Cummings D J, MacNeil I A, Domenico J, Matsuura E T
J Mol Biol. 1985 Oct 20;185(4):659-80. doi: 10.1016/0022-2836(85)90052-x.
During senescence in the filamentous fungus Podospora anserina, specific regions of the mitochondrial genome, termed senDNA are excised, ligated and amplified. We have cloned in their entirety three such autonomously replicating plasmids, alpha, beta and epsilon senDNA. None of these plasmids displayed cross-hybridization nor did we detect any significant DNA homology by computer analysis. The complete DNA sequence of the 2.5 kb alpha, the 5.5 kb epsilon and about 3.4 kb of the 9.8 kb beta senDNA is presented (kb = 10(3) base-pairs). These sequences were analyzed for the presence of consensus sequences common to introns, and it was found that alpha senDNA has the characteristics of a group II intron, epsilon senDNA contains three group I introns, and beta senDNA did not show relevant sequences in the 3.4 kb examined. Comparison of the 5' and 3'-flanking sequences of alpha senDNA with oxi 3 (Co I) amino acid sequences from Neurospora crassa and Saccharomyces cerevisiae revealed significant homology and provided strong support that the excised alpha senDNA itself consists entirely of an intron. Upstream from the oxi 3 gene a transfer RNA cysteine sequence was detected. beta senDNA contained four tRNA sequences, aspartic acid, serine, valine and tryptophan, and sequences homologous to URFC (untranslated reading frame C) as well as two new URFs. epsilon senDNA contained sequences homologous to ATPase 8 and URFl; URFl was interrupted by three group I introns. The excision site sequences, as located by S1 nuclease mapping were unique for each senDNA. Analysis for repeated units showed that each plasmid contained elements which could be involved in secondary structure required for the alignment of distal ends preparatory to excision. These results are interpreted in terms of the structural requirements of mobile elements including the possible involvement of reverse transcriptase in the excision-ligation-amplification process.
在丝状真菌栗疫霉衰老过程中，线粒体基因组的特定区域（称为senDNA）被切除、连接并扩增。我们已经完整克隆了三个这样的自主复制质粒，即α、β和ε senDNA。这些质粒均未显示出交叉杂交现象，通过计算机分析也未检测到任何显著的DNA同源性。本文给出了2.5 kb的α、5.5 kb的ε以及9.8 kb的β senDNA中约3.4 kb的完整DNA序列（kb = 10³个碱基对）。对这些序列进行内含子共有序列分析，发现α senDNA具有II类内含子的特征，ε senDNA包含三个I类内含子，而在所检测的3.4 kb的β senDNA中未发现相关序列。将α senDNA的5'和3'侧翼序列与粗糙脉孢菌和酿酒酵母的oxi 3（辅酶I）氨基酸序列进行比较，发现了显著的同源性，并有力支持了切除的α senDNA本身完全由一个内含子组成。在oxi 3基因上游检测到一个半胱氨酸转运RNA序列。β senDNA包含四个转运RNA序列，即天冬氨酸、丝氨酸、缬氨酸和色氨酸，以及与URFC（非翻译阅读框C）同源的序列和两个新的URF。ε senDNA包含与ATPase 8和URF1同源的序列；URF1被三个I类内含子打断。通过S1核酸酶作图确定的每个senDNA的切除位点序列都是独特的。重复单元分析表明，每个质粒都包含一些元件，这些元件可能参与切除前远端对齐所需的二级结构。这些结果根据移动元件的结构要求进行了解释，包括逆转录酶可能参与切除-连接-扩增过程。
