Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
Gene. 2014 Feb 10;535(2):336-44. doi: 10.1016/j.gene.2013.10.041. Epub 2013 Oct 28.
Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA - possibly a result of their low growth rates and deep-water lifestyle - has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences.
先前研究的三种玻璃海绵（多孔动物门，六放海绵纲）的线粒体基因组中，在蛋白质编码基因中推断出存在单个核苷酸插入，这些插入被认为是+1 翻译移框的位点。为了研究这些位点的分布和进化，并帮助阐明移框的机制，我们从玻璃海绵中确定了八个新的完整或近乎完整的 mtDNA 序列，并检查了另外三个的单个线粒体基因。我们在这些序列中发现了九个新的单核苷酸插入实例，并进行了比较和系统发育分析。这些碱基插入似乎在六放海绵 mt 蛋白基因中反复获得和丢失，表明移框位点没有功能意义。高度的序列保守性、不寻常的 tRNA 的存在以及独特的密码子使用模式表明翻译移框的“无框配对”模型。此外，我们提供的证据表明，玻璃海绵 mtDNA 受到的选择压力放松——可能是由于它们生长缓慢和生活在深水中——使得移框插入能够耐受数亿年。我们的研究提供了动物线粒体编码序列中转录移框在系统发育上多样化和广泛使用的第一个例子。
