Advances and prospects in genome-scale models of yeast

LI Yongzhu; CHEN Yu

doi:10.12211/2096-8280.2024-084

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Advances and prospects in genome-scale models of yeast

Invited Review | 更新时间：2025-07-07

- Advances and prospects in genome-scale models of yeast
- Synthetic Biology Journal Vol. 6, Issue 3, Pages: 585-602(2025)
- 作者机构：
  
  1.中国科学院深圳先进技术研究院，定量合成生物学全国重点实验室，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：
- 基金信息：
- DOI：10.12211/2096-8280.2024-084
  CLC： Q819
- Received：02 December 2024，
  
  Revised：2025-02-20，
  
  Published：30 June 2025
- 稿件说明：
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李永珠，陈禹. 酵母基因组规模模型进展及发展趋势［J］. 合成生物学， 2025， 6（3）： 585-602

LI Yongzhu， CHEN Yu. Advances and prospects in genome-scale models of yeast［J］. Synthetic Biology Journal， 2025， 6（3）： 585-602
李永珠，陈禹. 酵母基因组规模模型进展及发展趋势［J］. 合成生物学， 2025， 6（3）： 585-602 DOI： 10.12211/2096-8280.2024-084.

LI Yongzhu， CHEN Yu. Advances and prospects in genome-scale models of yeast［J］. Synthetic Biology Journal， 2025， 6（3）： 585-602 DOI： 10.12211/2096-8280.2024-084.

摘要

酵母作为常用的真核模式生物，在合成生物学和系统生物学研究中具有重要地位。然而，由于其代谢系统较为复杂，进行代谢网络研究和设计时存在一定困难，因此，研究人员提出了基因组规模的建模方法，利用基因组序列及注释信息，整合细胞内复杂的代谢反应和细胞过程，模拟细胞系统各部分的相互作用，得到对应的表型、功能和行为，辅助寻找代谢工程改造靶点，为理解复杂细胞系统提供了强有力的工具。本文介绍了基因组规模模型中传统代谢模型及整合多种生理学约束和多种细胞过程的模型的构建和分析方法，回顾了酵母属中多种酵母基因组规模模型的发展历程及主要应用，并基于此分析了当前酵母基因组规模模型研究中面临的主要问题，提出了提升模型准确率以及未来进一步优化模型的方法和趋势。

Abstract

Yeasts

particularly

Saccharomyces cerevisiae

are widely used eukaryotic organisms with relatively clear cellular structures and metabolic networks

and their cellular processes exhibit a certain degree of conservation among eukaryotes. These organisms play a crucial role in research with synthetic biology and systems biology as well. However

due to the complexity of their metabolic networks and the variability of cellular activities

study and design of pathways for yeasts still present considerable challenges. To address these issues

researchers have developed genome-scale models

which are mathematical framework that integrates genomic

biochemical

and physiological data to simulate cellular processes and predict the relationship between genotype and phenotype

which are further used to simulate cellular functions and predict cell behaviors under different conditions

providing a systematic approach for understanding and engineering biological systems. This review introduces methods for building and analyzing genome-scale models of yeasts

including traditional metabolic models and their derived multi-constraint and multi-process models. It also traces the development of yeast models over time. Furthermore

this article discusses recent applications of yeast models in areas such as designing yeasts as cell factories for producing valuable compounds

studying microbial physiology

optimizing cultivation conditions

and simulating microbial community interactions. These models also provide insights into identifying potential metabolic engineering targets for optimizing cellular functions. Despite the advantages of the genome-scale models

their develo

pment and application are still limited in several aspects

such as incomplete data on metabolic pathways

limited focus on secondary metabolism

and high barriers to use

particularly for users without programming backgrounds. This review proposes several strategies to address these challenges. To enhance the development of traditional models

it is crucial to incorporate more comprehensive datasets

with a particular emphasis on secondary metabolism and metabolic dark matters. Additionally

improving the accessibility of models requires the development of user-friendly platforms

the provision of clear and standardized tutorials. These strategies can lower barriers for users

and promote applications of the genome-scale models.

关键词

Keywords

references

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