经修饰的Cas9蛋白及其用途的制作方法

本发明涉及可靶的区域进一步扩张的、经修饰的cas9蛋白及其用途。
背景技术：
：：已知成簇的规律间隔短回文重复序列(clusteredregularlyinterspacedshortpalindromicrepeats：crispr)和cas(crispr-相关)基因一起在细菌和古细菌中构成提供对侵入外来核酸的获得耐性的适应免疫系统。crispr往往是由噬菌体或质粒dna引起的，由其间插入有大小类似的被称作间隔序列的独特可变dna序列的24～48bp的短保守重复序列构成。另外，在重复和间隔序列的附近存在编码cas蛋白家族的基因组。在crispr-cas系统中，外源性dna被cas蛋白家族切割成30bp左右的片段，并插入crispr中。作为cas蛋白家族之一的cas1和cas2蛋白识别外源性dna的被称作前间隔序列邻近基序(proto-spaceradjacentmotif，pam)的核苷酸序列(塩基配列)，切取其上游，插入到宿主的crispr序列中，这成为细菌的免疫记忆。包含免疫记忆的crispr序列转录生成的rna(称作pre-crrna。)与一部分互补的rna(反式激活crrna(trans-activatingcrrna：tracrrna))配对，被摄入到作为cas蛋白家族之一的cas9蛋白中。摄入到cas9中的pre-crrna和tracrrna被rnaseiii切割，成为包含外来序列(向导序列)的小的rna片段(crispr-rnas：crrnas)，形成cas9-crrna-tracrrna复合物。cas9-crrna-tracrrna复合物和与crrna互补的外来侵入性dna结合，作为切割dna的酶(核酸酶)的cas9蛋白切割外来侵入性dna，从而抑制和排除从外侵入的dna的功能。cas9蛋白识别外来侵入性dna中的pam序列，在其上游切割双链dna使形成平滑末端。pam序列的长度或核苷酸序列根据细菌种类而多种多样，在酿脓链球菌(streptococcuspyogenes)(s.pyogenes)中识别“ngg”这3个碱基(塩基)。嗜热链球菌(streptococcusthermophilus)(s.thermophilus)持有2个cas9，分别将“nggng”或“nnagaa”这5～6个碱基识别为pam序列。在新凶手弗朗西丝氏菌(francisellanovicida)(f.novicida)中识别“ngr”这3个碱基。切割pam序列上游的任何bp的位置还根据细菌种类而不同，但包含s.pyogenes的大部分的cas9直系同源物切割pam序列的3个碱基上游。近年来，正在积极开发将细菌中的crispr-cas系统应用于基因组编辑的技术。使crrna与tracrrna融合，作为tracrrna-crrna嵌合体(以下，称作向导rna(guiderna：grna)。)来表达，并进行有效利用。由此，称为核酸酶(rna-向导的核酸酶：rgn)，在目标部位(靶位点)切割基因组dna。crispr-cas系统有i、ii、iii型，但在基因组编辑中专门使用ii型crispr-cas系统，在ii型中使用cas9蛋白作为rgn。由于来自s.pyogenes的cas9蛋白识别ngg这3个碱基作为pam序列，所以只要有2个鸟嘌呤并列的序列，即可切割其上游。利用了crispr-cas系统的方法不仅可以合成与目标dna序列同源的短grna，还可以使用作为单一蛋白的cas9蛋白进行基因组编辑。因此，不必像以往使用的锌指核酸酶(zfn)或类反式激活因子激动剂(talen)那样合成每个dna序列都不同的大的蛋白，即可简便且快速地进行基因组编辑。专利文献1中公开了：有效利用了来自s.pyogenes的crispr-cas系统的基因组编辑技术。专利文献2中公开了：有效利用了来自s.thermophilus的crispr-cas系统的基因组编辑技术。而且，专利文献2中还公开了：cas9蛋白的d31a或n891a突变体起到仅其中一条dna链带有切口的dna切割酶即切口酶的作用。而且，在根据dna切割后的修复机制容易发生插入缺失等突变的非同源末端结合的发生率少时，仍具有与野生型cas9蛋白同等程度的同源重组效率。非专利文献1中公开了：利用2个cas9蛋白的d10a突变体和与该d10a突变体形成复合物的1对靶特异性向导rna的双切口酶系统，其是使用了来自s.pyogenes的cas9的crispr-cas系统。各cas9蛋白的d10a突变体和靶特异性向导rna的复合物在与向导rna互补的dna链上仅制作1个切口。一对向导rna有约20个碱基左右的错配(ずれ)，仅识别位于靶dna的相反链的靶序列。由各cas9蛋白的d10a突变体和靶特异性向导rna的复合物制作的2个切口形成模仿dna双链切割(dnadouble-strandbreak：dsb)的状态，通过使用一对向导rna，在维持高水平的效率的同时，可以改善cas9蛋白介导型基因编辑的特异性。专利文献3中公开了来自s.pyogenes的cas9蛋白的各种突变体，专利文献4中公开了来自f.novicida的cas9蛋白的各种突变体。现有技术文献专利文献专利文献1：wo2014/093661；专利文献2：日本特表2015-510778号公报；专利文献3：wo2016/141224；专利文献4：wo2017/010543；非专利文献非专利文献1：ran,f.a.等人,doublenickingbyrna-guidedcrisprcas9forenhancedgenomeeditingspecificity,cell,第154卷,第1380-1389页,2013。技术实现要素：发明所要解决的课题专利文献1中公开的来自s.pyogenes的cas9(在本说明书中也称作spcas9)蛋白可识别的pam序列是“ngg(n为任意碱基)”这2个碱基。另外，在非专利文献1所公开的双切口酶系统中使用了spcas9蛋白，需要在靶序列内的有义链和反义链中各有1处可识别的pam序列共计2处，因此可进一步编辑的靶序列受到限制。如此，在现有的cas9蛋白中，可识别的pam序列有限制，所以存在着可编辑的靶序列受到限制的问题。本发明的目的在于：提供一种在维持与向导rna的结合能力的同时靶序列的限制得到缓解的经修饰的cas9蛋白及其用途。用于解决课题的手段本发明人着眼于spcas9蛋白作为cas9蛋白，为了解决上述课题进行了深入研究。其结果，通过将spcas9蛋白的规定位置的氨基酸取代成特定的氨基酸(导入突变)，成功地在维持与向导rna的结合能力的同时将作为现有ngg(n为任意碱基)的2个碱基的pam序列转换成ng的1个碱基的序列，从而完成了本发明。本说明书中，有时将导入突变前的cas9蛋白称为野生型cas9蛋白，而将导入突变后的cas9蛋白称为经修饰的cas9蛋白或突变型cas9蛋白。即，本发明如下。[1]蛋白，该蛋白由包含在seqidno:1所表示的氨基酸序列中1335位的精氨酸被选自丙氨酸、甘氨酸、半胱氨酸、异亮氨酸、亮氨酸、蛋氨酸、苯丙氨酸、脯氨酸、缬氨酸、苏氨酸、天冬酰胺和天冬氨酸的1个氨基酸取代而得到的氨基酸序列的序列构成，并且具有与向导rna的结合能力。[2]上述[1]所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在1219位具有突变。[3]上述[1]或[2]所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在1322位具有突变。[4]蛋白，该蛋白由包含在seqidno:1所表示的氨基酸序列中1335位的精氨酸被选自丙氨酸、甘氨酸、半胱氨酸、异亮氨酸、亮氨酸、蛋氨酸、苯丙氨酸、脯氨酸、缬氨酸、苏氨酸、天冬酰胺和天冬氨酸的1个氨基酸取代、并进一步在1219位具有突变的氨基酸序列的序列构成，并且具有与向导rna的结合能力。[5]蛋白，该蛋白由包含在seqidno:1所表示的氨基酸序列中1335位的精氨酸被选自丙氨酸、甘氨酸、半胱氨酸、异亮氨酸、亮氨酸、蛋氨酸、苯丙氨酸、脯氨酸、缬氨酸、苏氨酸、天冬酰胺和天冬氨酸的1个氨基酸取代、并进一步在1322位具有突变的氨基酸序列的序列构成，并且具有与向导rna的结合能力。[6]上述[1]～[5]中任一项所述的蛋白，其中，1335位的精氨酸的取代是取代成丙氨酸。[7]上述[1]～[5]中任一项所述的蛋白，其中，1335位的精氨酸的取代是取代成异亮氨酸、蛋氨酸、苏氨酸或缬氨酸。[8]上述[2]或[4]所述的蛋白，其中，1219位的突变是谷氨酸被取代成苯丙氨酸。[9]上述[3]或[5]所述的蛋白，其中，1322位的突变是丙氨酸被取代成精氨酸、组氨酸或赖氨酸。[10]上述[9]所述的蛋白，其中，1322位的突变是丙氨酸被取代成精氨酸。[11]上述[1]～[10]中任一项所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在选自1111位、1135位、1218位和1337位的至少一个位置具有突变。[12]上述[11]所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在选自1111位、1135位、1218位和1337位的至少2个位置具有突变。[13]上述[11]所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在选自1111位、1135位、1218位和1337位的至少3个位置具有突变。[14]上述[11]所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中，进一步在1111位、1135位、1218位和1337位具有突变。[15]上述[11]～[14]中任一项所述的蛋白，其中，1111位的突变是亮氨酸被取代成精氨酸、组氨酸或赖氨酸；1135位的突变是天冬氨酸被取代成缬氨酸；1218位的突变是甘氨酸被取代成精氨酸、组氨酸或赖氨酸；1337位的突变是苏氨酸被取代成精氨酸、组氨酸或赖氨酸。[16]上述[1]～[15]中任一项所述的蛋白，其中，在seqidno:1的施行了突变的位置以外的位点具有80%以上的同源性。[17]上述[1]～[15]中任一项所述的蛋白，其中，在seqidno:1的施行了突变的位置以外的位点取代、缺失、插入和/或添加了1个～多个氨基酸。[18]上述[1]～[17]中任一项所述的蛋白，该蛋白具有rna诱导性dna核酸内切酶活性。[19]上述[1]～[16]中任一项所述的蛋白，其中，在seqidno:1所表示的氨基酸序列中进一步具有缺失一部分或全部的核酸酶活性的突变。[20]上述[19]所述的蛋白，其中，缺失一部分或全部的核酸酶活性的突变是seqidno:1所表示的氨基酸序列中的、(i)选自10位、762位、839位、983位和986位的至少1个位置或相当于此的位置、和/或(ii)选自840位和863位的位置或相当于此的位置的突变。[21]上述[20]所述的蛋白，其中，10位的天冬氨酸被取代成丙氨酸或天冬酰胺；或者840位的组氨酸被取代成丙氨酸、天冬酰胺或酪氨酸。[22]上述[19]～[21]中任一项所述的蛋白，该蛋白连接有转录调控因子蛋白或结构域。[23]上述[22]所述的蛋白，其中，转录调控因子为转录激活因子。[24]上述[22]所述的蛋白，其中，转录调控因子为转录沉默子或转录抑制因子。[25]核酸，该核酸编码上述[1]～[24]中任一项所述的蛋白。[26]蛋白-rna复合物，该复合物具备上述[1]～[24]中任一项所述的蛋白和向导rna，所述向导rna包含由与靶双链多核苷酸中的pam(前间隔序列邻近基序，proto-spaceradjacentmotif)序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成的多核苷酸。[27]用于位点特异性地修饰靶双链多核苷酸的方法，该方法具备以下步骤：将靶双链多核苷酸、蛋白和向导rna混合并进行培养的步骤；以及上述蛋白在位于pam序列上游的结合位点修饰上述靶双链多核苷酸的步骤，上述靶双链多核苷酸具有由ng(n是指任意碱基，g是指鸟嘌呤)构成的pam序列，上述蛋白为上述[1]～[24]中任一项所述的蛋白，上述向导rna包含由与上述靶双链多核苷酸中的上述pam序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成的多核苷酸。[28]上述[27]所述的方法，其中，修饰是指靶双链多核苷酸的位点特异性切割。[29]上述[27]所述的方法，其中，修饰是指靶双链多核苷酸中的位点特异性的1个以上的核苷酸的取代、缺失和/或添加。[30]增加细胞的靶基因表达的方法，该方法包括：使上述[23]所述的蛋白和针对上述靶基因的1个或多个向导rna在上述细胞内表达。[31]减少细胞的靶基因表达的方法，该方法包括：使上述[24]所述的蛋白和针对上述靶基因的1个或多个向导rna在上述细胞内表达。[32]上述[30]或[31]所述的方法，其中，细胞为真核细胞。[33]上述[30]或[31]所述的方法，其中，细胞为酵母细胞、植物细胞或动物细胞。发明效果根据本发明，可以获得在保持与向导rna的结合力的同时pam序列的识别变得广泛的cas9蛋白。另外，可以提供利用了上述cas9蛋白的简便且快速的靶序列位点特异性的基因组编辑技术。附图说明[图1a]图1a是表示实施例1中的dna切割活性测定试验的琼脂糖凝胶电泳的结果的图。使用“tgt”作为pam序列，使用ecori作为限制酶。[图1b]图1b是表示实施例1中的dna切割活性测定试验的琼脂糖凝胶电泳的结果的图。使用“tgg”作为pam序列，使用hindiii作为限制酶。[图1c]图1c是表示实施例1中的dna切割活性测定试验的琼脂糖凝胶电泳的结果的图。使用“tgna”作为pam序列，使用bamhi作为限制酶。[图1d]图1d是表示实施例1中的dna切割活性测定试验的琼脂糖凝胶电泳的结果的图。使用“tgn”作为pam序列，使用bamhi作为限制酶。[图2]图2是表示实施例2中的dna切割活性测定试验的琼脂糖凝胶电泳的结果的图。[图3]图3是表示实施例3中的dna切割活性测定试验的结果的图。使用“tga”作为pam序列，使用bamhi作为限制酶。[图4]图4是表示实施例4中的dna切割活性测定试验的结果的图。[图5]图5是表示实施例5中的dna切割活性测定试验的结果的图。具体实施方式以下，对本发明进行说明。本说明书中使用的术语只要没有特别说明，则具有该领域通常使用的意义。<pam序列的识别变得广泛的cas9蛋白>本实施方式的蛋白是在保持与向导rna的结合力的同时pam序列的识别变得广泛的cas9蛋白。根据本实施方式的蛋白，可以提供简便且快速、并且针对靶序列进行位点特异性的基因组编辑的技术。在本说明书中，“向导rna”是指模仿tracrrna-crrna的发夹结构的rna，在其5’末端区域包含多核苷酸，所述多核苷酸由与靶双链多核苷酸中的pam序列的从1个碱基上游到优选20个碱基以上且24个碱基以下、更优选22个碱基以上且24个碱基以下的核苷酸序列互补的核苷酸序列构成。该向导rna可以进一步包含1个以上的多核苷酸，所述多核苷酸由可获得发夹结构的核苷酸序列构成，该核苷酸序列由与靶双链多核苷酸不互补的核苷酸序列构成，并排列成以一点为轴对称性地互补的序列。向导rna具有与本发明的突变型cas9蛋白结合而将该蛋白引导至靶dna的功能。向导rna在其5’末端具有与靶dna互补的序列，经由该互补序列与靶dna结合，从而将本发明的突变型cas9蛋白引导至靶dna。在突变型cas9蛋白起到dna核酸内切酶的作用的情况下，可以在靶dna存在的位点切割dna，例如可以特异性地使靶dna的功能丧失。向导rna是根据应该切割或修饰的靶dna的序列信息设计、调制的。具体而言，可以列举如实施例中使用的序列。在本说明书中，“核酸内切酶”是指切割核苷酸链的中间位置的酶。因此，具有核酸内切酶活性的、使本实施方式的pam序列的识别变得广泛的cas9蛋白具有通过向导rna诱导而切割dna链的中间位置的酶活性。在本说明书中，“多肽”、“肽”和“蛋白”是指氨基酸残基的聚合物，且互换地使用。另外，还指下述的氨基酸聚合物：1个或多个氨基酸为天然存在的对应氨基酸的化学类似物或修饰衍生物。在本说明书中，“序列”是指任意长度的核苷酸序列，为脱氧核糖核苷酸或核糖核苷酸，呈线状、环状或支链状，为单链或双链。在本说明书中，“pam序列”是指存在于靶双链多核苷酸中、且可由cas9蛋白识别的序列，pam序列的长度或核苷酸序列根据细菌种类而不同。可由本实施方式的pam序列的识别变得广泛的cas9蛋白识别的序列可用“5’-ng-3’”表示。需要说明的是，在本说明书中，“n”是指选自腺嘌呤、胞嘧啶、胸腺嘧啶和鸟嘌呤的任意一种碱基，“a”是指腺嘌呤，“g”是指鸟嘌呤，“c”是指胞嘧啶，“t”是指胸腺嘧啶，“r”是指具有嘌呤骨架的碱基(腺嘌呤或鸟嘌呤)，“y”是指具有嘧啶骨架的碱基(胞嘧啶或胸腺嘧啶)。在本说明书中，“多核苷酸”是指呈线状或环状构象、且为单链或双链形态的任一种形态的脱氧核糖核苷酸或核糖核苷酸聚合物，关于聚合物的长度没有限制性的解释。另外，还包含天然核苷酸的已知的类似物、以及在碱基部分、糖部分和磷酸部分中的至少一个部分被修饰的核苷酸(例如，硫代磷酸盐骨架)。通常，特定核苷酸的类似物具有相同的碱基配对特异性，例如，a的类似物与t进行碱基配对。在一实施方式中，本发明提供蛋白(方案1)，该蛋白由在seqidno:1所表示的氨基酸序列中在1335位具有突变的氨基酸序列构成，并且具有与向导rna的结合能力。此外，方案1的蛋白还具有rna诱导性dna核酸内切酶活性。seqidno:1是spcas9蛋白的全长氨基酸序列。spcas9蛋白中的pam序列识别位点的序列是由seqidno:1的第1097位～第1368位的271个残基构成的氨基酸序列。具体而言，seqidno:1的1335位的突变是指1335位的精氨酸被取代成选自丙氨酸、甘氨酸、半胱氨酸、异亮氨酸、亮氨酸、蛋氨酸、苯丙氨酸、脯氨酸、苏氨酸、缬氨酸、天冬酰胺和天冬氨酸的1个氨基酸。优选取代成丙氨酸。另外，1335位的另一优选突变是取代成异亮氨酸、蛋氨酸、苏氨酸或缬氨酸。与pam序列中的第3位的鸟嘌呤(5’-ng“g”-3’)形成的氢键因1335位的突变而消失，因此可使该蛋白的pam序列的识别变得广泛。在本发明的另一实施方案中，本发明提供蛋白(方案2)，该蛋白除了具有上述方案1的突变以外，还进一步在1219位具有突变，并且具有与向导rna的结合能力。此外，方案2的蛋白还具有rna诱导性dna核酸内切酶活性。具体而言，该1219位的突变是指1219位的谷氨酸被取代成苯丙氨酸。1219位的突变可有助于提高(维持)rna诱导性dna核酸内切酶活性的表达速度。在本发明的又一实施方案中，本发明提供蛋白(方案3)，该蛋白除了具有上述方案1或2的突变以外，还进一步在1322位具有突变，并且具有与向导rna的结合能力。此外，方案3的蛋白还具有rna诱导性dna核酸内切酶活性。具体而言，该1322位的突变是指1322位的丙氨酸被取代成精氨酸、组氨酸或赖氨酸。优选取代成精氨酸。1322位的突变可有助于rna诱导性dna核酸内切酶活性的活性提高(活性维持)。在本发明的又一实施方案中，本发明提供蛋白(方案4)，该蛋白除了具有上述方案1、2或3的突变以外，还进一步在选自1111位、1135位、1218位和1337位的至少1个、优选2个、更优选3个、特别优选全部的4个位置具有突变，并且还具有与向导rna的结合能力。方案4的蛋白具有rna诱导性dna核酸内切酶活性。具体而言，该1111位的突变是指1111位的亮氨酸被取代成精氨酸、组氨酸或赖氨酸。优选取代成精氨酸。具体而言，该1135位的突变是指1135位的天冬氨酸被取代成缬氨酸。具体而言，该1218位的突变是指1218位的甘氨酸被取代成精氨酸、组氨酸或赖氨酸。优选取代成精氨酸。具体而言，该1337位的突变是指1337位的苏氨酸被取代成精氨酸、组氨酸或赖氨酸。优选取代成精氨酸。在本发明的又一实施方案中，本发明提供蛋白(方案5)，该蛋白除了具有上述方案1、2、3或4的突变以外，还进一步在(i)选自10位、762位、839位、983位、986位的至少1个位置和/或(ii)选自840位和863位的位置具有突变，并且具有与向导rna的结合能力。具体而言，该10位的突变是指10位的天冬氨酸被取代成丙氨酸或天冬酰胺。具体而言，该762位的突变是指762位的谷氨酸被取代成谷氨酰胺。具体而言，该839位的突变是指839位的天冬氨酸被取代成丙氨酸或天冬酰胺。具体而言，该983位的突变是指983位的组氨酸被取代成天冬酰胺或酪氨酸。具体而言，该986位的突变是指986位的天冬氨酸被取代成天冬酰胺。具体而言，该840位的突变是指840位的组氨酸被取代成丙氨酸、天冬酰胺或酪氨酸。具体而言，该863位的突变是指863位的天冬酰胺被取代成天冬氨酸、丝氨酸或组氨酸。作为方案5，优选为10位的天冬氨酸被取代成丙氨酸或天冬酰胺、或者840位的组氨酸被取代成丙氨酸、天冬酰胺或酪氨酸的蛋白。具有(i)的突变或(ii)的突变的方案5的蛋白具有切口酶活性。具有(i)的突变和(ii)的突变的方案5的蛋白虽然与向导rna结合而被运送到靶dna中，但丧失了核酸内切酶活性。在本发明的又一实施方案中，本发明提供在功能上与上述方案1～5的蛋白同等的蛋白(方案6)。为了在功能上与上述方案1～5的蛋白同等，在seqidno:1所表示的氨基酸序列中，在上述方案1～5中施行了突变的位置以外的位点具有80%以上的序列同源性，并且具有与向导rna的结合能力。在通过突变而使氨基酸有所增减的情况下，该“施行了突变的位置以外的位点”可理解为“相当于施行了突变的位置的位置以外的位点”。作为所涉及的同源性，优选80%以上，更优选85%以上，进一步优选90%以上，特别优选95%以上，最优选99%以上。氨基酸序列同源性可通过自身已知的方法来确定。例如，氨基酸序列同源性(%)可以按照初期设定利用该领域所惯用的程序(例如blast、fasta等)来确定。另一方面，同源性(%)可以利用该领域已知的任意算法、例如needleman等人(1970)(j.mol.biol.48:444-453)、myers和miller(cabios,1988,4:11-17)的算法等来确定。needleman等人的算法被整合到gcg软件包(可通过www.gcg.com获取)的gap程序中，例如可以通过使用blosum62matrix或pam250matrix、以及空位权重(加权)(gapweight):16、14、12、10、8、6或4和长度权重(lengthweight):1、2、3、4、5或6的任一者来确定同源性(%)。另外，myers和miller的算法被整合到作为gcg序列比对软件包的一部分的align程序中。在为了比较氨基酸序列而利用align程序的情况下，例如可以使用pam120权重残基表(weightresiduetable)、空位长度罚分(gaplengthpenalty)12、空位罚分(gappenalty)4。作为在功能上与上述方案1～5的蛋白同等的蛋白，提供下述蛋白(方案7)：该蛋白在seqidno:1所表示的氨基酸序列中在通过上述方案1～5施行了突变的位置以外的位点有1个～多个氨基酸被取代、缺失、插入和/或添加，并且具有与向导rna的结合能力。在通过突变而使氨基酸有所增减的情况下，该“施行了突变的位置以外的位点”可以理解为“相当于施行了突变的位置的位置以外的位点”。作为人为地进行“氨基酸的取代、缺失、插入和/或添加”的情形的手法，例如可以列举：对编码规定的氨基酸序列的dna施行惯用的位点特异性突变导入，之后利用常规方法使该dna表达的手法。这里，作为位点特异性突变导入法，例如可以列举：利用琥珀突变的方法(缺口双链体(gappedduplex)法、nucleicacidsres.,12,9441-9456(1984))、使用了突变导入用引物的pcr的方法等。上述修饰的氨基酸的数目至少是1个残基，具体而言，是指1个或多个、或其以上。另外，在上述取代、缺失、插入或添加中，特别优选氨基酸的取代。该取代更优选取代成具有在疏水性、电荷、pk、立体结构上的特征等类似的性质的氨基酸。作为这样的取代，例如可以列举下述组内的取代：i)甘氨酸、丙氨酸；ii)缬氨酸、异亮氨酸、亮氨酸；iii)天冬氨酸、谷氨酸、天冬酰胺、谷氨酰胺；iv)丝氨酸、苏氨酸；v)赖氨酸、精氨酸；vi)苯丙氨酸、酪氨酸。作为本发明的pam序列的识别变得广泛的cas9蛋白，优选列举包含下述氨基酸序列的蛋白：在seqidno:1中1335位的精氨酸突变成丙氨酸(r1335a)、1111位的亮氨酸突变成精氨酸(l1111r)、1135位的天冬氨酸突变成缬氨酸(d1135v)、1218位的甘氨酸突变成精氨酸(g1218r)、1219位的谷氨酸突变成苯丙氨酸(e1219f)、1322位的丙氨酸突变成精氨酸(a1322r)、1337位的苏氨酸突变成精氨酸(t1337r)而得到的氨基酸序列(seqidno:18)。另外，作为本发明的pam序列的识别变得广泛的cas9蛋白，还优选包含下述氨基酸序列的蛋白：在seqidno:1中1335位的精氨酸突变成异亮氨酸(r1335i)、蛋氨酸(r1335m)、苏氨酸(r1335t)或缬氨酸(r1335v)(更优选r1335m和r1335v)、1111位的亮氨酸突变成精氨酸(l1111r)、1135位的天冬氨酸突变成缬氨酸(d1135v)、1218位的甘氨酸突变成精氨酸(g1218r)、1219位的谷氨酸突变成苯丙氨酸(e1219f)、1322位的丙氨酸突变成精氨酸(a1322r)、1337位的苏氨酸突变成精氨酸(t1337r)而得到的氨基酸序列。该蛋白相当于分别包含在seqidno:18中1335位的丙氨酸突变成异亮氨酸、蛋氨酸、苏氨酸或缬氨酸而得到的氨基酸序列的蛋白。本说明书中，表示到取代位点为止的氨基酸残基数的数字的左侧显示的字母(alphabet)，表示取代前的氨基酸的单字母标记，而右侧显示的字母(alphabet)，表示取代后的氨基酸的单字母标记。本实施方式中的pam识别变得广泛的cas9蛋白例如可以通过如下所述的方法来制作。首先，使用包含编码上述pam识别变得广泛的cas9蛋白的核酸的载体转化宿主。然后，培养该宿主，使上述蛋白表达。培养基的组成、培养的温度、时间、诱导物质的添加等条件可由本领域技术人员按照已知的方法来确定，使转化体生长，高效率地产生上述蛋白。另外，例如在将抗生素抗性基因整合到表达载体中作为选择标志物的情况下，通过在培养基中加入抗生素，可以选择转化体。然后，通过将宿主所表达的上述蛋白按照自身已知的适当方法进行纯化，得到pam识别变得广泛的cas9蛋白。对宿主没有特别限定，可以列举：动物细胞、植物细胞、昆虫细胞、或大肠杆菌、枯草杆菌、酵母等微生物。<pam序列的识别变得广泛的cas9蛋白-向导rna复合物>在一实施方式中，本发明提供蛋白-rna复合物，该复合物具备：上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白和向导rna，所述向导rna包含多核苷酸，该多核苷酸由与靶双链多核苷酸中的pam(前间隔序列邻近基序，proto-spaceradjacentmotif)序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成的。根据本实施方式的蛋白-rna复合物，pam序列变得广泛，可以简便且快速、并且针对靶序列进行位点特异性的靶双链多核苷酸的编辑。上述蛋白和上述向导rna通过在体外和体内、在温和的条件下混合，可以形成蛋白-rna复合物。温和的条件表示蛋白不会分解或变性的程度的温度和ph，温度优选4℃以上且40℃以下，ph优选4以上且10以下。另外，混合上述蛋白和上述向导rna进行培养的时间优选0.5小时以上且1小时以下。由上述蛋白和上述向导rna形成的复合物稳定，即使在室温下静置数小时也可保持稳定性。<crispr-cas载体系统>在一实施方式中，本发明提供crispr-cas载体系统，该载体系统具备第1载体和第2载体，所述第1载体包含编码上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白的基因，所述第2载体包含向导rna，该向导rna包含由与靶双链多核苷酸中的pam序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成的多核苷酸。根据本实施方式的crispr-cas载体系统，pam序列变得广泛，可以简便且快速、并且针对靶序列进行位点特异性的靶双链多核苷酸的编辑。关于向导rna，只要适当设计在5’末端区域包含多核苷酸的向导rna即可，所述多核苷酸由与靶双链多核苷酸中的pam序列的从1个碱基上游到优选20个碱基以上且24个碱基以下、更优选22个碱基以上且24个碱基以下的核苷酸序列互补的核苷酸序列构成。该向导rna可以进一步包含1个以上的多核苷酸，所述多核苷酸由可获得发夹结构的核苷酸序列构成，该核苷酸序列由与靶双链多核苷酸不互补的核苷酸序列构成，并排列成以一点为轴对称性地互补的序列。本实施方式的载体优选为表达载体。对表达载体没有特别限定，例如可以使用：pbr322、pbr325、puc12、puc13等来自大肠杆菌的质粒；pub110、ptp5、pc194等来自枯草杆菌的质粒；psh19、psh15等来自酵母的质粒；λ噬菌体等噬菌体；腺病毒、腺相关病毒、慢病毒、牛痘病毒、杆状病毒等病毒；以及修饰这些载体而得到的载体等。在上述的表达载体中，对用于表达上述cas9蛋白和上述向导rna的启动子没有特别限定，例如可以使用：ef1α启动子、srα启动子、sv40启动子、ltr启动子、cmv(巨细胞病毒)启动子、hsv-tk启动子等用于在动物细胞中表达的启动子；花椰菜花叶病毒(camv)的35s启动子、ref(橡胶延伸因子，rubberelongationfactor)启动子等用于在植物细胞中表达的启动子；多角体蛋白启动子、p10启动子等用于在昆虫细胞中表达的启动子等。这些启动子可以根据上述cas9蛋白和上述向导rna、或者根据表达上述cas9蛋白和上述向导rna的细胞的种类而适当选择。上述的表达载体可以进一步具有多克隆位点、增强子、剪接信号、添加了聚a的信号、选择标志物、复制起点等。<用于位点特异性地修饰靶双链多核苷酸的方法>[第1实施方式]在一实施方式中，本发明提供用于位点特异性地修饰靶双链多核苷酸的方法，该方法具备以下步骤：将靶双链多核苷酸、蛋白和向导rna混合进行培养的步骤；以及上述蛋白在位于pam序列上游的结合位点修饰上述靶双链多核苷酸的步骤，上述靶双链多核苷酸具有由ng(n是指任意碱基，g是指鸟嘌呤)构成的pam序列，上述蛋白为上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白，上述向导rna包含多核苷酸，所述多核苷酸由与上述靶双链多核苷酸中的上述pam序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成。根据本实施方式的方法，通过使用pam序列变得广泛的突变型cas9蛋白，可以简便且快速、并且针对靶序列进行位点特异性地修饰靶双链多核苷酸。在本实施方式中，靶双链多核苷酸只要具有由ng(n是指任意碱基，g是指鸟嘌呤)构成的pam序列即可，没有特别限定。在本实施方式中，关于蛋白和向导rna，如上述的<pam序列的识别变得广泛的cas9蛋白>中所示。以下，对用于位点特异性地修饰靶双链多核苷酸的方法的细节进行说明。首先，在温和的条件下混合上述蛋白和上述向导rna，并进行培养。温和的条件如上所述。进行培养的时间优选0.5小时以上且1小时以下。由上述蛋白和上述向导rna形成的复合物稳定，即使在室温下静置数小时也可保持稳定性。接下来，上述蛋白和上述向导rna在上述靶双链多核苷酸上形成复合物。上述蛋白识别由“5’-ng-3’”构成的pam序列，在位于pam序列上游的结合位点与上述靶双链多核苷酸结合。在上述蛋白具有核酸内切酶活性的情况下在该位点切割该多核苷酸。上述cas9蛋白识别pam序列，以pam序列为起点，剥离上述靶双链多核苷酸的双螺旋结构，和上述向导rna中的与上述靶双链多核苷酸互补的核苷酸序列退火，从而使上述靶双链多核苷酸的一部分双螺旋结构解开。此时，上述cas9蛋白在位于pam序列上游的切割位点和位于与pam序列互补的序列的上游的切割位点，切割上述靶双链多核苷酸的磷酸二酯键。[第2实施方式]在本实施方式中，在培养步骤之前，可以进一步具备下述表达步骤：使用上述的crispr-cas载体系统，使上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白和向导rna表达。在本实施方式的表达步骤中，首先，使用上述的crispr-cas载体系统使cas9蛋白和向导rna表达。作为使之表达的具体方法，分别使用包含编码cas9蛋白的基因的表达载体和包含向导rna的表达载体来转化宿主。然后，培养该宿主，使cas9蛋白和向导rna表达。培养基的组成、培养的温度、时间、诱导物质的添加等条件可由本领域技术人员按照已知的方法确定，使转化体生长，高效率地产生融合蛋白。另外，例如在将抗生素抗性基因整合到表达载体中作为选择标志物的情况下，通过在培养基中加入抗生素，可以选择转化体。然后，通过利用适当的方法纯化宿主所表达的cas9蛋白和向导rna，获得cas9蛋白和向导rna。<用于位点特异性地修饰靶双链核苷酸的方法>[第1实施方式]在一实施方式中，本发明提供用于位点特异性地修饰靶双链多核苷酸的方法，该方法具备以下步骤：将靶双链多核苷酸、蛋白和向导rna混合进行培养的步骤；上述蛋白在位于pam序列上游的结合位点与上述靶双链多核苷酸结合的步骤；以及在通过上述向导rna与上述靶双链多核苷酸的互补性结合确定的区域得到被修饰的上述靶双链多核苷酸的步骤，上述靶双链多核苷酸具有由ng(n是指任意碱基，g是指鸟嘌呤)构成的pam序列，上述蛋白为上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白，上述向导rna包含多核苷酸，所述多核苷酸由与上述靶双链多核苷酸中的上述pam序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成。根据本实施方式的方法，通过使用pam序列变得广泛的rna诱导性dna核酸内切酶，可以简便且快速、并且针对靶序列进行位点特异性地修饰靶双链多核苷酸。在本实施方式中，关于靶双链多核苷酸、蛋白和向导rna，如上述的<pam序列的识别变得广泛的cas9蛋白>和<用于位点特异性地修饰靶双链多核苷酸的方法>中所示。以下，对用于位点特异性地修饰靶双链多核苷酸的方法的细节进行说明。直到与靶双链多核苷酸位点特异性地结合为止的步骤与上述的<用于位点特异性地切割靶双链多核苷酸的方法>中所示的步骤同样。然后，在通过上述向导rna与上述双链多核苷酸的互补性结合确定的区域可以获得根据目的施行了修饰的靶双链多核苷酸。在本说明书中，“修饰”是指靶双链多核苷酸的核苷酸序列发生变化。例如，除了通过靶双链多核苷酸的切割、切割后的外源性序列的插入(物理性插入或经由同源定向修复的复制进行的插入)而引起的靶双链多核苷酸的核苷酸序列的变化、切割后的非同源末端连接(nhej：通过切割生成的dna末端彼此再次结合)以外，还可以列举通过添加功能性的蛋白或核苷酸序列而引起的靶双链多核苷酸的核苷酸序列的变化等。通过本实施方式中的靶双链多核苷酸的修饰，可以向靶双链多核苷酸中导入突变，或者可以破坏、改变靶双链多核苷酸的功能。[第2实施方式]在本实施方式中，在培养步骤之前，可以进一步具备下述的表达步骤：使用上述的crispr-cas载体系统，使上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白和向导rna表达。在本实施方式的表达步骤中，首先，使用上述的crispr-cas载体系统使cas9蛋白和向导rna表达。作为使之表达的具体方法，与上述的<用于位点特异性地修饰靶双链多核苷酸的方法>的[第2实施方式]中例示的方法同样。<用于在细胞内位点特异性地修饰靶双链多核苷酸的方法>在一实施方式中，本发明提供用于在细胞内位点特异性地修饰靶双链多核苷酸的方法，该方法具备以下步骤：将上述的crispr-cas载体系统导入细胞中，使上述的<pam序列的识别变得广泛的cas9蛋白>中所示的蛋白和向导rna表达的表达步骤；上述蛋白在位于pam序列上游的结合位点与上述靶双链多核苷酸结合的步骤；以及在通过上述向导rna与上述靶双链多核苷酸的互补性结合确定的区域得到被修饰的上述靶双链多核苷酸的步骤，上述靶双链多核苷酸具有由ng(n是指任意碱基，g是指鸟嘌呤)构成的pam序列，上述向导rna包含多核苷酸，所述多核苷酸由与上述靶双链多核苷酸中的上述pam序列的从1个碱基上游到20个碱基以上且24个碱基以下上游的核苷酸序列互补的核苷酸序列构成。在本实施方式的表达步骤中，首先，利用上述的crispr-cas载体系统使cas9蛋白和向导rna在细胞内表达。作为本实施方式的方法的应用对象的细胞的来源的生物，例如可以列举：原核生物、酵母、动物、植物、昆虫等。对上述动物没有特别限定，例如可以列举：人、猴、狗、猫、兔、猪、牛、小鼠、大鼠等，不限于这些。另外，作为细胞来源的生物的种类，可以根据所期望的靶双链多核苷酸的种类、目的等任意选择。作为本实施方式的方法的应用对象的动物来源的细胞，例如可以列举：生殖细胞(精子、卵子等)、构成生物体的体细胞、干细胞、前体细胞、由生物体分离的癌细胞、由生物体分离并获得永生化能力而在体外稳定维持的细胞(细胞株)、由生物体分离且人为地进行了基因修饰的细胞、由生物体分离且人为地交换了核的细胞等，不限于这些。作为构成生物体的体细胞，例如可以列举：由皮肤、肾脏、脾脏、腎上腺、肝脏、肺、卵巢、胰腺、子宫、胃、结肠、小肠、大肠、膀胱、前列腺、睾丸、胸腺、肌肉、结缔组织、骨、软骨、血管组织、血液、心脏、眼、脑、神经组织等任意的组织采集的细胞等，不限于这些。作为体细胞，更具体而言，例如可以列举：成纤维细胞、骨髄细胞、免疫细胞(例如，b淋巴细胞、t淋巴细胞、嗜中性粒细胞、巨噬细胞、单核细胞等)、红细胞、血小板、骨细胞、骨髄细胞、周皮细胞(周细胞)、树突状细胞、角质形成细胞、脂肪细胞、间充质细胞、上皮细胞、表皮细胞、内皮细胞、血管内皮细胞、淋巴管内皮细胞、肝细胞、胰岛细胞(例如，α细胞、β细胞、δ细胞、ε细胞、pp细胞等)、软骨细胞、卵丘细胞、胶质细胞、神经细胞(神经元)、少突胶质细胞、小胶质细胞、星形胶质细胞、心肌细胞、食道细胞、肌肉细胞(例如，平滑肌细胞、骨骼肌细胞等)、黑色素细胞、单核细胞等，不限于这些。干细胞是指兼具自身复制能力和分化成其他多个系统的细胞的能力的细胞。作为干细胞，例如可以列举：胚胎干细胞(es细胞)、胚胎肿瘤细胞、胚胎生殖干细胞、人工多能性干细胞(ips细胞)、神经干细胞、造血干细胞、间充质干细胞、肝干细胞、胰干细胞、肌肉干细胞、生殖干细胞、肠干细胞、癌干细胞、毛囊干细胞等，但不限于这些。癌细胞是指由体细胞衍生而获得无限增殖能力的细胞。作为癌细胞来源的癌，例如可以列举：乳腺癌(例如，浸润性乳腺管癌、非浸润性乳腺管癌、炎症性乳腺癌等)、前列腺癌(例如，激素依赖性前列腺癌、激素非依赖性前列腺癌等)、胰腺癌(例如，胰腺管癌等)、胃癌(例如，乳头状腺癌、粘液性腺癌、腺鳞癌等)、肺癌(例如，非小细胞肺癌、小细胞肺癌、恶性间皮瘤等)、结肠癌(例如，胃肠道间质肿瘤等)、直肠癌(例如，胃肠道间质肿瘤等)、大肠癌(例如，家族性大肠癌、遗传性非息肉病性大肠癌、胃肠道间质肿瘤等)、小肠癌(例如，非霍奇金氏淋巴瘤、胃肠道间质肿瘤等)、食道癌、十二指肠癌、舌癌、咽癌(例如、鼻咽癌(上咽癌)、口咽癌、下咽癌等)、头颈部癌、唾液腺癌、脑肿瘤(例如，松果体星形细胞瘤、毛细胞性星形细胞瘤、弥漫性星形细胞瘤、间变性星形细胞瘤等)、神经鞘瘤、肝癌(例如，原发性肝癌、肝外胆管癌等)、肾癌(例如，肾细胞癌、肾盂与输尿管的移行上皮癌等)、胆囊癌、胆管癌、胰腺癌、子宫内膜癌、子宫颈癌、卵巢癌(例如，上皮性卵巢癌、性腺外胚细胞肿瘤、卵巢性胚细胞肿瘤、卵巢低度恶性肿瘤等)、膀胱癌、尿道癌、皮肤癌(例如，眼内(眼)黑色素瘤、merkel(梅克尔)细胞癌等)、血管瘤、恶性淋巴瘤(例如，网状细胞肉瘤、淋巴肉瘤、霍奇金病等)、黑色素瘤(恶性黑色素瘤)、甲状腺癌(例如，甲状腺髓样癌等)、甲状旁腺癌、鼻腔癌、鼻旁窦癌、骨肿瘤(例如，骨肉瘤、尤文氏肿瘤(尤文氏肉瘤)、子宫肉瘤、软组织肉瘤等)、转移性髓母细胞瘤、血管纤维瘤、隆突性皮肤纤维肉瘤、视网膜肉瘤、阴茎癌、睾丸肿瘤、儿童实体瘤(癌)(例如，威尔姆氏肿瘤、儿童肾脏肿瘤等)、卡波西肉瘤、因aids引起的卡波西肉瘤、上颌窦肿瘤、纤维组织细胞瘤、平滑肌肉瘤、横纹肌肉瘤、慢性骨髄增殖性疾病、白血病(例如，急性骨髄性白血病、急性淋巴母细胞白血病等)等，不限于这些。细胞株是指在生物体外通过人为操作获得了无限增殖能力的细胞。作为细胞株，例如可以列举：hct116、huh7、hek293(人胎肾细胞)、hela(人子宫颈癌细胞株)、hepg2(人肝癌细胞株)、ut7/tpo(人白血病细胞株)、cho(中国仓鼠卵巢细胞株)、mdck、mdbk、bhk、c-33a、ht-29、ae-1、3d9、ns0/1、jurkat、nih3t3、pc12、s2、sf9、sf21、highfive、vero等，不限于这些。作为向细胞内导入crispr-cas载体系统的方法，可以通过适合于使用的活细胞的方法来进行，可以列举：电穿孔法、热休克法、磷酸钙法、脂质转染法、deae葡聚糖法、微注射法、粒子枪法、使用了病毒的方法、或者使用了fugene(注册商标)6转染试剂(transfectionreagent)(roche公司制造)、转染胺(lipofectamine)2000试剂(invitrogen公司制造)、转染胺ltx试剂(invitrogen公司制造)、转染胺3000试剂(invitrogen公司制造)等市售的转染试剂的方法等。然后，关于修饰步骤，与上述的<用于位点特异性地修饰靶双链核苷酸的方法>的[第1实施方式]中所示的方法同样。通过本实施方式中的靶双链多核苷酸的修饰，可以获得向靶双链多核苷酸中导入了突变、或者靶双链多核苷酸的功能已被破坏、改变的细胞。作为本发明的突变型cas9蛋白，在采用不具有核酸内切酶活性的方案(例如，方案5)的情况下，该蛋白虽然可以在位于pam序列上游的结合位点与上述靶双链多核苷酸结合，但停留在此而无法进行切割。因此，例如若使该蛋白与荧光蛋白(例如gfp)等标记蛋白融合，则可经由向导rna-突变型cas9蛋白使标记蛋白与靶双链多核苷酸结合。通过适当选择与突变型cas9蛋白结合的物质，可以对靶双链多核苷酸赋予各种各样的功能。可以进一步在由突变型cas9蛋白或突变型cas9缺失了一部分或全部的切割酶活性的蛋白的n末端或c末端连接转录调控因子蛋白或结构域。作为转录调控因子或其结构域，可以列举：转录激活因子或其结构域(例如，vp64、nf-κbp65)和转录沉默子或其结构域(例如，异染色质蛋白1(hp1))或转录抑制因子或其结构域(例如，kruppel相关盒(krab)、erf阻遏域(erd)、msin3a相互作用结构域(sid))。还可以连接修饰dna的甲基化状态的酶(例如，dna甲基转移酶(dnmt)、tet)或修饰组蛋白亚单位的酶(例如，组蛋白乙酰转移酶(hat)、组蛋白脱乙酰酶(hdac)、组蛋白甲基转移酶、组蛋白去甲基化酶)。<基因治疗>在一实施方式中，本发明提供用于实行基因组编辑、进行基因治疗的方法和组合物。与以前已知的靶向化的基因重组方法相比，本实施方式的方法的实行有效且廉价，而且可适合于任意的细胞或生物。细胞或生物的双链核酸的任意片段可以通过本实施方式的基因治疗方法进行修饰。本实施方式的基因治疗方法采用在所有细胞中均为内在的同源重组工艺和非同源重组工艺两者。本说明书中，“基因组编辑”是指，通过利用crispr/cas9系统或转录激活因子样效应物核酸酶(transcriptionactivator-likeeffectornucleases，talen)等技术实行已靶向化的基因重组或已靶向化的突变，进行特异性的基因破坏或报道基因的敲入等新的基因修饰技术。另外，在一实施方式中，本发明提供：进行已靶向化的dna插入或已靶向化的dna缺失的基因治疗方法。该基因治疗方法包括：使用包含供体dna的核酸构建物来转化细胞的步骤。关于与靶基因切割后的dna插入和dna缺失相关的图解，本领域技术人员可以按照已知的方法确定。另外，在一实施方式中，本发明提供基因治疗方法：该方法在体细胞和生殖细胞中均被利用，于特定的基因座进行基因操作。另外，在一实施方式中，本发明提供：用于在体细胞内破坏基因的基因治疗方法。这里，基因过度表达对细胞或生物有害的产物，并表达对细胞或生物有害的产物。这样的基因能够在疾病中所产生的1个以上的细胞型中过度表达。通过本实施方式的基因治疗方法进行的上述过度表达的基因的破坏，可以对患有由上述过度表达的基因引起的疾病的个体带来更好的健康。即，细胞的微小比例的基因的破坏起作用，表达水平降低，产生治疗效果。另外，在一实施方式中，本发明提供：用于在生殖细胞内破坏基因的基因治疗方法。特定的基因被破坏的细胞可有效用于制作不具有特定的基因的功能的生物。在上述基因被破坏的细胞中，基因可以完全敲除。该特定细胞中的功能的缺失能够具有治疗效果。另外，在一实施方式中，本发明提供：插入编码基因产物的供体dna的基因治疗方法。该基因产物在构成性地表达的情况下具有治疗效果。例如可以列举下述方法：为了在胰细胞的个体组中进行活性启动子和编码胰岛素基因的供体dna的插入，而在患有糖尿病的个体(患者)中插入上述供体dna。然后，包含上述供体dna的胰细胞的上述个体组可以生成胰岛素，对糖尿病患者进行治疗。而且，将上述供体dna插入植物中，可以生成药剂相关基因产物。蛋白产物的基因(例如，胰岛素、脂肪酶或血红蛋白)可以和调控元件(组成型活性启动子、或诱导型启动子)一起插入到植物中，在植物中生成大量的药物。然后，可从植物中分离这样的蛋白产物。转基因植物或转基因动物可以通过采用核酸移入技术(mccreath,k.j.等人(2000)nature405:1066-1069；polejaeva,i.a.等人,(2000)nature407：86-90)的方法进行制作。组织型特异性载体或细胞型特异性载体可以为了仅在所选择的细胞内提供基因表达而利用。另外，在将上述方法用于生殖细胞的情况下，可以在靶基因中插入供体dna，通过之后的所有的细胞分裂，生成具有所设计的遗传变更的细胞。作为本实施方式的基因治疗方法的应用对象，例如可以列举：任意的生物、培养细胞、培养组织、培养核(在完整的培养细胞、培养组织或培养核中包含可用于再生生物的细胞、组织或核)、配子(例如，发育的各种阶段的卵或精子)等，并不限于这些。作为本实施方式的基因治疗方法的应用对象的细胞的来源，可以列举任意的生物(可以列举昆虫、真菌、啮齿类、牛、绵羊、山羊、鸡和其他的农业上重要的动物、以及其他哺乳动物(例如可以列举狗、猫和人，但并不限于这些)，并不限于这些)等，并不限于这些。本实施方式的基因治疗方法可以进一步在植物中使用。对作为本实施方式的基因治疗方法的应用对象的植物没有特别限定，可以在任意的各种植物种(例如，单子叶植物或双子叶植物等)中应用。以下，给出实施例，以更详细地说明本发明，但这些实施例并不限定本发明的范围。实施例实施例11.野生型和突变型spcas9的调制(1)结构体(construct)的设计将通过基因合成使密码子最优化的野生型或突变型spcas9基因整合到pet载体(novagen)中。进一步在his标记物与spcas9基因之间添加tev识别序列。在由完成的结构体表达的cas9的n末端连接6残基的组氨酸(his标记物)，形成添加有tev蛋白酶识别位点的设计。所使用的spcas9基因的核苷酸序列如下。wt：野生型spcas9的核苷酸序列：seqidno:2；m0：突变型spcas9基因(r1335a)的核苷酸序列：seqidno:3；m4：突变型spcas9基因(r1335a/g1218r)的核苷酸序列：seqidno:4；m18：突变型spcas9基因(r1335a/g1218r/t1337r)的核苷酸序列：seqidno:5；m19：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r)的核苷酸序列：seqidno:6；m20：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/d1332r)的核苷酸序列：seqidno:7；m21：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/d1332r/a1322r)的核苷酸序列：seqidno:8；m22：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/d1332r/a1322r/d1284r/a1285r)的核苷酸序列：seqidno:9；m23：突变型spcas9基因(r1335a/g1218r/l1111r/d1332r/a1322r)的核苷酸序列：seqidno:10；m24：突变型spcas9基因(r1335a/g1218r/l1111r/d1332r/a1322r/d1284r/a1285r)的核苷酸序列：seqidno:11；m25：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r)的核苷酸序列：seqidno:12；m26：突变型spcas9基因(r1335a/g1218r/l1111r/a1322r)的核苷酸序列：seqidno:13；m29：突变型spcas9基因(r1335a/g1218r/l1111r)的核苷酸序列：seqidno:14；m32：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r/e1219m)的核苷酸序列：seqidno:15；m33：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r/e1219f)的核苷酸序列：seqidno:16；m34：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r/e1219w)的核苷酸序列：seqidno:17；m43：突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：seqidno:18；m61：突变型spcas9基因(r1335i/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成atc而得到的核苷酸序列。m62：突变型spcas9基因(r1335l/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成ctg而得到的核苷酸序列。m63：突变型spcas9基因(r1335m/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成atg而得到的核苷酸序列。m64：突变型spcas9基因(r1335f/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成ttt而得到的核苷酸序列。m65：突变型spcas9基因(r1335t/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成acc而得到的核苷酸序列。m66：突变型spcas9基因(r1335v/g1218r/t1337r/l1111r/a1322r/e1219f/d1135v)的核苷酸序列：相对于m43的核苷酸序列(seqidno:18)将4003-4005位的gcc变换成gtg而得到的核苷酸序列。(2)在大肠杆菌中的表达将所制作的载体转化到大肠杆菌escherichiacolirosetta2(de3)株中。之后，使用含有20μg/ml的卡那霉素和20μg/ml的氯霉素的lb培养基进行培养。在培养直至od=0.8的时间点添加作为表达诱导剂的异丙基-β-硫代半乳糖吡喃糖苷(isopropylβ-d-1-thiogalactopyranoside：iptg)(终浓度为1mm)，在37℃下培养4小时。培养后，通过离心(5,000g、10分钟)回收大肠杆菌。(3)野生型和突变型spcas9的纯化将(2)中回收的菌体用缓冲液a悬浮，进行超声波破碎。通过离心(25,000g、30分钟)回收上清，与经缓冲液a调平衡的ni-nta　superflow树脂(qiagen)混合，平稳地颠倒混合1小时。回收流过的组分，之后用4柱容量的缓冲液a、进一步用2柱容量的高盐浓度缓冲液b进行洗涤。然后，再次用2柱容量的缓冲液a洗涤，之后用5柱容量的高咪唑浓度缓冲液c洗脱目标蛋白。然后，将粗制的样品加载到hitrapsp(gehealthcare)上。然后，用5柱容量份(容量分)的92.5%的缓冲液d(0m的nacl)和7.5%的缓冲液f(2m的nacl)的混合溶液进行洗涤，之后使用缓冲液e形成从10%到50%(nacl浓度从200mm到1m)的直线梯度，洗脱目标蛋白。缓冲液a～e的组成如下所示。缓冲液a：20mm的tris-hcl、ph8.0，300mm的nacl、20mm的咪唑；缓冲液b：20mm的tris-hcl、ph8.0，1000mm的nacl、20mm的咪唑；缓冲液c：20mm的tris-hcl、ph8.0，300mm的nacl、300mm的咪唑；缓冲液d：20mm的tris-hcl、ph8.0；缓冲液e：20mm的tris-hcl、ph8.0，2000mm的nacl。2.向导rna的调制进行了插入有目标向导rna序列(ggaaauuaggugcgcuuggcguuuuagagcuagaaauagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaagug;seqidno:19)的载体的制作。下划线显示20个碱基的向导序列，余部相当于支架部分(颈-环2，stem-loop2)。在向导rna序列的上游添加t7启动子序列，整合到已形成线状的puc119载体(takara)中。根据所制作的载体，利用pcr制作了体外转录反应的模板dna。使用该模板dna，在37℃下进行了4小时的t7rna聚合酶的体外转录反应。在包含转录产物的反应液中加入等量的苯酚氯仿进行混合，之后在20℃下离心(10,000g、2分钟)，回收上清。在上清中添加1/10量的3m的乙酸钠和2.5倍量的100%乙醇，在4℃下离心(10,000g、3分钟)，使转录产物沉淀。废弃上清，添加70%乙醇，在4℃下离心(10,000g、3分钟)，再次废弃上清。将沉淀风干后，再次悬浮于tbe缓冲液中，通过经7m脲改性的10%page进行纯化。切出位于目标rna的分子量的谱带，利用elutrap电洗脱系统(gehealthcare)提取rna。之后，使所提取的rna通过pd-10柱(gehealthcare)，将缓冲液换成缓冲液h(10mm的tris-hcl(ph8.0)、150mm的nacl)。3.质粒dna切割活性测定试验进行了插入有靶dna序列和pam序列的载体的制作，以便在dna切割活性测定试验中使用。在靶dna序列中分别添加pam序列1～4，整合到已形成线状的puc119载体中。靶序列和pam序列1～4见表1。[表1]核苷酸序列seqidno靶dna5’-ggaaattaggtgcgcttggc-3’seqidno:20pam序列15’-tgt-3’pam序列25’-tgg-3’pam序列35’-tgna-3’pam序列45’-tgn-3’使用所制作的载体转化大肠杆菌mach1株(lifetechnologies)，使用含有20μg/ml的氨苄青霉素的lb培养基，在37℃下进行培养。培养后，通过离心(8,000g、1分钟)回收菌体，使用qiaprepspinminiprep试剂盒(qiagen)纯化质粒dna。使用添加有已纯化的pam序列的靶质粒dna，进行了切割实验。质粒dna通过限制酶形成1根线状。若野生型或突变型的spcas9切割该线状化dna中的靶dna序列，则可产生约1,000bp和约2,000bp的切割产物。作为切割时的缓冲液，使用下述组成的裂解缓冲液b。b(×10)的组成200mm的hepes7.5；1000mm的kcl；50%的甘油；10mm的dtt；5mm的edta；20mm的mgcl2。使用1%浓度的琼脂糖凝胶对反应后的样品进行电泳，确认了切割产物的谱带。结果见图1a～d。图中，“substrate”显示底物，“product”显示切割产物。pam序列和反应条件如图中所示。在野生型spcas9中，仅识别pam序列的第3位的碱基为g的情形，靶质粒dna被切割，相对于此，在突变型spcas9中，还识别第3位的碱基为g以外的pam序列，可以切割靶质粒dna。因此，确认到了：在野生型的spcas9中识别pam序列“ngg”，相对于此，在突变型的spcas9中识别pam序列“ng”。由以上结果明确了：在突变型的spcas9中，pam序列变得广泛，可以简便且快速地针对靶序列进行位点特异性的靶双链多核苷酸的切割。实施例2使用实施例1中调制的突变型spcas9(m43)，进行与实施例1同样的操作，进行了质粒dna切割活性测定试验。结果见图2。在野生型spcas9中，仅识别pam序列的第3位的碱基为g的情形，靶质粒dna被切割，相对于此，在突变型spcas9中，还识别第3位的碱基为g以外的pam序列，可以切割靶质粒dna。因此，确认了：在野生型的spcas9中识别pam序列“ngg”，相对于此，在突变型的spcas9中识别pam序列“ng”。实施例3使用实施例1中调制的突变型spcas9(m43、m61～m66)，进行与实施例1同样的操作，进行了质粒dna切割活性测定试验。尚需说明的是，在切割产物的检测中使用了multina毛细管电泳装置(岛津制作所)。作为pam序列，使用了作为pam序列4的5’-tgc-3’。切割实验进行了0.5分钟(0.5m)和2分钟(2m)。结果见图3。在m61、m63、m65和m66中确认到了优异的dna切割活性。实施例4使用实施例1中调制的突变型spcas9(m43、m61、m63和m66)，进行与实施例1同样的操作，进行了质粒dna切割活性测定试验。切割实验进行了0.5分钟(0.5m)和2分钟(2m)。结果见图4。在野生型spcas9中，仅识别pam序列的第3位的碱基为g的情形，靶质粒dna被切割，相对于此，在突变型spcas9中，还识别第3位的碱基为g以外的pam序列，可以切割靶质粒dna。确认到：m61、m63和m66、特别是m63和m66，即使在使用在m43中效率低的tga和tgc的pam序列的情况下，也可以高效率地切割dna。实施例5使用实施例1中调制的野生型spcas9和突变型spcas9(wt、m43)和进行与实施例1同样的操作而调制的下述的突变型spcas9，进行与实施例1同样的操作，进行了质粒dna切割活性测定试验。切割实验随时间(0、0.5、1、2、5分钟)而进行。结果见图5。在m43中确认到了与wt相媲美的切割活性的提高。突变型spcas9基因(r1335a/g1218r/t1337r/l1111r/a1322r/d1135v)的核苷酸序列：相对于m25的核苷酸序列(seqidno:12)，将3403-3405位的gac变换成gtt而得到的核苷酸序列。产业实用性根据本发明，可以获得在保持与靶双链多核苷酸的结合力、进一步保持核酸内切酶活性的同时pam序列的识别变得广泛的cas9蛋白。另外，可以提供利用了上述cas9蛋白的简便且快速、并且针对靶序列进行位点特异性的基因组编辑的技术。本申请以在日本申请的特愿2017-108556(申请日：2017年5月31日)为基础，且其内容全部包含在本说明书中。<110>东京大学<120>经修饰的cas9蛋白及其用途<130>092761<150>jp2017-108556<151>2017-05-31<160>20<170>patentinversion3.5<210>1<211>1368<212>prt<213>酿脓链球菌<400>1metasplyslystyrserileglyleuaspileglythrasnserval151015glytrpalavalilethraspglutyrlysvalproserlyslysphe202530lysvalleuglyasnthrasparghisserilelyslysasnleuile354045glyalaleuleupheaspserglygluthralaglualathrargleu505560lysargthralaargargargtyrthrargarglysasnargilecys65707580tyrleuglngluilepheserasnglumetalalysvalaspaspser859095phephehisargleuglugluserpheleuvalglugluasplyslys100105110hisgluarghisproilepheglyasnilevalaspgluvalalatyr115120125hisglulystyrprothriletyrhisleuarglyslysleuvalasp130135140serthrasplysalaaspleuargleuiletyrleualaleualahis145150155160metilelyspheargglyhispheleuilegluglyaspleuasnpro165170175aspasnseraspvalasplysleupheileglnleuvalglnthrtyr180185190asnglnleupheglugluasnproileasnalaserglyvalaspala195200205lysalaileleuseralaargleuserlysserargargleugluasn210215220leuilealaglnleuproglyglulyslysasnglyleupheglyasn225230235240leuilealaleuserleuglyleuthrproasnphelysserasnphe245250255aspleualagluaspalalysleuglnleuserlysaspthrtyrasp260265270aspaspleuaspasnleuleualaglnileglyaspglntyralaasp275280285leupheleualaalalysasnleuseraspalaileleuleuserasp290295300ileleuargvalasnthrgluilethrlysalaproleuseralaser305310315320metilelysargtyraspgluhishisglnaspleuthrleuleulys325330335alaleuvalargglnglnleuproglulystyrlysgluilephephe340345350aspglnserlysasnglytyralaglytyrileaspglyglyalaser355360365glnglugluphetyrlyspheilelysproileleuglulysmetasp370375380glythrglugluleuleuvallysleuasnarggluaspleuleuarg385390395400lysglnargthrpheaspasnglyserileprohisglnilehisleu405410415glygluleuhisalaileleuargargglngluaspphetyrprophe420425430leulysaspasnargglulysileglulysileleuthrpheargile435440445protyrtyrvalglyproleualaargglyasnserargphealatrp450455460metthrarglysserglugluthrilethrprotrpasnphegluglu465470475480valvalasplysglyalaseralaglnserpheilegluargmetthr485490495asnpheasplysasnleuproasnglulysvalleuprolyshisser500505510leuleutyrglutyrphethrvaltyrasngluleuthrlysvallys515520525tyrvalthrgluglymetarglysproalapheleuserglyglugln530535540lyslysalailevalaspleuleuphelysthrasnarglysvalthr545550555560vallysglnleulysgluasptyrphelyslysileglucyspheasp565570575servalgluileserglyvalgluaspargpheasnalaserleugly580585590thrtyrhisaspleuleulysileilelysasplysasppheleuasp595600605asnglugluasngluaspileleugluaspilevalleuthrleuthr610615620leuphegluaspargglumetileglugluargleulysthrtyrala625630635640hisleupheaspasplysvalmetlysglnleulysargargargtyr645650655thrglytrpglyargleuserarglysleuileasnglyileargasp660665670lysglnserglylysthrileleuasppheleulysseraspglyphe675680685alaasnargasnphemetglnleuilehisaspaspserleuthrphe690695700lysgluaspileglnlysalaglnvalserglyglnglyaspserleu705710715720hisgluhisilealaasnleualaglyserproalailelyslysgly725730735ileleuglnthrvallysvalvalaspgluleuvallysvalmetgly740745750arghislysprogluasnilevalileglumetalaarggluasngln755760765thrthrglnlysglyglnlysasnserarggluargmetlysargile770775780glugluglyilelysgluleuglyserglnileleulysgluhispro785790795800valgluasnthrglnleuglnasnglulysleutyrleutyrtyrleu805810815glnasnglyargaspmettyrvalaspglngluleuaspileasnarg820825830leuserasptyraspvalasphisilevalproglnserpheleulys835840845aspaspserileaspasnlysvalleuthrargserasplysasnarg850855860glylysseraspasnvalproserglugluvalvallyslysmetlys865870875880asntyrtrpargglnleuleuasnalalysleuilethrglnarglys885890895pheaspasnleuthrlysalagluargglyglyleusergluleuasp900905910lysalaglypheilelysargglnleuvalgluthrargglnilethr915920925lyshisvalalaglnileleuaspserargmetasnthrlystyrasp930935940gluasnasplysleuilearggluvallysvalilethrleulysser945950955960lysleuvalseraspphearglysasppheglnphetyrlysvalarg965970975gluileasnasntyrhishisalahisaspalatyrleuasnalaval980985990valglythralaleuilelyslystyrprolysleuglusergluphe99510001005valtyrglyasptyrlysvaltyraspvalarglysmetileala101010151020lyssergluglngluileglylysalathralalystyrphephe102510301035tyrserasnilemetasnphephelysthrgluilethrleuala104010451050asnglygluilearglysargproleuilegluthrasnglyglu105510601065thrglygluilevaltrpasplysglyargaspphealathrval107010751080arglysvalleusermetproglnvalasnilevallyslysthr108510901095gluvalglnthrglyglypheserlysgluserileleuprolys110011051110argasnserasplysleuilealaarglyslysasptrpasppro111511201125lyslystyrglyglypheaspserprothrvalalatyrserval113011351140leuvalvalalalysvalglulysglylysserlyslysleulys114511501155servallysgluleuleuglyilethrilemetgluargserser116011651170pheglulysasnproileasppheleuglualalysglytyrlys117511801185gluvallyslysaspleuileilelysleuprolystyrserleu119011951200phegluleugluasnglyarglysargmetleualaseralagly120512101215gluleuglnlysglyasngluleualaleuproserlystyrval122012251230asnpheleutyrleualaserhistyrglulysleulysglyser123512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