Lavrov Dennis V, Adamski Marcin, Chevaldonné Pierre, Adamska Maja
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011, USA.
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.
Curr Biol. 2016 Jan 11;26(1):86-92. doi: 10.1016/j.cub.2015.11.043. Epub 2015 Dec 24.
One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate.
一般而言，含DNA的细胞器，尤其是线粒体，其一个不同寻常的特征是RNA编辑频繁发生[1]。“RNA编辑”一词指的是多种机制不相关的生化过程，这些过程在转录期间或之后改变RNA序列[2]。编辑可以是插入、缺失或替换，并且已在所有主要类型的RNA中发现[3,4]。虽然线粒体mRNA编辑在一些真核生物谱系中广泛存在[5-7]，但在动物中很少见，报道的案例在范围和系统发育分布上都有限[8-11]（另见[12]）。在分析来自钙质海绵纲的纤毛Sycon和复杂白枝海绵的基因组数据时，我们对缺乏可识别的线粒体编码序列感到困惑。对这些物种的基因组和转录组数据进行比较后发现，存在线粒体隐基因，其转录本会经历广泛的编辑。这种编辑包括在预先存在的短聚尿苷酸（U）序列中插入单个或双个尿苷酸（U）。随后的分析表明，在Sycon coactum中也存在类似的编辑，而在高度钙化的钙质海绵纲的马西利亚石海绵中编辑缺失。此外，发现至少一些钙质海绵纲的线粒体基因组具有非常不寻常的结构，几乎所有基因都位于单个且可能是线性的染色体上。对线粒体编码序列的系统发育分析表明，该类群的序列进化速度加快。后一观察结果对突变风险假说[13]提出了挑战，该假说认为，在突变率升高的谱系中不应发生mRNA编辑。
