Di Giulio Massimo
Laboratory for Molecular Evolution, Institute of Genetics and Biophysics 'Adriano Buzzati Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Napoli, Italy.
Gene. 2008 Dec 15;426(1-2):39-46. doi: 10.1016/j.gene.2008.07.024. Epub 2008 Jul 29.
The paradigm of the monophyletic origin of genes is deeply rooted in us all. For instance, this stems from the observation that the possibility of obtaining a good multiple alignment using the same protein from organisms from the three domains of life (Bacteria, Archaea and Eukarya) would seem to imply that the last universal common ancestor (LUCA) must have had that protein and, therefore, the origin of that gene must necessarily be monophyletic. The hypothesis of a polyphyletic origin of genes has to explain how it was possible to evolve highly conserved regions of multiple alignments of orthologous proteins from the three domains of life when these regions clearly seem to define a monophyletic origin of genes. If mRNAs were assembled at the stage of the LUCA through the trans-splicing of pieces of RNA representing mini-genes, and the translation of these mRNAs resulted in proteins whose genes (DNA) actually only evolved much later, i.e. only after the main domains of life were established, then this would explain why multiple alignments of orthologous proteins can be obtained from the three domains of life. Therefore, this makes these multiple alignments compatible with a polyphyletic origin of genes. I have analysed many multiple alignments of orthologous proteins from the three domains of life, reaching a conclusion that seems to suggest that these alignments are also compatible with a polyphyletic origin of genes because, for instance, they contain protein motifs characterising the domains of life. These motifs, and also genes, might have evolved late on, thus making their polyphyletic origin likely.
基因单系起源的范式在我们所有人心中都根深蒂固。例如，这源于这样的观察：使用来自生命三个域（细菌、古菌和真核生物）的生物体中的同一种蛋白质获得良好的多重比对的可能性，似乎意味着最后的共同祖先（LUCA）必定拥有该蛋白质，因此，该基因的起源必定是单系的。基因多系起源的假说必须解释，当这些区域明显似乎定义了基因的单系起源时，如何能够从生命的三个域中进化出直系同源蛋白质多重比对的高度保守区域。如果mRNA在LUCA阶段是通过代表小基因的RNA片段的反式剪接组装而成，并且这些mRNA的翻译产生的蛋白质，其基因（DNA）实际上是在很久之后才进化出来的，也就是说，仅在生命的主要域建立之后才进化出来，那么这将解释为什么可以从生命的三个域中获得直系同源蛋白质的多重比对。因此，这使得这些多重比对与基因的多系起源相兼容。我分析了来自生命三个域的许多直系同源蛋白质的多重比对，得出的结论似乎表明这些比对也与基因的多系起源相兼容，因为例如它们包含表征生命域的蛋白质基序。这些基序以及基因可能是后来才进化出来的，因此使得它们的多系起源成为可能。
