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.

Keywords: Helitron; mobile genetic element; rolling-circle replication; viral evolution.

Figure 1

Modular diversity of HUH endonucleases. Schematic representation of the rolling-circle replication (RCR) proteins included in the present analysis. Rolling-circle replication endonuclease (RCRE) domains have the first two motifs (I and II), in addition to the third motif represented by one or two tyrosines (Y) in the catalytic core (dots represent variable amino acid residues). Domains are not drawn to scale, and segments after helicase domains are not represented. Based on information from Chandler et al. [1], Koonin and Dolja [8], and the Conserved Domain Database (CDD) search tool [10].

Figure 2

Phylogenetic analysis of RCRE domain sequences. Clade colors indicate each tyrosine group: Y1 (green), Y2 (red), and Yx (blue). Taxa colors represent the family of each element (box on the upper right). See Table S1 for taxa information. Phylogeny inferred by the Maximum Likelihood method (LG+G+I). The same phylogeny, with the numerical support values represented, is shown on Figure S1.

Figure 3

Non-metric multidimensional scaling (NMDS) of evolutionary divergence between RCRE domains. (A) Ordinations with taxa represented by their sequence abbreviations. Colors indicate the different classes of mobile genetic elements. (B) Same ordinations of (A), with colors indicating the tyrosine group of each taxa. The scaling represents euclidean distances for two dimensions (stress: 0.26382).

Figure 4

Proposed scenario for the origin of Helitrons and other RCR elements. Arrows represent putative pathways to explain the observed relationship among RCR elements. Virion images were obtained from VIPERdb (http://viperdb.scripps.edu) [31].