通过深度学习支持的元基因组挖掘,探索核糖体在 prokaryote-phage 相互作用中的作用
Ying Gao1, Zheng Zhong1, Dengwei Zhang1
1CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China.
Microbiome
|May 24, 2024
概括
我们在海洋生态系统中发现了新的微生物,称为核糖体合成和翻译后修饰 (RiPPs). 这些RiPP与细菌和病毒之间的相互作用有关,揭示了它们的生态作用.
科学领域:
- 微生物学 微生物学
- 转基因组学是指转基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 微生物的二次代谢产物,包括核糖体合成和翻译后改性 (RiPPs),在环境相互作用中至关重要.
- RiPPs具有结构多样性和功能多样性,具有潜在的治疗应用,但其生物合成能力和生态作用在很大程度上是未知的.
- 海洋微生物组在化学上仍未得到充分探索,但它拥有丰富的微生物相互作用的多样化生物组.
研究的目的:
- 探索海洋元基因组中的RiPPs的生物合成概况.
- 研究RiPPs在海洋生态系统中的微生物-病毒相互作用中的潜在作用.
- 发现新的RiPP家族,了解它们的生态功能.
主要方法:
- 开发TrRiPP,这是一种深度学习方法,用于在元基因组数据中标志性基因独立的RiPP前体检测.
- 将TrRiPP应用于全球海洋元基因组,以识别新的RiPP家族.
- 对元转录组数据的相关性分析,以将RiPP与菌素相关蛋白联系起来.
- 构建一个海洋病毒数据库 (OVD) 和一个涉及RiPP的宿主-菌体交互网络.
主要成果:
- 从海洋元基因组中识别出各种各样的新型,未经表征的假定RiPP家族.
- 观察RiPP家族和抗/相关蛋白家族之间的共同表达,这表明它们在 prokaryote-phage 相互作用中的作用.
- 在涉及RiPP编码 prokaryotes,RiPPs 和病毒蛋白的宿主-菌体相互作用网络中的复杂连接的阐明.
结论:
- 对全球海洋微生物群中的RiPP生物合成潜力的系统研究揭示了重要的新奇性.
- RiPPs涉及 prokaryote-phage 相互作用和共同进化,为它们在海洋环境中的生态功能提供了关键的见解.
- 这项研究例证了在复杂微生物相互作用中探索细菌二次代谢物功能的研究.
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