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. 2024 Feb 13;13(2):119.
doi: 10.3390/biology13020119.

Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements

Kenji K Kojima  1
Affiliations

Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements

Kenji K Kojima. Biology (Basel). .

Abstract

Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3.

Keywords: 5S rRNA; Ajax; Cassandra; Helenus; LTR retrotransposon; RNA polymerase III promoter; SINE; TRIM; TRIMp3; tRNA.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Schematic structures of autonomous LTR retrotransposons and TRIMs. LTRs are shown as triangles, while protein-coding regions are as gray rectangles. TSDs are shown as diamonds. PBSs are shown as black rectangles, and PPTs are shown as red rectangles. Small RNA-like sequences are colored in orange (5S rRNA) or in green (tRNA). Solo LTR is generated by the recombination between the two LTRs of an LTR retrotransposon. Some TRIMs are revealed to be generated by the deletion of a part of the internal portion of an autonomous LTR retrotransposon.
Figure 2
Figure 2
tRNA-derived sequences in Helenus LTRs. Boxes A and B for RNA polymerase III promoter are shown above the alignment with their motif sequences. The positions of the aligned sequence in the respective consensus is shown at both sides. (a) tRNA-derived sequences in representative fungal Helenus LTRs aligned with tRNA-Thr-CGT from Saccharomyces cerevisiae. (b) tRNA-derived sequences in representative hymenopteran Helenus LTRs aligned with tRNA-Lys-CTT from Apis mellifera. (c) tRNA-derived sequences in representative fish Helenus LTRs aligned with tRNA-Val-CAC from Homo sapiens. (d) tRNA-derived sequences in representative molluscan Helenus LTRs aligned with tRNA-Lys-TTT from Aplysia californica.
Figure 3
Figure 3
The evolution and PBS sequences of the fungal Helenus families. The phylogeny shown on the left is based on the tRNA-derived sequences in Helenus LTRs. The line and leaf color indicate the primer tRNA type. The bootstrap support value over 50% is shown at the branch of Helenus families not using 3′-truncated tRNA-iMet-CAT as a primer. PBS sequences are shown on the right. tRNA sequences are shown in red and in the reverse orientation. The anticodons are shown in bold. The site of intron is indicated by “|”. The PBS nucleotides complementary to the tRNA are highlighted in yellow.
Figure 4
Figure 4
The alignment of Copia-9_PGr and LTR-1_PTrit. (A) Internal portion. (B) LTR. tRNA-like sequence is shown in bold.
Figure 5
Figure 5
The sequence alignments of the 5S rRNA-like sequences in Ajax, Cassandra, and lepidopteran SINE3 along with 5S rRNA genes. Box A, IE and box C for RNA polymerase III promoter are shown above the alignment with their motif sequences. 5S rDNA sequences are from Oryza sativa (5S_OS), Homo sapiens (5S_HS), and Notospermus geniculatus (5S_NGe). Lepidopteran SINE3 are from Helicoverpa armigera (HaSE3), Lycaena phlaeas (SINE3-1_LycPhl), Plutella xylostella (PxSE4 and PxSE5), Chrysoteuchia culmella (SINE3-1_ChrCul and SINE3-2_ChrCul), Lerema accius (LaSE2), Ennomos fuscantarius (SINE3-1_EnnFus), and Chilo suppressalis (CsSE2). The positions of the aligned sequence in the respective consensus is shown at both sides.
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