Kostygov Alexei Yu, Skýpalová Karolína, Kraeva Natalia, Kalita Elora, McLeod Cameron, Yurchenko Vyacheslav, Field Mark C, Lukeš Julius, Butenko Anzhelika
Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic.
Zoological Institute of the Russian Academy of Sciences, St. Petersburg, 199034, Russia.
BMC Biol. 2024 Dec 3;22(1):281. doi: 10.1186/s12915-024-02080-z.
In trypanosomatids, a group of unicellular eukaryotes that includes numerous important human parasites, cis-splicing has been previously reported for only two genes: a poly(A) polymerase and an RNA helicase. Conversely, trans-splicing, which involves the attachment of a spliced leader sequence, is observed for nearly every protein-coding transcript. So far, our understanding of splicing in this protistan group has stemmed from the analysis of only a few medically relevant species. In this study, we used an extensive dataset encompassing all described trypanosomatid genera to investigate the distribution of intron-containing genes and the evolution of splice sites.
We identified a new conserved intron-containing gene encoding an RNA-binding protein that is universally present in Kinetoplastea. We show that Perkinsela sp., a kinetoplastid endosymbiont of Amoebozoa, represents the first eukaryote completely devoid of cis-splicing, yet still preserving trans-splicing. We also provided evidence for reverse transcriptase-mediated intron loss in Kinetoplastea, extensive conservation of 5' splice sites, and the presence of non-coding RNAs within a subset of retained trypanosomatid introns.
All three intron-containing genes identified in Kinetoplastea encode RNA-interacting proteins, with a potential to fine-tune the expression of multiple genes, thus challenging the perception of cis-splicing in these protists as a mere evolutionary relic. We suggest that there is a selective pressure to retain cis-splicing in trypanosomatids and that this is likely associated with overall control of mRNA processing. Our study provides new insights into the evolution of introns and, consequently, the regulation of gene expression in eukaryotes.
锥虫是一类单细胞真核生物，包含许多重要的人类寄生虫。此前报道，在锥虫中只有两个基因存在顺式剪接，即一个聚腺苷酸聚合酶基因和一个RNA解旋酶基因。相反，几乎每个蛋白质编码转录本都存在反式剪接，即涉及连接一个剪接前导序列。到目前为止，我们对这个原生生物类群剪接的理解仅源于对少数医学相关物种的分析。在本研究中，我们使用了一个广泛的数据集，涵盖了所有已描述的锥虫属，以研究含内含子基因的分布和剪接位点的进化。
我们鉴定出一个新的保守的含内含子基因，该基因编码一种RNA结合蛋白，普遍存在于动基体目中。我们发现，变形虫的动基体共生体珀金斯氏菌属是第一个完全没有顺式剪接但仍保留反式剪接的真核生物。我们还提供了证据，证明动基体目中存在逆转录酶介导的内含子丢失、5'剪接位点的广泛保守以及保留的锥虫内含子子集中存在非编码RNA。
在动基体目中鉴定出的所有三个含内含子基因都编码与RNA相互作用的蛋白，有可能微调多个基因的表达，从而挑战了人们对这些原生生物中顺式剪接仅仅是进化遗迹的看法。我们认为，锥虫中存在保留顺式剪接的选择压力，这可能与mRNA加工的整体控制有关。我们的研究为内含子的进化以及真核生物中基因表达的调控提供了新的见解。
