Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Abstract

Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and non-metric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.

Systematic annotation ofHelitron-like elements in eukaryote genomes using HELIANO

“…Using a large set of eukaryote genomes, we found that HELIANO could quickly produce a range of annotations, from a lack of full-length HLE to predictions of thousands of full-length and non-autonomous copies. We did not predict any HLE using HELIANO on 4,491 bacterial genomes, in accordance with the current model on the evolution of HLEs (46). Similarly, we did not detect HLEs in 139 of the 404 screened eukaryote genomes, a finding underscoring that false positives are not a central issue.…”

“…Recent studies have identified variants of Helitrons named Helentron and Helitron2 (12)(13)(14)(15)(16)(17). To avoid confusion, we will collectively use the term Helitron-like elements (HLEs) to refer to all variants (Figure 1).…”

“…HLEs also vary in their insertion site preferences: the Helitron variant usually inserts between A and T nucleotides, while Helitron2/Helentrons generally insert between T and T nucleotides (12,15,16) (Figure 1A). Based on their transposase sequence similarity, Helitron and Helentron/Helitron2 variants are phylogenetically distinguishable (12,13,25).…”

Genome-Wide Identification of G-Quadruplex forming regions in Arabidopsis: Unraveling the Role of Pif like Helicase (AtPLH1) in Gene Regulation and Stress Response

“…These protein sequences showed higher similarity to ScPif1 (38% for AtPLH1, 46% for AtPLH2 and 47% for AtPLH3) as compared to HsPif1 (~30%) (Supplementary Table 2a). A recent study suggested that Pif sequences in Arabidopsis emerged from Helitron/Helentron helicase domains (Heringer and Kuhn, 2022).…”

Structural Studies of Pif1 Helicases from Thermophilic Bacteria

“…However, Pif1 is related to cancer in humans since mutations in Pif1 have been linked to oncogenesis [ 14 , 15 , 16 , 17 ]. Sequences related to Pif1 were also found in some genomes, mostly of plants and bats, as being part of helitron transposons [ 18 ] and these Pif1-like sequences forming Hel domains of helitron transposases may have originated from bacteria [ 19 ].…”