Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).
复制标题
DOI：
10.1186/1759-8753-4-5
复制
发表时间：
2013-02-01
期刊：
影响因子：
4.9
通讯作者：
Blomberg J
中科院分区：
文献类型：
--
作者：
Benachenhou F;Sperber GO;Bongcam-Rudloff E;Andersson G;Boeke JD;Blomberg J
长末端重复序列（LTR，由U3-R-U 5部分组成）是逆转录病毒和相关逆转录转座子的重要元件。由于其可变性，很难对其进行分析。目的是获得比以往更全面的关于长期贸易关系的结构、多样性和起源的看法。为属于逆转录病毒科（III类逆转录病毒）、动物变病毒科（Gypsy/Ty 3）元件和植物假病毒科（Copia/Ty 1）元件的11个LTR进化枝创建隐马尔可夫模型（HMM），补充了我们对正逆转录病毒的工作。植物偏病毒科和少数分歧的动物假病毒科的LTR长度的巨大变化阻止了从这两个组构建障碍物。动物Metaviridae LTR具有与逆转录病毒LTR相同的保守基序，证实了这两组病毒密切相关。保守的基序是短反向重复序列（SIR），整合酶识别信号（5“TGTTRNR... YNYAACA 3”）;多聚腺苷酸化信号或AATAAA基序;多聚腺苷酸化信号下游的富含GT的片段;以及对应于核心启动子元件TATA盒的不太保守的富含AT的片段。植物假病毒科LTR略有不同，有一个保守的TATA盒，TATATA，但没有保守的多聚腺苷酸化信号，加上一个短得多的R区。对于大多数模型，用于基因组序列中检测的HIBR的灵敏度约为50%，具有相对较高的特异性，适合于基因组筛选。Hacker产生了共有序列，通过创建HMM模型（"Superviterbi“比对）对其进行比对。这产生了一个系统发育树，与波尔为基础的树进行了比较。LTR和Pol树均支持逆转录病毒的单系性。在这两种病毒中，假病毒科是所有其他LTR逆转录转座子的祖先。然而，LTR树显示偏病毒科的有色病毒部分与假病毒科聚在一起，将偏病毒科分成具有不同同源性的两个部分。HALOY清楚地证明了LTR的单一保守结构，支持它们在进化过程中出现过一次。我们试图通过追踪其功能基础来跟踪LTR的进化，即获得RNA酶H、组合的启动子/多聚腺苷酸化位点、整合酶、发夹引发和引物结合位点（PBS）。现有的信息并不支持一个简单的事件演变链。
Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability. The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible. Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups. Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region. The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening. The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny. The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.
登录
查看更多内容
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
3.7
作者：
Anderssen, S;Sjottem, E;Johansen, T
通讯作者：
Johansen, T
影响因子：
5.4
作者：
Chatterjee, Atreyi Ghatak;Leem, Young Eun;Levin, Henry L.
通讯作者：
Levin, Henry L.
影响因子：
5.3
作者：
FRIESEN, PD;NISSEN, MS
通讯作者：
NISSEN, MS
影响因子：
3.3
作者：
Jern P;Sperber GO;Blomberg J
通讯作者：
Blomberg J