The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei
The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei
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DOI：
10.1093/molbev/msh045
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发表时间：
2004-03-01
影响因子：
10.7
通讯作者：
Baltz, T
中科院分区：
文献类型：
--
作者：
Bringaud, F;Biteau, N;Baltz, T
ingi（长且自主）和 RIME（短且非自主）非长末端重复反转录转座子是迄今为止在非洲锥虫布氏锥虫基因组中表征的最丰富的移动元件。这些逆转录转座子被认为是随机分布的，但迄今为止尚未对其基因组分布进行详细而全面的分析。为了解决这个问题，我们分析了正在进行的布氏锥虫基因组测序项目（TREU927/4 株）的ingi/RIME 序列和侧翼序列。在分析的 81 个 ingi/RIME 元件中，60% 是完整的，7% 的 ingi 元件（每个单倍体基因组大约 15 个拷贝）似乎编码其自身的转座。 ingi/RIME 逆转录转座子侧翼的直接重复序列的大小是保守的（即 12-bp），并且在 5'-直接重复序列之前有一个强的 11-bp 共有模式。通过分析包含 5'-相邻 ingi/RIME 序列的 294 GSS 中的碱基出现情况，证实了逆转录元件上游共有模式的存在。保守序列存在于 ingis 和 RIME 的上游，表明 ingis 编码的酶活性用于 RIME 的逆转录转座，RIME 是短的非自主逆转录元件。总之，ingi和RIME逆转录元件在布氏锥虫基因组中并不是随机分布的，其前面有一个保守序列，该序列可能是ingi编码的核酸内切酶的识别位点。
The ingi (long and autonomous) and RIME (short and nonautonomous) non-long-terminal repeat retrotransposons are the most abundant mobile elements characterized to date in the genome of the African trypanosome Trypanosoma brucei. These retrotransposons were thought to be randomly distributed, but a detailed and comprehensive analysis of their genomic distribution had not been performed until now. To address this question,we analyzed the ingi/RIME sequences and flanking sequences from the ongoing T. brucei genome sequencing project (TREU927/4 strain). Among the 81 ingi/ RIME elements analyzed, 60% are complete, and 7% of the ingi elements (approximately 15 copies per haploid genome) appear to encode for their own transposition. The size of the direct repeat flanking the ingi/RIME retrotransposons is conserved (i.e., 12-bp), and a strong 11-bp consensus pattern precedes the 5'-direct repeat. The presence of a consensus pattern upstream of the retroelements was confirmed by the analysis of the base occurrence in 294 GSS containing 5'-adjacent ingi/RIME sequences. The conserved sequence is present upstream of ingis and RIMEs, suggesting that ingi-encoded enzymatic activities are used for retrotransposition of RIMEs, which are short nonautonomous retroelements. In conclusion, the ingi and RIME retroelements are not randomly distributed in the genome of T. brucei and are preceded by a conserved sequence, which may be the recognition site of the ingi-encoded endonuclease.