功能预测来自人类肠道考古组的蛋白质
Polina V Novikova1, Susheel Bhanu Busi1,2, Alexander J Probst3
1Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg.
ISME communications
|March 15, 2024
概括
这项研究通过整合蛋白质序列和结构数据来提高功能注释,并识别新的肠道特异性蛋白质,从而提高对关键肠道古典体Methanobrevibacter smithii的理解.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 结构生物学 结构生物学
背景情况:
- 人的肠道有多种古老的社区,包括Methanobrevibacter smithii,这是一种重要的甲原体,与胃肠道疾病有关.
- 对M. smithii蛋白质的准确功能注释对于理解其在健康和疾病中的作用至关重要.
研究的目的:
- 通过整合序列和结构信息来改善M. smithii蛋白质的功能注释.
- 为了识别独特的肠特异性古老蛋白及其潜在的功能.
- 探索涉及M. smithii.的潜在水平基因转移事件.
主要方法:
- 使用了先进的蛋白质结构预测工具 (AlphaFold2,trRosetta) 和注释软件 (ProFunc,DeepFri).
- 分析了来自人类肠道的大量考古和细菌蛋白质数据集.
- 预测和特征的功能域和结构,考古蛋白质集群.
主要成果:
- 鉴定了707,754种仅在人类肠道中存在的古老蛋白质.
- 通过结合预测的结构,扩展基于序列的信息来改进蛋白质注释.
- 发现了肠道特定的古老蛋白质,可能与防御,毒性,粘附和排毒有关.
- 鉴定了潜在的糖系转移酶,并提供了从Clostridia物种水平基因转移的证据.
结论:
- 整合序列和结构数据显著增强了对肠道古生物的蛋白质功能预测,如M. smithii.
- 这项研究揭示了新的肠道特异性古老蛋白和肠道微生物组内的潜在相互作用机制.
- 这些发现有助于更深入地了解考古生物学及其临床相关性.
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