Novikova Olga, Jayachandran Pradeepa, Kelley Danielle S, Morton Zachary, Merwin Samantha, Topilina Natalya I, Belfort Marlene
Department of Biological Sciences and RNA Institute, University at Albany.
Department of Biomedical Sciences, School of Public Health, University at Albany.
Mol Biol Evol. 2016 Mar;33(3):783-99. doi: 10.1093/molbev/msv271. Epub 2015 Nov 25.
Inteins, also called protein introns, are self-splicing mobile elements found in all domains of life. A bioinformatic survey of genomic data highlights a biased distribution of inteins among functional categories of proteins in both bacteria and archaea, with a strong preference for a single network of functions containing replisome proteins. Many nonorthologous, functionally equivalent replicative proteins in bacteria and archaea carry inteins, suggesting a selective retention of inteins in proteins of particular functions across domains of life. Inteins cluster not only in proteins with related roles but also in specific functional units of those proteins, like ATPase domains. This peculiar bias does not fully fit the models describing inteins exclusively as parasitic elements. In such models, evolutionary dynamics of inteins is viewed primarily through their mobility with the intein homing endonuclease (HEN) as the major factor of intein acquisition and loss. Although the HEN is essential for intein invasion and spread in populations, HEN dynamics does not explain the observed biased distribution of inteins among proteins in specific functional categories. We propose that the protein splicing domain of the intein can act as an environmental sensor that adapts to a particular niche and could increase the chance of the intein becoming fixed in a population. We argue that selective retention of some inteins might be beneficial under certain environmental stresses, to act as panic buttons that reversibly inhibit specific networks, consistent with the observed intein distribution.
内含肽，也被称为蛋白质内含子，是在生命的所有领域中发现的自我剪接移动元件。对基因组数据的生物信息学调查突出了内含肽在细菌和古菌蛋白质功能类别中的偏向分布，强烈偏好包含复制体蛋白的单一功能网络。细菌和古菌中许多非直系同源、功能等效的复制蛋白都携带内含肽，这表明内含肽在生命各领域特定功能的蛋白质中具有选择性保留。内含肽不仅聚集在具有相关作用的蛋白质中，还聚集在这些蛋白质的特定功能单元中，如ATP酶结构域。这种特殊的偏向并不完全符合将内含肽完全描述为寄生元件的模型。在这类模型中，内含肽的进化动力学主要通过其与内含肽归巢内切核酸酶（HEN）的移动性来观察，HEN是内含肽获得和丢失的主要因素。虽然HEN对于内含肽在群体中的入侵和传播至关重要，但HEN的动力学并不能解释观察到的内含肽在特定功能类别蛋白质中的偏向分布。我们提出，内含肽的蛋白质剪接结构域可以作为一种环境传感器，适应特定的生态位，并可能增加内含肽在群体中固定的机会。我们认为，在某些环境压力下，一些内含肽的选择性保留可能是有益的，可作为应急按钮来可逆地抑制特定网络，这与观察到的内含肽分布一致。
