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IsoPairFinder:一种使用稳定同位素追踪代谢学来发现生化途径的工具

Zhiwei Zhou¹, Yuanyuan Liu¹, Mingxun Wang²

¹Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

bioRxiv : the preprint server for biology

|September 2, 2025

概括

通过稳定同位素追踪 (SIT) 代谢和基因编辑识别微生物中的代谢途径中间体. 这有助于研究人员更有效地发现和验证微生物代谢途径.

科学领域:

微生物学
代谢学
系统生物学

背景情况:

微生物基因和代谢途径的功能注释落后于基因组测序.
稳定同位素追踪 (SIT) 代谢学与基因操纵相结合显示出途径发现的前景.
现有的计算工具缺乏分析基因扰动实验的专业能力.

研究的目的:

开发一个计算工具,IsoPairFinder,用于识别代谢途径中间体.
来自基因编辑微生物的配对未标记 (12C) 和同位素标记 (13C) 代谢组数据的分析.
加速发现和验证新的微生物代谢途径.

主要方法:

开发了一个开源的R软件包IsoPairFinder.
分析基因编辑微生物的未标记 (12C) 和13C标记的代谢组数据.
优先考虑基质特征对,以确定生物相关的中间体.
整合到GNPS2生态系统中的IsoPairFinder.

主要成果:

通过分析配对的代谢学数据,IsoPairFinder有效地识别路径中间体.
该工具根据基质的特异性优先考虑生物相关的中间体.
为研究人员提供一个可访问的平台来进行途径发现.

结论:

IsoPairFinder解决了微生物基因扰乱代谢学的专门工具的需求.
促进了微生物代谢途径的加速发现和验证.
通过计算分析增强对微生物代谢的理解.

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