Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages
Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages
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DOI：
10.1186/s12862-019-1488-y
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发表时间：
2019-08-02
影响因子：
3.4
通讯作者：
Russell, Anthony G.
中科院分区：
文献类型：
--
作者：
Hudson, Andrew J.;McWatters, David C.;Russell, Anthony G.
两种剪接体内含子类型共存于真核生物前体mRNA中，并由不同的U2依赖性和U12依赖性剪接体切除。在蓝氏贾第鞭毛虫，小核（sn）RNA显示U2和U12依赖的剪接体snRNA的杂交特性和5的11个确定的剩余剪接体内含子的反式剪接。不寻常的内含子和剪接体特征是否在其他的单胞菌中是保守的还不清楚。结果我们从另外两个已获得基因组信息的螺旋体（Spironucleus vortens）和杀鲑螺旋体（Spironucleus salmonicida）及其近缘种中鉴定出剪接体内含子、snRNA和蛋白质，包括在S.漩涡。内含子剪接信号在螺核菌和G.兰布利亚。类似于“长”G。在Lamblia内含子中，RNA二级结构潜力对于“长”（> 50 nt）螺旋核内含子以及在副担子毛滴虫中鉴定的内含子是明显的。预测这些内含子内的碱基配对将剪接点之间的空间距离限制为在这些生物体中较短且大小均匀的内含子中所见的类似距离。我们发现，几个剩余的螺旋核剪接体内含子是古老的。我们从S中鉴定出了一个候选U2 snRNA。vortens和S.杀鲑纲;累积起来，说明在某些微藻纲内存在显著的snRNA差异。最后，我们研究了剪接体蛋白互补物，并发现贾第虫、螺旋核虫和螺旋藻属PC 1中的蛋白集高度减少，但在整个进化枝中保持良好，在174种研究的剪接体蛋白中有44至62种可检测。与更远的亲戚比较，揭示了一个高度嵌套的模式，与更多的内含子丰富的fornicate Kipferlia bialata保留87个总蛋白，包括几乎所有的观察到的所有在Escheronad的代表，和oxymonad Monocercomonoides保留115个总蛋白，包括几乎所有的观察到的K。比阿拉塔。结论在单胞菌代表和其他密切相关的metamonad组物种的比较表明，内含子结构的保守性和剪接体蛋白的组成相似的模式，但显着分歧的snRNA结构的基因组减少的物种。相对于其他真核生物，进化上保守的snRNA结构域和常见的剪接体蛋白质组的丢失指向一个更精简的剪接机制，其中内含子序列和结构可能在功能上补偿剪接体组分的最小化。
Background Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. Results We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to 'long' G. lamblia introns, RNA secondary structural potential is evident for 'long' (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S. salmonicida; cumulatively, illustrating significant snRNA differences within some diplomonads. Finally, we studied spliceosomal protein complements and find protein sets in Giardia, Spironucleus and Trepomonas sp. PC1 highly- reduced but well conserved across the clade, with between 44 and 62 out of 174 studied spliceosomal proteins detectable. Comparison with more distant relatives revealed a highly nested pattern, with the more intron-rich fornicate Kipferlia bialata retaining 87 total proteins including nearly all those observed in the diplomonad representatives, and the oxymonad Monocercomonoides retaining 115 total proteins including nearly all those observed in K. bialata. Conclusions Comparisons in diplomonad representatives and species of other closely-related metamonad groups indicates similar patterns of intron structural conservation and spliceosomal protein composition but significant divergence of snRNA structure in genomically-reduced species. Relative to other eukaryotes, loss of evolutionarily-conserved snRNA domains and common sets of spliceosomal proteins point to a more streamlined splicing mechanism, where intron sequences and structures may be functionally compensating for the minimalization of spliceosome components.