Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles
Genomic organization of Trypanosoma brucei kinetoplast DNA minicircles
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DOI：
10.1078/143446103322166554
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发表时间：
2003-07-01
期刊：
影响因子：
2.5
通讯作者：
Simpson, L
中科院分区：
文献类型：
--
作者：
Hong, M;Simpson, L
获得了7个新的布氏锥虫动基体DNA微环的序列。对这些序列和数据库中18个布氏锥虫完整kDNA小环序列进行了详细的比较分析。这25个不同的微环含有86个推定的gRNA基因。每个小环的gRNA基因的数量从2到5不等。在大多数情况下，基因位于短的不完美反向重复序列之间，但在几个微环中存在不含可识别gRNA基因的反向重复序列盒。五个微环含有未被可识别的重复序列包围的单个gRNA基因。两对密切相关的小环可能最近从共同的祖先进化而来：KTMH1和KTMH3包含相同顺序的相同gRNA基因，而KTCSGRA和KTCSGRB包含相同顺序的两个gRNA基因和一个gRNA基因。所有小环可以根据高度保守区域内的短取代分为两类，但这两类中的小环在gRNA含量或基因组织方面似乎没有差异。存在许多含有相同编辑信息但不同序列的冗余gRNA。预测的gRNA与编辑的mRNA序列的比对从没有空位的完美比对到具有多个错配的比对变化。多个gRNA与上游gRNA重叠，但在任何情况下都没有获得覆盖整个编辑结构域的重叠gRNA的完整集合。我们估计，对于完全重叠的集合，将需要大约65个额外gRNA的最小集合。这一分析应提供一个基础，详细研究的演变和作用，在RNA编辑的kDNA微环在这个物种。
The sequences of seven new Trypanosoma brucei kinetoplast DNA minicircles were obtained. A detailed comparative analysis of these sequences and those of the 18 complete kDNA minicircle sequences from T brucei available in the database was performed. These 25 different minicircles contain 86 putative gRNA genes. The number of gRNA genes per minicircle varies from 2 to 5. In most cases, the genes are located between short imperfect inverted repeats, but in several minicircles there are inverted repeat cassettes that did not contain identifiable gRNA genes. Five minicircles contain single gRNA genes not surrounded by identifiable repeats. Two pairs of closely related minicircles may have recently evolved from common ancestors: KTMH1 and KTMH3 contained the same gRNA genes in the same order, whereas KTCSGRA and KTCSGRB contained two gRNA genes in the same order and one gRNA gene specific to each. All minicircles could be classified into two classes on the basis of a short substitution within the highly conserved region, but the minicircles in these two classes did not appear to differ in terms of gRNA content or gene organization. A number of redundant gRNAs containing identical editing information but different sequences were present. The alignments of the predicted gRNAs with the edited mRNA sequences varied from a perfect alignment without gaps to alignments with multiple mismatches. Multiple gRNAs overlapped with upstream gRNAs, but in no case was a complete set of overlapping gRNAs covering an entire editing domain obtained. We estimate that a minimum set of approximately 65 additional gRNAs would be required for complete overlapping sets. This analysis should provide a basis for detailed studies of the evolution and role in RNA editing of kDNA minicircles in this species.