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在流量平衡分析中减轻生物质组成的不确定性,使用集体表示
Yoon-Mi Choi1,2, Dong-Hyuk Choi1, Yi Qing Lee1
1School of Chemical Engineering, Sungkyunkwan University, Suwon-si, Gyeonggi-do, Republic of Korea.
Computational and structural biotechnology journal
|August 7, 2023
概括
基因组规模代谢模型 (GEMs) 中的细胞生物质方程因条件而异. 综合生物质表示通过考虑这些自然变化来改善流量平衡分析 (FBA) 预测.
科学领域:
- 系统生物学 系统生物学
- 代谢工程是代谢工程.
- 计算生物学 计算生物学
背景情况:
- 基因组规模代谢模型 (GEMs) 在流量平衡分析 (FBA) 中使用生物质方程作为客观函数.
- 细胞的宏分子组成可以在不同的环境条件下发生变化,从而质疑单一生物质方程的使用.
- 这种变化需要重新评估FBA中的生物质方程假设.
研究的目的:
- 为了研究关键宿主生物体在不同条件下的宏分子组成的变化.
- 评估这些变化对FBA预测的影响.
- 为FBA中生物质代表性提出一个改进的方法.
主要方法:
- 对大分子组成 (RNA,蛋白质,脂质) 和单体单位 (核酸,氨基酸) 在大肠杆菌,谷类菌和灰色菌中的分析.
- 使用FBA中的单个与集合生物质方程进行流量预测的比较.
- 对FBA预测对宏分子和单体化合物的敏感度的评估.
主要成果:
- 宏分子组合 (RNA,蛋白质,脂质) 在各种条件中显示出显著的变化,而单体组合则保持相对稳定.
- FBA流量预测对宏分子组成的变化敏感,但对单体组成的变化不敏感.
- 综合生物质表示提高了通过合成反应预测流量的准确性.
结论:
- 细胞的宏分子组成是条件依赖的,影响FBA的准确性.
- 集合生物质方程为在不同条件下建模细胞代谢提供了更强大的方法.
- 这项研究强调了需要在FBA中纳入动态生物质表示,以避免模拟不准确.
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