page_title: Helitron (biology)
section_title: Structure
hierarchical_section_title: Helitron (biology) / Structure
caption_attribution_description: English: Structure and coding capacity of canonical animal and plant Helitrons
context_page_description: Helitrons are one of the three groups of eukaryotic class 2 transposable elements so far described. They are the eukaryotic rolling-circle transposable elements which are hypothesized to transpose by a rolling circle replication mechanism via a single-stranded DNA intermediate. They were first discovered in plants and in the nematode Caenorhabditis elegans, and now they have been identified in a diverse range of species, from protists to mammals. Helitrons make up a substantial fraction of many genomes where non-autonomous elements frequently outnumber the putative autonomous partner. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for Helitron transposition.
context_section_description: Helitrons are structurally asymmetric and are the only class of DNA transposons that do not generate duplications of target sites during transposition. Canonical Helitrons typically begin with a 5′ T (C/T) and terminate with the nucleotides CTRR (most frequently CTAG, but occasionally variation has been noted) but do not contain terminal inverted repeats. In addition, they frequently have a short palindromic sequence (16 to 20 nucleotides) hairpin about ∼ 11 bp from the 3′ end. They integrate between an AT host dinucleotide. Some families of Helitrons also carry tandem repeats, like microsatellites and minisatellites which are generally highly mutable sequences.
  Most Helitrons are non-autonomous elements and share common termini and other structural hallmarks with autonomous Helitrons, but they do not encode any complete set of proteins encoded by the autonomous elements.  The main enzymatic hallmarks of Helitrons are the rolling-circle (RC) replication initiator (Rep) and DNA helicase (Hel) domains, which are present in a protein comprising 1000–3000 amino acids (aa) (Rep/Hel) encoded by all autonomous Helitron elements. The Rep/Helicase protein includes zinc finger motifs, the Rep domain (which is a ~100-aa and has HUH endonuclease activity), and an eight-domain PiF1 family helicase (SuperFamily1) which are universally conserved in Helitrons. The zinc finger-like-motifs have been associated with DNA binding. The ~400-aa Hel domain is classified as a 5’ to 3’ DNA Hel which is involved in the breaking and joining of single-stranded DNA and are characterized by both the presence of the HUH motif (two histidine residues separated by a hydrophobic residue) and the Y motif (one or two tyrosine residues that are separated by several amino acids). The PiF1 family of helicases (Hel) has 5′ to 3′ unwinding activity which for many rolling-circle entities this activity is host encoded. Plant Helitrons also encode an open reading frame with homology to single-stranded DNA-binding proteins (RPA). Typically, the RPA proteins in Helitrons are 150 – 500-aa long and are encoded by several exons. In all Helitrons, the Rep domain precedes the Hel domain.
caption: Structure and coding capacity of canonical animal and plant Helitrons
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