Are Most Human-Specific Proteins Encoded by Long Noncoding RNAs?

IF 2.1 3区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Evolution Pub Date : 2024-08-01 Epub Date: 2024-06-25 DOI:10.1007/s00239-024-10174-z

Yves-Henri Sanejouand

引用次数: 0

Abstract

By looking for a lack of homologs in a reference database of 27 well-annotated proteomes of primates and 52 well-annotated proteomes of other mammals, 170 putative human-specific proteins were identified. While most of them are deemed uncertain, 2 are known at the protein level and 23 at the transcript level, according to UniProt. Interestingly, 23 of these 25 proteins are found to be encoded or to have close homologs in an open reading frame of a long noncoding human RNA. However, half of them are predicted to be at least 80% globular, with a single structural domain, according to IUPred, and with at least 80% of ordered residues, according to flDPnn. Strikingly, there is a near-complete lack of structural knowledge about these proteins, with no tertiary structure presently available in the Protein Data Bank and a fair prediction for one of them in the AlphaFold Protein Structure Database. Moreover, knowledge about the function of these possibly key proteins remains scarce.

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大多数人类特异性蛋白质都是由长非编码 RNA 编码的吗？

通过在参考数据库中寻找缺乏同源物的灵长类动物的 27 个完善注释的蛋白质组和其他哺乳动物的 52 个完善注释的蛋白质组，发现了 170 种推测的人类特异性蛋白质。根据 UniProt 的数据，虽然其中大部分被认为是不确定的，但有 2 个在蛋白质水平上是已知的，23 个在转录本水平上是已知的。有趣的是，在这 25 种蛋白质中，有 23 种在人类长非编码核糖核酸的开放阅读框中被编码或有近似的同源物。然而，根据 IUPred 预测，其中一半的蛋白质至少有 80% 是球状的，只有一个结构域，根据 flDPnn 预测，至少有 80% 的有序残基。令人吃惊的是，关于这些蛋白质的结构知识几乎完全缺乏，蛋白质数据库（Protein Data Bank）中目前没有三级结构，而 AlphaFold 蛋白结构数据库（AlphaFold Protein Structure Database）中对其中一种蛋白质的预测尚可。此外，有关这些可能是关键蛋白的功能的知识仍然匮乏。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Evolution 生物-进化生物学

CiteScore

5.50

自引率

2.60%

发文量

审稿时长

3 months

期刊介绍： Journal of Molecular Evolution covers experimental, computational, and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems through their evolution at the molecular level, the co-evolution of their functions in cellular and organismal systems, and their influence on organismal adaptation, speciation, and ecology. Topics addressed include the evolution of informational macromolecules and their relation to more complex levels of biological organization, including populations and taxa, as well as the molecular basis for the evolution of ecological interactions of species and the use of molecular data to infer fundamental processes in evolutionary ecology. This coverage accommodates such subfields as new genome sequences, comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA, molecular evolutionary ecology, and the development of methods and theory that enable molecular evolutionary inference, including but not limited to, phylogenetic methods.