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Open Access Open Badges Research article

Transfer of rice mitochondrial ribosomal protein L6 gene to the nucleus: acquisition of the 5'-untranslated region via a transposable element

Nakao Kubo1*, Masaru Fujimoto2, Shin-ichi Arimura2, Masashi Hirai1 and Nobuhiro Tsutsumi2

Author Affiliations

1 Graduate School of Agriculture, Kyoto Prefectural University, Seika, Kyoto 619-0244, Japan

2 Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku 113-8657, Japan

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BMC Evolutionary Biology 2008, 8:314  doi:10.1186/1471-2148-8-314

Published: 14 November 2008



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.