保守的 A 到 I RNA 编辑与非保守的重新编码扩大了功能性编辑位点的候选范围。

IF 2.4 4区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Fly Pub Date : 2024-12-01 Epub Date: 2024-06-18 DOI:10.1080/19336934.2024.2367359
Yuange Duan, Ling Ma, Tianyou Zhao, Jiyao Liu, Caiqing Zheng, Fan Song, Li Tian, Wanzhi Cai, Hu Li
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引用次数: 0

摘要

腺苷-肌苷(A-to-I)RNA 编辑对基因组进行重新编码,赋予生物适应环境的灵活性。人们认为,RNA 重编码位点非常适合通过在时间和空间上增加蛋白质组的多样性来促进适应性进化。一些保守的重编码位点的功能和重要性已得到公认。然而,实验发现的功能位点只占总位点的一小部分,因此仍需要利用生物信息学方法来扩大这些功能位点的范围。在这项研究中,我们定义了一类新的RNA编辑位点,称为 "保守编辑与非保守重编码",并在果蝇编辑组中系统地鉴定了这类位点,在种间和种内水平上弄清了它们的选择压力和适应信号。令人惊讶的是,果蝇中具有非保守重编码的保守编辑位点并没有受到抑制,甚至还略有高出。在进化过程中,导致这种情况的DNA突变也受到青睐,这表明在不同物种中,这些重编码事件的功能可能是分化、特化和保持的。最后,结构预测表明,钾通道 Shab 中的这种重编码可能会增加离子通透性并补偿低温效应。总之,带有非保守重编码的保守编辑也可能具有功能性。我们的研究为考虑 RNA 编辑位点的适应性进化提供了新的视角,同时也扩大了功能性重编码位点的候选范围,为未来的验证提供了可能。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

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来源期刊
Fly
Fly 生物-生化与分子生物学
CiteScore
2.90
自引率
0.00%
发文量
17
审稿时长
>12 weeks
期刊介绍: Fly is the first international peer-reviewed journal to focus on Drosophila research. Fly covers a broad range of biological sub-disciplines, ranging from developmental biology and organogenesis to sensory neurobiology, circadian rhythm and learning and memory, to sex determination, evolutionary biology and speciation. We strive to become the “to go” resource for every researcher working with Drosophila by providing a forum where the specific interests of the Drosophila community can be discussed. With the advance of molecular technologies that enable researchers to manipulate genes and their functions in many other organisms, Fly is now also publishing papers that use other insect model systems used to investigate important biological questions. Fly offers a variety of papers, including Original Research Articles, Methods and Technical Advances, Brief Communications, Reviews and Meeting Reports. In addition, Fly also features two unconventional types of contributions, Counterpoints and Extra View articles. Counterpoints are opinion pieces that critically discuss controversial papers questioning current paradigms, whether justified or not. Extra View articles, which generally are solicited by Fly editors, provide authors of important forthcoming papers published elsewhere an opportunity to expand on their original findings and discuss the broader impact of their discovery. Extra View authors are strongly encouraged to complement their published observations with additional data not included in the original paper or acquired subsequently.
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