The rice genome has various transposable elements. Many of these elements
exist in intergenic spacer regions or introns of various genes and thus
contribute to genome diversity. In some cases, insertions of these elements
cause specific effects. For example, the insertion of retrotransposon
Tos17 into one of the introns of OsABA1 inhibited normal
splicing of the gene and greatly reduced the steady state mRNA level of
the gene (Agrawal et al. 2001).
Tnr1 is a repetitive sequence in the rice genome. Its copy number
was estimated to be about 3500 per haploid genome. This sequence is about
230 bp long, which is too short to encode transposase. However, it has
the characteristics of transposable DNA elements; it has terminal inverted
repeats of about 75 bp and makes target sequence duplications upon transition.
Tnr1 has some other unique features, including transposition to
the specific sequence 5'-PuTAPy-3', duplicating the TA sequence. Therefore,
Tnr1 is thought to be a kind of transposable DNA element, and it
is probably non-autonomous (Umeda et al 1991; Tenzen et al.
We previously characterized a cDNA of a novel rice nuclear-encoded gene
for the subunit VIb of cytochrome c oxidase (COX) (Ohtsu et
al. 1999). COX is the terminal oxidase of the cytochrome electron
transport pathway that produces ATP in mitochondria. The deduced amino
acid sequence of this gene, designated OsCOX6b1, has an extended
N-terminal sequence compared with the human (Taanman et al. 1989)
and yeast (LaMarche et al. 1992) COX6bs. We subsequently determined
the genomic nucleotide sequence of OsCOX6b1.
First, we obtained genomic DNA fragments containing the whole OsCOX6b1
coding region by PCR using rice total DNA as a template. The nucleotide
sequence of the fragments was completely determined (accession number:
AB047975). Based on the OsCOX6b1 cDNA sequence, the OsCOX6b1
gene contained four introns. As shown in Figure 1A, we found two Tnr1-like
transposable DNA elements in the first intron. The upstream and downstream
Tnr1-like elements had 56% and 60% identities to Tnr1A (previously
identified Tnr1), respectively. Arabidopsis has a similar
gene (designated AtCOX6b1). The nucleotide sequence of this gene
(determined from Arabidopsis EST clone E10B10) was found to have
four introns at the same positions as OsCOX6b1, and its deduced
amino acid sequence has a long N-terminal sequence like OsCOX61.
However, no transposable elements such as Tnr1 were found in the
introns of AtCOX6b1 (Fig. 1A).
To determine the effect of Tnr1 insertion into the first intron
of OsCOX6b1, we investigated the steady-state mRNA levels of both
OsCOX6b1 and AtCOX6b1 in various organs. As shown in Figure
1B, the steady-state level of OsCOX6b1 mRNA, as well as that of
AtCOX6b1, was detected in the mature form in all organs examined
in this report. Based on the sizes of the transcripts, the first introns
of both OsCOX6b1 and AtCOX6b1 were normally spliced out
at the same positions. Based on the results obtained with AtCOX6b1,
the amounts of the steady-state
mRNA of OsCOX6b1 appeared to be normal. These results indicate
that the insertion of Tnr1-like transposable DNA elements into
the first intron of OsCOX6b1, unlike the insertion of Tos17
into one of the introns of OsABA1, does not affect the splicing
position of the intron, and likely does not affect the steady-state mRNA
level of the gene.
Agrawal, G.K., M. Yamazaki, M. Kobayashi, R. Hirochika, A. Miyao and H.
Hirochika, 2001. Screening of the rice viviparous mutants generated by
endogenous retrotransposon Tos17 insertion. Tagging of a zeaxanthion
epoxidase gene and a novel OsTATC gene. Plant Physiol. 125:
LaMarche, A.E.P., M.I. Abate, S.H.P. Chan and B.L. Trumpower, 1992. Isolation
and characterization of COX12 the nuclear gene for a previously
unrecognized subunit of Saccharomyces cerevisiae cytochrome c
oxidase. J. Biol. Chem. 267: 22473-22480.
Ohtsu, K., S. Hamanaka, K. Yamazaki, M. Nakazono and A. Hirai, 1999. Characterization
of a cDNA encoding a novel subunit for cytochrome c oxidase (COX6b)
from rice. Breed. Sci. 49: 211-215.
Taanman, J.W., C. Schrage, N. Ponne, P. Bolhuis, H. Vries and E. Agsteribbe,
1989. Nucleotide sequence of cDNA encoding subunit VIb of human cytochrome
c oxidase. Nucleic Acid Res. 17: 1766.
Tenzen, T., Y. Matsuda, H. Ohtsubo and E. Ohtsubo, 1994. Transposition
of Tnr 1 in rice genomes to 5'-PuTAPy-3' sites, duplicating the
TA sequence. Mol. Gen. Genet. 245: 441-448.
Umeda, M., H. Ohtsubo and E. Ohtsubo, 1991. Diversification of the rice
Waxy gene by insertion of mobile DNA elements into introns. Jpn.
J. Genet. 66: 569-586.