Progress in the study of genetic code expansion related methods, principles and applications

doi:10.12211/2096-8280.2020-007

Synthetic Biology Journal ›› 2020, Vol. 1 ›› Issue (1): 103-119.DOI: 10.12211/2096-8280.2020-007

Progress in the study of genetic code expansion related methods, principles and applications

Xian FU^1,², Tao LIN¹, Fan ZHANG³, Huiming ZHANG¹, Wenwei ZHANG¹, Huanming YANG^1,⁴, Shida ZHU^1,⁵, Xun XU^1,², Yue SHEN^1,^2,^5,⁶

^1.BGI-Shenzhen, Shenzhen 518083, Guangdong, China
^2.Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
^3.BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
^4.Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
^5.Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen 518120, Guangdong, China
^6.China National GeneBank, BGI-Shenzhen, Shenzhen 518120, Guangdong, China

Received:2020-02-28 Revised:2020-03-25 Online:2020-07-07 Published:2020-02-25
Contact: Yue SHEN

基因密码子拓展技术的方法原理和前沿应用研究进展

付宪^1,², 林涛¹, 张帆³, 张惠铭¹, 章文蔚¹, 杨焕明^1,⁴, 朱师达^1,⁵, 徐讯^1,², 沈玥^1,^2,^5,⁶

^1.深圳华大生命科学研究院, 广东深圳 518083
^2.广东省高通量基因组测序与合成编辑应用重点实验室，深圳华大生命科学研究院，广东深圳 518120
^3.中国科学院大学华大教育中心，广东深圳 518083
^4.（广东省）华大基因合成基因组学院士工作站, 深圳华大基因科技有限公司，广东深圳 518120
^5.深圳创新分子诊断技术工程实验室，深圳华大生命科学研究院，广东深圳 518120
^6.深圳国家基因库，广东深圳 518120

通讯作者: 沈玥
作者简介:付宪（1989-），男，博士，副研究员，研究方向为合成生物学、合成基因组学、蛋白质定向进化。E-mail:fuxian1@genomics.cn|沈玥（1986-)，女，博士，研究员，研究方向为合成生物学、合成基因组学、DNA合成技术与工具开发。E-mail:shenyue@genomics.cn
基金资助:
国家重点研发计划（2018YFA0900100）国家自然科学基金?(31901029、31800078)

Abstract

Abstract:

All life on the earth uses a set of 20 amino acids to synthesize proteins according to the highly conservative codon table, and these limited kinds of amino acids serve as the building blocks for the natural protein synthesis. During the long-term evolution, nature is able to expand the structure and function of cellular proteins via changing the sequence order of amino acids. However, the evolution process is random and lack of controllability. Manipulating the structure and function of target proteins can also be realized by incorporating an expanded set of building blocks with new chemical and physical properties. Genetic code expansion for synthesis of proteins containing unnatural amino acids at any designed position can be achieved via the manipulation of the cellular components responsible for the translation step of the central dogma, which could endow target proteins with new and expanded properties. This review will be focused on the introduction of principles, strategies, techniques to engineer and rewire translational machinery and chassis underpinning genetic code expansion technology. Furthermore, emerging applications in the field of protein function regulation, innovative biomedicine and biocontainment relying on this technology will also be discussed.

Most lifes on the earth use a set of 20 naturally occurring amino acids as the building blocks for protein synthesis, according to the highly conserved codon table. Natural evolution modulates the structure and function of cellular proteins via random mutations among the limited, canonical collection of basic units. Instead, an expanded set of unnatural amino acids with new chemical and physical properties can be incorporated into proteins by synthetic biologists with molecular precision. Genetic code expansion for proteins can be achieved by engineering the translation step of the central dogma. This review will first introduce the principles, strategies, and techniques underpinning genetic code expansion technology, which targets the translational machinery in model chassis. Furthermore, related, emerging applications including protein function regulation, innovative biomedicine, and enhanced biocontainment will be discussed. We conclude with future perspectives.

Key words: unnatural amino acid, genetic codon expansion system, translational tool, adaptive cell chassis, orthogo-nality

摘要：

自然界生物根据其高度保守的密码子表来对20种天然氨基酸进行基因编码，这些种类有限的氨基酸构成了天然蛋白质合成的基本构筑单元。生物在漫长进化中通过改变蛋白质中氨基酸的排列顺序来丰富其结构与功能,但上述过程是随机的，缺乏可控性。拓展用于蛋白质合成的氨基酸种类亦可实现对蛋白质结构和功能的改变与操纵。通过对中心法则中翻译系统的设计与改造，基因密码子拓展技术可将非天然氨基酸特异性地引入到细胞内目标蛋白的指定位点，利用非天然氨基酸中特殊的官能团赋予目标蛋白新的物理化学性质，最终达到蛋白质功能创新的目的。本文主要介绍基因密码子拓展技术中翻译工具开发和适配底盘改造研究相关的原理、技术和前沿进展，讨论其在蛋白质功能调控、生物医药、生物防控等新兴领域应用中的成果进展与未来展望。

关键词: 非天然氨基酸, 密码子拓展系统, 翻译工具, 适配底盘细胞, 正交性

CLC Number:

Q755

Xian FU, Tao LIN, Fan ZHANG, Huiming ZHANG, Wenwei ZHANG, Huanming YANG, Shida ZHU, Xun XU, Yue SHEN. Progress in the study of genetic code expansion related methods, principles and applications[J]. Synthetic Biology Journal, 2020, 1(1): 103-119.

付宪, 林涛, 张帆, 张惠铭, 章文蔚, 杨焕明, 朱师达, 徐讯, 沈玥. 基因密码子拓展技术的方法原理和前沿应用研究进展[J]. 合成生物学, 2020, 1(1): 103-119.

Figures/Tables 2

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Progress in the study of genetic code expansion related methods, principles and applications

基因密码子拓展技术的方法原理和前沿应用研究进展

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