进化视角下的定量生物学规律与人工生命合成

赵晓宇; 张浩; 李雪飞; 胡政

doi:10.12211/2096-8280.2021-092

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进化视角下的定量生物学规律与人工生命合成

特约评述 | 更新时间：2025-03-20

- 进化视角下的定量生物学规律与人工生命合成
- An evolutionary perspective on quantitative biological principles and synthetic life design
- 合成生物学 2022年3卷第1期页码：6-21
- 作者机构：
  
  1.中国科学院深圳先进技术研究院，深圳合成生物学创新研究院，广东深圳 518055
  2.中国科学院大学，北京 100049
- 作者简介：
  
  [ "赵晓宇（1999—），女，硕士研究生。主要研究方向为细菌与肿瘤。E-mail：xy.zhao1@siat.ac.cn" ]
  [ "胡政（1987—），男，研究员，博士生导师。研究方向为基因组学、进化生物学和定量生物学。E-mail：zheng.hu@siat.ac.cn" ]
- 基金信息：
  
  国家自然科学基金青年基金(32000886);广东省自然科学基金杰出青年基金(2021B1515020042);广东省自然科学基金面上项目(2114050001502)
- DOI：10.12211/2096-8280.2021-092
  中图分类号： Q812
- 收稿：2021-09-18，
  
  修回：2021-11-08，
  
  纸质出版：2022-02-28
- 稿件说明：
移动端阅览
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

ZHAO Xiaoyu， ZHANG Hao， LI Xuefei， HU Zheng. An evolutionary perspective on quantitative biological principles and synthetic life design［J］. Synthetic Biology Journal， 2022， 3（1）： 6-21
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 DOI： 10.12211/2096-8280.2021-092.

ZHAO Xiaoyu， ZHANG Hao， LI Xuefei， HU Zheng. An evolutionary perspective on quantitative biological principles and synthetic life design［J］. Synthetic Biology Journal， 2022， 3（1）： 6-21 DOI： 10.12211/2096-8280.2021-092.

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。

Abstract

Genetic evolution is a defining feature of all biological systems

whereby lives are able to adapt to the rapidly changing environments. Quantitative synthetic biology

an emerging field in life science

mainly studies how to apply synthetic biosystems to reveal quantitative biological rules

which in turn guides the rational design of synthetic life. Although such artificial biosystems are created in the laboratory

they are also governed by the rules of evolution

such as mutation

genetic drift

Darwinian selection

etc. However

the evolutionary potential of a synthetic biosystem might have been underrated

which often leads to the circuit failures or the emergence of undesigned function. Therefore

overcoming evolutionary perturbations is one of grand challenges in robust circuit design

and harnessing the rules of evolution would be important for more robust design of artificial biosystems. On the other hand

bottom-up synthetic systems provide favorable biological models to test and explore the evolutionary principles that are hard to study based on natural biosystems. In this review

we first summarize the current progress in screening functional proteins through continuous directed-evolution guided by the evolutionary principles. We assess advantages and disadvantages for different architectures in continuous directed-evolution through evolutionary perspective. We also review the evolutionary strategies that are used to improve the stability of synthetic circuits in host cells

including reducing mutation rate

the coupling of host cell fitness with target gene expression

synthetic addiction

compartmentalization

feedback control

orthogonal system

etc. Furthermore

we discuss how to use the synthetic biology approaches to address some basic theories in evolutionary biology

such as the origin of life

the development of multicellularity

genetic constraint and epistasis

and the evolutionary tradeoff of complex life system

etc. We believe that a real-time precise control of the evolutionary process would enhance the quantitative features and predictability in the field of synthetic biology

and greatly advance the applications of robust synthetic biosystems for human sustainable goals.

关键词

Keywords

references

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