Celis Juan Sebastián, Edgell David R, Stelbrink Björn, Wibberg Daniel, Hauffe Torsten, Blom Jochen, Kalinowski Jörn, Wilke Thomas
Animal Ecology and Systematics, Justus Liebig University, Giessen, Hessen, Germany.
Corporation Center of Excellence in Marine Sciences CEMarin, Bogotá, Colombia.
PLoS One. 2017 Mar 9;12(3):e0173734. doi: 10.1371/journal.pone.0173734. eCollection 2017.
Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as 'homing'. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (Ka) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower Ka rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals.
I 组内含子和归巢内切酶基因（HEGs）是可移动遗传元件，能够侵入无内含子基因组中的靶序列。LAGLIDADG HEGs是最大的内切酶家族，在I组内含子通过一种称为“归巢”的过程进行移动中起关键作用。I组内含子和HEGs在后生动物中很少见，主要可发现插入在一些海绵动物和刺胞动物的COXI基因中，包括石珊瑚（石珊瑚目）和蘑菇珊瑚（珊瑚藻目）。垂直和水平内含子转移机制已被提出作为刺胞动物中内含子出现的解释。然而，LAGLIDADG基序在内含子移动机制中的核心作用仍知之甚少。为了解决关于I组内含子和HEGs在石珊瑚目和珊瑚藻目中的进化起源和分布的问题，我们在一个全面的系统发育框架内检查了内含子/HEGs序列。对LAGLIDADG基序保守性的分析表明，在复杂的石珊瑚目和珊瑚藻目中有高度的降解。此外，这两个基序缺乏金属离子结合和催化所需的各自酸性残基，可能会损害水平内含子移动。相比之下，这两个基序在强壮的石珊瑚目中高度保守，表明存在一种能够促进水平内含子转移的功能完整的内切酶。在复杂的石珊瑚目和珊瑚藻目的HEGs中检测到较高的非同义替换率（Ka），表明HEG发生了降解，而在强壮的石珊瑚目中较低的Ka率与纯化选择的情况一致。分子钟分析和内含子类型的祖先推断表明，与强壮的石珊瑚目相比，复杂的石珊瑚目和珊瑚藻目中的内含子插入更早。这些发现表明，前两组中缺乏水平内含子转移与内切酶活性的年龄依赖性降解有关。此外，它们还解释了石珊瑚和蘑菇珊瑚中内含子独特的地理分布模式。
