WO2017209280A1 - Novel protein identification method using yeast and fragmented cdna library - Google Patents

Novel protein identification method using yeast and fragmented cdna library Download PDF

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WO2017209280A1
WO2017209280A1 PCT/JP2017/020614 JP2017020614W WO2017209280A1 WO 2017209280 A1 WO2017209280 A1 WO 2017209280A1 JP 2017020614 W JP2017020614 W JP 2017020614W WO 2017209280 A1 WO2017209280 A1 WO 2017209280A1
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protein
cdna
yeast
gene encoding
vector
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昭世 岸田
小山 浩史
想子 岸田
幹雄 飯島
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国立大学法人鹿児島大学
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    • CCHEMISTRY; METALLURGY
    • C40COMBINATORIAL TECHNOLOGY
    • C40BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00Libraries per se, e.g. arrays, mixtures
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    • C40B40/06Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries

Definitions

  • the present invention relates to a protein identification method using, for example, yeast and a fragmented cDNA library.
  • the yeast two-hybrid method is known as a method for identifying binding of intracellular (cytoplasmic) molecules (Non-Patent Documents 1 to 3).
  • the yeast two-hybrid method uses a gene vector to add a known gene to which a nuclear translocation signal has been added and a full-length cDNA chimeric gene to which the nuclear translocation signal has been added (usually reverse transcribed with an oligo dT primer in a commercial product)
  • the types are expressed and a bond between molecules is formed in the nucleus, the bond between the molecules is detected by the activity of the reporter gene whose expression is induced, light emission, or the like.
  • yeast two-hybrid method when a gene encoding a membrane protein such as a ligand molecule or a receptor is inserted into a vector, the chimeric gene is nucleated by expression of the signal peptide at the 5 'end or the transmembrane region near the 3' end.
  • the yeast two-hybrid method is not suitable for analysis of ligand-receptor binding.
  • yeast two-hybrid method many modifications have been reported.
  • the cells to be used can be changed to organisms other than yeast, or can be improved by developing a reporter gene portion.
  • a modification of the yeast two-hybrid method which is intended to be detected in the nucleus as a partial region library of (membrane) protein and to detect the interaction that originally occurs outside the nucleus, is known. There wasn't.
  • the conventional yeast two-hybrid method is not suitable for analysis of ligand-receptor binding due to the expression of the signal peptide at the 5 ′ end and the transmembrane region near the 3 ′ end. Therefore, the present invention aims to provide a method suitable for analyzing the binding between proteins containing a ligand-receptor by modifying the yeast two-hybrid method.
  • the present invention includes the following.
  • a protein identification method comprising a step of culturing a yeast transformant into which the first and second vectors have been introduced, wherein the first vector comprises a gene encoding a nuclear translocation signal and a DNA binding protein
  • a gene encoding a decoy protein and a second vector comprising a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA
  • the fragmented partial cDNA encodes a prey protein lacking a signal peptide, a cell membrane or organelle localization sequence or a transmembrane region, and in the nucleus of the yeast transformant,
  • a fusion protein comprising a translocation signal, a DNA binding protein and a decoy protein, and said translocation signal and transcription-activating protein Fusion protein was expressed containing the prey proteins encoded by fragmented partial cDNA, the binding of the bait protein and ⁇ product protein, detecting the activity of
  • a vector comprising a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA, wherein the fragmented partial cDNA is described in (4) or (5) The vector, which is cDNA.
  • the present invention it is possible to contribute to the elucidation of signal molecules involved in various diseases by elucidating the receptors for orphan ligands and searching for and identifying molecules to which membrane proteins bind.
  • the protein identification method according to the present invention includes a step of culturing a yeast transformant into which the first and second vectors have been introduced, wherein
  • the first vector includes a gene encoding a nuclear translocation signal, a gene encoding a DNA binding protein, and a gene encoding a bait protein
  • the second vector includes a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA.
  • the fragmented partial cDNA is a signal peptide, a cell membrane, or an organelle.
  • a fusion protein comprising the nuclear translocation signal, a DNA binding protein, and a decoy protein, and a prey encoded by the partial cDNA fragmented with the nuclear translocation signal, the transcriptional activation protein A fusion protein containing a protein is expressed, and the binding between the decoy protein and the prey protein is detected using the activity of a reporter gene as an indicator, Is the method.
  • a fusion protein of a DNA-binding protein and a molecule of interest (bait protein) and a cDNA library (derived from) a transcription library and a full-length cDNA (prey protein)
  • a cDNA library derived from) a transcription library and a full-length cDNA (prey protein)
  • the activity of the reporter gene that induces expression is used as an index to bind the decoy protein to the library-derived molecule. Is detected.
  • the yeast two-hybrid method has become widespread as an inexpensive large-scale screening technique using the binding of two molecules as an index.
  • a protein derived from a cDNA library contains a signal peptide, a sequence that localizes to cell membranes or various organelles, the molecule cannot be expressed in the nucleus, and a bond with a decoy protein is formed in the nucleus. And reporter gene expression cannot be detected.
  • the yeast two-hybrid method is generally used as a technique for detecting the binding between intracellular proteins.
  • a library commercially available in the prior art is one in which a cDNA that has been reverse-transcribed and synthesized from the 3 ′ end of mRNA using an oligoolidT primer (substantially full length) is inserted.
  • this method uses a cDNA library with intentionally fragmented cDNA inserted, partial regions of molecules including membrane proteins and various localized sequences that were missed in the conventional method are expressed in the yeast nucleus. By doing so, binding to a decoy protein can be detected, and ligand-receptor binding that usually occurs outside the cell and association of membrane proteins can be detected inside the yeast nucleus, both inside and outside the cell.
  • first, first and second vectors are prepared.
  • the first vector includes a fusion gene in which a gene encoding a nuclear translocation signal, a gene encoding a DNA binding protein, and a gene encoding a decoy protein are functionally linked.
  • the first vector may be any vector that functions in yeast, and examples thereof include pBTM116, pGBKT7, and pGBT9.
  • a nuclear transfer signal is sent.
  • Encoding gene is included in the fusion gene or added in advance (eg, Large T antigen residues 47 to 54 (PKKKRKVE: SEQ ID NO: 1), LexA protein endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2), etc.) Must have been.
  • DNA binding protein examples include a DNA binding domain (DBD) of Gal4 protein, a DBD of LexA protein, and the like.
  • DBD DNA binding domain
  • decoy proteins include orphan ligands whose receptors are unknown, proteins encoded by partial cDNAs excluding various localization signals (such as transmembrane domains and signal sequences localized to organelles) Is mentioned.
  • each gene is included in a functionally linked form in order to express a fusion protein including a nuclear translocation signal-DBD-bait protein.
  • the second vector includes a fusion gene in which a gene encoding a nuclear translocation signal, a gene encoding a transcription activation protein, and a fragmented partial cDNA are functionally linked.
  • the second vector may be any vector that functions in yeast, and examples thereof include pACT2, pGADT7, and pGAD10.
  • the transfer signal in order to transfer the fusion protein encoded by the fusion gene comprising the gene encoding the transcriptional activation protein and the fragmented partial cDNA into the yeast nucleus,
  • the transfer signal must be endogenous or previously added (for example, Large T antigen residuesres47 to 54 (PKKKRKVE: SEQ ID NO: 1), LexA protein endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2), etc.) Don't be.
  • the transcription activation protein includes a DNA binding protein encoded by the fusion gene contained in the first vector and transcription activity when located close to a reporter gene control sequence (promoter etc.) in yeast. And activates transcription of a reporter gene, such as an activator domain (AD) of Gal4 protein corresponding to DBD of Gal4 protein.
  • a reporter gene control sequence promoter etc.
  • AD activator domain
  • the fragmented partial cDNA is different from a full-length gene cDNA library prepared using an oligo dT primer, for example, a known cDNA library preparation (e.g., cDNA Library Construction Kit (Takara Bio Inc.)).
  • a known cDNA library preparation e.g., cDNA Library Construction Kit (Takara Bio Inc.)
  • a random primer for example, a random primer comprising the base sequence described in SEQ ID NO: 3 used in the following Examples
  • the cDNA obtained by random prime reverse transcription has, for example, a length of 100 to 1800 bp (preferably 100 to 1000 bp).
  • a cDNA library fragmented by cleavage using sonication or the like is prepared, for example, by adding an EcoRI adapter to the end and binding it to a large excess of vector having an EcoRI stump.
  • Such partial cDNAs include those encoding a prey protein that binds to a ligand or membrane protein, lacking a signal peptide, a cell membrane or organelle localization sequence or a transmembrane region. Examples of the prey protein include a receptor protein.
  • a fusion protein containing a nuclear protein a prey protein encoded by a Gal4 activator domain (AD) -fragmented cDNA is sequentially expressed.
  • AD Gal4 activator domain
  • the first and second vectors are then transformed into yeast to produce yeast transformants that express the first and second vectors.
  • yeast include budding yeast (Saccharomyces cerevisiae).
  • transcription is activated by the DNA binding protein encoded by the fusion gene contained in the first vector and the transcription activation protein encoded by the fusion gene contained in the second vector.
  • control sequences to be converted and a reporter gene located downstream thereof include a base sequence called UASG (UpstreamUpActivation Sequences for galactose) for the Gal4 protein.
  • the reporter gene include a gene encoding ⁇ -galactosidase and HIS3. The control sequence and the reporter gene located downstream thereof are present in the yeast nucleus because they are integrated into the genomic DNA.
  • the method for introducing the first and second vectors into yeast is not particularly limited as long as it is a method for introducing DNA into yeast, and examples thereof include an electroporation method, a spheroplast method, and a lithium acetate method.
  • the obtained yeast transformant is cultured under conditions that allow it to grow.
  • a fusion protein comprising a nuclear translocation signal, a DNA-binding protein and a decoy protein, and a prey protein encoded by the nuclear translocation signal, a transcriptional activation protein and a fragmented partial cDNA
  • the decoy protein and the prey protein interact with each other so that the DNA-binding protein and the transcriptional activation protein are close to each other and bind to a control sequence located upstream of the reporter gene. , Transcription of the reporter gene is promoted. Therefore, the binding of the decoy protein and the prey protein can be confirmed using the activity of the reporter gene as an index, and the prey protein corresponding to the decoy protein can be identified.
  • the temperature is set to, for example, 25 to 30 ° C.
  • the pH of the medium is, for example, pH 5 so that the transformants grow and the reporter protein encoded by the reporter gene is not inactivated. Set at around .8 and continue culturing until the required amount of cells for each assay is obtained.
  • the gene fragment encoding the partial prey protein can be identified by determining the sequence of the fragmented partial cDNA contained in the second vector. . Furthermore, by comparing the gene fragment encoding the identified partial prey protein with, for example, a gene sequence registered in a known database, the gene encoding the prey protein (if registered) or the gene concerned The full-length prey protein encoded by can also be identified.
  • the detection sensitivity of binding up to about 1 ⁇ M Kd binding is expected to be detected by using the yeast reporter gene system, compared to the case of panning in cultured cells.
  • Improved S / N ratio, faster screening (normally about 14 days are required to determine the binding of about 1 million clones), stability of recovered genes, faster cloning, economy, etc. Be expected.
  • receptor identification of orphan ligands may be directly linked to drug discovery, and this method can be applied to receptor identification of orphan ligands.
  • the present method can be widely applied to the binding screening between membrane proteins.
  • the present invention also relates to a reagent kit for the present method comprising the cDNA itself obtained by the above-mentioned random prime reverse transcription, the second vector itself, the cDNA obtained by the random prime reverse transcription or the second vector.
  • the reagent kit can further include, for example, a buffer and a container used in the present method, instructions for use, and the like.
  • reverse transcriptase (PrimeScript RTase Takara Bio Inc.) (200 U / ⁇ l) 1 ⁇ l, RNase inhibitor (40 U / ⁇ l) 1 ⁇ l, reaction buffer (250 mM Tris-HCl (pH 8.3 ), 375 mM KCl, 15 mM MgCl 2 ) 4 ⁇ l and RNase-free water 4 ⁇ l were added to make 20 ⁇ l, and a reverse transcription reaction was performed at 42 ° C. for 1 hour. After 1 hour, it was cooled on ice for 2 minutes. The cDNA synthesized by this reaction was designated as 1st strand cDNA.
  • 2nd strand cDNA synthesis 1st strand cDNA is mixed with dNTP mixture (dATP, dCTP, dGTP, dTTP) 4.5 ⁇ l, RNaseH and DNA ligase mixture 2 ⁇ l, DNA polymerase I (20 U / ⁇ l) 2 ⁇ l, 30 ⁇ l of reaction buffer and 87.5 ⁇ l of RNase-free water were added to make 146 ⁇ l, followed by reaction at 16 ° C. for 2 hours. After 2 hours, the mixture was allowed to stand at 70 ° C. for 10 minutes and then allowed to stand at room temperature for 5 minutes or more. The double-stranded cDNA synthesized by this reaction was designated as 2nd strand cDNA.
  • dNTP mixture dATP, dCTP, dGTP, dTTP
  • RNaseH and DNA ligase mixture 2 ⁇ l
  • DNA polymerase I 20 U / ⁇ l
  • reaction buffer 30 ⁇ l
  • the XhoI recognition sequence in the random primer is cleaved, but the XhoI recognition sequence in the cDNA is not cleaved by XhoI because 5-methyl dCTP is used during the synthesis of the first strand cDNA.
  • the vector and EcoRI-XhoI-cleaved cDNA combined were introduced into E. coli by electroporation, and any 10 clones were selected and analyzed for the size of the fragmented cDNA inserted by PCR. After confirming that it was 100 to 1000 bases, a cDNA library was recovered from E. coli.
  • the vector pBTM116-HA-KM-hENHO contains an endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2) and DNA binding domain (DBD) of the LexA protein in order from the 5 ′ end to the 3 ′ end. It has a gene that encodes it and a gene that encodes human adropin (hENHO) as a gene that encodes a decoy protein.
  • Saccharomyces cerevisiae L40 has a gene (reporter gene) encoding ⁇ -galactosidase and an HIS3 gene under the control of UASG downstream. When molecules expressed from the two plasmids are combined in the cell, yeast cells can grow even in a His-deficient medium due to the expression of the HIS3 gene.
  • the seeded medium was transferred to a 30 ° C. incubator and cultured for several days until colonies were visible. Colonies were transferred to fresh SD-Leu-Trp medium and cultured in a 30 ° C. incubator. Using a part of the grown yeast, ⁇ -galactosidase assay was performed, and a group of clones positive for ⁇ -galactosidase activity was analyzed. As a result, those containing partial cDNA of membrane protein were included.

Abstract

The purpose of the present invention is to provide a novel method for identifying a protein in a yeast nucleus. More specifically, the present invention relates to a protein identification method which comprises: in a yeast nucleus, expressing a fusion protein comprising a nuclear localization signal, a DNA-binding protein and a bait protein, and another fusion protein comprising a nuclear localization signal, a transcriptional activation protein and a prey protein encoded by a fragmented partial cDNA, said prey protein lacking a signal peptide, a cell membrane or intracellular organelle localization sequence or a transmembrane domain; and then detecting the binding of the bait protein to the prey protein using the activity, luminescence, etc. of a reporter gene as an indication.

Description

酵母と断片化cDNAライブラリーを用いたタンパク質の新しい同定法A new method for protein identification using yeast and fragmented cDNA libraries.
 本発明は、例えば酵母と断片化cDNAライブラリーを用いたタンパク質の同定方法に関する。 The present invention relates to a protein identification method using, for example, yeast and a fragmented cDNA library.
 細胞内外での複数の分子の会合又は結合が、細胞の増殖や分化、接着等を制御する生体シグナルとして働くことが知られている。特に、ホルモン等各種のリガンド分子の生理作用を解明するためには、細胞膜上のレセプター分子の同定が有用である。これらの目的には、免疫沈降等でレセプター分子を含むタンパク質複合体を濃縮し、質量分析を行う方法や培養細胞を用いたパンニング法等が一般化しつつある。しかしながら、未だに受容体の不明な「オーファンリガンド」が多数知られている。その受容体同定は、各種疾患病態と関連する可能性が高く注目されているが、スクリーニング方法の煩雑さ、検出感度の不足等から進んでいない。 It is known that the association or binding of a plurality of molecules inside and outside the cell acts as a biological signal that controls cell proliferation, differentiation, adhesion, and the like. In particular, identification of receptor molecules on cell membranes is useful for elucidating the physiological effects of various ligand molecules such as hormones. For these purposes, a method of concentrating a protein complex containing a receptor molecule by immunoprecipitation and performing mass spectrometry, a panning method using cultured cells, and the like are becoming common. However, many “orphan ligands” whose receptors are unknown are still known. Receptor identification has attracted attention because it is highly likely to be associated with various disease pathologies, but has not progressed due to the complexity of screening methods and lack of detection sensitivity.
 一方、細胞内(細胞質)の分子の結合同定法として、酵母two-hybrid法が知られている(非特許文献1~3)。酵母two-hybrid法では、遺伝子ベクターを用いて核内移行シグナルを付加した既知遺伝子と核内移行シグナルを付加した全長cDNAキメラ遺伝子(市販品では通常はオリゴdTプライマーで逆転写したもの)を2種類発現させ、分子同士の結合が核内で形成された場合、発現誘導されるレポーター遺伝子の活性や発光等で分子間の結合を検出する。 On the other hand, the yeast two-hybrid method is known as a method for identifying binding of intracellular (cytoplasmic) molecules (Non-Patent Documents 1 to 3). The yeast two-hybrid method uses a gene vector to add a known gene to which a nuclear translocation signal has been added and a full-length cDNA chimeric gene to which the nuclear translocation signal has been added (usually reverse transcribed with an oligo dT primer in a commercial product) When the types are expressed and a bond between molecules is formed in the nucleus, the bond between the molecules is detected by the activity of the reporter gene whose expression is induced, light emission, or the like.
 酵母two-hybrid法において、リガンド分子や受容体等の膜タンパク質をコードする遺伝子をベクターに挿入した場合、5'末端のシグナルペプチドや3'末端付近の細胞膜貫通領域の発現により、キメラ遺伝子を核内で発現させることが困難であり、従来の酵母two-hybrid法はリガンド-受容体の結合の解析には適していない。 In the yeast two-hybrid method, when a gene encoding a membrane protein such as a ligand molecule or a receptor is inserted into a vector, the chimeric gene is nucleated by expression of the signal peptide at the 5 'end or the transmembrane region near the 3' end. The yeast two-hybrid method is not suitable for analysis of ligand-receptor binding.
 また、酵母two-hybrid法の改変が多数報告されている。例えば、使用する細胞を酵母以外の生物に変えたり、レポータージーン部分の開発による改良を目指したものが挙げられる。しかしながら、従来において、(膜)タンパク質の部分領域ライブラリーとして核内で発現させて、本来細胞外で起こる相互作用を核内で検出しようとする意図の酵母two-hybrid法の改変は知られていなかった。 In addition, many modifications of the yeast two-hybrid method have been reported. For example, the cells to be used can be changed to organisms other than yeast, or can be improved by developing a reporter gene portion. However, conventionally, a modification of the yeast two-hybrid method, which is intended to be detected in the nucleus as a partial region library of (membrane) protein and to detect the interaction that originally occurs outside the nucleus, is known. There wasn't.
 上述のように、5'末端のシグナルペプチドや3'末端付近の細胞膜貫通領域の発現により、従来の酵母two-hybrid法はリガンド-受容体の結合の解析には適していない。そこで、本発明は、酵母two-hybrid法を改変し、リガンド-受容体を含むタンパク質間の結合の解析に好適な方法を提供することを目的とする。 As mentioned above, the conventional yeast two-hybrid method is not suitable for analysis of ligand-receptor binding due to the expression of the signal peptide at the 5 ′ end and the transmembrane region near the 3 ′ end. Therefore, the present invention aims to provide a method suitable for analyzing the binding between proteins containing a ligand-receptor by modifying the yeast two-hybrid method.
 上記課題を解決するため鋭意研究を行った結果、従来の酵母two-hybrid法(オリゴdTプライマーによる逆転写での作製)とは異なり、cDNAライブラリー作製時に、ランダムプライマーを用いて任意の個所から逆転写したcDNAや超音波処理等で切断して意図的に断片化したcDNAをベクターに挿入した断片化cDNAライブラリーを用いて、酵母two-hybrid法を行うことで、当該断片化cDNAライブラリーには、膜タンパク質であっても5'末端のシグナルペプチドや3'末端付近の細胞膜貫通領域の欠損したクローンが含まれているので、核内で安定して発現させることが可能となり、細胞外でのリガンドと受容体の細胞外部分との結合を核内で再現し、レポータージーンを利用した結合の検出という過程で従来法では行えなかった結合解析が可能となることを見出し、本発明を完成するに至った。 As a result of earnest research to solve the above problems, unlike the conventional yeast two-hybrid method (preparation by reverse transcription with oligo dT primer), random primers are used to create cDNA libraries from any location. Using a fragmented cDNA library in which reverse-transcribed cDNA or cDNA that has been intentionally fragmented by sonication or the like is inserted into a vector, the fragmented cDNA library can be obtained by performing the yeast two-hybrid method. Contains a clone lacking the signal peptide at the 5 'end and the transmembrane region near the 3' end even if it is a membrane protein, allowing stable expression in the nucleus, In this process, the binding between the ligand and the extracellular part of the receptor is reproduced in the nucleus, and in the process of detecting the binding using the reporter gene, binding analysis that could not be performed by the conventional method becomes possible. Which resulted in the completion of the Akira.
 すなわち、本発明は、以下を包含する。
(1)第1及び第2のベクターを導入した酵母形質転換体を培養する工程を含む、タンパク質の同定方法であって、第1のベクターは、核内移行シグナルをコードする遺伝子とDNA結合タンパク質をコードする遺伝子とおとりタンパク質をコードする遺伝子とを含み、第2のベクターは、核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含み、該断片化した部分cDNAは、シグナルペプチド、細胞膜若しくは細胞内小器官局在化配列又は細胞膜貫通領域が欠損した獲物タンパク質をコードするものであり、且つ、前記酵母形質転換体の核内において、前記核内移行シグナルとDNA結合タンパク質とおとりタンパク質とを含む融合タンパク質、及び前記核内移行シグナルと転写活性化タンパク質と断片化した部分cDNAによりコードされる獲物タンパク質とを含む融合タンパク質が発現し、該おとりタンパク質と該獲物タンパク質との結合を、レポーター遺伝子の活性を指標に検出する、前記方法。
(2)おとりタンパク質がリガンドであり、且つ獲物タンパク質が受容体タンパク質である、(1)記載の方法。
(3)おとりタンパク質が各種局在シグナル配列を除いた部分cDNAによりコードされるタンパク質である、(1)記載の方法。
(4)ランダムプライム逆転写によって得られた、長さ100~1800bpを有するcDNA。
(5)長さが100~1000bpである、(4)記載のcDNA。
(6)核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含むベクターであって、該断片化した部分cDNAが(4)又は(5)記載のcDNAである、前記ベクター。
(7)(4)若しくは(5)記載のcDNA又は(6)記載のベクターを含む、(1)~(3)のいずれか1記載のタンパク質の同定方法用試薬キット。
That is, the present invention includes the following.
(1) A protein identification method comprising a step of culturing a yeast transformant into which the first and second vectors have been introduced, wherein the first vector comprises a gene encoding a nuclear translocation signal and a DNA binding protein A gene encoding a decoy protein and a second vector comprising a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA, The fragmented partial cDNA encodes a prey protein lacking a signal peptide, a cell membrane or organelle localization sequence or a transmembrane region, and in the nucleus of the yeast transformant, A fusion protein comprising a translocation signal, a DNA binding protein and a decoy protein, and said translocation signal and transcription-activating protein Fusion protein was expressed containing the prey proteins encoded by fragmented partial cDNA, the binding of the bait protein and 該獲 product protein, detecting the activity of the reporter gene as an index, said method.
(2) The method according to (1), wherein the decoy protein is a ligand and the prey protein is a receptor protein.
(3) The method according to (1), wherein the decoy protein is a protein encoded by a partial cDNA excluding various localization signal sequences.
(4) cDNA having a length of 100 to 1800 bp obtained by random prime reverse transcription.
(5) The cDNA according to (4), wherein the length is 100 to 1000 bp.
(6) A vector comprising a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA, wherein the fragmented partial cDNA is described in (4) or (5) The vector, which is cDNA.
(7) A reagent kit for the protein identification method according to any one of (1) to (3), comprising the cDNA according to (4) or (5) or the vector according to (6).
 本明細書は本願の優先権の基礎となる日本国特許出願番号2016-112107号の開示内容を包含する。 This specification includes the disclosure of Japanese Patent Application No. 2016-112107, which is the basis of the priority of the present application.
 本発明によれば、オーファンリガンドの受容体解明や、膜タンパク質が結合する分子を検索同定することで各種疾患に関わるシグナル分子の解明に寄与できる。 According to the present invention, it is possible to contribute to the elucidation of signal molecules involved in various diseases by elucidating the receptors for orphan ligands and searching for and identifying molecules to which membrane proteins bind.
 本発明に係るタンパク質の同定方法(以下、「本方法」と称する)は、第1及び第2のベクターを導入した酵母形質転換体を培養する工程を含み、ここで、
 第1のベクターは、核内移行シグナルをコードする遺伝子とDNA結合タンパク質をコードする遺伝子とおとり(bait)タンパク質をコードする遺伝子とを含み、
 第2のベクターは、核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含み、該断片化した部分cDNAは、シグナルペプチド、細胞膜若しくは細胞内小器官局在化配列又は細胞膜貫通領域が欠損した獲物(prey)タンパク質をコードするものであり、且つ、
 該酵母形質転換体の核内において、該核内移行シグナルとDNA結合タンパク質とおとりタンパク質とを含む融合タンパク質、及び該核内移行シグナルと転写活性化タンパク質と断片化した部分cDNAによりコードされる獲物タンパク質とを含む融合タンパク質が発現し、該おとりタンパク質と該獲物タンパク質との結合を、レポーター遺伝子の活性を指標に検出する、
方法である。
The protein identification method according to the present invention (hereinafter referred to as “the present method”) includes a step of culturing a yeast transformant into which the first and second vectors have been introduced, wherein
The first vector includes a gene encoding a nuclear translocation signal, a gene encoding a DNA binding protein, and a gene encoding a bait protein,
The second vector includes a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA. The fragmented partial cDNA is a signal peptide, a cell membrane, or an organelle. Encodes a prey protein lacking a localization sequence or transmembrane region, and
In the nucleus of the yeast transformant, a fusion protein comprising the nuclear translocation signal, a DNA binding protein, and a decoy protein, and a prey encoded by the partial cDNA fragmented with the nuclear translocation signal, the transcriptional activation protein A fusion protein containing a protein is expressed, and the binding between the decoy protein and the prey protein is detected using the activity of a reporter gene as an indicator,
Is the method.
 一般に、従来の酵母two-hybrid法では、DNA結合タンパク質と興味のある分子(おとりタンパク質)との融合タンパク質及び転写活性化タンパク質と全長cDNAから成るcDNAライブラリー(由来の)分子(獲物タンパク質)との融合タンパク質を酵母の核内で発現させ、おとりタンパク質とライブラリー由来分子との結合が生じたときに発現誘導が起こるレポーター遺伝子の活性を指標に、当該おとりタンパク質とライブラリー由来分子との結合を検出する。 In general, in the conventional yeast two-hybrid method, a fusion protein of a DNA-binding protein and a molecule of interest (bait protein) and a cDNA library (derived from) a transcription library and a full-length cDNA (prey protein) When the fusion protein is expressed in the yeast nucleus and binding of the decoy protein to the library-derived molecule occurs, the activity of the reporter gene that induces expression is used as an index to bind the decoy protein to the library-derived molecule. Is detected.
 酵母two-hybrid法は、二分子の結合を指標とする安価な大規模スクリーニングの手法として広く普及した。しかしながら、cDNAライブラリー由来のタンパク質がシグナルペプチド、細胞膜や各種細胞内小器官へ局在させる配列を含む場合、核内で該当分子を発現させられないため、おとりタンパク質との結合を核内で形成させることができず、レポーター遺伝子の発現を検出できない。そのため、酵母two-hybrid法は、一般に細胞内タンパク質同士の結合を検出する手法という位置づけで利用されている。また、従来において市販されているライブラリーは、oligo dTプライマーを用いてmRNAの3'末端側から逆転写合成した(ほぼ完全長の)cDNAを挿入したものである。 The yeast two-hybrid method has become widespread as an inexpensive large-scale screening technique using the binding of two molecules as an index. However, when a protein derived from a cDNA library contains a signal peptide, a sequence that localizes to cell membranes or various organelles, the molecule cannot be expressed in the nucleus, and a bond with a decoy protein is formed in the nucleus. And reporter gene expression cannot be detected. For this reason, the yeast two-hybrid method is generally used as a technique for detecting the binding between intracellular proteins. In addition, a library commercially available in the prior art is one in which a cDNA that has been reverse-transcribed and synthesized from the 3 ′ end of mRNA using an oligoolidT primer (substantially full length) is inserted.
 一方、本方法では、意図的に断片化したcDNAを挿入したcDNAライブラリーを使用するため、従来法において見逃していた膜タンパク質や各種の局在配列を含む分子の部分領域を酵母核内で発現させることで、おとりタンパク質との結合を検出でき、通常細胞外で起こるリガンド-受容体の結合や、細胞内外を問わず膜タンパク質同士の会合を酵母の核内で検出することができる。 On the other hand, since this method uses a cDNA library with intentionally fragmented cDNA inserted, partial regions of molecules including membrane proteins and various localized sequences that were missed in the conventional method are expressed in the yeast nucleus. By doing so, binding to a decoy protein can be detected, and ligand-receptor binding that usually occurs outside the cell and association of membrane proteins can be detected inside the yeast nucleus, both inside and outside the cell.
 本方法では、先ず、第1及び第2のベクターを準備する。 In this method, first, first and second vectors are prepared.
 第1のベクターは、核内移行シグナルをコードする遺伝子とDNA結合タンパク質をコードする遺伝子とおとりタンパク質類をコードする遺伝子とを機能的に連結した融合遺伝子を含む。第1のベクターとしては、酵母で機能するベクターであればよく、例えばpBTM116、pGBKT7、pGBT9等が挙げられる。 The first vector includes a fusion gene in which a gene encoding a nuclear translocation signal, a gene encoding a DNA binding protein, and a gene encoding a decoy protein are functionally linked. The first vector may be any vector that functions in yeast, and examples thereof include pBTM116, pGBKT7, and pGBT9.
 第1のベクターにおいては、上記のDNA結合タンパク質をコードする遺伝子とおとりタンパク質類をコードする遺伝子とを含む融合遺伝子によりコードされる融合タンパク質を酵母の核内に移行すべく、核内移行シグナルをコードする遺伝子が当該融合遺伝子に内包、あるいは予め付加(例えばLarge T 抗原 residues 47 to 54 (PKKKRKVE:配列番号1)、LexAタンパク質の内在性の核局在シグナル配列(KRLKK:配列番号2)等)されていなければならない。 In the first vector, in order to transfer the fusion protein encoded by the fusion gene comprising the gene encoding the DNA binding protein and the gene encoding the decoy protein into the nucleus of the yeast, a nuclear transfer signal is sent. Encoding gene is included in the fusion gene or added in advance (eg, Large T antigen residues 47 to 54 (PKKKRKVE: SEQ ID NO: 1), LexA protein endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2), etc.) Must have been.
 また、DNA結合タンパク質としては、例えばGal4タンパク質のDNA結合ドメイン(DBD)、LexAタンパク質のDBD等が挙げられる。 Examples of the DNA binding protein include a DNA binding domain (DBD) of Gal4 protein, a DBD of LexA protein, and the like.
 さらに、おとりタンパク質類としては、例えば受容体の不明なオーファンリガンド、各種局在シグナル(細胞膜貫通ドメインや細胞内小器官への局在シグナル配列等)を除いた部分cDNAによりコードされるタンパク質等が挙げられる。 In addition, examples of decoy proteins include orphan ligands whose receptors are unknown, proteins encoded by partial cDNAs excluding various localization signals (such as transmembrane domains and signal sequences localized to organelles) Is mentioned.
 このように、第1のベクターでは、例えばN末端からC末端の方向に、順に核内移行シグナル-DBD-おとりタンパク質を含む融合タンパク質を発現させるべく、各遺伝子を機能的に連結した形で含む。 Thus, in the first vector, for example, in the direction from the N-terminal to the C-terminal, each gene is included in a functionally linked form in order to express a fusion protein including a nuclear translocation signal-DBD-bait protein. .
 第2のベクターは、核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを機能的に連結した融合遺伝子を含む。第2のベクターとしては、酵母で機能するベクターであればよく、例えばpACT2、pGADT7、pGAD10等が挙げられる。 The second vector includes a fusion gene in which a gene encoding a nuclear translocation signal, a gene encoding a transcription activation protein, and a fragmented partial cDNA are functionally linked. The second vector may be any vector that functions in yeast, and examples thereof include pACT2, pGADT7, and pGAD10.
 第2のベクターにおいては、上記の転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含む融合遺伝子によりコードされる融合タンパク質を酵母の核内に移行すべく、当該融合遺伝子に核内移行シグナルが内在又は予め付加(例えば、Large T 抗原residues 47 to 54 (PKKKRKVE:配列番号1)、LexAタンパク質の内在性の核局在シグナル配列(KRLKK:配列番号2)等)されていなくてはならない。 In the second vector, in order to transfer the fusion protein encoded by the fusion gene comprising the gene encoding the transcriptional activation protein and the fragmented partial cDNA into the yeast nucleus, The transfer signal must be endogenous or previously added (for example, Large T antigen residuesres47 to 54 (PKKKRKVE: SEQ ID NO: 1), LexA protein endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2), etc.) Don't be.
 また、転写活性化タンパク質としては、第1のベクター中に含まれる融合遺伝子によりコードされるDNA結合タンパク質と共に、酵母中のレポーター遺伝子の制御配列(プロモーター等)上に近接に位置した場合に転写活性能を有し、レポーター遺伝子の転写を活性化するものであり、例えば、Gal4タンパク質のDBDに対応するGal4タンパク質のアクティベータードメイン(AD)等が挙げられる。 In addition, the transcription activation protein includes a DNA binding protein encoded by the fusion gene contained in the first vector and transcription activity when located close to a reporter gene control sequence (promoter etc.) in yeast. And activates transcription of a reporter gene, such as an activator domain (AD) of Gal4 protein corresponding to DBD of Gal4 protein.
 一方、断片化した部分cDNAは、オリゴdTプライマーを用いて作製した全長遺伝子のcDNAライブラリーと異なり、例えば公知のcDNAライブラリー作製(例えば、cDNA Library Construction Kit(タカラバイオ株式会社)等の市販のキットを用いたcDNAライブラリー作製)において、任意の生物や組織から採取したmRNAとランダムプライマー(例えば、下記の実施例で使用される配列番号3に記載の塩基配列から成るランダムプライマー)を用いて任意の個所から逆転写したcDNAライブラリー、又は超音波処理等で切断して意図的に断片化したcDNAライブラリーである。ランダムプライム逆転写によって得られたcDNAは、例えば長さ100~1800bp(好ましくは、100~1000bp)を有する。超音波処理等を用いた切断による断片化したcDNAライブラリーは、例えば、EcoRIアダプターを末端に付加し、EcoRI断端を持つ大過剰のベクターと結合させることにより作製する。当該部分cDNAは、シグナルペプチド、細胞膜若しくは細胞内小器官局在化配列又は細胞膜貫通領域が欠損した、リガンドや膜タンパク質と結合する獲物タンパク質をコードするものを含む。獲物タンパク質としては、例えば受容体タンパク質等が挙げられる。 On the other hand, the fragmented partial cDNA is different from a full-length gene cDNA library prepared using an oligo dT primer, for example, a known cDNA library preparation (e.g., cDNA Library Construction Kit (Takara Bio Inc.)). In preparation of a cDNA library using a kit), using an mRNA collected from an arbitrary organism or tissue and a random primer (for example, a random primer comprising the base sequence described in SEQ ID NO: 3 used in the following Examples) A cDNA library reversely transcribed from an arbitrary location, or a cDNA library intentionally fragmented by cutting with ultrasonic treatment or the like. The cDNA obtained by random prime reverse transcription has, for example, a length of 100 to 1800 bp (preferably 100 to 1000 bp). A cDNA library fragmented by cleavage using sonication or the like is prepared, for example, by adding an EcoRI adapter to the end and binding it to a large excess of vector having an EcoRI stump. Such partial cDNAs include those encoding a prey protein that binds to a ligand or membrane protein, lacking a signal peptide, a cell membrane or organelle localization sequence or a transmembrane region. Examples of the prey protein include a receptor protein.
 このように、第2のベクターでは、例えばN末端からC末端の方向に、順に核内移行シグナル-Gal4アクティベータードメイン(AD)-断片化cDNAによりコードされる獲物タンパク質を含む融合タンパク質を発現させるべく、各遺伝子を機能的に連結した形で含む。 Thus, in the second vector, for example, in the direction from the N-terminal to the C-terminal, a fusion protein containing a nuclear protein, a prey protein encoded by a Gal4 activator domain (AD) -fragmented cDNA is sequentially expressed. Each gene in a functionally linked form.
 本方法では、次に第1及び第2のベクターを酵母に形質転換し、第1及び第2のベクターを発現する酵母形質転換体を作製する。酵母としては、例えば出芽酵母(サッカロマイセス・セレビシエ(Saccharomyces cerevisiae))等が挙げられる。なお、酵母の核内には、第1のベクター中に含まれる融合遺伝子によりコードされるDNA結合タンパク質と第2のベクター中に含まれる融合遺伝子によりコードされる転写活性化タンパク質とにより転写が活性化される制御配列とその下流に位置するレポーター遺伝子が存在する。当該制御配列としては、例えば、Gal4タンパク質についてはUASG(Upstream Activation Sequences for galactose)と称される塩基配列等が挙げられる。また、レポーター遺伝子としては、例えばβ-ガラクトシダーゼをコードする遺伝子やHIS3等が挙げられる。制御配列とその下流に位置するレポーター遺伝子は、ゲノムDNAに組み込まれているために酵母の核内に存在する。 In this method, the first and second vectors are then transformed into yeast to produce yeast transformants that express the first and second vectors. Examples of yeast include budding yeast (Saccharomyces cerevisiae). In the yeast nucleus, transcription is activated by the DNA binding protein encoded by the fusion gene contained in the first vector and the transcription activation protein encoded by the fusion gene contained in the second vector. There are control sequences to be converted and a reporter gene located downstream thereof. Examples of the control sequence include a base sequence called UASG (UpstreamUpActivation Sequences for galactose) for the Gal4 protein. Examples of the reporter gene include a gene encoding β-galactosidase and HIS3. The control sequence and the reporter gene located downstream thereof are present in the yeast nucleus because they are integrated into the genomic DNA.
 酵母への第1及び第2のベクターの導入方法としては、酵母にDNAを導入する方法であれば特に限定されず、例えばエレクトロポレーション法、スフェロプラスト法、酢酸リチウム法等が挙げられる。 The method for introducing the first and second vectors into yeast is not particularly limited as long as it is a method for introducing DNA into yeast, and examples thereof include an electroporation method, a spheroplast method, and a lithium acetate method.
 次いで、得られた酵母形質転換体を生育可能な条件下で培養する。当該酵母形質転換体の核内において、核内移行シグナルとDNA結合タンパク質とおとりタンパク質とを含む融合タンパク質、及び核内移行シグナルと転写活性化タンパク質と断片化した部分cDNAによりコードされる獲物タンパク質とを含む融合タンパク質が発現し、該おとりタンパク質と該獲物タンパク質とが相互作用することで該DNA結合タンパク質と該転写活性化タンパク質とが近接し、レポーター遺伝子上流に位置する制御配列に結合することで、レポーター遺伝子の転写が促進される。従って、当該レポーター遺伝子の活性を指標に、おとりタンパク質と獲物タンパク質との結合を確認し、おとりタンパク質に対応する獲物タンパク質を同定することができる。 Next, the obtained yeast transformant is cultured under conditions that allow it to grow. In the nucleus of the yeast transformant, a fusion protein comprising a nuclear translocation signal, a DNA-binding protein and a decoy protein, and a prey protein encoded by the nuclear translocation signal, a transcriptional activation protein and a fragmented partial cDNA The decoy protein and the prey protein interact with each other so that the DNA-binding protein and the transcriptional activation protein are close to each other and bind to a control sequence located upstream of the reporter gene. , Transcription of the reporter gene is promoted. Therefore, the binding of the decoy protein and the prey protein can be confirmed using the activity of the reporter gene as an index, and the prey protein corresponding to the decoy protein can be identified.
 酵母形質転換体の培養においては、形質転換体が生育し、且つレポーター遺伝子によりコードされるレポータータンパク質が失活しないように、温度は、例えば25~30℃に設定し、培地のpHは例えばpH5.8付近に設定し、各種アッセイに必要な量の菌体が得られるまでの期間は培養を続ける。 In culturing yeast transformants, the temperature is set to, for example, 25 to 30 ° C., and the pH of the medium is, for example, pH 5 so that the transformants grow and the reporter protein encoded by the reporter gene is not inactivated. Set at around .8 and continue culturing until the required amount of cells for each assay is obtained.
 レポーター遺伝子の活性が確認された酵母形質転換体において、第2のベクターに含まれる断片化した部分cDNAの配列を決定することで、部分的な獲物タンパク質をコードする遺伝子断片を同定することができる。さらに、同定した部分的な獲物タンパク質をコードする遺伝子断片を、例えば既知のデータベースに登録された遺伝子配列と比較することで、(登録されている場合には)獲物タンパク質をコードする遺伝子や当該遺伝子によりコードされる全長の獲物タンパク質を同定することもできる。 In a yeast transformant in which the activity of the reporter gene is confirmed, the gene fragment encoding the partial prey protein can be identified by determining the sequence of the fragmented partial cDNA contained in the second vector. . Furthermore, by comparing the gene fragment encoding the identified partial prey protein with, for example, a gene sequence registered in a known database, the gene encoding the prey protein (if registered) or the gene concerned The full-length prey protein encoded by can also be identified.
 本方法によれば、培養細胞でのパンニング法を行った際に比べて、酵母のレポーター遺伝子のシステムを利用することにより、結合の検出感度(最大で1μM程度のKdの結合まで検出できると見込まれる)とS/N比の向上、スクリーニングの迅速化(100万クローン程度の結合判定に通常は14日間程度が必要となる)、回収する遺伝子の安定性、クローニングの迅速化、経済性等が期待される。また、オーファンリガンドの受容体同定は、創薬に直結する可能性があり、本方法をオーファンリガンドの受容体同定に適用することができる。さらに、本方法を幅広く膜タンパク質同士の結合スクリーニングに適用することも可能である。 According to this method, the detection sensitivity of binding (up to about 1 μM Kd binding is expected to be detected by using the yeast reporter gene system, compared to the case of panning in cultured cells. Improved S / N ratio, faster screening (normally about 14 days are required to determine the binding of about 1 million clones), stability of recovered genes, faster cloning, economy, etc. Be expected. In addition, receptor identification of orphan ligands may be directly linked to drug discovery, and this method can be applied to receptor identification of orphan ligands. Furthermore, the present method can be widely applied to the binding screening between membrane proteins.
 また、本発明は、上記のランダムプライム逆転写によって得られたcDNA自体、第2のベクター自体、当該ランダムプライム逆転写によって得られたcDNA又は第2のベクターを含む本方法用試薬キットに関する。当該試薬キットは、例えば、本方法に使用するバッファーや容器、使用説明書等を更に含むことができる。 The present invention also relates to a reagent kit for the present method comprising the cDNA itself obtained by the above-mentioned random prime reverse transcription, the second vector itself, the cDNA obtained by the random prime reverse transcription or the second vector. The reagent kit can further include, for example, a buffer and a container used in the present method, instructions for use, and the like.
 以下、実施例を用いて本発明をより詳細に説明するが、本発明の技術的範囲はこれら実施例に限定されるものではない。
1.断片化cDNAの合成
 断片化cDNAの合成は、cDNA Library Construction Kit(タカラバイオ株式会社)の方法を、一部条件を改変して行った。
EXAMPLES Hereinafter, although this invention is demonstrated in detail using an Example, the technical scope of this invention is not limited to these Examples.
1. Synthesis of Fragmented cDNA Fragmented cDNA was synthesized using the method of cDNA Library Construction Kit (Takara Bio Inc.) with partial modification.
(1) 1st strand cDNAの合成
 制限酵素XhoIの認識配列(5'-CTCGAG-3')の3'側に、dATPとdCTPとdGTPとdTTPの4種類のヌクレオチドをランダムに6個付加したプライマー(配列5'-TAGAACTCGAGNNNNNN-3'(配列番号3);以下、「ランダムプライマー」と称する)(600 μM、1 μl)と、任意の生物や組織から採取したmRNA 5 μgと、dNTP混合液(dATP, 5-methyl dCTP, dGTP, dTTP)(各10 mM) 1.2 μlをマイクロ遠心チューブ内で混合し、RNaseを含まない水で10 μlにした。これを65℃で5分間加熱して、氷上で急冷して変性させた。これに、逆転写酵素(PrimeScript RTase タカラバイオ株式会社)(200 U/μl) 1 μlと、RNase阻害剤(40 U/μl) 1 μlと、反応用緩衝液(250 mM Tris-HCl(pH 8.3), 375 mM KCl, 15 mM MgCl2) 4 μlと、RNaseを含まない水4 μlを加え20 μlにし、42℃で1時間逆転写反応を行なった。1時間経過後、氷上で2分間冷却した。この反応で合成されたcDNAを1st strand cDNAとした。
(1) Synthesis of 1st strand cDNA Primer with 4 kinds of 4 nucleotides of dATP, dCTP, dGTP and dTTP randomly added to the 3 'side of the restriction enzyme XhoI recognition sequence (5'-CTCGAG-3') ( Sequence 5′-TAGAACTCGAGNNNNNN-3 ′ (SEQ ID NO: 3); hereinafter referred to as “random primer” (600 μM, 1 μl), 5 μg of mRNA collected from any organism or tissue, and dNTP mixture (dATP , 5-methyl dCTP, dGTP, dTTP) (10 mM each) was mixed in a microcentrifuge tube and made up to 10 μl with RNase-free water. This was heated at 65 ° C. for 5 minutes and denatured by rapid cooling on ice. To this, reverse transcriptase (PrimeScript RTase Takara Bio Inc.) (200 U / μl) 1 μl, RNase inhibitor (40 U / μl) 1 μl, reaction buffer (250 mM Tris-HCl (pH 8.3 ), 375 mM KCl, 15 mM MgCl 2 ) 4 μl and RNase-free water 4 μl were added to make 20 μl, and a reverse transcription reaction was performed at 42 ° C. for 1 hour. After 1 hour, it was cooled on ice for 2 minutes. The cDNA synthesized by this reaction was designated as 1st strand cDNA.
(2) 2nd strand cDNAの合成
 1st strand cDNAにdNTP混合液(dATP, dCTP, dGTP, dTTP) 4.5 μlと、RNaseHとDNA ligaseの混合液 2 μl、DNA polymerase I(20 U/μl) 2 μl、反応用緩衝液 30 μl、RNaseを含まない水87.5 μlを加え146 μlにし、16℃で2時間反応させた。2時間経過後、70℃で10分間静置後、室温で5分間以上静置した。この反応で合成された二本鎖cDNAを2nd strand cDNAとした。
(2) 2nd strand cDNA synthesis 1st strand cDNA is mixed with dNTP mixture (dATP, dCTP, dGTP, dTTP) 4.5 μl, RNaseH and DNA ligase mixture 2 μl, DNA polymerase I (20 U / μl) 2 μl, 30 μl of reaction buffer and 87.5 μl of RNase-free water were added to make 146 μl, followed by reaction at 16 ° C. for 2 hours. After 2 hours, the mixture was allowed to stand at 70 ° C. for 10 minutes and then allowed to stand at room temperature for 5 minutes or more. The double-stranded cDNA synthesized by this reaction was designated as 2nd strand cDNA.
(3) 2nd strand cDNAの末端の平滑化
 2nd strand cDNAに、T4 DNA polymerase(1 U/μl) 4 μlを加え、37℃で10分間反応させ、2nd strand cDNAの末端を平滑化した。これに等量のフェノール/クロロホルム/イソアミルアルコール(25:24:1混合液)を添加し、よく混合後、遠心分離を行い、上層を新しいマイクロ遠心チューブに移した。これに等量のクロロホルム/イソアミルアルコール(24:1混合液)を添加し、よく混合後、遠心分離を行い、上層を新しいマイクロ遠心チューブに移した。これに1/10量の3 M 酢酸ナトリウム緩衝液(pH 5.2)と、2.5倍量のエタノールを加え、よく混合後、室温で15,000 rpmで30分間遠心分離を行い、上清を除去した。沈殿に70%エタノールを200 μl加え、沈殿をリンス後、室温で15,000 rpmで3分間遠心分離を行い、上清を除去した。沈殿を乾燥させた後、RNaseを含まない水を12.5 μl加え沈殿を溶解した。これを末端平滑化2nd strand cDNAとした。
(3) Smoothing of the ends of the 2nd strand cDNA 4 μl of T4 DNA polymerase (1 U / μl) was added to the 2nd strand cDNA and reacted at 37 ° C. for 10 minutes to smooth the ends of the 2nd strand cDNA. An equal amount of phenol / chloroform / isoamyl alcohol (25: 24: 1 mixed solution) was added thereto, mixed well, centrifuged, and the upper layer was transferred to a new microcentrifuge tube. An equal amount of chloroform / isoamyl alcohol (24: 1 mixed solution) was added thereto, and after mixing well, the mixture was centrifuged and the upper layer was transferred to a new microcentrifuge tube. 1/10 volume of 3 M sodium acetate buffer (pH 5.2) and 2.5 volumes of ethanol were added to this, and after mixing well, the mixture was centrifuged at 15,000 rpm for 30 minutes at room temperature, and the supernatant was removed. After adding 200 μl of 70% ethanol to the precipitate and rinsing the precipitate, the mixture was centrifuged at 15,000 rpm for 3 minutes at room temperature, and the supernatant was removed. After drying the precipitate, 12.5 μl of RNase-free water was added to dissolve the precipitate. This was used as the end-blunted 2nd strand cDNA.
(4) 末端平滑化2nd strand cDNAへのEcoRIアダプターの付加
 末端平滑化2nd strand cDNA溶液12.5 μlに、EcoRI-SmaIアダプター(5'末端を脱リン酸化した5'-AATTCCCGGG-3'の一本鎖DNA(配列番号4)と、5'-CCCGGG-3'の一本鎖DNAをアニーリングさせたもの)(0.4 μg/μl) 3.5 μlと、T4 DNA ligase(350 U/μl) 2 μlと、反応用緩衝液2 μlを加え、全量を20 μlとした。これを、よく混合した後、8℃で一晩以上反応させた。反応後、70℃で30分間静置し、T4 DNA ligaseを失活させた後、室温でさらに5分間静置した。これをアダプター付加2nd strand cDNAとした。
(4) Addition of EcoRI adapter to end-blunted 2nd strand cDNA Add 12.5 μl of end-blunted 2nd strand cDNA solution to EcoRI-SmaI adapter (5′-AATTCCCGGG-3 ′ single strand with 5 ′ end dephosphorylated) DNA (SEQ ID NO: 4) and 5′-CCCGGG-3 ′ single-stranded DNA annealed) (0.4 μg / μl) 3.5 μl and T4 DNA ligase (350 U / μl) 2 μl 2 μl of working buffer was added to make a total volume of 20 μl. This was mixed well and then reacted at 8 ° C. overnight or longer. After the reaction, the mixture was allowed to stand at 70 ° C. for 30 minutes to inactivate T4 DNA ligase, and then allowed to stand at room temperature for another 5 minutes. This was designated as adapter-added 2nd strand cDNA.
(5) アダプター付加2nd strand cDNAの制限酵素XhoIによる切断
 アダプターを付加した2nd strand cDNA溶液20 μlに、XhoI(10 U/μl) 3 μlと、反応用緩衝液(500 mM Tris-HCl(pH 7.5), 100 mM MgCl2, 10 mM dithiothreitol, 1 M NaCl) 5 μlと、0.1% BSA(ウシ血清アルブミン) 5 μlと、RNaseを含まない水を17 μl加え、全量を50 μlとした。これを、よく混合した後、37℃で3時間反応させた。この反応で、ランダムプライマー内のXhoI認識配列が切断されるが、cDNA内のXhoI認識配列には1st strand cDNA合成時に5-methyl dCTPが使用されている為、XhoIで切断されない。
(5) Cleavage of adapter-added 2nd strand cDNA with restriction enzyme XhoI 20 μl of adapter-added 2nd strand cDNA solution, 3 μl of XhoI (10 U / μl) and reaction buffer (500 mM Tris-HCl (pH 7.5)) ), 100 mM MgCl 2 , 10 mM dithiothreitol, 1 M NaCl) 5 μl, 0.1 μl BSA (bovine serum albumin) 5 μl, and RNase-free water 17 μl were added to make a total volume of 50 μl. This was mixed well and then reacted at 37 ° C. for 3 hours. In this reaction, the XhoI recognition sequence in the random primer is cleaved, but the XhoI recognition sequence in the cDNA is not cleaved by XhoI because 5-methyl dCTP is used during the synthesis of the first strand cDNA.
(6) 短鎖DNAの除去
 ゲル濾過やシリカベースのビーズを用いて未反応のアダプターや数十残基以下の短鎖DNAの除去を行う。TE緩衝液(10 mM Tris-HCl(pH 8.0), 1 mM EDTA)で平衡化したゲル濾過カラム(目的とするcDNAのサイズによりゲルの種類を選択する)に、XhoIで切断した2nd strand cDNAを添加し、遠心分離(条件はカラムによる)を行った。この遠心操作で、未反応のEcoRI-SmaIアダプターや、XhoIで切断された短いDNA断片を含まない、一定サイズ以上のcDNAを取得した。これに等量のフェノール/クロロホルム/イソアミルアルコール(25:24:1混合液)を添加し、よく混合後、遠心分離を行い、上層を新しいマイクロ遠心チューブに移した。これに等量のクロロホルム/イソアミルアルコール(24:1混合液)を添加し、よく混合後、遠心分離を行い、上層を新しいマイクロ遠心チューブに移した。これに1/10量の3 M 酢酸ナトリウム緩衝液(pH 5.2)と、2.5倍量のエタノールを加え、よく混合後、室温で15,000 rpmで30分間遠心分離を行い、上清を除去した。沈殿に70%エタノールを200 μl加え、沈殿をリンス後、室温で15,000 rpmで3分間遠心分離を行い、上清を除去した。沈殿を乾燥させた後、RNaseを含まない水を15 μl加え、沈殿を溶解し、これをEcoRI-XhoI切断処理済みcDNAとした。
(6) Removal of short-chain DNA Using gel filtration or silica-based beads, unreacted adapters and short-chain DNAs of several tens of residues or less are removed. 2nd strand cDNA cleaved with XhoI is applied to a gel filtration column (select the gel type according to the size of the target cDNA) equilibrated with TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). The mixture was added and centrifuged (conditions depend on the column). By this centrifugation operation, cDNAs of a certain size or larger were obtained, which did not contain unreacted EcoRI-SmaI adapters or short DNA fragments cleaved with XhoI. An equal amount of phenol / chloroform / isoamyl alcohol (25: 24: 1 mixed solution) was added thereto, mixed well, centrifuged, and the upper layer was transferred to a new microcentrifuge tube. An equal amount of chloroform / isoamyl alcohol (24: 1 mixed solution) was added thereto, and after mixing well, the mixture was centrifuged and the upper layer was transferred to a new microcentrifuge tube. 1/10 volume of 3 M sodium acetate buffer (pH 5.2) and 2.5 volumes of ethanol were added to this, and after mixing well, the mixture was centrifuged at 15,000 rpm for 30 minutes at room temperature, and the supernatant was removed. After adding 200 μl of 70% ethanol to the precipitate and rinsing the precipitate, the mixture was centrifuged at 15,000 rpm for 3 minutes at room temperature, and the supernatant was removed. After drying the precipitate, 15 μl of RNase-free water was added to dissolve the precipitate, which was designated as EcoRI-XhoI-cleaved cDNA.
(7) ベクターへのEcoRI-XhoI切断処理済みcDNAの結合
 目的に応じたベクターをEcoRIとXhoIで切断したものと、EcoRI-XhoI切断処理済みcDNAをDNA ligaseを用い結合した。
(7) Binding of EcoRI-XhoI-cleaved cDNA to a vector A vector according to purpose was cleaved with EcoRI and XhoI, and EcoRI-XhoI-cleaved cDNA was ligated using DNA ligase.
 次いで、ベクターとEcoRI-XhoI切断処理済みcDNAを結合したものを、大腸菌にエレクトロポレーション法で導入し、任意の10クローンを選んでPCR法で挿入されている断片化cDNAのサイズを解析したところ100~1000塩基であることを確認した後、大腸菌からcDNAライブラリーを回収した。 Next, the vector and EcoRI-XhoI-cleaved cDNA combined were introduced into E. coli by electroporation, and any 10 clones were selected and analyzed for the size of the fragmented cDNA inserted by PCR. After confirming that it was 100 to 1000 bases, a cDNA library was recovered from E. coli.
2.マウス脳由来分子のスクリーニング
 上記第1節に準じて、マウスの脳から回収したmRNAを元に作製したcDNAをベクターpACT2に挿入したライブラリーを、pBTM116-HA-KM-hENHOで形質転換した出芽酵母L40に導入し、SD-Leu-Trp-His+3-AT培地に播種した(3-AT = 3-amino-1,2,4-triazole)。ここで、cDNAを挿入したベクターpACT2は、5'末端から3'末端の方向に、順にLarge T 抗原 residues 47 to 54 (PKKKRKVE:配列番号1)をコードする遺伝子とGal4タンパク質のアクティベータードメイン(AD)をコードする遺伝子と作製したcDNAとを有する。また、ベクターpBTM116-HA-KM-hENHOは、5'末端から3'末端の方向に、順にLexAタンパク質の内在性の核局在シグナル配列(KRLKK:配列番号2)とDNA結合ドメイン(DBD)をコードする遺伝子と、おとりタンパク質をコードする遺伝子としてヒトのアドロピン(hENHO)をコードする遺伝子とを有する。さらに、出芽酵母L40は、UASGの下流の制御下にβ-ガラクトシダーゼをコードする遺伝子(レポーター遺伝子)とHIS3遺伝子を有する。細胞内で二つのプラスミドから発現される分子が結合するとHIS3遺伝子の発現により、His欠乏培地でも酵母細胞は生育可能となる。
2. Screening of mouse brain-derived molecules Saccharomyces cerevisiae transformed with pBTM116-HA-KM-hENHO, a library in which cDNA prepared based on mRNA recovered from mouse brain was inserted into vector pACT2 according to Section 1 above. It was introduced into L40 and seeded on SD-Leu-Trp-His + 3-AT medium (3-AT = 3-amino-1,2,4-triazole). Here, the vector pACT2 into which the cDNA is inserted has a gene encoding the Large T antigen residues 47 to 54 (PKKKRKVE: SEQ ID NO: 1) in order from the 5 ′ end to the 3 ′ end and an activator domain (AD) of the Gal4 protein. And a prepared cDNA. In addition, the vector pBTM116-HA-KM-hENHO contains an endogenous nuclear localization signal sequence (KRLKK: SEQ ID NO: 2) and DNA binding domain (DBD) of the LexA protein in order from the 5 ′ end to the 3 ′ end. It has a gene that encodes it and a gene that encodes human adropin (hENHO) as a gene that encodes a decoy protein. Furthermore, Saccharomyces cerevisiae L40 has a gene (reporter gene) encoding β-galactosidase and an HIS3 gene under the control of UASG downstream. When molecules expressed from the two plasmids are combined in the cell, yeast cells can grow even in a His-deficient medium due to the expression of the HIS3 gene.
 播種した培地を30℃の培養器に移し、コロニーが視認出来るまで数日間培養した。コロニーを新しいSD-Leu-Trp培地に移し、30℃の培養器で培養した。増殖した酵母の一部を使用し、β-ガラクトシダーゼアッセイを行い、β-ガラクトシダーゼ活性陽性のクローン群を解析したところ、膜タンパク質の部分cDNAを含むものが含まれていた。 The seeded medium was transferred to a 30 ° C. incubator and cultured for several days until colonies were visible. Colonies were transferred to fresh SD-Leu-Trp medium and cultured in a 30 ° C. incubator. Using a part of the grown yeast, β-galactosidase assay was performed, and a group of clones positive for β-galactosidase activity was analyzed. As a result, those containing partial cDNA of membrane protein were included.
 本明細書で引用した全ての刊行物、特許及び特許出願はそのまま引用により本明細書に組み入れられるものとする。 All publications, patents and patent applications cited in this specification are incorporated herein by reference in their entirety.

Claims (7)

  1.  第1及び第2のベクターを導入した酵母形質転換体を培養する工程を含む、タンパク質の同定方法であって、
     第1のベクターは、核内移行シグナルをコードする遺伝子とDNA結合タンパク質をコードする遺伝子とおとりタンパク質をコードする遺伝子とを含み、
     第2のベクターは、核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含み、該断片化した部分cDNAは、シグナルペプチド、細胞膜若しくは細胞内小器官局在化配列又は細胞膜貫通領域が欠損した獲物タンパク質をコードするものであり、且つ、
     前記酵母形質転換体の核内において、前記核内移行シグナルとDNA結合タンパク質とおとりタンパク質とを含む融合タンパク質、及び前記核内移行シグナルと転写活性化タンパク質と断片化した部分cDNAによりコードされる獲物タンパク質とを含む融合タンパク質が発現し、該おとりタンパク質と該獲物タンパク質との結合を、レポーター遺伝子の活性を指標に検出する、
    前記方法。
    A method for identifying a protein comprising the step of culturing a yeast transformant into which the first and second vectors have been introduced,
    The first vector includes a gene encoding a nuclear translocation signal, a gene encoding a DNA binding protein, and a gene encoding a decoy protein,
    The second vector includes a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA. The fragmented partial cDNA is a signal peptide, a cell membrane, or an organelle. Encodes a prey protein lacking a localization sequence or transmembrane region, and
    Prey encoded in the nucleus of the yeast transformant by a fusion protein comprising the nuclear translocation signal, a DNA-binding protein and a decoy protein, and a partial cDNA fragmented with the nuclear translocation signal, a transcriptional activation protein A fusion protein containing a protein is expressed, and the binding between the decoy protein and the prey protein is detected using the activity of a reporter gene as an indicator,
    Said method.
  2.  おとりタンパク質がリガンドであり、且つ獲物タンパク質が受容体タンパク質である、請求項1記載の方法。 The method according to claim 1, wherein the decoy protein is a ligand and the prey protein is a receptor protein.
  3.  おとりタンパク質が各種局在シグナル配列を除いた部分cDNAによりコードされるタンパク質である、請求項1記載の方法。 The method according to claim 1, wherein the decoy protein is a protein encoded by a partial cDNA excluding various localization signal sequences.
  4.  ランダムプライム逆転写によって得られた、長さ100~1800bpを有するcDNA。 A cDNA having a length of 100 to 1800 bp obtained by random prime reverse transcription.
  5.  長さが100~1000bpである、請求項4記載のcDNA。 The cDNA according to claim 4, wherein the length is 100 to 1000 bp.
  6.  核内移行シグナルをコードする遺伝子と転写活性化タンパク質をコードする遺伝子と断片化した部分cDNAとを含むベクターであって、該断片化した部分cDNAが請求項4又は5記載のcDNAである、前記ベクター。 A vector comprising a gene encoding a nuclear translocation signal, a gene encoding a transcriptional activation protein, and a fragmented partial cDNA, wherein the fragmented partial cDNA is the cDNA according to claim 4 or 5. vector.
  7.  請求項4若しくは5記載のcDNA又は請求項6記載のベクターを含む、請求項1~3のいずれか1項記載のタンパク質の同定方法用試薬キット。 A reagent kit for the protein identification method according to any one of claims 1 to 3, comprising the cDNA according to claim 4 or 5 or the vector according to claim 6.
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