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真菌王国绒泡菌调控因子的系统发生基因组学分析。

Phylogenomics analysis of velvet regulators in the fungal kingdom.

机构信息

School of Food Science and Biotechnology, Kyungpook National University, Daegu, South Korea.

Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA.

出版信息

Microbiol Spectr. 2024 Feb 6;12(2):e0371723. doi: 10.1128/spectrum.03717-23. Epub 2024 Jan 5.

Abstract

All life forms have evolved to respond appropriately to various environmental and internal cues. In the animal kingdom, the prototypical regulator class of such cellular responses is the Rel homology domain proteins including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Fungi, the close relatives of animals, have also evolved with their own NF-κB-like regulators called velvet family proteins to govern cellular and chemical development. Here, we conducted a detailed investigation of the taxonomic broad presence of velvet proteins. We observed that velvet proteins are widely distributed in the fungal kingdom. Moreover, we have identified and characterized 21 major velvet clades in fungi. We have further revealed that the highly conserved velvet domain is composed of three distinct motifs and acts as an evolutionarily independent domain, which can be shuffled with various functional domains. Such rearrangements of the velvet domain have resulted in the functional and type diversity of the present velvet regulators. Importantly, our in-deep analyses of the primary and 3D structures of the various velvet domains showed that the fungal velvet domains can be divided into two major clans: the VelB and the VosA clans. The 3D structure comparisons revealed a close similarity of the velvet domain with many other eukaryotic DNA-binding proteins, including those of the Rel, Runt, and signal transducer and activator of transcription families, sharing a common β-sandwich fold. Altogether, this study improves our understanding of velvet regulators in the fungal kingdom.IMPORTANCEFungi are the relatives of animals in Opisthokonta and closely associated with human life by interactive ways such as pathogenicity, food, and secondary metabolites including beneficial ones like penicillin and harmful ones like the carcinogenic aflatoxins. Similar to animals, fungi have also evolved with NF-κB-like velvet family regulators. The velvet proteins constitute a large protein family of fungal transcription factors sharing a common velvet domain and play a key role in coordinating fungal secondary metabolism, developmental and differentiation processes. Our current understanding on velvet regulators is mostly from Ascomycota fungi; however, they remain largely unknown outside Ascomycota. Therefore, this study performed a taxonomic broad investigation of velvet proteins across the fungal kingdom and conducted a detailed analysis on velvet distribution, structure, diversity, and evolution. The results provide a holistic view of velvet regulatory system in the fungal kingdom.

摘要

所有生命形式都进化到能够对各种环境和内部线索做出适当反应。在动物王国中,这种细胞反应的典型调节类蛋白是 Rel 同源结构域蛋白,包括核因子 kappa-轻链增强子的 B 细胞(NF-κB)。真菌是动物的近亲,它们也进化出了自己的 NF-κB 样调节剂,称为 velvet 家族蛋白,以控制细胞和化学发育。在这里,我们对 velvet 蛋白在真菌界的广泛存在进行了详细的研究。我们观察到 velvet 蛋白在真菌界广泛分布。此外,我们已经鉴定并描述了真菌中的 21 个主要 velvet 分支。我们还进一步揭示了高度保守的 velvet 结构域由三个不同的基序组成,并且作为一个独立进化的结构域,可以与各种功能结构域重组。这种 velvet 结构域的重排导致了现有 velvet 调节剂的功能和类型多样性。重要的是,我们对各种 velvet 结构域的一级和 3D 结构的深入分析表明,真菌的 velvet 结构域可以分为两大族:VelB 和 VosA 族。3D 结构比较表明,velvet 结构域与许多其他真核 DNA 结合蛋白非常相似,包括 Rel、Runt 和信号转导和转录激活因子家族的蛋白,它们具有共同的β-三明治折叠。总之,这项研究提高了我们对真菌王国中 velvet 调节剂的认识。

重要性真菌是后生动物界(Opisthokonta)的动物近亲,通过致病性、食物和次级代谢物(包括有益的青霉素和有害的黄曲霉毒素)等相互作用方式与人类生活密切相关。与动物一样,真菌也进化出了与 NF-κB 类似的 velvet 家族调节剂。velvet 蛋白是真菌转录因子的一个大家族,它们共享一个共同的 velvet 结构域,在协调真菌次级代谢、发育和分化过程中起着关键作用。我们目前对 velvet 调节剂的了解主要来自子囊菌真菌;然而,它们在子囊菌之外的真菌中仍然知之甚少。因此,本研究对真菌界的 velvet 蛋白进行了广泛的分类学调查,并对 velvet 分布、结构、多样性和进化进行了详细分析。研究结果提供了真菌王国 velvet 调控系统的整体视图。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a77f/10845976/7becda1056b3/spectrum.03717-23.f001.jpg

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