本发明属于蛋白质工程
技术领域:
:,具体涉及基于结构的crispr蛋白的优化设计方法,还涉及由该优化设计方法得到的spcas9的新型突变体,以及作为基因编辑工具的应用。
背景技术:
::crispr是细菌和古细菌中抵抗外源核酸入侵的免疫系统。近年来,已被人们开发成一种特异性切割dna片段的基因编辑工具[1]。目前人们最常使用的是ii型crispr系统中的化脓性链球菌cas9(spcas9)[2]。但是,spcas9存在pam(protospaceradjacentmotifs)识别范围有限以及基因编辑时易脱靶的问题,从而使其更广泛应用受到限制[3-5]。因此,只有拓展pam识别范围和降低脱靶效应,才能使spcas9技术在基因编辑领域发挥更大的作用。为了达到以上目标,人们已提出多种研究方法:一种是利用细菌选择系统来筛选设计spcas9,通过该方法获得了pam识别范围扩大的vqr、eqr和vrer突变体[6]。另一种是基于spcas9结构指导的改造方法,也获得了高保真突变体espcas9、spcas9-hf、hypacas9和evocas9[7、8]。此外,还有人通过pace定向进化的方法获得了一个spcas9突变体(xcas9)。该突变体不仅有高特异性,而且pam识别更加灵活[9]。虽然,这些方法可以帮助人们获得cas9的新型突变体,但是这些方法盲目性比较大,且耗时耗力。随着计算机运算速度的快速增长,很多计算软件被用来辅助蛋白质设计。这个方法不受体系的限制,只要有蛋白质的三维结构,就可以将蛋白结构模型先精细化,再通过模拟自由能方法计算一些物理和化学过程的自由能变化,从而进行蛋白设计与改造。生物分子结构预测和设计的rosetta软件包(https://www.rosettacommons.org)包含140个应用程序,该软件可进行蛋白质结构从头预测、蛋白质结构设计和蛋白质重设计等[10、11]。用rosetta进行蛋白质设计的方法盲目性低,操作更简单,效率更高。基于上述问题,开发一种利用rosetta软件的优化设计crispr蛋白的方法十分有必要。技术实现要素:本发明的第一个目的是提供一种基于结构的crispr蛋白的优化设计方法,以获得spcas9的新型突变体。本发明的第二个目的是利用本发明方法获得spcas9的新型突变体(ycas9),为生物学领域提供有应用价值的新型基因编辑工具。本发明提供的基于结构的crispr蛋白的优化设计方法,从能量角度出发,使用rosetta来优化cas9蛋白与dna有相互作用的重要氨基酸,以增强cas9对dna的结合力,从而获得pam兼容性高或脱靶率低的突变体,记该突变体为ycas9。具体而言,本发明提供基于结构的crispr蛋白的优化设计方法,流程如附图1所示,其具体步骤如下。第一步:确定对cas9特性有重要影响的氨基酸位点。蛋白优化设计的第一步就是确定对cas9特性有重要影响的氨基酸位点。从蛋白质数据库(http://www.rcsb.org/)中下载蛋白结构,通过分析和比较蛋白的电子密度图,找出对cas9的pam识别或者脱靶作用有重要影响的氨基酸位点;具体地,xcas9突变的7个定向进化位点(a262t、r324l、s409i、e480k、e543d、m694i和e1219v)分布在sgrna-dna异源双链体的两侧(附图2)。这7个氨基酸共同作用,拓展了xcas9的pam识别范围并降低了其脱靶效应。因此,选取这7个位点作为rosetta优化设计的氨基酸位点。第二步:relax能量最小化。relax[12、13]是rosetta软件里结构预测中的一个模块。在rosetta力场中,使用该模块通过多次迭代使结构的氨基酸侧链重排,并且在每轮迭代中不断地调整范德华作用力,以能量最小化的方式搜索该结构的局部最优构象。所以,此步骤是将第一步中选择的结构用relax模块处理,使其处于能量最低的状态。本发明用relax模块对spcas9结构(pdbid:4un3)进行多轮(25轮)迭代,并根据rosetta的打分函数,选出能量最低的结构作为初始结构。第三步:fixbb优化protein-dna相互作用界面。fixbb(fixedbackbonedesign)[14、15]是rosetta软件里蛋白设计中一个模块。该模块可在固定蛋白主链骨架的同时,使侧链自由旋转,寻找其最佳的位置,并设计最适合该位置的氨基酸。所以,此步骤是把步骤二处理过的结构用fixbb模块固定它的蛋白骨架,然后针对步骤一中选出的氨基酸位点进行20种氨基酸随机组合设计,设置程序输出10000个组合结果。具体地,本发明使用fixbb模块固定第二步中筛选出的初始结构的主链原子,并对第一步中确定的7个氨基酸位点(262、324、409、480、543、694、1219)进行20种氨基酸组合突变设计,使程序输出10000个排列组合。第四步:去除重复性结果,筛选突变体。虽然每个氨基酸位点都有20种氨基酸可以选择,n个氨基酸位点就有20n种随机组合,但是适合该固定骨架且能量低的情况并不多,所以fixbb模块输出的结果中,会有很多重复的结果。此步骤就通过对输出的10000个结果进行序列比对,去除重复的结果,把剩余结果按能量从低到高的顺序排列,并从中进行挑选。最终选择分数值低即更接近自然构象的突变体,并将其命名为ycas9。第五步:突变体的表达与验证。将筛选到的突变体首先进行质粒构造,然后表达与纯化蛋白,最后对蛋白的剪切活性进行检测,以鉴定上述基于relax和fixbb等多种rosetta模块设计出的突变体的性能。本发明得到的ycas9,其氨基酸序列如seqidno.6所示,是将野生型spcas9的第409位的氨基酸s、第480位的e、第543位的e、第694位的m和第1219位的e分别突变成了n、k、d、l和t。ycas9具有和xcas9相当的基因编辑活性:宽泛的pam识别范围,可识别ngg、nga、ngt、ngc、gaa和gat,且在基因编辑时脱靶率低。本发明中,所述野生型spcas9核酸酶的核苷酸序列和氨基酸序列分别为seqidno.1和seqidno.2所示。所述xcas9核酸酶的核苷酸序列和氨基酸序列分别为seqidno.3和seqidno.4所示。所述ycas9核酸酶的核苷酸序列和氨基酸序列分别为seqidno.5和seqidno.6所示。本发明还提供一种多核苷酸序列,可以转录和翻译成所述的ycas9核酸酶,其序列为seqidno.7。本发明还提供一种表达载体,其含有上述多核苷酸序列。本发明还提供一种宿主细胞,可以用于转化上述表达载体。本发明还提供所述ycas9核酸酶的制备方法,具体步骤包括:首先,构建所述ycas9核酸酶的多核苷酸序列表达载体;然后,将所述表达载体转化至宿主细胞,筛选并挑出单克隆;最后,将所述单克隆诱导表达,并通过亲和层析从表达产物中分离出所述的ycas9核酸酶。本发明提供的上述crispr/cas9(ycas9)核酸酶、多核苷酸序列以及表达载体均可作为编辑基因组dna的编辑工具,用于基因组dna片段的相关编辑。本发明中,所述的基因编辑可以是单点编辑,也可以是编辑位点大于等于两个的多点编辑。所述编辑的手段包括删除、突变、插入、倒位、移位、重复或易位。本发明中,所述crispr/cas9编辑工具包括与靶标dna片段匹配的引导sgrna。所述的crispr/cas9核酸酶与能够介导它的sgrna组合,从而对目的基因进行编辑。附图说明图1为rosetta组合突变设计流程图。图2为xcas9定向进化位点的三维分布。图3为pet21-6his-tev-ycas9质粒构造。图4为含有ycas9的突变氨基酸的质粒测序。图5为crispr/cas9目标蛋白纯化的电泳鉴定。图6为sgrna的在靶和脱靶序列。图7为spcas9pam识别的检测。图8为xcas9pam识别的检测。图9为ycas9pam识别的检测。图10为spcas9脱靶效应的检测。图11为xcas9脱靶效应的检测。图12为ycas9脱靶效应的检测。具体实施方式下述实施例中所用的实验方法,如无特定说明,均为常规方法。下述实施例中所用的材料、试剂等,如无特定说明,均为从商业途径获得。一、spcas9的组合突变设计第一步:确定对cas9特性有重要影响的氨基酸位点。xcas9突变的7个定向进化位点(a262t、r324l、s409i、e480k、e543d、m694i和e1219v)分布在sgrna-dna异源双链体的两侧(附图2)。这7个氨基酸共同作用,拓展了xcas9的pam识别范围并降低了其脱靶效应。因此,选取这7个位点作为rosetta优化设计的氨基酸位点。第二步:relax能量最小化。用relax模块将spcas9结构(pdbid:4un3)进行25轮迭代,并根据rosetta的打分函数选出能量最低的结构作为初始结构。第三步:fixbb优化protein-dna相互作用界面。用fixbb模块固定第二步中筛选出的初始结构的主链原子,并对第一步中确定的7个氨基酸位点(262、324、409、480、543、694、1219)进行20种氨基酸组合突变设计,使程序输出10000个排列组合。第四步:去除重复性结果,筛选突变体。对这10000个组合进行序列比对,去除重复性结果,并将剩余结果按分数大小排列。最终选择分数值低即更接近自然构象的突变体,并将其命名为ycas9。第五步:突变体的表达与验证。本发明的ycas9是将野生型spcas9的第409位的氨基酸s、第480位的e、第543位的e、第694位的m和第1219位的e分别突变成了n、k、d、l和t。ycas9具有和xcas9相当的基因编辑活性。所述ycas9含有如seqidno.6所示的氨基酸序列。二、突变体ycas9的质粒构造、蛋白表达与纯化、检测(1)ycas9质粒构造:本文分别以质粒pet21-6his-tev-spcas9(seqidno.8)和pet21-6his-tev-xcas9(seqidno.9)为模板,通过一步定向克隆和点突变的方式构建突变体质粒,其具体质粒构建策略如附图3所示。质粒构建完成后,通过上海杰李生物技术有限公司测序,其结果如附图4所示,表明ycas9质粒构建成功。(2)ycas9蛋白表达与纯化:首先,将上述获得的ycas9质粒转入rosetta(de3)细胞中表达,当菌液的od600达到0.9时,加入终浓度为0.5μm的iptg,16℃过夜培养。其次,离心收集菌体,并用裂解液重悬菌体,超声破碎20min,12000rpm离心1h。然后,用ni柱亲和层析的方式纯化蛋白。最后,用sds-page鉴定,收集目的蛋白并将其浓缩至250μl,保存于蛋白储存液中。将浓缩后的蛋白再次进行电泳鉴定,结果如附图5所示,ycas9的杂蛋白已经非常少了,可用于后续实验。(3)底物dna的获取:底物dna序列如seqidno.10所示,通过pcr扩增和割胶回收的方式获得。底物dna为920bp,其中包含20bp靶序列和pam序列,pam序列又分别为5'-tgg-3'、5'-tga-3'、5'-tgc-3'、5'-tgt-3'、5'-gaa-3'和5'-gat-3'。原始底物dna的pam序列为tgg(seqidno.10),通过点突变的方式获得带有其他pam序列的dna。(4)sgrna的获取:sgrna序列如seqidno.11所示,通过pcr扩增,体外转录和纯化的方式获得。野生型sgrna(seqidno.11)中与底物dna的靶序列匹配的间隔序列为5'-uaccgcuccagucguucaug-3'(seqidno.12)。从pam远端开始依次将sgrna间隔序列的两个碱基突变为其互补碱基,共改8次,最终获得9个sgrna,其序列如附图6所示,这些sgrna将用于脱靶检测。(5)ycas9的pam识别检测:利用带有不同的pam序列的底物dna检测ycas9的pam识别能力,其反应体系为20μl体系:200nmcas9、200nmsgrna、30nmdna和反应缓冲液(20mmhepes,150mmkcl,1mmdtt,10mmmgcl2,ph7.5)。首先在反应缓冲液中加入cas9和sgrna,混合均匀后将其放置在37℃预孵育10min,然后将dna加入混合物中,继续孵育2h。反应结束后,使用琼脂糖凝胶电泳检测cas9的底物切割情况,其结果如附图7、8和9所示。由图可见,野生型spcas9主要识别tgg、tga和tgc,表明其可识别的pam的类型非常有限(图7,lanes2-4)。从图8可以看出,xcas9不仅可以识别tgg、tga和tgc,而且可以识别tgt、gaa和gat序列。而ycas9对包含这些pam序列的dna的剪切活性与xcas9相当(图9)。值得注意的是,ycas9对gat的识别能力比xcas9高(图9,lane7)。由此说明,rosetta设计的ycas9突变体的pam识别范围比野生型spcas9大,并且其对gat的识别能力优于xcas9。(6)ycas9的脱靶效应检测:利用不同的sgrna,如附图6中所示的0到8号sgrna检测ycas9的体外切割活性,从而评价ycas9的脱靶效应,其反应体系为20μl体系:200nmcas9、200nmsgrna、30nmdna和反应缓冲液(20mmhepes,150mmkcl,1mmdtt,10mmmgcl2,ph7.5)。首先在反应缓冲液中加入cas9和sgrna,混合均匀后将其放置在37℃预孵育10min,然后将dna加入混合物中,继续孵育3h。反应结束后,使用琼脂糖凝胶电泳检测cas9的底物切割情况,其结果如附图10、11和12所示。由图可见,1-8号sgrna均可以引导spcas9剪切底物dna。其中,1-5号sgrna引导的剪切活性与0号sgrna相当(图10,lanes3-8),这表明spcas9的脱靶效应比较严重。与spcas9相比,xcas9的脱靶效率明显降低。在1-8号sgrna的引导下,xcas9对底物的切割活性都有下降(图11,lanes3-11)。其中,泳道9和11的结果表明6号和8号sgrna几乎不引导xcas9切割底物dna。由图12可见,ycas9的脱靶效应与xcas9相当,在相同的反应时间内,ycas9对dna的剪切与xcas9几乎一致。因此,ycas9的脱靶率远远低于野生型spcas9。综上,ycas9突变体在功能上与xcas9相当,既拓展了pam识别能力,又降低了基因编辑时的脱靶效应,是一个有潜在应用价值的基因编辑工具,可以加强crispr系统介导的基因编辑技术的实用性和有效性。所以,本文所设计的基于结构的理性设计方法是可行有效的,为人们继续开发多pam识别和低脱靶的多功能型cas9蛋白提供了新的途径。参考文献[1]sanderjd,joungjk.crispr-cassystemsforediting,regulatingandtargetinggenomes[j].natbiotechnol,2014,32(4):347-355.[2]lierc,baticlee,horvathp,etal.analysisofthetypeii-acrispr-cassystemofstreptococcusagalactiaerevealsdistinctivefeaturesaccordingtogeneticlineages[j].frontgenet,2015,6:214.[3]hsupd,scottda,weinsteinja,etal.dnatargetingspecificityofrna-guidedcas9nucleases[j].natbiotechnol,2013,31(9):827-832.[4]fuy,sanderjd,reyond,etal.improvingcrispr-casnucleasespecificityusingtruncatedguidernas[j].natbiotechnol,2014,32(3):279-284.[5]congl,ranfa,coxd,etal.multiplexgenomeengineeringusingcrispr/cassystems[j].science,2013,339(6121):819-823.[6]kleinstiverbp,prewms,tsaisq,etal.engineeredcrispr/cas9nucleaseswithalteredpamspecificities[j].nature,2015,523(7561):481-485.[7]chenjs,dagdasys,kleinstiverbp,etal.enhancedproofreadinggovernscrispr/cas9targetingaccuracy[j].nature,2017,550(7676):407-410.[8]kleinstiverbp,pattanayakv,prewms,etal.high-fidelitycrispr/cas9nucleaseswithnodetectablegenome-wideoff-targeteffects[j].nature,2016,529(7587):490-495.[9]hujh,millersm,geurtsmh,etal.evolvedcas9variantswithbroadpamcompatibilityandhighdnaspecificity[j].nature,2018,556(7699):57-63.[10]leaver-faya,tykam,lewissm,etal.rosetta3:anobject-orientedsoftwaresuiteforthesimulationanddesignofmacromolecules[j].methodsenzymol,2011,487:545-574.[11]kerstins.broo,larsbrive,perahlberg,etal.catalysisofhydrolysisandtransesterifificationreactionsofp-nitrophenylestersbyadesignedhelix-loophelixdimer[j].amchemsoc,1997,119:11362–11372.[12]nivonlg,morettir,bakerd.apareto-optimalrefinementmethodforproteindesignscaffolds[j].plosone.2013,8(4):e59004.[13]conwayp,tykamd,dimaiof,etal.relaxationofbackbonebondgeometryimprovesproteinenergylandscapemodeling[j].proteinsci.2014,23(1):47-55.[14]kuhlmanb,dantasg,iretongc,etal.designofanovelglobularproteinfoldwithatomic-levelaccuracy[j].science.2003,302(5649):1364-1368.[15]hux,wangh,keh,etal.high-resolutiondesignofaproteinloop[j].procnatlacadsciusa.2007,104(45):17668-17673。序列表<110>复旦大学<120>一种基于结构的crispr蛋白的优化设计方法<130>001<160>12<170>siposequencelisting1.0<210>1<211>4104<212>dna<213>人工序列(artificialsequence)<400>1ggcgacaagaagtactccattgggctcgatatcggcacaaacagcgtcggctgggccgtc60attacggacgagtacaaggtgccgagcaaaaaattcaaagttctgggcaataccgatcgc120cacagcataaagaagaacctcattggcgccctcctgttcgactccggggagacggccgaa180gccacgcggctcaaaagaacagcacggcgcagatatacccgcagaaagaatcggatctgc240tacctgcaggagatctttagtaatgagatggctaaggtggatgactctttcttccatagg300ctggaggagtcctttttggtggaggaggataaaaagcacgagcgccacccaatctttggc360aatatcgtggacgaggtggcgtaccatgaaaagtacccaaccatatatcatctgaggaag420aagcttgtagacagtactgataaggctgacttgcggttgatctatctcgcgctggcgcat480atgatcaaatttcggggacacttcctcatcgagggggacctgaacccagacaacagcgat540gtcgacaaactctttatccaactggttcagacttacaatcagcttttcgaagagaacccg600atcaacgcatccggagttgacgccaaagcaatcctgagcgctaggctgtccaaatcccgg660cggctcgaaaacctcatcgcacagctccctggggagaagaagaacggcctgtttggtaat720cttatcgccctgtcactcgggctgacccccaactttaaatctaacttcgacctggccgaa780gatgccaagcttcaactgagcaaagacacctacgatgatgatctcgacaatctgctggcc840cagatcggcgaccagtacgcagacctttttttggcggcaaagaacctgtcagacgccatt900ctgctgagtgatattctgcgagtgaacacggagatcaccaaagctccgctgagcgctagt960atgatcaagcgctatgatgagcaccaccaagacttgactttgctgaaggcccttgtcaga1020cagcaactgcctgagaagtacaaggaaattttcttcgatcagtctaaaaatggctacgcc1080ggatacattgacggcggagcaagccaggaggaattttacaaatttattaagcccatcttg1140gaaaaaatggacggcaccgaggagctgctggtaaagcttaacagagaagatctgttgcgc1200aaacagcgcactttcgacaatggaagcatcccccaccagattcacctgggcgaactgcac1260gctatcctcaggcggcaagaggatttctacccctttttgaaagataacagggaaaagatt1320gagaaaatcctcacatttcggataccctactatgtaggccccctcgcccggggaaattcc1380agattcgcgtggatgactcgcaaatcagaagagaccatcactccctggaacttcgaggaa1440gtcgtggataagggggcctctgcccagtccttcatcgaaaggatgactaactttgataaa1500aatctgcctaacgaaaaggtgcttcctaaacactctctgctgtacgagtacttcacagtt1560tataacgagctcaccaaggtcaaatacgtcacagaagggatgagaaagccagcattcctg1620tctggagagcagaagaaagctatcgtggacctcctcttcaagacgaaccggaaagttacc1680gtgaaacagctcaaagaa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