Abstract
BackgroundLong interspersed nuclear elements (LINES) are the most common transposable element (TE) in almost all metazoan genomes examined. In most LINE superfamilies there are two open reading frames (ORFs), and both are required for transposition. The ORF2 is well characterized, while the structure and function of the ORF1 is less well understood. ORF1s have been classified into five types based on structural organization and the domains identified. Here we perform a large scale analysis of ORF1 domains of 448 elements from the Jockey superfamily using multiple alignments and Hidden Markov Model (HMM)-HMM comparisons.ResultsThree major lineages, Chicken repeat 1 (CR1), LINE2 (L2) and Jockey, were identified. All Jockey lineage elements have the same type of ORF1. In contrast, in the L2 and CR1 lineage elements, all five ORF1 types are found, with no one type of ORF1 predominating. A plant homeodomain (PHD) is much more prevalent than previously suspected. ORF1 type variations involving the PHD domain were found in many subgroups of the L2 and CR1 lineages. A Jockey lineage-like ORF1 with a PHD domain was found in both lineages. A phylogenetic analysis of this ORF1 suggests that it has been horizontally transferred. Likewise, an esterase containing ORF1 type was only found in two exclusively vertebrate L2 and CR1 groups, indicating that it may have been acquired in a vertebrate common ancestor and then transferred between the lineages.ConclusionsThe ORF1 of the CR1 and L2 lineages is very structurally diverse. The presence of a PHD domain in many ORF1s of the L2 and CR1 lineages is suggestive of domain shuffling. There is also evidence of possible horizontal transfer of entire ORF1s between lineages. In conclusion, while the structure of the ORF2 appears to be highly constrained and its evolution tree-like, the structure of the ORF1 within the CR1 and L2 lineages is much more variable and its evolution reticulate.
Highlights
Long interspersed nuclear elements (LINES) are the most common transposable element (TE) in almost all metazoan genomes examined
All Jockey lineage elements have the same type of ORF1, with one to two RNA recognition motif (RRM) domains upstream of three Cys2HisCys zinc-knuckle domains (CCHC) domains
The plant homeodomain (PHD) domain is much more prevalent than previously suspected; it was identified in four ORF1 types in many subgroups within the L2 and Chicken repeat 1 (CR1) lineages and both upstream and downstream of the RRM domain
Summary
Long interspersed nuclear elements (LINES) are the most common transposable element (TE) in almost all metazoan genomes examined. Transposable elements (TEs) are mobile genetic elements found in most eukaryotic genomes and are the major contributor to variation in genome size [1]. They are genomic ‘invaders’, one type of genomic component involved in genomic conflict with the host genome. Fourteen clades were assigned to five groups based on reverse transcriptase (RT) phylogeny by Eickbush and Malik [8]. These five groups were converted to superfamilies in the TE classification system proposed by Wicker et al [7]. The CR1 and L2 clades are widely distributed in metazoans, while the Jockey clade is confined to the arthropods
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