The DIRS1 group of retrotransposons
The DIRS1 group of retrotransposons
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DOI：
10.1093/oxfordjournals.molbev.a003748
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发表时间：
2001-11-01
影响因子：
10.7
通讯作者：
Poulter, RTM
中科院分区：
文献类型：
--
作者：
Goodwin, TJD;Poulter, RTM
此前仅有3个DIRS1组的逆转录转座子被描述过：DIRS1来自粘菌盘状盘齿骨菌，PAT来自再病毒线虫，Prt1来自合菌真菌黑藻。对这些元件编码的逆转录酶序列的分析表明，它们与长末端重复（LTR）逆转录元件有关，如Ty3/gypsy逆转录转座子和脊椎动物逆转录病毒。然而，dirs1组元件具有与典型LTR元件不同的几个不同寻常的结构特征：(1)它们缺乏编码dde型整合酶或天冬氨酸蛋白酶的能力；(2)具有未知功能的开放阅读框（or - f）；(3)在不复制目标站点的情况下进行整合；(4)尽管它们以末端重复序列为边界，但这些序列与典型的ltr不同，它们要么是反向重复序列，要么是“分裂”的直接重复序列。由于描述的类似dirs1的元素数量很少，而且这些元素的结构不寻常，因此对它们的进化、分布和复制机制知之甚少。在这里，我们报道了几个新的类似dirs1的逆转录转座子的鉴定，包括来自线虫、海胆、鱼类和两栖动物的元件。我们也提出证据证明在人类基因组中存在类似dirs1的序列。此外，我们发现DIRS1组的元件缺乏dde型整合酶基因，这可以通过发现这些元件先前未被表征的orf编码与噬菌体lambda的位点特异性重组酶相关的蛋白质来解释。在DIRS1元件中存在lambda-recombinase样基因也解释了这些元件缺乏目标位点复制，并可能与它们末端重复序列的不寻常结构有关。
Only three retrotransposons of the DIRS1 group have previously been described: DIRS1 from the slime mold Dictyostelium discoideum, PAT from the nematode Panagrellus redivivus, and Prt1 from the zygomycetous fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (LTR) retroelements, such as the Ty3/gypsy retrotransposons and the vertebrate retroviruses. The DIRS1-group elements, however, have several unusual structural features which distinguish them from typical LTR elements: (1) they lack the capacity to encode DDE-type integrases or aspartic proteases; (2) they have open reading frames (OR-Fs) of unknown function; (3) they integrate without creating duplications of their target sites; and (4) although they are bordered by terminal repeats, these sequences differ from typical LTRs in that they are either inverted repeats or "split" direct repeats. Because of the small number of DIRS1-like elements described, and the unusual structures of these elements, little is known about their evolution, distribution, and replication mechanisms. Here, we report the identification of several new DIRS1-like retrotransposons, including elements from nematodes, sea urchins, fish, and amphibia. We also present evidence for the existence of DIRS1-like sequences in the human genome. In addition, we show that the lack of DDE-type integrase genes from elements of the DIRS1 group is explained by the finding that the previously uncharacterized ORFs of these elements encode proteins related to the site-specific recombinase of bacteriophage lambda. The presence of lambda-recombinase-like genes in DIRS1 elements also accounts for the lack of target-site duplications for these elements and may be related to the unusual structures of their terminal repeats.