The modern bio-fermentation industry requires design and creation of efficient microbial cell factories for directed conversion of raw materials to target products. The main criteria for assessing the performance of microbial cell factories are their product synthesis capacity and stability. Due to the deficiencies of plasmids in gene expression such as instability and being easy to lose, integration of genes into chromosome is often a better choice for stable expression in microbial hosts. To this end, chromosomal gene integration technology has received much attention and has developed rapidly. In this review, we summarize the recent research progresses of chromosomal integration of large DNA fragments in microorganisms, illustrate the principles and features of various technologies, highlight the opportunity brought by the CRISPR-associated transposon systems, and prospect future research direction of this technology.
微生物大片段DNA整合染色体整合细胞工厂microorganismslarge DNA fragmentschromosomal integrationcell factories国家重点研发计划2021YFC2103500上海市科学技术委员会科研计划21DZ1209100中国科学院洁净能源创新研究院合作基金DNL202013天津市合成生物技术创新能力提升行动TSBICIP-KJGG-016-01国家重点研发计划(2021YFC2103500);上海市科学技术委员会科研计划(21DZ1209100);中国科学院洁净能源创新研究院合作基金(DNL202013);天津市合成生物技术创新能力提升行动(TSBICIP-KJGG-016-01)the National Key Research and Development Program of China2021YFC2103500the Science and Technology Commission of the Shanghai Municipality21DZ1209100the DNL Cooperation Fund, Chinese Academy of SciencesDNL202013the Tianjin Synthetic Biotechnology Innovation Capacity Improvement ProjectTSBICIP-KJGG-016-01This work was supported by the National Key Research and Development Program of China (2021YFC2103500), the Science and Technology Commission of the Shanghai Municipality (21DZ1209100), the DNL Cooperation Fund, Chinese Academy of Sciences (DNL202013), and the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-KJGG-016-01)
tfoX表达促使含有同源臂的外源tDNA的吸收. C:无水四环素诱导Cas9蛋白和gRNA的合成]]>V. natriegens cells. B: IPTG-induced expression of tfoX for tDNA introduction. C: ATc-induced production of Cas9 and gRNA.]]>
值得一提的是,除同源重组外,生物体内还有两种修复DNA双链断裂的方式——非同源末端连接(nonhomologous end-joining, NHEJ)和微同源介导的末端连接(microhomology-mediated end-joining, MMEJ)。这两种修复机制也被研究者开发成分子工具用于染色体上的DNA片段整合。非同源末端连接不需要同源序列,是一种依赖于多功能酶(核酸酶、聚合酶、连接酶) ligase D (LigD)和DNA结合蛋白Ku的双组分系统。Ku蛋白以同二聚体化的形式结合DNA末端,招募LigD,催化DNA末端的加工和连接[37]。目前,研究者已利用NHEJ在多种微生物如枯草芽孢杆菌(Bacillus subtilis)、解脂耶氏酵母(Yarrowia lipolitica)和某些丝状真菌的染色体上成功整合了外源DNA片段[38-40]。这一方法的不足是可能会产生双链断裂连接处的小片段的插入或者缺失[37]。微同源介导的末端连接主要是应用于哺乳动物细胞中,在细菌中极少使用,在此就不作详细阐述了。
整合酶介导的染色体基因定点整合
温和性噬菌体感染新宿主后会在适当的条件下将自身核酸整合至宿主的染色体中,该过程由噬菌体编码的整合酶介导。根据序列的同源性和作用机制的不同,噬菌体编码的整合酶被分为两大类,丝氨酸整合酶(DNA断裂和重新连接的过程中形成磷酸丝氨酰键)和酪氨酸整合酶(DNA断裂和重新连接的过程中形成磷酸酪氨酰键)[41]。酪氨酸整合酶家族中最为人们熟知的是来自P1噬菌体的Cre蛋白和其识别位点loxP。loxP是一段34 bp的两端含有13 bp反向重复的且具有方向性的特殊序列。Cre蛋白分别与loxP上的反向重复序列结合形成二聚体,然后和另一个结合有loxP的Cre蛋白结合形成四聚体,通过Cre的催化和基团之间的相互取代,形成一个类似于Holliday的接头并完成链置换[42]。当一个环形双链DNA分子上含有一个loxP且菌株基因组上也含有一个loxP时,环形分子上的DNA片段就能够整合到基因组DNA上。在宿主微生物的染色体上引入loxP,并对loxP的方向进行设计,还可以实现特定DNA片段的剪切、易位和倒位[43]。绝大多数酪氨酸整合酶的重组机制都和Cre-loxP类似,但λ Int (来源于λ噬菌体的酪氨酸整合酶)发挥功能还需要宿主菌的IHF蛋白参与[44]。
Integrases and the "cut-and-paste" transposon system.
除了噬菌体编码的酪氨酸整合酶和丝氨酸整合酶外,在细菌中还广泛存在一类特殊的整合和接合元件(integrative and conjugative element, ICE)。ICE是一大类可移动遗传元件,能够像接合质粒一样通过接合转移到新的宿主中,并被整合到受体细胞染色体中,通过宿主复制和细胞分裂被动繁殖[49-50]。不同菌株来源的ICE的大小差异很大(20–500 kb),通常含有抗生素抗性基因,共生或毒力相关基因,因此其整合到受体菌株中后能够促进受体菌的进化[51-52]。2018年,Christopher A. Voigt团队利用枯草芽孢杆菌来源的ICE Bs1构建了一个工程菌株XPORT,该菌株能够将含有异源DNA的mini-ICE转移到来源于土壤、肠道和皮肤的几十种细菌中,并整合至受体菌株的染色体上。即使在非标准的实验条件下,例如直接将XPORT和受体菌株一起添加到无菌土壤中共孵育,一周后也能在受体菌株中检测到整合事件的发生[53]。
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