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CN103343120A - 一种小麦基因组定点改造方法 - Google Patents

一种小麦基因组定点改造方法 Download PDF

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CN103343120A
CN103343120A CN2013102793037A CN201310279303A CN103343120A CN 103343120 A CN103343120 A CN 103343120A CN 2013102793037 A CN2013102793037 A CN 2013102793037A CN 201310279303 A CN201310279303 A CN 201310279303A CN 103343120 A CN103343120 A CN 103343120A
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wheat
cas9 nuclease
rna
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guide rna
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CN103343120B (zh
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高彩霞
王延鹏
单奇伟
陈坤玲
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Suzhou Qihe Biotechnology Co ltd
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Institute of Genetics and Developmental Biology of CAS
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Abstract

本发明公开了一种小麦基因组定点改造方法。本发明的小麦基因改造方法,包含以下步骤:使小麦组织中含有向导RNA和Cas9核酸酶,然后在向导RNA和Cas9核酸酶共同作用下,目的基因上的双链靶标片段被剪切,再通过小麦细胞的自身DNA修复功能,最终实现小麦目的基因中靶标片段上的随机插入和/或随机缺失。实验证明,本发明方法能够成功地对小麦进行基因突变。

Description

一种小麦基因组定点改造方法
技术领域
本发明属于植物基因工程领域,涉及一种小麦基因组改造方法。
背景技术
小麦是世界上最重要且广泛种植的农作物之一,对小麦基因组的改造有利于小麦基因组的研究,对提高产量,增强其对病虫害的抗性和农业发展有重要意义。目前,小麦突变体的创制和染色体改造主要是通过EMS诱变,物理诱变和染色体工程来获得,但这些方法费时费力,盲目性较大。当前的植物基因组工程(Genome engineering)技术中,主要通过锌指核酸酶(ZFNs)和转录激活子样效应因子核酸酶(TALENs)来做基因改造,但是在小麦基因定点改造还没有报道,而且这些技术操作过程复杂,成本高,技术难度较大,因此,亟待开发更加高效、廉价并且简单的小麦基因改造新技术。
最近发现的原核生物的第二类适应性免疫系统CRISPR(成簇的规律间隔的短回文重复序列)提供了另一个基因组改造的方法。第二类CRISPR系统广泛存在于细菌中,它们利用一个核酸内切酶Cas9为它们自身提供了防御病毒和质粒入侵的手段。Cas9可以和一个人工合成的引导RNA(guide RNA,gRNA)组成复合体,引导RNA由crRNA(CIRSPR RNA)和tracr RNA(trans-activating crRNA)融合产生。由gRNA引导Cas9核酸内切酶识别并切断靶向DNA。Cas9有两个关键的结构域:HNH和RuvC,它们分别切开DNA双链中的一条单链。产生DNA双链断裂(DSB),细胞启动修复机制,通过非同源末端连接(NHEJ)这种不精确的修复方式可以产生基因定点突变,通过同源重组(HR)方式修复可以实现精确的基因定点插入或基因替换。Cas9已经在细菌、人类细胞、斑马鱼和小鼠中成功进行基因组工程研究。
发明内容
本发明的一个目的,是提供一种实现小麦目的基因中靶标片段上的随机插入和/或随机缺失的基因改造方法。
本发明的实现小麦目的基因中靶标片段上的随机插入和/或随机缺失的基因改造方法,是利用CRISPR/Cas系统在小麦中对目的基因进行改造,该系统包括向导RNA和Cas9核酸酶,所述方法包含以下步骤:使小麦组织中含有向导RNA和Cas9核酸酶,然后在向导RNA和Cas9核酸酶共同作用下,目的基因上的双链靶标片段被剪切,再通过小麦细胞的自身DNA修复功能,最终实现小麦目的基因中靶标片段上的随机插入和/或随机缺失;
所述靶标片段位于所述目的基因上;所述双链靶标片段中的一条链具有如下结构:5’-NX-NGG-3’,N表示A、G、C和T中的任一种,14≤X≤30;
所述向导RNA依次由能够与所述靶标片段互补结合的RNA片段和骨架RNA片段连接而成;所述骨架RNA片段依次由tracrRNA、crRNA嵌合形成类似发夹结构的RNA,所述骨架RNA片段可与Cas9核酸酶结合。
所述5’-NX-NGG-3’中,19≤X≤21,具体X为19或20。
所述向导RNA中能够与所述靶标片段互补结合的RNA片段为能与所述5’-NX-NGG-3’中NX片段互补结合的RNA片段。
所述向导RNA中骨架RNA片段是由SEQ ID No.3中第386-469位核苷酸所示DNA转录出来的RNA。
所述使小麦组织中含有向导RNA和Cas9核酸酶的方法为:向小麦组织中直接转入所述向导RNA和带有核定位信号肽的Cas9核酸酶。
所述使小麦组织中含有向导RNA和Cas9核酸酶的方法为:向小麦组织中导入含有所述向导RNA的表达盒的重组克隆载体和含有所述带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体,所述向导RNA的表达盒在小麦组织中表达出向导RNA,所述带有核定位信号肽的Cas9核酸酶的表编码基因在小麦组织中表达出带有核定位信号肽的Cas9核酸酶。
所述向导RNA的表达盒由U6启动子和所述向导RNA的编码基因组成;所述向导RNA的编码基因由所述能与所述靶标序列互补结合的RNA片段的编码基因和所述骨架RNA片段的编码基因组成。
所述U6启动子的核苷酸序列如SEQ ID No.3中第1-363位核苷酸序列所示。
所述重组表达载体中的出发载体为任一能够在小麦中表达外源基因的表达载体。如在构建含有带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体时,可使用出发载体pJIT163。
所述重组克隆载体中的出发载体为任一能够在小麦中使外源DNA转录出RNA的克隆载体。如在构建含有所述向导RNA的表达盒的重组克隆载体时,可使用出发载体pUC-T。
所述向导RNA的表达盒中启动子为U6启动子时,所述靶标片段的一条链具有如下结构:5’-G-NX-NGG-3’,N及X与权利要求1或2中定义相同。
所述带有核定位信号肽的Cas9核酸酶的编码基因中,所述Cas9核酸酶的编码基因的核苷酸序列如SEQ ID No.1中第37-4161位核苷酸所示。
所述带有核定位信号肽的Cas9核酸酶为在Cas9核酸酶的N端和/或C端带有核定位信号肽。
所述带有核定位信号肽的Cas9核酸酶的编码基因的核苷酸序列如SEQ ID No.1中第7-4212位核苷酸所示。
所述小麦组织为小麦原生质体。
本发明的另一个目的是提供一种用于实现小麦目的基因的靶标片段上的随机插入和/或随机缺失的基因改造试剂盒。
本发明的用于实现小麦目的基因的靶标片段上的随机插入和/或随机缺失的基因改造试剂盒,包括如下(1)和(2):
(1)SEQ ID No.1中第37-4161位核苷酸所示Cas9核酸酶的编码基因、或SEQ IDNo.1中第7-4212位核苷酸所示的带有核定位信号肽的Cas9核酸酶的编码基因、含有SEQ ID No.1中第37-4161位核苷酸所示Cas9核酸酶的编码基因的重组表达载体、或含有SEQ ID No.1中第7-4212位核苷酸所示的带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体;
(2)含有如下DNA片段的重组克隆载体:依次由U6启动子、两个BbsI酶切位点和骨架RNA片段的编码DNA依次连接而成;
所述骨架RNA片段的编码DNA的核苷酸序列如SEQ ID No.3中第386-469位核苷酸所示。
所述U6启动子的核苷酸序列如SEQ ID No.3中第1-363位核苷酸序列所示。
所述重组表达载体中的出发载体为任一能够在小麦中表达外源基因的表达载体。如在构建含有带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体时,可使用出发载体pJIT163。
所述重组克隆载体中的出发载体为任一能够在小麦中使外源DNA转录出RNA的克隆载体。如在构建含有所述向导RNA的表达盒的重组克隆载体时,可使用出发载体pUC-T。
所述的试剂盒中,所述(2)中所述DNA片段如SEQ ID No.3所示。
本发明带有小麦U6启动子的gRNA:Cas9系统原则上可以靶向形式为5’-G-N(20)-GG-3’的小麦基因组序列。对小麦A基因组进行生物信息分析,在全基因组和cDNA中分别含有约34,896,754个和约247,868个gRNA结合位点,即具有5’-G-N(20)-GG-3’序列结构的位点。如果放宽这个限制为5’-G-N(19-21)-GG-3’,则A基因组每条cDNA中含有21.4个gRNA结合位点。对小麦D基因组进行生物信息分析,在全基因组和cDNA中分别含有约30,621,909个和约308,244个gRNA结合位点,即具有5’-G-N(20)-GG-3’序列结构的位点。如果放宽这个限制为5’-G-N(19-21)-GG-3’,则D基因组每条cDNA中含有21.7个gRNA结合位点。
附图说明
图1为gRNA:Cas9系统对小麦内源基因TaMLO的定点突变结果图,其中图1a中,泳道1和2为导入了gRNA:Cas9系统的原生质体PCR产物经内切酶AvaII酶切结果,泳道3为野生型的原生质体PCR产物,泳道4为野生的原生质体PCR产物经内切酶AvaII酶切结果;图1b为测序结果,其中,WT表示野生型基因序列,“-”表示发生了删除突变的序列,“+”表示发生了插入突变的序列,“-/+”后边的数字表示删除或插入的核苷酸的数量。
具体实施方式
下述实施例中所使用的实验方法如无特殊说明,均为常规方法。
下述实施例中所用的材料、试剂等,如无特殊说明,均可从商业途径得到。
以下实施例便于更好地理解本发明,但并不限定本发明。
本发明列列举的实施例中进行基因改造时使用的具体工具如下:
1、Cas9核酸酶重组表达载体的制备
对酿脓链球菌Cas9(SpCas9,S.pyogenes Cas9)基因进行了密码子优化,并在基因编码序列的两端添加核定位信号(NLS)和BamH Ⅰ/Mfe Ⅰ限制酶切位点,使优化后的Cas9可更好地在小麦中表达和定位。两端添加NLS和限制酶切位点且密码子优化后的Cas9的核苷酸编码序列如序列表中SEQ ID№:1所示。SEQ ID№:1中,第1-6位为BamH Ⅰ酶切位点,第4213-4218位为Mfe Ⅰ酶切位点,第10-36位为N端NLS序列,第4162-4209位为C端NLS序列,第37-4161位为Cas9蛋白的编码基因。SEQ ID№:1中编码框为SEQ ID №:1的第7-4212位核苷酸,编码SEQ ID №:2所示蛋白,即为带有核定位信号肽的Cas9核酸酶。
人工合成SEQ ID №:1所示DNA。
将上述人工合成的核苷酸片段经BamH Ⅰ和Mfe Ⅰ双酶切,连接入表达载体pJIT163(pJIT163相关参考文献:Guerineau,F.,Lucy,A.&Mullineaux,P.Effect of twoconsensus sequences preceding the translation initiator codon on geneexpression in plant protoplasts.Plant Molecular Biology18,815-818<1992>,公众可从中国科学院遗传与发育生物学研究所获得该载体)中,即得Cas9表达载体,命名为pJIT163-2NLSCas9。经测序证明,在pJIT163表达载体的BamH Ⅰ和EcoRI(EcoRI与MfeI为同尾酶)酶切位点间插入了具有SEQ ID №:1的所示序列的核苷酸片段。
2、带有小麦U6启动子和小麦gRNA骨架编码序列的载体pU6-gRNA的制备
人工合成带有小麦U6启动子的gRNA骨架序列的U6-gRNA核酸片段,U6-gRNA的核苷酸序列如序列表中SEQ ID №:3所示;将该人工合成的U6-gRNA核酸片段克隆至pUC-T载体(购自CWBIO)中。具体克隆过程:合成扩增引物F:CCCAAGCTTGACCAAGCCCGTTATTCT R:GGTACCAAAAAAAGCACCGACTCGG,用Transgen EASYTaq扩增U6-gRNA片段,扩增产物经纯化,可直接连到pUC-T载体中,即得pU6-gRNA载体。
对pU6-gRNA载体进行测序,测序结果表明,pUC-T载体中插入了序列表中SEQ ID№:3所示序列的核苷酸片段,将该插入了具有序列表中SEQ ID №:3所示序列的核苷酸片段的pUC-T载体命名为pU6-gRNA。其中,SEQ ID №:3的第1-363位核苷酸为U6启动子的编码序列,第386-469位核苷酸为小麦gRNA的骨架编码序列;在小麦U6启动子和小麦gRNA骨架编码序列之间还含有两个BbsI酶切位点,待突变靶序列的识别序列可插入两个酶切位点之间。
实施例1、gRNA:Cas9系统对小麦内源基因TaMLO的定点突变
(一)靶标片段target-SP6的设计
target-SP6:GGAGATTGGGTCCTGCGTGACGG;(Genbank No为AF384144的TaMLO基因负链中的第429-451位核苷酸)
(二)含有SP6核苷酸片段的pU6-gRNA质粒的制备
SP6是能与靶标target-SP6互补结合的RNA的编码DNA。
合成下述带有粘性末端(下划线部分)的单链引物:
SP6-F:CTTGGAGATTGGGTCCTGCGTGA;
SP6-R:AAACTCACGCAGGACCCAATCTC。
经过引物退火程序形成有粘性末端的双链DNA,分别插入到pU6-gRNA质粒的两个BbsI酶切位点之间,即得含有SP6的pU6-gRNA质粒,质粒经测序验证阳性质粒。
(三)转化gRNA:Cas9系统至小麦原生质体
将pJIT163-2NLSCas9和含有SP6的pU6-gRNA质粒转化至小麦原生质体(小麦所用品种为科农199,可从遗传发育所获得),原生质体制备和转化具体过程为:
1.小麦原生质体制备和转化所用溶液的配制,见表1-表4。
表1 50ml酶解液
Figure BDA00003462819900051
表2 500ml W5
Figure BDA00003462819900052
Figure BDA00003462819900061
表3 10ml MMG溶液
加入量 终浓度
Mannitol(0.8M) 5ml 0.4M
MgCl2(1M) 0.15ml 15mM
MES(200mM) 0.2ml 4mM
DDW 至10ml
表4 4ml PEG溶液
加入量 终浓度
PEG4000 1.6g 40%
Mannitol(0.8M) 1ml 0.2M
CaCl2(1M) 0.4ml 0.1M
DDW 至4ml
2.小麦苗的培养:
种小麦种子于培养室,置于温度25±2℃,光照度1000Lx,光照14~16h/d的条件下培养。培养时间约1-2周。
3.原生质体分离:
1)取小麦幼嫩的叶片,用刀片将其中间部分切成0.5-1mm的丝,放入0.6M的Mannitol溶液中避光处理10分钟,再用滤网过滤,将其放入50ml酶液中消化5小时(先抽真空酶解0.5h,再10rmp缓慢摇晃4.5h)。
注:酶解温度要保持在20-25℃,且要避光,酶解完轻轻摇晃酶解液,使原生质体释放出来。
2)加10ml W5稀释酶解产物,用75um尼龙滤膜过滤酶解液于圆底离心管中(50ml)。
注:尼龙滤膜要浸泡在75%酒精里,用时要用水冲洗,再用W5浸泡2min再过滤。
3)23℃,100g,离心3min,弃上清。
4)用W5 10ml轻轻悬起,冰上放置30min;原生质体逐渐沉降,弃上清。
5)加适量MMG悬浮,至于冰上,待转化。
注:此时需要确定原生质体的浓度,镜检(×100),原生质体数为2×105/ml-1×106/ml.
4.小麦原生质体转化
1)加10ug pJIT163-2NLSCas9和10ug含有SP6的pU6-gRNA质粒于2ml离心管,用枪头吸取200ul原生质体轻弹混匀,静止3-5min,再加250ul PEG4000,轻弹混匀,避光诱导转化30min;
2)加900ul W5(室温)颠倒混匀,100g,离心3min,弃上清;
3)加2ml W5,颠倒混匀,轻轻转至6孔板中,已预先加入1ml W5,23℃培养过夜。
(四)PCR/RE实验分析gRNA:Cas9系统对小麦内源基因TaMLO的突变结果
小麦原生质体转化后48小时提取基因组DNA,以该DNA为模板,进行PCR/RE(Polymerase Chain Reaction/Restriction digestion)实验分析。PCR/RE分析方法参考了文献Shan,Q.et al.Rapid and efficient gene modification in rice andBrachypodium using TALENs.Molecular Plant(2013),其中,PCR扩增所用引物为:
TaMLO-F:TCATCGTCTCCGTCCTCCTGGAGCA,
TaMLO-R:TGGTATTCCAAGGAGGCGGTCTCTGTCT;
PCR/RE实验分析结果见图1a,图1a结果表明在TaMLO基因靶位点发生了突变,根据条带强度用软件计算的突变效率在27.9-28.5%之间。分别回收测序图1a中的条带,测序结果见图1b,测序结果表明在TaMLO基因的两个靶位点都发生了碱基插入/删除(insertion/deletion,indel)类型的突变。图1b中是target-SP6的互补链的测序结果。DNA正链或负链都能被设计的gRNA结合,并进而由Cas9切断,正负链没有区别。
Figure IDA00003462820700011
Figure IDA00003462820700031
Figure IDA00003462820700041
Figure IDA00003462820700051
Figure IDA00003462820700061
Figure IDA00003462820700071
Figure IDA00003462820700081
Figure IDA00003462820700091

Claims (13)

1.一种实现小麦目的基因中靶标片段上的随机插入和/或随机缺失的基因改造方法,是利用CRISPR/Cas系统在小麦中对目的基因进行改造,该系统包括向导RNA和Cas9核酸酶,其特征在于:所述方法包含以下步骤:使小麦组织中含有向导RNA和Cas9核酸酶,然后在向导RNA和Cas9核酸酶共同作用下,目的基因上的双链靶标片段被剪切,再通过小麦细胞的自身DNA修复功能,最终实现小麦目的基因中靶标片段上的随机插入和/或随机缺失;
所述靶标片段位于所述目的基因上;所述双链靶标片段中的一条链具有如下结构:5’-NX-NGG-3’,N表示A、G、C和T中的任一种,14≤X≤30;
所述向导RNA依次由能够与所述靶标片段互补结合的RNA片段和骨架RNA片段连接而成;所述骨架RNA片段依次由tracrRNA、crRNA嵌合形成类似发夹结构的RNA,所述骨架RNA片段可与Cas9核酸酶结合。
2.根据权利要求1所述的方法,其特征在于:所述5’-NX-NGG-3’中,19≤X≤21,具体X为19或20。
3.根据权利要求1或2所述的方法,其特征在于:所述向导RNA中能够与所述靶标片段互补结合的RNA片段为能与所述5’-NX-NGG-3’中NX片段互补结合的RNA片段。
4.根据权利要求1-3任一所述的方法,其特征在于:所述向导RNA中骨架RNA片段是由SEQ ID No.3中第386-469位核苷酸所示DNA转录出来的RNA。
5.根据权利要求1-4任一所述的方法,其特征在于:所述使小麦组织中含有向导RNA和Cas9核酸酶的方法为:向小麦组织中直接转入所述向导RNA和带有核定位信号肽的Cas9核酸酶。
6.根据权利要求1-5任一所述的方法,其特征在于:所述使小麦组织中含有向导RNA和Cas9核酸酶的方法为:向小麦组织中导入含有所述向导RNA的表达盒的重组克隆载体和含有所述带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体,所述向导RNA的表达盒在小麦组织中表达出向导RNA,所述带有核定位信号肽的Cas9核酸酶的表编码基因在小麦组织中表达出带有核定位信号肽的Cas9核酸酶。
7.根据权利要求1-6任一所述的方法,其特征在于:所述向导RNA的表达盒由U6启动子和所述向导RNA的编码基因组成;所述向导RNA的编码基因由所述能与所述靶标序列互补结合的RNA片段的编码基因和所述骨架RNA片段的编码基因组成。
8.根据权利要求1-7任一所述的方法,其特征在于:所述向导RNA的表达盒中启动子为U6启动子时,所述靶标片段的一条链具有如下结构:5’-G-NX-NGG-3’,N及X与权利要求1或2中定义相同。
9.根据权利要求1-8任一所述的方法,其特征在于:所述带有核定位信号肽的Cas9核酸酶的编码基因中,所述Cas9核酸酶的编码基因的核苷酸序列如SEQ ID No.1中第37-4161位核苷酸所示。
10.根据权利要求1-9任一所述的方法,其特征在于:所述带有核定位信号肽的Cas9核酸酶的编码基因的核苷酸序列如SEQ ID No.1中第7-4212位核苷酸所示。
11.根据权利要求1-10任一所述的方法,其特征在于:所述小麦组织为小麦原生质体。
12.一种用于实现小麦目的基因的靶标片段上的随机插入和/或随机缺失的基因改造试剂盒,包括如下(1)和(2):
(1)SEQ ID No.1中第37-4161位核苷酸所示Cas9核酸酶的编码基因、或SEQ IDNo.1中第7-4212位核苷酸所示的带有核定位信号肽的Cas9核酸酶的编码基因、含有SEQ ID No.1中第37-4161位核苷酸所示Cas9核酸酶的编码基因的重组表达载体、或含有SEQ ID No.1中第7-4212位核苷酸所示的带有核定位信号肽的Cas9核酸酶的编码基因的重组表达载体;
(2)含有如下DNA片段的重组克隆载体:依次由U6启动子、两个BbsI酶切位点和骨架RNA片段的编码DNA依次连接而成;
所述骨架RNA片段的编码DNA的核苷酸序列如SEQ ID No.3中第386-469位核苷酸所示。
13.根据权利要求12所述的试剂盒,其特征在于:所述(2)中所述DNA片段如SEQ ID No.3所示。
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