A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons
复制标题
DOI：
10.1007/s10709-012-9654-9
复制
发表时间：
2011-12
期刊：
影响因子：
1.5
通讯作者：
V. Steinbauerová;P. Neumann;P. Novák;J. Macas
中科院分区：
文献类型：
--
作者：
V. Steinbauerová;P. Neumann;P. Novák;J. Macas
长末端重复序列(LTR)反转录转座子构成了大多数高等植物基因组的重要组成部分，由于其复制的转座方式，它们在那里积累。虽然转座受到所有自主元件共同的Gag-Pol区内编码的蛋白质的促进，但一些LTR反转录转座子被发现可能携带额外的蛋白质编码能力，由位于Ofgag-Pol1上游或下游的额外开放阅读框表示。在这项研究中，我们对Ty3/Gypsy LTR反转录转座子组中的这些额外的开放阅读框(ORF)进行了全面的电子扫描和比较分析，作为了解它们的来源和功能的第一步。我们发现，在植物Ty3/吉普赛元素的所有三个主要谱系中都存在额外的ORF，其中最常见的是TAT谱系，其中大多数(77%)已确定的元素包含额外的ORF。这一谱系的特征也是元素内额外ORF排列(位置和方向)的最高多样性。另一方面，根据它们的相似性或它们推断的蛋白质序列中是否存在短的保守基序，所有这些ORF都只能被分为两大类。在Athila谱系中，额外的ORF局限于元素3‘区，但与Tat中发现的ORF相比，它们显示出更高的序列多样性。在铬病毒的谱系中，额外的ORF相对较少，仅出现在单一植物科(Poaceae)中一组元素的5‘端区域。在所有三个谱系中，除两个Athila类元件与LOGL4基因相似，以及部分ChromoVirus额外ORF与组蛋白H3基因部分相似外，大多数额外ORF缺乏与特征基因序列或功能蛋白结构域的序列相似性。因此，在这些情况下，额外的ORF很可能起源于细胞基因序列的转导或重组。此外，在部分类似TAT的额外ORF中检测到了与DNA转座子相关的蛋白质结构域，表明它们来自可移动元件的插入事件。
Long terminal repeat (LTR) retrotransposons make up substantial parts of most higher plant genomes where they accumulate due to their replicative mode of transposition. Although the transposition is facilitated by proteins encoded within thegag-polregion which is common to all autonomous elements, some LTR retrotransposons were found to potentially carry an additional protein coding capacity represented by extra open reading frames located upstream or downstream ofgag-pol. In this study, we performed a comprehensive in silico survey and comparative analysis of these extra open reading frames (ORFs) in the group of Ty3/gypsy LTR retrotransposons as the first step towards our understanding of their origin and function. We found that extra ORFs occur in all three major lineages of plant Ty3/gypsy elements, being the most frequent in the Tat lineage where most (77 %) of identified elements contained extra ORFs. This lineage was also characterized by the highest diversity of extra ORF arrangement (position and orientation) within the elements. On the other hand, all of these ORFs could be classified into only two broad groups based on their mutual similarities or the presence of short conserved motifs in their inferred protein sequences. In the Athila lineage, the extra ORFs were confined to the element 3′ regions but they displayed much higher sequence diversity compared to those found in Tat. In the lineage of Chromoviruses the extra ORFs were relatively rare, occurring only in 5′ regions of a group of elements present in a single plant family (Poaceae). In all three lineages, most extra ORFs lacked sequence similarities to characterized gene sequences or functional protein domains, except for two Athila-like elements with similarities toLOGL4gene and part of the Chromoviruses extra ORFs that displayed partial similarity to histone H3 gene. Thus, in these cases the extra ORFs most likely originated by transduction or recombination of cellular gene sequences. In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element.