使用新的基于网络的工具RepRanger,对在细菌和古生物中发现的重复性外原性帕林德罗姆序列进行了全面分析
Oleg N Murashko1, Connor Morgan-Lang2, Chen-Hsin Albert Yu1
1Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
mSphere
|July 7, 2025
概括
重复的外原性帕林德罗姆序列 (REP) 是细菌适应的关键. 一个名为RepRanger的新工具识别了这些REP序列在细菌和古生物中,揭示了它们的多样化作用和保护.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 微生物学 微生物学
背景情况:
- 在细菌的基因间区域中发现了重复的外基因帕林德罗姆 (REP) 序列,但它们的功能和保存尚未完全理解.
- 目前用于识别REP序列的工具有限,尽管微生物基因组数据不断增加,但这阻碍了研究.
研究的目的:
- 开发RepRanger,这是一个基于Web的新平台,用于快速识别和注释包括REP在内的palindromic元素.
- 研究REPs在细菌和古生物中的生物学作用,序列保存和多样性.
主要方法:
- 开发用于REP序列识别的RepRanger网络平台.
- 对大肠杆菌MG1655中的REP序列的分析,包括它们与小非编码RNA (sRNA) 的关联.
- 在不同的大肠杆菌菌株和其他细菌和古生物基因组中对REP基因进行比较分析.
主要成果:
- RepRanger在大肠杆菌MG1655中发现了4000多个REP,其中52%在小非编码RNA (sRNA) 中发现.
- 确定了十个REP共识动机,与翻译控制和sRNA相关的独特动机.
- 发现REPs在致病性,环境和共生性大肠杆菌 (E. coli) 中保存,并且存在于具有序列相似性的细菌和古生物中.
结论:
- RepRanger是一个多功能工具,用于在各种 prokaryotic 基因组中发现 REP.
- REPs可能在细菌适应中发挥重要作用,特别是通过它们与调节代谢途径的sRNA的关联.
- 这项研究为REPs在细菌和古生物学中的功能多样性和序列保护提供了新的见解.
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