Genomic Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
Research Laboratory and Department of Microbiology, Nordland Hospital Trust, 8005 Bodø, Norway.
Genes (Basel). 2022 May 25;13(6):944. doi: 10.3390/genes13060944.
Group I introns are mobile genetic elements encoding self-splicing ribozymes. Group I introns in nuclear genes are restricted to ribosomal DNA of eukaryotic microorganisms. For example, the myxomycetes, which represent a distinct protist phylum with a unique life strategy, are rich in nucleolar group I introns. We analyzed and compared 75 group I introns at position 516 in the small subunit ribosomal DNA from diverse and distantly related myxomycete taxa. A consensus secondary structure revealed a conserved group IC1 ribozyme core, but with a surprising RNA sequence complexity in the peripheral regions. Five S516 group I introns possess a twintron organization, where a His-Cys homing endonuclease gene insertion was interrupted by a small spliceosomal intron. Eleven S516 introns contained direct repeat arrays with varying lengths of the repeated motif, a varying copy number, and different structural organizations. Phylogenetic analyses of S516 introns and the corresponding host genes revealed a complex inheritance pattern, with both vertical and horizontal transfers. Finally, we reconstructed the evolutionary history of S516 nucleolar group I introns from insertion of mobile-type introns at unoccupied cognate sites, through homing endonuclease gene degradation and loss, and finally to the complete loss of introns. We conclude that myxomycete S516 introns represent a family of genetic elements with surprisingly dynamic structures despite a common function in RNA self-splicing.
I 类内含子是编码自我剪接核酶的移动遗传元件。真核微生物核基因中的 I 类内含子局限于核糖体 DNA。例如，黏菌代表了一个独特的原生生物门，具有独特的生活策略，富含核仁 I 类内含子。我们分析和比较了来自不同和远缘黏菌类群的小亚基核糖体 DNA 位置 516 的 75 个 I 类内含子。一个共识的二级结构揭示了保守的 IC1 核酶核心，但在周边区域具有惊人的 RNA 序列复杂性。五个 S516 类内含子具有双内含子组织，其中一个 His-Cys 归巢内切核酸酶基因插入被一个小剪接体内含子中断。11 个 S516 内含子包含具有不同重复基序长度、重复拷贝数和不同结构组织的直接重复阵列。S516 内含子和相应宿主基因的系统发育分析揭示了一种复杂的遗传模式，既有垂直和水平转移。最后，我们通过移动型内含子在未占据的同源位点的插入、归巢内切核酸酶基因的降解和丢失，以及最终完全丢失内含子，重建了 S516 核仁 I 类内含子的进化历史。我们得出结论，尽管在 RNA 自我剪接方面具有共同的功能，但黏菌 S516 内含子代表了一类具有惊人动态结构的遗传元件。
