Fuertes Miguel Angel, Rodrigo José Ramón, Alonso Carlos
Centro de Biología Molecular ''Severo Ochoa'' (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain.
Telefónica de España S.A., Gran Vía, 28, Madrid, Spain.
J Mol Evol. 2017 Jan;84(1):29-38. doi: 10.1007/s00239-016-9763-7. Epub 2016 Nov 3.
The analysis of a large number of human and mouse genes codifying for a populated cluster of transmembrane proteins revealed that some of the genes significantly vary in their primary nucleotide sequence inter-species and also intra-species. In spite of that divergence and of the fact that all these genes share a common parental function we asked the question of whether at DNA level they have some kind of common compositional structure, not evident from the analysis of their primary nucleotide sequence. To reveal the existence of gene clusters not based on primary sequence relationships we have analyzed 13574 human and 14047 mouse genes by the composon-clustering methodology. The data presented show that most of the genes from each one of the samples are distributed in 18 clusters sharing the common compositional features between the particular human and mouse clusters. It was observed, in addition, that between particular human and mouse clusters having similar composon-profiles large variations in gene population were detected as an indication that a significant amount of orthologs between both species differs in compositional features. A gene cluster containing exclusively genes codifying for transmembrane proteins, an important fraction of which belongs to the Rhodopsin G-protein coupled receptor superfamily, was also detected. This indicates that even though some of them display low sequence similarity, all of them, in both species, participate with similar compositional features in terms of composons. We conclude that in this family of transmembrane proteins in general and in the Rhodopsin G-protein coupled receptor in particular, the composon-clustering reveals the existence of a type of common compositional structure underlying the primary nucleotide sequence closely correlated to function.
对大量编码跨膜蛋白密集簇的人类和小鼠基因进行分析后发现，其中一些基因在种间以及种内的一级核苷酸序列上存在显著差异。尽管存在这种差异，且所有这些基因都具有共同的亲本功能，但我们还是提出了一个问题：在DNA水平上，它们是否具有某种共同的组成结构，而这种结构从其一级核苷酸序列分析中并不明显。为了揭示不基于一级序列关系的基因簇的存在，我们采用组成聚类方法分析了13574个人类基因和14047个小鼠基因。所呈现的数据表明，每个样本中的大多数基因分布在18个簇中，特定人类和小鼠簇之间具有共同的组成特征。此外，还观察到，在具有相似组成谱的特定人类和小鼠簇之间，检测到基因群体存在很大差异，这表明两个物种之间大量的直系同源基因在组成特征上存在差异。还检测到一个仅包含编码跨膜蛋白基因的基因簇，其中很大一部分属于视紫红质G蛋白偶联受体超家族。这表明，尽管其中一些基因显示出低序列相似性，但在组成方面，两个物种中的所有这些基因都具有相似的组成特征。我们得出结论，在这个跨膜蛋白家族中，特别是在视紫红质G蛋白偶联受体中，组成聚类揭示了一种与功能密切相关的、位于一级核苷酸序列之下的共同组成结构的存在。
