摘要
CRISPR-Cas(clustered regularly interspaced short palindromic repeats and CRISPR-associated)系统是在细菌和古细菌基因组中发现的一种由RNA介导、抵挡外源核酸入侵的适应性免疫系统。通过对靶标位点的特异性识别,结合细胞自身的DNA修复功能或转录调控机制,CRISPR-Cas系统可高效编辑靶标序列或精准调控基因的表达,目前已被开发成为基因编辑领域的有力工具。根据效应复合物组成形式的不同,CRISPR-Cas系统分为1类(Ⅰ型、Ⅳ型和Ⅲ型)和2类(Ⅱ型、Ⅴ型和Ⅵ型)两大类。2类中的CRISPR-Cas9系统作为最早发现且被研究透彻的系统之一,应用范围已十分广泛;而1类系统虽占整个CRISPR-Cas系统的90%,但目前还未有开发成熟的应用工具。本综述以1类中的Ⅰ型系统为例,从亚型分类、效应复合物组装与结构、Cas3蛋白的切割降解机制以及近几年在基因编辑中的应用等方面进行总结,为更好地研究该类别的作用机制及后期的开发应用提供新的思路和方法。
CRISPR-Cas(clustered regularly interspaced short palindromic repeats and CRISPR associated)系统是一种在细菌和古细菌基因组中发现的适应性免疫系统,由RNA介导来抵挡外源核酸的入侵。1987年,日本大阪大学在研究大肠埃希菌的碱性磷酸酶同工酶时发现其基因组中存在一些串联间隔重复序
CRISPR-Cas基因簇包含储存外源核酸序列信息的CRISPR基因座以及编码不同功能蛋白的cas基因。CRISPR基因座是一段由前导序列、重复序列和间隔序列组成的簇状规则间隔的短回文重复片段。前导序列是CRISPR基因座的启动子,转录重复序列和间隔序列,但不翻译为蛋白;长度相近的间隔序列则是来源于噬菌体、质粒、转座酶基因或内源性的有害核酸片段等;重复序列区将不同的间隔序列隔开,转录后在内部通过碱基互补作用形成发卡结构。cas基因位于CRISPR基因座附近,根据在系统中执行的功能不同来命名区分,可编码几十种结构和性质不同的Cas蛋白(
CRISPR-Cas系统的适应性免疫过程分为3步:(1)第1步是适应过程。外源核酸片段被Cas蛋白特异性识别,整合特定长度的序列到CRISPR基因座
根据效应复合物的组成形式不同,CRISPR-Cas系统分成1类和2类两大部分:1类又分为3个类型(Ⅰ型、Ⅳ型和Ⅲ型)和16个亚型,该类别的共同特征是利用多Cas蛋白效应物复合物实现干扰靶标核酸;2类包括有Ⅱ型、Ⅴ型和Ⅵ型3个类型,该系统只利用单一效应蛋白如Cas9和Cas12发挥活性。2020年,科学家对已经发现的Cas蛋白进行了系统整
Ⅰ型系统目前分为I-A至F和I-U 7个亚型(

Figure 1 Representative strains and gene cluster information of type I CRISPR-Cas system subtypes.Grey rectangle represents repeat,and pink diamond means different spacers. Cas1 and Cas2 are conserved in all systems
Ⅰ型CRISPR-Cas系统的效应复合物结构具有一些共同特征,目前通过冷冻电镜或X射线解析得到的结构有I-E、I-F、I-C以及I-D型,其中关于I-E型和I-F型系统的研究最为透彻。以大肠埃希菌的I-E型为例,其效应复合物有5种Cas蛋白,包括11个亚基(Cas76Cas51Cas61Cse11Cse22)和61个碱基的成熟crRNA(

Figure 2 Cascade complex assembly of type I CRISPR-Cas system subtypes and protein-nucleic acid interaction
A: CRISPR RNA-guided surveillance complex binding to dsDNA in Thermobifida fusca (PDB: 5U07); B: The base at the 6th position of spacer is blocked by the residues (sky blue) and does not bind to DNA; C: Cascade consists of only three proteins (Cas7fv-Cas5fv-Cas6fv) in the I-Fv system (PDB: 5O7H); D: Type I-F Cascade complex from Pseudomonas aeruginosa (PDB: 6NE0); E: Cas3 binds to the large subunit in Cascade,and the nuclease domain is close to the non-target DNA (PDB: 6C66); F:Detail of Cas3 and DNA in the E.Grey: Cas7 (backbone); Green: Cas6; Purple: Cse2; Dark blue: Cse1 or Cas8; Orange: Cas5; Light blue: Cas3. Red chain: crRNA; Yellow chain: target DNA; Violet purple chain: non-target DNA.Ball in F: metal ions in Cas3
不同系统中crRNA的长度不同,在Ⅰ型系统中作为确定效应复合物大小的分子尺,即与一些Cas蛋白的拷贝数有关。在Zymomonas mobilis的I-F亚型系统中,研究者发现在制备体外复合物时,添加的crRNA中间隔序列长度不同,溶液中单体ZmCsy3会转变为不同的低聚状
在复合物的结构中,各亚型一般都包括骨架蛋白、大亚基和小亚基。由于进化或生存环境的影响,一些蛋白的结构有差异,同时效应复合物的扭曲角度也会有所不同(
效应复合物识别底物dsDNA时,需要满足两个基本条件:一是识别前间隔序列附近的PAM序列,二是DNA序列与crRNA产生特定长度的互补配对区域。PAM序列位于前间隔序列非靶标链中(不与crRNA互补的链),Ⅱ型系统一般在前间隔序列的3′
实验表明,效应复合物必须与靶标DNA形成完整的R-loop结构,才能招募Cas3蛋
从结构上来看,Ⅰ型CRISPR-Cas系统的效应复合物由多种蛋白组成,分工明确,遵循着严格的分子组装方式,每种亚型都有各自的特点;在寻找靶标DNA并干扰时,有着严谨的识别机制,与Ⅱ型系统如CRISPR-Cas9的过程相比,要求更加严格,这可能是Ⅰ型CRISPR-Cas系统在自然界存在更为广泛的原因之一。
CRISPR-Cas9系统是研究者最早发现并且其分子机制研究透彻的系统之一,已经成为基础和应用生物学研究中普遍选择的基因编辑工
Cas3切割靶向DNA之后,核酸酶活性对DNA进行持续降解,对比Cas9的单碱基突变,这一特性为基因编辑领域提供了新思路。Thermobifida fusca I-E型的效应复合物可以在人类细胞中产生一系列大的基因组缺失,通过电转效应复合物和Cas3蛋白,在单个CRISPR靶向位点的上游引起长片段DNA损伤(几百碱基到100 kb)而引起基因沉默,效率最高可达60%,显示了它们在大范围基因组操作中的潜

Figure 3 Gene editing applications of type I CRISPR-Cas system
A: Cas3 deletes large fragments of non-essential genes and minimizes the genome; B: Insert a gene into the target fragment through homologous recombination; C: Design different spacers in one CRISPR array to target different genes and edit two genes at the same time; D: Regulatory protein is fused with Cascade,and reaches the transcriptional regulatory region through the targeting effect of Cascade,controlling gene expression or silence
基因敲除后,DNA的修复方式之一是细胞内的同源重组机制,当人为给予修复模板时,该系统可以在基因组中的指定位点插入指定片段。一般方法是在表达CRISPR阵列的质粒上携带一段非靶向的待插入片段,同时在两侧加上基因组插入位点两侧的同源序列,这段特定片段即被插入到基因组中(
除了对单个基因进行编辑,CRISPR 阵列的序列特点使得多基因同时编辑变得非常容易。Ⅰ型系统中,只需要在表达crRNA质粒中增加几十个碱基,设计多个间隔序列即可(
CRISPR-Cas系统精准的靶向性使其可以作为体内引导工具。效应复合物在PAM序列和crRNA的引导下,能够将融合表达的蛋白带到调控位点,从而激活基因(CRISPRa)或沉默基因(CRISPRi)的表达,且该融合一般不会影响效应复合物本身的组装(
CRISPR-Cas系统存在于约90%的古细菌以及40%的细菌基因组中,为了应对复杂的生存环境,很多细菌同时具有多个CRISPR-Cas系统,这广泛性揭示了CRISPR-Cas系统作用机制的高效和精确性。通过优化改造Ⅰ型系统的效应复合物,可以实现精准地插入、敲除或替换目的基因。例如通过改变Cas蛋白的某些氨基酸序列改变效应复合物的最佳活性温度,从而更适合在人类细胞中应用;同时,效应复合物的含量在一定范围内与编辑效率呈现正相关。融合表达调控基因时,延长间隔序列的长度可以增加骨架蛋白的拷贝数,从而增强调控作用,一定程度上提高编辑效率;此外由于重复序列具有同源重组效应,可能丢失中间的间隔序列而降低效率,这一问题可以通过改变引起重组反应的部分碱基来解决。选择靶标序列时,crRNA与前间隔序列之间的核苷酸错配影响CRISPR复合物干扰的效率,相对于鸟嘌呤,胞嘧啶突变更容易被耐
对于Cas3而言,其长基因片段缺失功能将有助于对非编码区基因的探究,有望开发成为大规模检测基因组功能的工具,对遗传学研究具有深远的意义。此外,CRISPR激活(CRISPRa)和CRISPR抑制(CRISPRi)的应用范围广泛,无论在实验方案设计或实验操作中,融合不同调控蛋白过程的可操控性较强,Ⅰ型CRISPR-Cas系统的效应复合物在基因编辑的各个方面都具有很大的应用价值。未来应用中,在动物模型搭建、基因组功能研究、基因检测以及基因编辑为原理的疾病治疗、药物递送等领域,Ⅰ型CRISPR-Cas系统的特点和功能为人们提供更多的方法和思路。
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