由细菌XRE家族转录调节器结合的Palindromic图案的计算-实验识别
Linjia Wang1, Shitong Zhong1, Liangyan Wang1
1MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Life (Basel, Switzerland)
|October 29, 2025
概括
研究人员开发了一种计算方法来识别细菌的Xenobiotic Response Element (XRE) 转录调节器结合动机. 这种方法成功地预测并实验验证了许多XRE-DNA相互作用,进步了我们对细菌基因调节的理解.
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.
- 分子生物学分子生物学
背景情况:
- 细菌利用转录调节剂,如Xenobiotic Response Element (XRE) 家族,进行新陈代谢控制.
- XRE调节器经常二元化以结合平行体DNA基因,但它们的结合基因在大规模上没有很好的特征.
研究的目的:
- 开发一种有效的计算方法来识别细菌XRE转录调节器识别动机.
- 建立一个预测和验证XRE-DNA相互作用的框架.
主要方法:
- 利用螺旋转螺旋 (HTH) 域的XRE家族蛋白质 (n=27,732) 的结构对齐和序列扫描.
- 使用生物信息学工具 (MEME,motifStack) 来识别和集群潜在的DNA动机 (5622个动机,223个集群).
- 使用AlphaFold预测的蛋白质-DNA相互作用模型和通过电泳运动转移试验 (EMSAs) 验证的结合.
主要成果:
- 确定了5622个潜在的图案,分为223个组,并分为7个主要类型.
- 计算预测经过实验验证,10个测试的XRE-DNA相互作用中有9个被EMSA证实.
- 该研究建立了一个可靠的计算框架,用于XRE模式识别.
结论:
- 开发的计算框架有效地识别了XRE家族的转录调节器识别动机.
- 实验验证证证实了计算预测的高准确性,为细菌基因调节提供了洞察力.
- 虽然计算方法很强大,但实验验证对于确定生物相互作用至关重要.
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