Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease

Abstract

HUH endonucleases of the Rep (replication protein) class mediate the replication of highly diverse plasmids and viral genomes across all domains of life. Reps also function as transposases, and three evolutionarily independent groups of transposable elements (TEs) mobilised by Reps have been described: the prokaryotic insertion sequences IS200/IS605and IS91/ISCR, and the eukaryotic Helitrons. Here I present Replitrons, a new group of eukaryotic transposons encoding Rep HUH endonuclease. Replitron transposases feature Rep with one catalytic Tyr (Y1) as their only recognised domain, contrasting with Helitron transposases that feature Rep with two Tyr (Y2) and a fused helicase domain (i.e. RepHel). Protein clustering found no link between Replitron transposases and described Rep transposases, and instead recovered a weak association with Reps of circular Rep-encoding single stranded (CRESS) DNA viruses and their related plasmids (pCRESS). The predicted tertiary structure of the transposase ofReplitron-1, the founding member of the group that is active in the green algaChlamydomonas reinhardtii, closely resembles that of CRESS-DNA viruses and other HUH endonucleases. Replitrons are present in at least three eukaryotic supergroups and reach high copy numbers in non-seed plant genomes. Replitron DNA sequences generally feature short direct repeats at, or potentially near, their termini. Finally, I characterisecopy-and-paste de novoinsertions ofReplitron-1using long-read sequencing ofC. reinhardtiiexperimental lines. Overall, these results support an ancient and evolutionarily independent origin of Replitrons, in line with other major groups of eukaryotic TEs. This work substantially expands the known diversity of both transposons and HUH endonucleases in eukaryotes.

Rates and spectra of de novo structural mutations inChlamydomonas reinhardtii

“…4 B). We also observed an unusual pair of copy-and-paste transposons, the autonomous Replitron-1 and nonautonomous Replitron-N1 , which are the founding elements of a new group of eukaryotic transposons named Replitrons that will be described elsewhere ( Craig 2022 ). Like Helitrons, Replitron-1 encodes an HUH endonuclease of the Rep class, although it features only one catalytic tyrosine (i.e., Y1 rather than Y2) in the Rep domain and does not feature a C-terminal helicase domain ( Fig.…”

Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution

“…While the association of these gene groups likely has a mechanistic basis, the nature of that basis is hard to predict. SF1B helicases of the Pif1 family provide mobility functions for the helitron and replitron classes of mobile elements (Chandler et al 2013;Craig 2023). Helitron and replitron helicases possess an HUH single strand endonuclease domain that nicks DNA to initiate transposition through a rolling circle replication mechanism.…”

HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-tags

“…HUH-endonucleases are a diverse group of mechanistically similar enzymes that contain a unifying metal-coordinating motif most often comprised of a pair of histidines (H) separated by a hydrophobic residue (U) [1,2]. The HUH superfamily includes nucleases that mediate a host of biological processes, ranging from replication, to conjugation, and even transposition [1][2][3][4][5][6][7]. These enzymes mediate their functions through a common single-stranded DNA (ssDNA) processing mechanism in which a coordinated divalent cation polarizes the phosphate backbone of the substrate to enable the catalytic tyrosine to cleave and covalently bind to the substrate's newly exposed 5' end via a phosphotyrosine linkage (Figure 1A) [1].…”