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对特定环境的基因组规模代谢模型的修改和分析:利用甲作为案例研究的微生物底盘

M A Kulyashov¹, R Hamilton², Y Afshin²

¹Department of Computational Biology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.

|December 19, 2024

概括

我们开发了一种计算工作流程,用于为非模型微生物 (如Methylotuvimicrobium alcaliphilum) 重建特定环境的基因组规模代谢模型 (CS-GSMs). 该工具有助于理解基因型-表型关系,并优化微生物平台的甲捕获和利用.

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:

特定环境的基因组规模模型 (CS-GSM) 重建整合了多个规模的数据,用于基因型-表型探索.
对非传统微生物来说,CS建模具有挑战性,阻碍了基础研究和应用研究.
甲基微生物 (Methylotuvimicrobium alcaliphilum 20Z^R) 是一种用于捕获和利用甲的关键微生物底盘.

研究的目的:

提供一个用户友好的计算工作流来重建和查询CS-GSMs.
通过使用集成的Python工具,简化非模型生物的CS-GSM开发.
通过使用来自M. alcaliphilum 20Z^R的多omics数据来验证工作流.

主要方法:

开发了一个图形用户界面,将COBRApy,EscherPy和RIPTiDe集成到BioUML平台中.
使用Jupyter笔记本用于自动化CS-GSM重建和查询.
使用基因表达数据优化了以前重建的全基因组代谢网络.

主要成果:

对M. alcaliphilum 20Z^R进行自动重建的CS-GSM显示了与手动策划的模型相似的结果.
该模型确定了基酶路径可逆性的潜在问题,并突出了在甲-甲酸盐节点上的碳分区.
对于甲酸盐脱酶 (fdhAB) 和甲氧化酶 (fae1-2) 同类物质的突变性实验验证实了模型的预测.

结论:

开发的计算工作流有效支持对非模型微生物的CS-GSM的重建和验证.
这项研究推进了M. alcaliphilum 20Z^R的C1代谢的基本知识.
工作流程有助于为生物技术和环境应用开发微生物平台.

关键词:

甲基otuvimicrobium alcaliphilum 20ZRR 20ZRR 20ZRR 甲基otuvimicrobium 20ZRR 20ZRR 20ZRR 20ZRR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 20ZR 特定背景的基因组规模代谢建模.使用甲的细菌利用甲.在这种情况下,甲醇缩会导致甲醇缩.

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