Vicient Carlos M
Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
Mob DNA. 2025 Apr 2;16(1):15. doi: 10.1186/s13100-025-00354-z.
Plant Gypsy LTR-retrotransposons are classified into lineages according to the phylogenetic relationships of the reverse transcriptase. Retand is a lineage of non-chromovirus elements characterized by the presence of a long internal region compared to other lineages.
This work focuses on the identification and characterization of Potentially Recently Active Retand Elements (PRAREs) in 617 genomic sequence assemblies of Viridiplantae species. The Retand elements were considered PRAREs if their LTRs and insertion sequences were identical, and the sizes of their internal regions and LTRs did not differ by more than 2% from the consensus. A total of 2,735 PRAREs were identified, distributed in 122 clusters corresponding to 34 species, with copy numbers per cluster varying between 1 and 180. They are present in Eudicotyledons and Liliopsida but not in other groups of plants. Some PRAREs are non-autonomous elements, lacking some of the typical LTR retrotransposon coding domains. The size of the POL-3'LTR regions varies between 2,933 and 6,566 bp, and in all cases, includes potential coding regions oriented antisense to the gag and pol genes. 97% of the clusters contain antisense ORFs encoding the TRP28 protein domain of unknown function. The analysis of the consensus TRP28 domain indicates that it probably can bind DNA. About half of the PRAREs contain arrays of tandem repeats in the POL-3'LTR region.
The large internal region of the Retand elements is due to the presence of a long POL-3'LTR region. This region frequently contains arrays of tandem repeats that contribute to the expansion of this area. The presence of antisense ORFs in the POL-3'LTR region is also a common feature in these elements, many of which encode proteins with conserved domains, especially the TRP28 domain. The possible function of these TRP28-containing proteins is unknown, but their potential DNA binding capacity and the comparison with similar genes in some retroviruses suggest that they may play a regulatory role in the Retand transposition process.
植物吉普赛LTR反转录转座子根据反转录酶的系统发育关系分为不同谱系。Retand是一类非染色体病毒元件谱系，与其他谱系相比，其特征在于存在一个长的内部区域。
本研究聚焦于绿藻门物种617个基因组序列组装中潜在近期活跃的Retand元件（PRAREs）的鉴定与表征。如果Retand元件的LTR和插入序列相同，且其内部区域和LTR的大小与共有序列的差异不超过2%，则这些元件被视为PRAREs。共鉴定出2735个PRAREs，分布在对应于34个物种的122个簇中，每个簇的拷贝数在1到180之间。它们存在于双子叶植物和单子叶植物中，但不存在于其他植物类群中。一些PRAREs是非自主元件，缺少一些典型的LTR反转录转座子编码结构域。POL - 3'LTR区域的大小在2933至6566 bp之间，在所有情况下，都包括与gag和pol基因呈反义方向的潜在编码区域。97%的簇含有编码功能未知的TRP28蛋白结构域的反义ORF。对共有TRP28结构域的分析表明它可能能够结合DNA。约一半的PRAREs在POL - 3'LTR区域含有串联重复序列阵列。
Retand元件的大内部区域是由于存在一个长的POL - 3'LTR区域。该区域经常含有串联重复序列阵列，这有助于该区域的扩展。POL - 3'LTR区域中反义ORF的存在也是这些元件的一个共同特征，其中许多编码具有保守结构域的蛋白质，尤其是TRP28结构域。这些含TRP28蛋白的可能功能尚不清楚，但它们潜在的DNA结合能力以及与一些逆转录病毒中相似基因的比较表明，它们可能在Retand转座过程中发挥调节作用。
