Exploring the Remote Ties between Helitron Transposases and Other Rolling-Circle Replication Proteins

Abstract

Rolling-circle replication (RCR) elements constitute a diverse group that includes viruses, plasmids, and transposons, present in hosts from all domains of life. Eukaryotic RCR transposons, also known as Helitrons, are found in species from all eukaryotic kingdoms, sometimes representing a large portion of their genomes. Despite the impact of Helitrons on their hosts, knowledge about their relationship with other RCR elements is still elusive. Here, we compared the endonuclease domain sequence of Helitron transposases with the corresponding region from RCR proteins found in a wide variety of mobile genetic elements. To do that, we used a stepwise alignment approach followed by phylogenetic and multidimensional scaling analyses. Although it has been suggested that Helitrons might have originated from prokaryotic transposons or eukaryotic viruses, our results indicate that Helitron transposases share more similarities with proteins from prokaryotic viruses and plasmids instead. We also provide evidence for the division of RCR endonucleases into three groups (Y1, Y2, and Yx), covering the whole diversity of this protein family. Together, these results point to prokaryotic elements as the likely closest ancestors of eukaryotic RCR transposons, and further demonstrate the fluidity that characterizes the boundaries separating viruses, plasmids, and transposons.

Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

“…It has been previously suggested that helitrons might represent a missing link between eukaryotic CRESS-DNA viruses, namely, geminiviruses, and bacterial HUH replicons 41 or that helitrons evolved from geminiviruses 42 . However, in our analysis, helitrons do not connect to any of the groups of CRESS-DNA viruses, suggesting independent evolutionary trajectories, consistent with the recent findings 43 .…”

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

“…Before conducting searches to retrieve genomic Pif1-like helicases, we first expanded our sample of Helitrons from different variants ( Helitrons , Helentrons , and Helitron2 ) selected previously ( Heringer and Kuhn 2018 ). Consensus sequences from the helicase domains (Hel) found in those Helitrons were used as queries to obtain Pif1-like helicases from a wide diversity of organisms (see Materials and Methods).…”

“…Conversely, because geminiviruses had been found integrated into plant chromosomes, it was also proposed that Helitrons could likewise be derived from an ancient genomic integration of a eukaryotic RCR virus ( Feschotte and Wessler 2001 ). However, as revealed by recent findings, Rep domains from Helitrons are distantly related to proteins from prokaryotic TEs and eukaryotic viruses, and share more similarities with RCR plasmids and viruses from bacteria ( Heringer and Kuhn 2018 ; Kazlauskas et al 2019 ). In spite of these similarities, the prokaryotic plasmid and viral elements which are more closely related to Helitrons do not encode a helicase domain ( Heringer and Kuhn 2018 ), what makes the origin of Hel domains a still unsolved issue.…”

“…However, as revealed by recent findings, Rep domains from Helitrons are distantly related to proteins from prokaryotic TEs and eukaryotic viruses, and share more similarities with RCR plasmids and viruses from bacteria ( Heringer and Kuhn 2018 ; Kazlauskas et al 2019 ). In spite of these similarities, the prokaryotic plasmid and viral elements which are more closely related to Helitrons do not encode a helicase domain ( Heringer and Kuhn 2018 ), what makes the origin of Hel domains a still unsolved issue. The absence of helicases on the coding sequences of prokaryotic RC TEs, together with the presence of introns in some Hel domains from plants and Caenorhabditis elegans Helitrons , have been considered as tentative evidences that a Helitron ancestor acquired its Hel domain by capturing a helicase gene from its eukaryotic host ( Kapitonov and Jurka 2001 , 2007 ; Thomas and Pritham 2015 ).…”

“…Helitrons can be classified into four structural and coding variants, namely Helitron , Helentron , Helitron2 , and Proto-Helentron ( Thomas and Pritham 2015 ). In contrast to the first three variants, which have been shown to represent distinct phylogenetic groups ( Poulter et al 2003 ; Thomas et al 2014 ; Heringer and Kuhn 2018 ), Proto-Helentron elements seem to constitute a subtype of Helentrons with derived Helitron -like structural features ( Thomas et al 2014 ). Although all Helitrons have RepHel proteins with two major domains, distinct variants, or specific variant lineages, can encode additional domains in their transposase or/and additional genes.…”