Designing, building and rapid prototyping of biosynthesis module based on cell-free system

TANG Shiming; HU Jiyuan; ZHENG Suiping; HAN Shuangyan; LIN Ying

doi:10.12211/2096-8280.2022-024

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Designing, building and rapid prototyping of biosynthesis module based on cell-free system

Invited Review | 更新时间：2026-01-19

- Designing, building and rapid prototyping of biosynthesis module based on cell-free system
- Synthetic Biology Journal Vol. 3, Issue 6, Pages: 1250-1261(2022)
- 作者机构：
  
  华南理工大学，生物科学与工程学院，广东广州 510006
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2022-024
  CLC： Q816
- Received：21 April 2022，
  
  Revised：2022-09-06，
  
  Published：31 December 2022
- 稿件说明：
移动端阅览
唐士茗，胡纪元，郑穗平，韩双艳，林影. 基于无细胞体系的生物合成代谢模块设计、构建与快速途径原型［J］. 合成生物学， 2022， 3（6）： 1250-1261

TANG Shiming， HU Jiyuan， ZHENG Suiping， HAN Shuangyan， LIN Ying. Designing， building and rapid prototyping of biosynthesis module based on cell-free system［J］. Synthetic Biology Journal， 2022， 3（6）： 1250-1261
唐士茗，胡纪元，郑穗平，韩双艳，林影. 基于无细胞体系的生物合成代谢模块设计、构建与快速途径原型［J］. 合成生物学， 2022， 3（6）： 1250-1261 DOI： 10.12211/2096-8280.2022-024.

TANG Shiming， HU Jiyuan， ZHENG Suiping， HAN Shuangyan， LIN Ying. Designing， building and rapid prototyping of biosynthesis module based on cell-free system［J］. Synthetic Biology Journal， 2022， 3（6）： 1250-1261 DOI： 10.12211/2096-8280.2022-024.

摘要

随着代谢工程及合成生物学技术的发展，化学品高效生物合成与绿色制造成为可能。高效生物合成体系的设计与构建是绿色生物制造的核心，其理论体系建立及关键技术突破，将为实现绿色生物制造领域高效生产及资源与环境可持续发展提供有力支撑。本文借助代谢途径模块设计的案例，探讨化合物生物合成过程中潜在通用模块设计原则、设计工具，以及基于无细胞蛋白合成体系的代谢模块快速构建及测试的方法，将突破生物合成途径多基因、多模块“设计-构建-测试”（Design-Build-Test cycle，DBT cycle）高效循环迭代的技术瓶颈。结合机器学习方法的应用，将使“设计-构建-测试”向“设计-构建-测试-学习”（Design-Build-Test-Learn cycle，DBTL cycle）进一步延伸，对高效合成模块的“精准-鲁棒性”设计与构建、推动合成生物学科学与技术发展具有重要意义。

Abstract

Bio-based chemical production has drawn attention regarding the realization of a sustainable society. With the development of metabolic engineering and synthetic biology

it is possible to make more efficient biosynthesis and scale-up commercial production of useful metabolites by metabolic pathway modification. Usually

some microorganisms are utilized as platforms by increasing the expression of desired genes and/or decreasing

that of undesired genes. Precise control of natural metabolism is

however

still challenging due to the complicated regulatory architecture at the levels of transcription

translation

and post-translation. Hence

various strategies of design and construction of biosynthesis modules have been proposed to optimize and expedite the design-build-test cycles of developing biosynthetic system for renewable chemical synthesis

in vitro

to avoid laborious and expensive ways for the optimization of metabolism pathway

strain and biocatalysts for each new product. In this review

we discuss the strategies of modules design and their rapid prototyping based on cell-free protein synthesis for assembling biosynthetic pathway

in vitro

. Biosynthetic modules could b

e sets of enzymes that catalyze a cascade reaction for a specific purpose or chemical

containing the conversion of starting materials to intermediary metabolites

biosynthesis of target products from the intermediates

cofactor balance and phosphorylation. Enzymes from distinct sources can be combined to construct desired reaction cascades with fewer biological constraints in one vessel

enabling easier pathway design with high modularity. Multiple modules could then been designed by different groups for different purpose with the help of metabolic pathway database

computational design tool and some general module design rules. Cell-free protein synthesis was here utilized to build and rapidly prototype the functionality of biosynthesis pathway and module. The further application of machine learning methods might also contribute to better “precision-robustness” design and construction of these modules. This process is also called cell-free pathway engineering which has been proved to be a powerful and flexible enabling technology

providing simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system.

关键词

Keywords

references

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