烟草NtNHX1 3基因的克隆及表达特性

以栽培烟草‘云烟87’为材料,通过同源克隆方法分离了烟草NHX（Na⁺,K⁺/H⁺ exchanger）基因NtNHX1 3。结果表明：NtNHX1 3基因CDS长度1 617 bp,编码蛋白质长度为538 aa,蛋白理论等电点为8.67,分子量为59.34 kD。预测NtNHX1 3属于膜蛋白,含有11个跨膜区,且含有NHX类蛋白保守位点氨氯吡嗪咪结合位点。进化树分析显示,NtNHX1 3与菊苣、野菊花NHX遗传距离最近。qRT PCR组织特异性表达分析表明,NtNHX1 3在烟草叶片中表达量最高,根、茎、花中也有表达;盐胁迫处理后NtNHX1 3基因的表达上调,表明该基因参与了盐胁迫反应;打顶初期NtNHX1 3基因的表达呈逐渐上调的趋势,与该时期钾含量逐渐升高相吻合。研究推测,NtNHX1 3具有将钾离子从细胞质转运至液泡的功能。     

苹果属垂丝海棠MhPPOX1基因克隆及抗缺铁性功能鉴定

原卟啉原氧化酶(Protoporphyrinogen oxidase, PPOX1) 是叶绿素生物合成途径中的关键酶,为深入探究苹果PPOX1基因的功能,该研究以苹果砧木垂丝海棠(Malus halliana)为试材,采用PCR方法,克隆MhPPOX1基因,并进行生物信息学分析及功能鉴定;采用农杆菌介导法转化烟草和拟南芥,进一步分析MhPPOX1在缺铁胁迫中的功能,并对转基因烟草与拟南芥进行抗性分析。结果表明：(1)成功克隆获得 垂丝海棠MhPPOX1基因片段,经序列比对鉴定为苹果的 MhPPOX1基因(序列号：LOC103444480)。MhPPOX1基因的开放阅读框为1 644 bp,编码547个氨基酸,等电点为8.98;系统进化树分析表明,苹果属垂丝海棠MhPPOX1与白梨该家族蛋白的亲缘关系最近。(2)成功克隆获得垂丝海棠MhPPOX1启动子序列片段(2 016 bp),对该启动子顺式作用元件预测结果显示,MhPPOX1启动子序列中存在干旱、低温、光、生长素以及与叶绿素相关等响应元件。(3)成功构建过表达载体 MhPPOX1 pRI101,并成功获得转MhPPOX1基因烟草和拟南芥。(4)qRT PCR分析表明,垂丝海棠幼苗在缺铁( Fe)胁迫下植株叶片黄化枯死,且MhPPOX1基因表达量较对照显著升高;转MhPPOX1基因烟草和拟南芥在缺铁胁迫中与野生型相比均生长良好,不易黄化,且缺铁条件下转基因拟南芥和烟草的叶绿素a、叶绿素b总量以及总铁含量明显高于野生型植株,表明MhPPOX1基因过量表达提高了拟南芥和烟草对缺铁胁迫的抗性。研究认为,MhPPOX1基因在植物抵抗缺铁胁迫中可能发挥重要作用。     

绣球‘杜丽'AP3基因克隆与基因编辑载体构建

绣球(Hydrangea macrophylla)是以花序为主要观赏部位的园林植物,多用作切花装饰和景观营造,在亚洲、美洲、欧洲广泛栽培。为探究AP3基因在绣球花萼形成过程中的功能,加快重瓣绣球新品种培育进程,该研究以绣球‘杜丽''为材料,克隆其MADS-box B类基因HmAP3,并结合生物信息学方法预测基因功能; 根据HmAP3序列信息,筛选出高特异性编辑靶点并构建CRISPR/Cas9基因编辑载体,通过农杆菌转化法将载体整合到绣球基因组中。结果表明:(1)克隆到1段HmAP3基因的cDNA序列,其序列全长546 bp,共编码181个氨基酸,测序结果表明其氨基酸序列与参考序列一致性为100%,与拟南芥AtAP3相似度为58.8%。(2)不同属植物AP3氨基酸序列差异较大,在同属不同物种中,AP3蛋白主要结构较为保守,仅在少数基序上存在差异。(3)在HmAP3中共鉴定到2个高特异性靶点,并成功构建2个单靶点CRISPR/Cas9基因编辑载体。(4)该研究共获得5株基因组内含有Cas9序列的抗性芽,但其靶点均未突变,在抗性芽中没有检测到Cas9表达。该研究探讨了AP3基因在重瓣绣球育种中的价值,对绣球的CRISPR/Cas9基因编辑技术进行了初探,为绣球优良品种繁育工作奠定了基础。     

忽地笑LaSUVH1基因克隆与功能分析

为了深入探究忽地笑(Lycoris aurea)组蛋白赖氨酸甲基转移酶(histone lysine methyltransferase, HKMT)基因的功能,该研究根据前期转录组测序结果,采用RT PCR方法克隆得到一个组蛋白赖氨酸甲基转移酶基因LaSUVH1。序列分结果表明, LaSUVH1基因的编码区(coding sequences, CDs)序列长2 007 bp,编码668个氨基酸残基;LaSUVH1蛋白不具有信号肽结构,无跨膜结构,为亲水性蛋白,含有SET、YDG/SRA、Pre SET和Post SET结构域;序列比对和系统进化树分析发现,LaSUVH1与芦笋AoSUVH1 like蛋白亲缘关系最近。实时荧光定量PCR分析表明,LaSUVH1基因在忽地笑不同组织部位均有表达,且在叶中表达量最高。经潮霉素筛选成功获得3个反义过表达LaSUVH1的转基因拟南芥株系。进一步功能分析发现,反义过表达LaSUVH1促进了拟南芥幼苗侧根的发生,降低了拟南芥对NaCl的耐受性,增加了拟南芥种子萌发对脱落酸(ABA)的敏感性,表明LaSUVH1基因响应盐胁迫应答可能依赖ABA信号通路。     

三倍体枇杷花期调控基因EjAGL6的表达特性和功能分析

以三倍体枇杷(Eriobotrya japonica) ‘华玉无核1号’的花芽为材料,采用基因克隆技术获得EjAGL6基因,分析其序列、亚细胞定位特性以及在二倍体和三倍体枇杷早晚花品种中的表达水平。采用花序浸染转化拟南芥,并利用实时荧光定量PCR分析转基因拟南芥植株的EjAGL6基因表达量,进一步观察野生型与EjAGL6转基因拟南芥的表型差异,分析EjAGL6基因的功能,为解析EjAGL6基因参与三倍体枇杷花期调控机制提供理论依据。结果显示：(1)成功获得MADS box基因EjAGL6;该基因的编码区序列(CDS)为732 bp,编码243个氨基酸,分子质量为27.88 kD,等电点为 9.05,脂溶指数为 79.05;系统进化树分析表明,枇杷EjAGL6与苹果MdAGL6蛋白质的相似性较高,聚在同一分支。(2)蛋白序列比对发现,EjAGL6的M区有57个氨基酸,I区有30个氨基酸,K区有82个氨基酸,C区有74个氨基酸,其中C区包含高度保守的AGL6基序Ⅰ和AGL6基序Ⅱ。(3)亚细胞定位分析表明,EjAGL6蛋白定位在细胞核,具有典型的MADS box转录因子亚细胞定位特性。(4)实时荧光定量PCR分析表明,EjAGL6基因在二倍体和三倍体枇杷早、晚花品种中均有表达,主要集中于小花分化期(S6)、花蕾露白期(S7)和盛花期(S8),且EjAGL6基因在二倍体和三倍体早花品种中的花蕾露白期的表达量均较高。(5) 转基因拟南芥株系的EjAGL6基因表达量显著高于野生型拟南芥;转EjAGL6基因植株表型观察显示,EjAGL6基因在拟南芥中过量表达能够使转EjAGL6基因拟南芥的开花时间提前1周左右。研究认为,EjAGL6基因可促使枇杷开花时间提前,推测EjAGL6基因在花蕾露白期发挥调控花期的关键作用。     

中国南瓜CmNPR1基因的克隆和表达分析

从实验室前期对中国南瓜雌花败育转录组测序结果推测,CmNPR1基因可能在南瓜花发育过程中发挥重要功能。该研究以中国南瓜自交系‘3 1’为试验材料,采用同源克隆方法获得中国南瓜CmNPR1基因CDS序列,通过生物信息学、基因表达以及亚细胞定位分析对该基因进行初步研究, 为进一步研究CmNPR1基因在南瓜花发育中的功能和作用机制奠定基础。结果表明：(1)中国南瓜CmNPR1基因CDS全长1 442 bp,编码480个氨基酸;蛋白序列包含有一个BTB/POZ和一个锚蛋白重复序列(Ank)保守结构域;该蛋白无信号肽和跨膜结构;多序列比对分析结果显示,CmNPR1氨基酸序列与美洲南瓜的亲缘关系最近,为96.05%,其次是印度南瓜,为95.63%。(2)CmNPR1基因在所取样品中花纵径0.5 cm时期表达量最高,且在花不同结构中柱头的表达量最高。(3)通过拟南芥原生质体亚细胞定位分析发现,该蛋白定位于细胞质和细胞核。     

一种新型的CRISPR/Cas9-hLacI双链DNA供体适配基因编辑系统

在CRISPR/Cas9系统介导的基因编辑中,借助于双链DNA （double-stranded DNA,dsDNA）供体模板的重组效应能够实现对目标基因组靶位点的精确编辑和基因敲入,然而高等真核生物细胞中同源重组的低效性限制了该基因编辑策略的发展和应用。为提高CRISPR/Cas9系统介导dsDNA供体模板的同源重组效率,本研究利用大肠杆菌（Escherichia coli）乳糖操纵子阻遏蛋白LacI与操纵序列LacO特异性结合的特点,通过重组DNA技术将密码子人源化优化的阻遏蛋白基因LacI分别与脓链球菌（Streptococcus pyogenes）源的SpCas9和路邓葡萄球菌（Staphylococcus lugdunensis）源的SlugCas9-HF融合表达,通过PCR将操纵序列LacO与dsDNA供体嵌合,构建了新型的CRISPR/Cas9-hLacI供体适配系统（donor adapting system,DAS）。首先在报告载体水平上对Cas9核酸酶活性、DAS介导的同源引导修复（homology-directed repair,HDR）效率进行了验证和优化,其次在基因组水平对其介导的基因精确编辑进行了检测,并最终利用CRISPR/SlugCas9-hLacI DAS在HEK293T细胞中实现了VEGFA位点的精确编辑,效率高达30.5%,显著高于野生型。综上所述,本研究开发了新型的CRISPR/Cas9-hLacI供体适配基因编辑系统,丰富了CRISPR/Cas9基因编辑技术种类,为以后的基因编辑及分子设计育种研究提供了新的工具。     

基于CRISPR/Cas9系统筛选猪流行性腹泻病毒复制相关基因及其验证

【背景】成簇规律间隔的短回文重复序列相关蛋白(clustered regularly interspaced short palindromic repeats/CRISPR-associated protein,CRISPR/Cas9)已被广泛证实是高效、强大的第三代基因编辑工具,在发现功能基因等领域取得了重要进展,但至今尚无利用该方法挖掘猪流行性腹泻病毒(porcine epidemic diarrhea virus,PEDV)宿主基因的报道。【目的】利用CRISPR/Cas9系统在全基因组范围内筛选PEDV复制相关基因,并进行候选基因的初步验证,为培育抗PEDV种猪提供科学参考。【方法】通过CRISPR/Cas9技术构建人肝癌细胞系(Huh-7)全基因组敲除文库,利用PEDV感染Huh-7文库细胞,随后经过高通量测序筛选影响PEDV复制的关键宿主因子,结合基因干扰和检测病毒效价等相关试验对影响PEDV复制的候选基因进行初步验证。【结果】构建了CRISPR/Cas9系统在全基因组范围内筛选PEDV复制相关基因的方法,将富集程度排名靠前的整合素α11(integrin α11,ITGA11)、哺乳动物复制蛋白A2(replication protein A2,RPA2)、驱动蛋白家族成员2A(kinesin family member 2A,KIF2A)、诱导髓系白血病细胞分化蛋白1(induced myeloid leukemia cell differentiation protein 1,MCL1)、多聚ADP核糖化酶1[poly(ADP-ribose)polymerase 1,PARP1]和囊泡单胺转运蛋白(vesicular monoamine transporter,SLC18A1)基因进行了验证;采用siRNA对上述基因分别进行干扰后,结果与对照组相比,干扰ITGA11可显著降低PEDV猪源靶向细胞IPEC-J2中PEDV-NmRNA、蛋白表达水平及子代病毒滴度。【结论】基于CRISPR/Cas9系统的全基因组敲除文库可作为挖掘PEDV复制相关功能基因的有效工具,ITGA11基因可作为一种制备抗PEDV猪种潜在的靶基因。     

CRISPR/Cas9介导靶向敲除拟南芥GGB基因突变体的鉴定

GGB是抗旱负调控基因。为了获得拟南芥ggb突变体材料,构建了以拟南芥U6启动子驱动GGB sgRNA的CRISPR/Cas9基因组编辑载体。将构建好的编辑载体利用农杆菌介导的浸花法转化野生型拟南芥。对转基因后代GGB基因的测序结果分析发现,在靶位点处有缺失4个碱基和增加1个T碱基的2种突变体产生。分别对野生型拟南芥和上述2种ggb突变体进行半定量RT PCR分析结果显示,突变体材料中几乎检测不到GGB基因表达,说明获得了GGB基因敲除突变体。对野生型和ggb突变体叶片失水率、耐旱表型及单株种子量的测定结果表明,与野生型相比,拟南芥GGB基因突变后,叶片失水率显著减少,抗旱性明显增强,而单株种子量却并没有改变。研究表明,GGB是一种理想的作物分子育种的候选靶基因,获得的突变体为今后从农作物中克隆的GGB同源基因进行功能互补验证提供了有用的遗传材料。     

呼伦贝尔黄花苜蓿MfMYB30基因的克隆及表达分析

该研究在呼伦贝尔黄花苜蓿(Medicago falcata L. cv. Hulunbuir)转录组测序基础上,通过RT PCR方法克隆获得了MfMYB30基因,并通过生物信息学和表达分析进行初步研究,为深入研究MfMYB30基因的功能和开发利用奠定基础。结果表明：(1)成功克隆获得呼伦贝尔黄花苜蓿MfMYB30基因,其ORF序列长为957 bp,编码318个氨基酸,相对分子质量为86.85 kD,理论等电点为5.11。MfMYB30蛋白为疏水性蛋白,无跨膜结构,无信号肽序列。(2)系统进化分析表明黄花苜蓿MfMYB30蛋白与紫花苜蓿MsMYB4、拟南芥AtMYB30、木豆CcMYB30、蒺藜苜蓿MtMYB30和大豆GmMYB60聚为一个类群,亲缘关系较近。(3)实时荧光定量PCR结果显示,MfMYB30在黄花苜蓿模拟刈割不同天数后的相对表达量呈先降低后升高的趋势,在刈割7 d后相对表达量达到峰值。(4)通过在拟南芥原生质体亚细胞定位分析发现,该蛋白定位于细胞核。研究推测,MfMYB30基因可能在黄花苜蓿刈割或放牧胁迫响应过程中发挥重要调控作用。     

An efficient CRISPR/Cas9 platform for targeted genome editing in rose (Rosa hybrida)

The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-related nuclease 9(Cas9) system enables precise, simple editing of genes in many animals and plants.However, this system has not been applied to rose(Rosa hybrida) due to the genomic complexity and lack of an efficient transformation technology for this plant. Here, we established a platform for screening single-guide RNAs(sgRNAs) with high editing efficiency for CRISPR/Cas9-mediated gene editing in rose using suspensio...     

CRISPR/Cas9-mediated targeted T-DNA integration in rice

Key message

Combining with a CRISPR/Cas9 system, Agrobacterium-mediated transformation can lead to precise targeted T-DNA integration in the rice genome.

Abstract

Agrobacterium-mediated T-DNA integration into the plant genomes is random, which often causes variable transgene expression and insertional mutagenesis. Because T-DNA preferentially integrates into double-strand DNA breaks, we adapted a CRISPR/Cas9 system to demonstrate that targeted T-DNA integration can be achieved in the rice genome. Using a standard Agrobacterium binary vector, we constructed a T-DNA that contains a CRISPR/Cas9 system using SpCas9 and a gRNA targeting the exon of the rice AP2 domain-containing protein gene Os01g04020. The T-DNA also carried a red fluorescent protein and a hygromycin resistance (hptII) gene. One version of the vector had hptII expression driven by an OsAct2 promoter. In an effort to detect targeted T-DNA insertion events, we built another T-DNA with a promoterless hptII gene adjacent to the T-DNA right border such that integration of T-DNA into the targeted exon sequence in-frame with the hptII gene would allow hptII expression. Our results showed that these constructs could produce targeted T-DNA insertions with frequencies ranging between 4 and 5.3% of transgenic callus events, in addition to generating a high frequency (50?80%) of targeted indel mutations. Sequencing analyses showed that four out of five sequenced T-DNA/gDNA junctions carry a single copy of full-length T-DNA at the target site. Our results indicate that Agrobacterium-mediated transformation combined with a CRISPR/Cas9 system can efficiently generate targeted T-DNA insertions.

     

Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress

The CRISPR/Cas9 system has greatly improved our ability to engineer targeted mutations in eukaryotic genomes. While CRISPR/Cas9 appears to work universally, the efficiency of targeted mutagenesis and the adverse generation of off‐target mutations vary greatly between different organisms. In this study, we report that Arabidopsis plants subjected to heat stress at 37°C show much higher frequencies of CRISPR‐induced mutations compared to plants grown continuously at the standard temperature (22°C). Using quantitative assays relying on green fluorescent protein (GFP) reporter genes, we found that targeted mutagenesis by CRISPR/Cas9 in Arabidopsis is increased by approximately 5‐fold in somatic tissues and up to 100‐fold in the germline upon heat treatment. This effect of temperature on the mutation rate is not limited to Arabidopsis, as we observed a similar increase in targeted mutations by CRISPR/Cas9 in Citrus plants exposed to heat stress at 37°C. In vitro assays demonstrate that Cas9 from Streptococcus pyogenes (SpCas9) is more active in creating double‐stranded DNA breaks at 37°C than at 22°C, thus indicating a potential contributing mechanism for the in vivo effect of temperature on CRISPR/Cas9. This study reveals the importance of temperature in modulating SpCas9 activity in eukaryotes, and provides a simple method to increase on‐target mutagenesis in plants using CRISPR/Cas9.     

Site-directed mutagenesis by biolistic transformation efficiently generates inheritable mutations in a targeted locus in soybean somatic embryos and transgene-free descendants in the T1 generation

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system is being rapidly developed for mutagenesis in higher plants. Ideally, foreign DNA introduced by this system is removed in the breeding of edible crops and vegetables. Here, we report an efficient generation of Cas9-free mutants lacking an allergenic gene, Gly m Bd 30K, using biolistic transformation and the CRISPR/Cas9 system. Five transgenic embryo lines were selected on the basis of hygromycin resistance. Cleaved amplified polymorphic sequence analysis detected only two different mutations in e all of the lines. These results indicate that mutations were induced in the target gene immediately after the delivery of the exogenous gene into the embryo cells. Soybean plantlets (T₀ plants) were regenerated from two of the transgenic embryo lines. The segregation pattern of the Cas9 gene in the T₁ generation, which included Cas9-free plants, revealed that a single copy number of transgene was integrated in both lines. Immunoblot analysis demonstrated that no Gly m Bd 30K protein accumulated in the Cas9-free plants. Gene expression analysis indicated that nonsense mRNA decay might have occurred in mature mutant seeds. Due to the efficient induction of inheritable mutations and the low integrated transgene copy number in the T₀ plants, we could remove foreign DNA easily by genetic segregation in the T₁ generation. Our results demonstrate that biolistic transformation of soybean embryos is useful for CRISPR/Cas9-mediated site-directed mutagenesis of soybean for human consumption.

     

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis,tobacco, sorghum and rice

The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5′ coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.     

应用CRISPR/Cas9系统构建MTHFD1基因敲除的HEK-293细胞系

目的:利用成簇的、规律间隔的短回文重复序列/Cas9核酸酶(CRISPR/Cas9)基因编辑技术构建亚甲基四氢叶酸脱氢酶1(methylenetetrahydrofolate dehydrogenase 1, MTHFD1))基因敲除人胚肾(HEK-293)稳定细胞系。方法:利用在线软件筛选出评分最高的3条针对MTHFD1基因的单向导RNA (sg RNA),然后合成sg RNA序列并将其插入到含有GFP标签的质粒中;重组质粒转染HEK-293细胞后通过流式细胞仪分选出已被转入sg RNA的单细胞,通过测序确认单克隆细胞系中MTHFD1的DNA序列突变状态;最后应用实时荧光定量多聚核苷酸链式反应(real-time quantitative Polymerase Chain Reaction, RT-q PCR)和蛋白质印迹(Western blot)方法检测单克隆细胞中MTHFD1的m RNA和蛋白表达水平。结果:重组载体中含有正确的sg RNA序列;测序结果显示该细胞系中MTHFD1基因发生了单个碱基插入突变和6个碱基的缺失突变;RT-qPCR结果显示单克隆细胞系中MTHFD1在m RNA水平显著降低;Western blot检测成功构建MTHFD1蛋白缺失的HEK-293细胞。结论:本研究利用CRISPR/Cas9技术成功构建的MTHFD1敲除HEK-293细胞系。