Kubo Nakao, Fujimoto Masaru, Arimura Shin-ichi, Hirai Masashi, Tsutsumi Nobuhiro
Graduate School of Agriculture, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan.
BMC Evol Biol. 2008 Nov 14;8:314. doi: 10.1186/1471-2148-8-314.
The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they must have acquired cis-regulatory elements compatible with eukaryotic gene expression. However, most of such processes remain unknown.
The ribosomal protein L6 gene (rpl6) has been lost in presently-known angiosperm mitochondrial genomes. We found that each of the two rice rpl6 genes (OsRpl6-1 and OsRpl6-2) has an intron in an identical position within the 5'-untranslated region (UTR), which suggests a duplication of the rpl6 gene after its transfer to the nucleus. Each of the predicted RPL6 proteins lacks an N-terminal extension as a mitochondrial targeting signal. Transient assays using green fluorescent protein indicated that their mature N-terminal coding regions contain the mitochondrial targeting information. Reverse transcription-PCR analysis showed that OsRpl6-2 expresses considerably fewer transcripts than OsRpl6-1. This might be the result of differences in promoter regions because the 5'-noncoding regions of the two rpl6 genes differ at a point close to the center of the intron. There are several sequences homologous to the region around the 5'-UTR of OsRpl6-1 in the rice genome. These sequences have characteristics similar to those of the transposable elements (TE) belonging to the PIF/Harbinger superfamily.
The above evidences suggest a novel mechanism in which the 5'-UTR of the transferred mitochondrial gene was acquired via a TE. Since the 5'-UTRs and introns within the 5'-UTRs often contain transcriptional and posttranscriptional cis-elements, the transferred rice mitochondrial rpl6 gene may have acquired its cis-element from a TE.
当代生物的线粒体所含基因比预计的原始细菌所含基因要少。由于大多数线粒体蛋白是由细胞核编码的，这些基因在进化的某个阶段必定从线粒体转移到了细胞核，并且它们一定获得了与真核基因表达兼容的顺式调控元件。然而，大多数此类过程仍不清楚。
核糖体蛋白L6基因（rpl6）在目前已知的被子植物线粒体基因组中已经丢失。我们发现，水稻的两个rpl6基因（OsRpl6 - 1和OsRpl6 - 2）在5'非翻译区（UTR）的相同位置都有一个内含子，这表明rpl6基因转移到细胞核后发生了复制。每个预测的RPL6蛋白都缺乏作为线粒体靶向信号的N端延伸。使用绿色荧光蛋白的瞬时分析表明，它们成熟的N端编码区包含线粒体靶向信息。逆转录 - PCR分析表明，OsRpl6 - 2表达的转录本比OsRpl6 - 1少得多。这可能是启动子区域差异的结果，因为两个rpl6基因的5'非编码区在内含子中心附近的一个点上有所不同。水稻基因组中有几个与OsRpl6 - 1的5'UTR周围区域同源的序列。这些序列具有与属于PIF/Harbinger超家族的转座元件（TE）相似的特征。
上述证据表明了一种新机制，即转移的线粒体基因的5'UTR是通过一个TE获得的。由于5'UTR和5'UTR内的内含子通常包含转录和转录后顺式元件，转移的水稻线粒体rpl6基因可能从一个TE获得了其顺式元件。
