and pU5Fluc constructed in sample 4 were co-transfected into HEK293 cells in 24 well plates, cell culture, transfection and induction method were the same as described in example 10. Total RNA of these samples was extracted using RNA isolation kit according to the instructions (Tiangen). RNA concentration was determined and 0.5 μg RNA was reverse transcripted into cDNA using ImpromII reverse transcriptase. Refer to P109 and P110 for primers for Flue, and refer to P111 and P112 for primers for internal reference gene actin. Approach of RT-PCR was the same as routine PCR using Taq DNA polymerase with 1 kb/min for 28 cycles. The result showed that no visible band was observed when cells transfected with pU5Fluc or pGAVP (N56K+C71V) alone, and a bright band existed in co-transfection and light irradiation cells but only a faint band in dark cells, indicating that recombinant light-switchable transcription factor GAVP (N56K+C71V) could activate gene transcription after light illumination, there was significant difference between samples kept in darkness and in light (FIG. 41).
RT-PCR primer for Flue gene:









Forward primer (P109):



5′-GAGATACGCCCTGGTTCCTG-3′



 



Reverse primer (P110):



5′-CGAAATGCCCATACTGTTGAG-3′






RT-PCR primer for Actin gene:









Forward primer (P111):



5′-CATGTACGTTGCTATCCAGGC-3′



 



Reverse primer (P112):



5′-CTCCTTAATGTCACGCACGAT-3′






Example 14: Regulation Gene Expression by Recombinant Light-Hormone Dual-Regulated Transcription Factors in Mammalian Cells
To evaluate gene expression regulated by recombinant light-hormone dual-regulated transcription factors, Glue was used as the reporter gene to detect the gene expression regulated by light and ligand of EcR, ER or hPR in HEK293 cells. pU5Gluc with pGAVPEcR, pGAVPER or pGAVPhPR constructed in sample 9 were co-transfected into two identical plates of HEK293 cells. Cells were cultured in the dark for 8 hours, ligands of receptors (EcR: Tebufenozide; ER: 4-OHTamxoifen; the hPR: Mifepristone) were added at the final concentration of 1 μM under red light illumination; then one plate was wrapped in aluminum foil and placed in dark while the other was illuminated for 1 s every 30 s. After 22 h induction, medium was collected and Glue activity was analyzed. Cells transfected with pU5Gluc and pEGFP-N1 containing no recombinant light-switchable transcription factor was used as negative control. The result showed that Glue activity of cells in negative control group was very low both in dark and in light conditions, Glue activity of cells with those three recombinant light-hormone dual-regulated transcription factors were higher in the presence of both light and hormone than cells in dark condition without ligand or cells in dark condition with ligand or cells in light condition without ligand, indicating the recombinant light-hormone dual-regulated transcription factors could utilize light and hormone to co-regulated gene expression in cells. In detailed, Gluc activity of cells transfected with pGAVPEcR, pGAVPER or pGAVPhPR in the absence of ligand and in dark conditions was extremely low and was similar to the cells containing no recombinant light-hormone dual-regulated transcription factors, Gluc activity in HEK293 cells increased 4-5 folds with light illumination but no ligand or in the presence of ligand but without light, while in the presence of both light and ligand (EcR: Tebufenozide; ER: 4-OHTamxoifen; hPR: Mifepriston), Gluc activity increased 1000, 500, 60 folds in pGAVPEcR, pGAVPER, pGAVPhPR expressing cells respectively (FIG. 42), indicating that recombinant light-hormone dual-regulated transcription factor could regulate gene expression in mammalian cells.
Example 15: Spatiotemporally Regulate Gene Expression by Recombinant Light-Switchable Transcription Factors in Mammalian Cells
On the one hand, neutral density filter as photomask was used to study recombinant light-switchable transcription factors regulated gene expression in spatiotemporal resolution. mCherry was used as the reporter gene, pU5mCherry vector and pGAVP (N56K+C71V) vector were co-transfected into HEK293 cells in 96 quadrate well plate. 10 h after transfection, cells were illuminated by blue light for 1 s every 30 s, graded light intensity was adjusted by neutral density filter. 24 h after illumination, the medium was removed and the imaging was conducted using the In-Vivo Multispectral System FX (Kodak) with 550 nm excitation and 600 nm emission filters for the mCherry, image was collected in 4×4 binning for 5 min exposure. The result indicated that cells showed graded expression level by neutral density filter adjustment, and mCherry achieved the highest expression level when no neutral density filter was added (FIG. 43).
On the other hand, to display spatiotemporally regulated gene expression capacity, printed laser transparency film was used as photomask to “take photos” for cells. A “ECUST” pattern was printed and a gradient slider on laser transparency film using a laser printer was used as photomask, the light intensity of transparent space detected by a luminator was 30 times more than the black space. HEK293 cells were seeded in glass bottom dish (NEST), pU5mCherry with pGAVP (N56K+C71V) were co-transfected and the photomask was pasted on the bottom of the dish, the cells were illuminated 10 h after transfection for 1 s every 30 s. 24 h after illumination, the medium was removed and the imaging was conducted using the In-Vivo Multispectral System FX (Kodak) with 550 nm excitation and 600 nm emission filters for the mCherry, image was collected in 4×4 binning for 5 min exposure. The result showed that the mCherry fluorescence image of the cells had the pattern of the original image used as the mask, that was an “ECUST” and a gradient slider (FIG. 44), indicating that the system could spatiotemporally regulate gene expression.
Example 16: Characteristics of Recombinant Light-Switchable DNA Binding Protein and DNA Recognization/Binding Analysis
To evaluate spectrum and DNA binding capacity of the recombinant light-switchable DNA binding protein in this invention, the recombinant light-switchable DNA binding protein was purified first. Gal4-VIVID(WT) was amplified from pGAVP(WT) described in sample 2 by PCR using primers P113 and P114 and ligated into pET28a by NdeI/XhoI digestion, the resulting vector was named as pET28a-GAV(WT) containing recombinant protein GAV(WT), there is a His-tag in its N-terminal for nickel ion affinity chromatograph.









Forward primer (P113):



5′-CTTTCATATGATGAAGCTACTGTCTTCTATCGAAC-3′



 



Reverse primer (P114):



5′-CTTTCTCGAGTTATTCCGTTTCGCACTGGAAACCCATG-3′






pET28a-GAV (WT) was transformed into JM109 (DE3) competent cell, a positive clone was picked for GAV (WT) expression, the expressed protein was purified using 1 ml Hitrap column (GE Healthcare), and further desalting by 5 ml Hitrap Desalting column (GE Healthcare). The purified protein with 90% purity identified by SDS-PAGE was kept in 20 mM Hepes, 150 mM NaCl, 20 μM ZnCl2, 10% glycerol, pH7.5 and in dark at 4° C. (FIG. 45).
For analysis of the spectrum of GAV (WT), protein was kept at 4° C. for 30 h for recovering back to the dark state. 40 μL sample was added into 384 UV-star plate in dim red light (light intensity<0.05 W/cm2), absorbance spectrum was determined from 300 nm to 700 nm by Synergy 2 multi-mode microplate reader (BioTek). Then the sample was irradiated by blue light (460-470 nm, 0.4 W/cm2) for 5 min and the spectrum was determined. It has been reported that dark state of wild type VIVID-36 has peaks in 428 nm, 450 nm, 478 nm and only a 390 nm peak in light state [Zoltowski, B. D. et al, Science 316 (5827), 1054-1057 (2007)]. The result showed that spectrum of GAV (WT) was similar to VIVID-36, indicating that recombinant protein GAV (WT) retained the absorbance spectrum of wild-type VIVID-36 (FIG. 46).
DNA recognization/binding capacity of recombinant protein GAV(WT) was evaluated by EMSA, protein was kept in 4° C. for 30 h for recovering back to the dark state. DNA probe was as follows:









Sense strand (P105):



5′-TCTTCGGAGGGCTGTCACCCGAATATA-3′,



 



Anti-sense strand (P106):



5′-ACCGGAGGACAGTCCTCCGG-3′,






To obtain double strand DNA probe, DNA was diluted to 10 μM, 1:1 mixed and annealed in PCR instrument which began from 95° C. for 5 min and reduced 1° C. every minute from 95° C. to 25° C. GAV (WT) protein was diluted in RnB (20 mM Hepes 7.5, 50 mM NaCl, 100 μg/mL BSA) by 2 fold serial dilution. Protein and DNA (125 μM) were mixed with an additional 5% w/v Ficol and divided into two replicates, one was illuminated by blue light and the other was kept in darkness at room temperature for 30 min. After incubation, the two samples were loaded onto two 6% polyacryamide gel in 0.5× Tris-borate-EDTA (TBE) buffer and run at 100V for 30-50 min at 4° C. upon light exposure or in darkness, then the gels were stained by Gelred nucleic acid gel stain. The result was shown in FIG. 47, GAV (WT) bound with probe shifted slowly and located in the top band due to its high molecular weight, while GAV (WT) bound with no probe shifted fast and located in the bellow band due to its small molecular weight. The left figure showed that GAV (WT) could bind probe only at high concentration in the darkness, the right figure showed GAV (WT) could bind probe at all concentration used after blue light exposure, indicating that blue light could regulate the binding of recombinant GAV (WT) with DNA probe.
Sample 17: The Study of Light-Switchable Gene Expression System on the Gene Therapy of Type I Diabetic Mice
1. Establishment of Type I diabetic mice models induced by Streptozotocin (STZ).
(1) Male Kunming (KM) mice (Four-week-old,  ̃20 g body weight, FUDAN University) were dealt with sufficient water but no food overnight, and were weighed and labeled the next day.
(2) Citrate solution (0.1 M, pH 5) was prepared as injection solution of STZ and placed on ice away from light.
(3) Streptozotocin (STZ) was intraperitoneally injected into the mice at a dose of 150 mg·kg−1 body weight.
(4) The mice were fed with sufficient water and food and 10% sugar solution overnight.
(5) The mice were fed with sufficient water and food without 10% sugar solution in the next two weeks.
(6) After 5-7 days, the glucose levels of each mouse were determined using the ACCU-CHEK Integra Glucose Meter (Roche), and mice with glucose levels of approximately 30 mM (Type I diabetic mice) were selected for use in the following experiment.
2. Drug administration: 20 μg of pU5-insulin described in example 4 and 10 μg of pGAVP (C71V+N56K) described in example 2 were tail intravenously injected into the selected mice in 5-7 seconds (the injection volume was 0.12 ml/g, about 3 mL each mice), the vectors were dissolved in Ringer's solution (147 mM NaCl, 4 mM KCl, 1.13 mM CaCl2). The control vector was pGAVPO (C108S) described in example 2.
3. Determination of blood glucose levels: a shaver was utilized to shave off most of the fur firstly, and then cotton ball was dipped with 8% sodium sulfide to remove the residual fur. The residual sodium sulfide was washed off with warm water and dried the skin of abdomen. The mice were illuminated under blue light with 90 mW cm−2 intensity without food for 8 h, and then the mice were allowed to rest in darkness for another 4 hours with sufficient food. The blood glucose levels of each mouse were determined using the ACCU-CHEK Integra Glucose Meter (Roche).
FIG. 48 indicated that the expression of insulin could significantly decrease the blood glucose levels upon blue light exposure, while the mice kept in darkness or the control group (got injection of control vector pGAVP (C108S)) decreased insignificantly. So the light-switchable gene expression system could be used in gene therapy of Type I diabetic mice.
It will be understood that the dosages, reaction conditions, etc., in the examples are approximate values unless noted otherwise, and they can be exactly changed base on the situations to obtain similar results. All of the professional terms used in the Description, except those specially defined, have identical meanings to those known by persons skilled in the art. All the references referred to are incorporated into the application as a whole. The preferable embodiments are only exemplified for the illustration of the invention. Those skilled in the art can adopt similar methods or materials to obtain similar results. All the changes and modifications are within the scope of the attached claims.
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## Claims

1. A light-switchable gene expression system, comprising: a) a gene encoding a photosensitive recombinant light-switchable eukaryotic transcription factor, said recombinant light-switchable eukaryotic transcription factor is one protein including a first polypeptide as DNA-binding domain, a second polypeptide as light-switchable domain and a third polypeptide as transcriptional regulatory domain; b) a target transcription unit, including at least one reaction element recognized/bound by the first polypeptide, a promoter regulated by the third polypeptide and a nucleic acid sequence to be transcribed; wherein said second polypeptide is selected from LOV2 domain of Neurospora crassa VIVID, AsLOV2 domain of oat phytochrome gene 1 and AuLOV domain in Aureochrome1 of Stramenopile algae Vaucheria frigida.

2. The light-switchable gene expression system according to claim 1, wherein said first polypeptide, second polypeptide and third polypeptide were linked each other operatively and/or wherein said reaction element, promoter and nucleic acid sequence to be transcribed were linked each other operatively.

3. The light-switchable gene expression system according to claim 1, wherein said first polypeptide is selected from helix-turn-helix DNA-binding domain, zinc finger motif or zinc cluster DNA-binding domain, leucine zipper DNA-binding domain, winged helix DNA-binding domain, winged helix-turn-helix DNA-binding domain, helix-loop-helix DNA-binding domain, high mobility family DNA-binding domain and B3 DNA-binding domain.

4. The light-switchable gene expression system according to claim 3, wherein said first polypeptide is selected from DNA binding domain of yeast Gal4 protein.

5. The light-switchable gene expression system according to claim 1, wherein said third polypeptide is selected from transcriptional activation domains rich in acidic amino acids, transcriptional activation domains rich in proline, transcriptional activation domains rich in serine/threonine and transcriptional activation domains rich in glutamine, and Kruppel-retated box transcriptional repression domain.

6. The light-switchable gene expression system according to claim 5, wherein the third polypeptide is selected from transcriptional activation domains of the herpes simplex virus VP16 particle protein, transcriptional activation domains of yeast Gal4 protein, transcriptional activation domains of NF-κB p65 subunit, transcriptional activation domains of yeast general control protein 4, and Kruppel-retated box transcriptional repression domain of the zinc finger 354A protein.

7. The light-switchable gene expression system according to claim 1, further comprising a fourth polypeptide, i.e., nuclear localization signal peptide, which can promote the transportation of the recombinant light-switchable transcription factor into the nucleus, said fourth polypeptide links with the first, the second and the third polypeptides directly or via a linker peptide.

8. The light-switchable gene expression system according to claim 1, further comprising a fifth polypeptide regulated by hormones, said fifth polypeptide links with the first, the second and the third polypeptides directly or via a linker peptide.

9. The light-switchable gene expression system according to claim 1, wherein said reaction element is a DNA motif which can be specifically recognized and bound by the first polypeptide.

10. The light-switchable gene expression system according to claim 9, wherein said reaction element is selected from Gal4 binding element.

11. The light-switchable gene expression system according to claim 1, wherein the promoter is selected from the adenovirus late promoter, cytomegalovirus (CMV) minimal promoter, yeast Gal1 gene promoter and SV40 promoter.

12. The light-switchable gene expression system according to claim 1, wherein said first polypeptide and said second polypeptide constitute a light-switchable DNA-binding protein.