合成生物学 ›› 2022, Vol. 3 ›› Issue (1): 6-21.DOI: 10.12211/2096-8280.2021-092
赵晓宇1,2, 张浩1, 李雪飞1, 胡政1
收稿日期:
2021-09-18
修回日期:
2021-11-08
出版日期:
2022-02-28
发布日期:
2022-03-14
通讯作者:
胡政
作者简介:
基金资助:
Xiaoyu ZHAO1,2, Hao ZHANG1, Xuefei LI1, Zheng HU1
Received:
2021-09-18
Revised:
2021-11-08
Online:
2022-02-28
Published:
2022-03-14
Contact:
Zheng HU
摘要:
遗传进化是生物系统的一个基本特征,生物系统的结构与功能都是动态变化的,生物通过进化更好地适应环境。定量合成生物学作为一门新兴交叉学科,主要研究如何利用合成系统定量刻画生物学规律,以及基于理性设计和改造人工生命系统来解答生命科学前沿问题。然而,目前掌握的知识还不足以满足理性设计和定量可控的要求。尽管人工生命系统产生于实验室,但其同样受到进化法则的支配,比如突变、遗传漂变、达尔文自然选择等,因此需要利用进化规律帮助设计和构建更加稳定的人工生命系统;反过来,简单、周期短且可控的定量合成生物系统也可帮助研究生物进化原理提供更佳的生物模型,两者相互促进,为更好地探索生命法则提供了理论支撑和技术手段。本文主要综述了目前应用进化原理筛选目标蛋白的连续定向进化方法,总结了利用进化原理提高合成线路稳定性的策略;同时,介绍了用定量合成生物学的手段研究生物进化原理的进展,并提出了基于进化原理的人工生命设计的研究方向。未来合成生物学与进化生物学的融合发展将为精确控制生命系统提供思路和方法,增进合成生物学改善人类可持续发展的应用。
中图分类号:
赵晓宇, 张浩, 李雪飞, 胡政. 进化视角下的定量生物学规律与人工生命合成[J]. 合成生物学, 2022, 3(1): 6-21.
Xiaoyu ZHAO, Hao ZHANG, Xuefei LI, Zheng HU. An evolutionary perspective on quantitative biological principles and synthetic life design[J]. Synthetic Biology Journal, 2022, 3(1): 6-21.
方法 | 框架 | 原理 | 进化对象 | 突变速率 | 实例 | 突破性与局限性 | 方法延伸 |
---|---|---|---|---|---|---|---|
PACE[ | 病毒框架 | 将目的蛋白与噬菌体生命周期耦联,利用宿主的致突变质粒和辅助质粒完成突变与扩增,通过自动化连续培养实现选择与连续进化 | 包含目的基因的噬菌体 | 2.3×10-3 bp/代;突变文库数量可达到109个 | 碱基编辑器[ | 优点:应用范围最广且优化速度较快,是其他进化方法的100倍 缺点:只适用于能被噬菌体感染的原核生物;只能突变引起gⅢ基因表达变化的蛋白;操作和设备复杂 | SE-PACE系统[ |
CRISPR-X[ | “外部”突变框架 | CRISPR系统融合胞苷脱氨酶(AID),将目标基因的C脱氨并修复为T,实现碱基对直接替换 | 哺乳细胞 | 1×10-3 bp/代 | 慢性髓系白血病细胞中的耐药突变[ | 优点:适用于哺乳细胞,实现特定碱基对替换 缺点:只能实现C到T的突变,突变率较低,未实现真正的连续进化 | 胞嘧啶剪辑编辑器[ |
OrthoRep[ | 直接突变框架 | 含有目标基因和突变的DNAP的质粒、含有所有必需基因的质粒负责靶基因的复制与突变,与基因组的复制正交 | 酵母中的正交突变质粒 | 1×10-5 bp/代;能保持超过300 代的高突变率 | 进化耐药性疟疾二氢叶酸还原酶[ | 优点:正交系统可保持细胞基因组的稳定,实现连续进化 缺点:局限于酵母;系统设计复杂;外源性基因低表达 | OrthoRep基因表达盒[ |
表1 连续定向进化的原理和应用
Table 1 Principles and methods for continuous directed-evolution
方法 | 框架 | 原理 | 进化对象 | 突变速率 | 实例 | 突破性与局限性 | 方法延伸 |
---|---|---|---|---|---|---|---|
PACE[ | 病毒框架 | 将目的蛋白与噬菌体生命周期耦联,利用宿主的致突变质粒和辅助质粒完成突变与扩增,通过自动化连续培养实现选择与连续进化 | 包含目的基因的噬菌体 | 2.3×10-3 bp/代;突变文库数量可达到109个 | 碱基编辑器[ | 优点:应用范围最广且优化速度较快,是其他进化方法的100倍 缺点:只适用于能被噬菌体感染的原核生物;只能突变引起gⅢ基因表达变化的蛋白;操作和设备复杂 | SE-PACE系统[ |
CRISPR-X[ | “外部”突变框架 | CRISPR系统融合胞苷脱氨酶(AID),将目标基因的C脱氨并修复为T,实现碱基对直接替换 | 哺乳细胞 | 1×10-3 bp/代 | 慢性髓系白血病细胞中的耐药突变[ | 优点:适用于哺乳细胞,实现特定碱基对替换 缺点:只能实现C到T的突变,突变率较低,未实现真正的连续进化 | 胞嘧啶剪辑编辑器[ |
OrthoRep[ | 直接突变框架 | 含有目标基因和突变的DNAP的质粒、含有所有必需基因的质粒负责靶基因的复制与突变,与基因组的复制正交 | 酵母中的正交突变质粒 | 1×10-5 bp/代;能保持超过300 代的高突变率 | 进化耐药性疟疾二氢叶酸还原酶[ | 优点:正交系统可保持细胞基因组的稳定,实现连续进化 缺点:局限于酵母;系统设计复杂;外源性基因低表达 | OrthoRep基因表达盒[ |
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