Ehara M, Watanabe K I, Ohama T
Department of Biology, Faculty of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, 560-0043, Osaka, Japan.
Gene. 2000 Oct 3;256(1-2):157-67. doi: 10.1016/s0378-1119(00)00359-0.
We identified group IIA introns that contain an open reading frame (ORF) in the mitochondrial cytochrome oxidase subunit I (cox1) genes of yellow algae, a diatom Thalassiosira (Th.) nordenskioeldii CCMP 992 collected from the east coast of USA, and a haptophyte Pavlova (Pa.) lutheri CCMP 1325 collected from Finland. Cognate introns of CCMP 1325 were detected in all Pa. lutheri strains investigated, which were collected from various oceans. In contrast, the intron was absent from closely related species belonging to the same genus Pavlova. This was also the case for the group II intron detected in a diatom Th. nordenskioeldii CCMP 992. The group II intron of CCMP 992 was located at the corresponding site to the group IIA intron found in Pylaiella (synonym, Pilayella) littoralis. The deduced secondary structures of these introns, one of which is from a diatom and the other from a brown alga, were virtually identical. In contrast, the haptophyte group II intron was inserted at a novel locus, and shares no particularly high sequence homology with any intron known to date. The phylogenetic tree based on the intronic ORF domain was not congruent with that based on the cox1 exon. The most prominent property of the intronic ORF tree was that introns located at homologous sites made robust pair clades irrespective of the phylogenetic relationships of the organisms. This suggests that mitochondrial group II introns often invade intronless alleles across the species barrier with site specificity. Homology analysis of the haptophyte intronic ORF suggested that it comprises three domains: reverse transcriptase (RT), RNA maturase (Ma), and H-N-H endonuclease. However, the intronic ORF of the diatom contains the Ma domain but is apparently missing the H-N-H domain, and its RT domain is most probably partly or completely lacking in function.
我们在黄藻、一种从美国东海岸采集的硅藻——诺氏海链藻（Thalassiosira (Th.) nordenskioeldii）CCMP 992以及一种从芬兰采集的定鞭藻——鲁氏巴夫藻（Pavlova (Pa.) lutheri）CCMP 1325的线粒体细胞色素氧化酶亚基I（cox1）基因中鉴定出了含有开放阅读框（ORF）的IIA类内含子。在所研究的所有从不同海洋采集的鲁氏巴夫藻菌株中均检测到了CCMP 1325的同源内含子。相比之下，在属于同一属——巴夫藻属的近缘物种中该内含子缺失。在硅藻诺氏海链藻CCMP 992中检测到的II类内含子情况也是如此。CCMP 992的II类内含子位于与在潮间带皮丝藻（Pylaiella (synonym, Pilayella) littoralis）中发现的IIA类内含子相对应的位点。这些内含子（其中一个来自硅藻，另一个来自褐藻）推导的二级结构几乎相同。相比之下，定鞭藻的II类内含子插入到一个新位点，并且与迄今为止已知任何内含子均无特别高的序列同源性。基于内含子ORF结构域的系统发育树与基于cox1外显子的系统发育树不一致。内含子ORF树最显著的特性是位于同源位点的内含子形成了稳健的配对分支，而与生物的系统发育关系无关。这表明线粒体IIA类内含子经常以位点特异性跨物种屏障侵入无内含子的等位基因。对定鞭藻内含子ORF的同源性分析表明它由三个结构域组成：逆转录酶（RT）、RNA成熟酶（Ma）和H-N-H核酸内切酶。然而，硅藻的内含子ORF包含Ma结构域，但显然缺少H-N-H结构域，并且其RT结构域很可能部分或完全缺乏功能。
