基于隐藏的马尔科夫模型的原生生物基因组空间挖掘揭示了复杂I的广泛蔓延及其潜在的进化方案
Akshay Shirsath1, Snehal V Khairnar1, Abhirath Anand1
1Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.
Genome biology and evolution
|August 12, 2025
概括
研究人员使用隐藏的马尔科夫模型追溯了原核生物中呼吸复合体I (C-I) 子单元的进化起源. 他们确定了多种C-I变体及其分布,揭示了进化途径,并通过等离子体传播.
科学领域:
- 生物化学 生化学
- 进化生物学 进化生物学
- 基因组学就是基因组学.
背景情况:
- 细胞反应往往形成相互依赖的途径,其中一些蛋白质组装成复合体.
- 呼吸系统复合物I (C-I),也称为NADH-氨酸氧降解酶 (Nuo),是一种大型膜蛋白复合物,对生物能学,氧化还原稳定和运输至关重要.
- 由于难以识别同类的原因,C-I的进化历史和亚单元祖先尚未得到充分理解.
研究的目的:
- 研究原核生物中呼吸复合体I子单元的进化起源和分布.
- 开发和应用一个敏感的计算工作流程来分析跨多种物种的C-I子单位分布.
- 阐明C-I的进化传播和潜在变体,包括辅助子单元.
主要方法:
- 利用定制隐藏的马尔科夫模型 (HMM) 配置文件来分析14个核心C-I (Nuo) 子单位的 prokaryotic 基因组空间.
- 开发并应用基于HMMER的工作流程,用于对Nuo子单元的全面注释和分析.
- 扩展了工作流程,以检查 prokaryotes 中的线粒体 C-I 辅助子单元.
主要成果:
- 建立了一个基于HMMER的敏感工作流来分析Nuo子单元,可适应类似的研究.
- 创建了Nuo子单位的第一个物种级分布图.
- 在大约11,000个物种中确定了多个C-I变异,其中51.2%具有完整的复杂性.
- 在等离子体上发现了C-I变体,这表明它在进化传播中的作用.
- 揭示了线粒体C-I辅助子单元的进化根源.
结论:
- 这项研究提供了C-I亚单元分布的全面描述,以及 prokaryotes 中可能的进化方案.
- 开发的计算工作流和Web应用程序是未来对C-I进化研究的宝贵资源.
- 了解C-I分布和进化对于生物能量学和细胞功能研究至关重要.
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