Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species

Abstract

Some families of mobile elements in bacterial genomes encode not only a transposase but also an accessory TnpB gene. This gene has been shown to encode an RNA-guided DNA endonuclease, co-evolving with Y1 transposase and serine recombinase in mobile elements IS605 and IS607. In this paper, we reveal the evolutionary relationships among TnpB-containing mobile elements (TCMEs) in well-assembled genomes of six bacterial species: Bacillus cereus, Clostridioides difficile, Deinococcus radiodurans, Escherichia coli, Helicobacter pylori and Salmonella enterica. In total, 9996 TCMEs were identified in 4594 genomes. They belonged to 39 different insertion sequences (ISs). Based on their genetic structures and sequence identities, the 39 TCMEs were classified into three main groups and six subgroups. According to our phylogenetic analysis, TnpBs include two main branches (TnpB-A and TnpB-B) and two minor branches (TnpB-C and TnpB-D). The key TnpB motifs and the associated Y1 and serine recombinases were highly conserved across species, even though their overall sequence identities were low. Substantial variation was observed for the rate of invasion across bacterial species and strains. Over 80% of the genomes of B. cereus, C. difficile, D. radiodurans and E. coli contained TCMEs; however, only 64% of the genomes of H. pylori and 44% of S. enterica genomes contained TCMEs. IS605 showed the largest rate of invasion in these species, while IS607 and IS1341 had a relatively narrow distribution. Co-invasions of IS605, IS607 and IS1341 elements were observed in various genomes. The largest average copy number was observed for IS605b elements in C. difficile. The average copy numbers of most other TCMEs were smaller than four. Our findings have important implications for understanding the co-evolution of TnpB-containing mobile elements and their biological roles in host genome evolution.

Keywords: IS1341; IS605; IS607; TnpB; transposable elements.

Figure 1

Structure organization of TCME elements. ORFs are presented as boxes with arrowheads showing the direction of transcription: LE and RE are red and blue boxes, respectively. (A) Three genetic structures of IS605 elements. (B) Two genetic structures of IS607 elements. (C) Genetic structure of IS1341 elements.

Figure 2

The overall identity of Y1, SR, and TnpB. (A) The identity of 39 mined TnpB proteins in six species. (B) The identity of 15 mined Y1 proteins in six species. (C) The identity of 6 mined SR proteins in six species.

Figure 3

The phylogenetic tree of SR, Y1, and TnpB. The bootstrap values are indicated with a black circle (>90%) and a grey circle (70–90%). (A) The phylogenetic tree of TnpB and IscB. The TnpB proteins are classified into two main branches (TnpB-A and TnpB-B) and two minor branches (TnpB-C and TnpB-D), are indicated with blue, green, purple, and orange circles, respectively. The IscB formed a single branch shown with red circles. The mined TnpBs from six species are also shown in orange background. The IS1341 subgroup is shown in blue background. The IS605 subgroup is shown in green background. The IS607 family is shown with purple background. (B) The phylogenetic tree of SR. The SR proteins from ISfinder are shown in green background. The mined SR proteins are shown in blue background. (C) The phylogenetic tree of Y1. The Y1 proteins from ISfinder are shown in orange. The mined-Y1 proteins are shown in green.

Figure 4

The alignments of TnpB, Y1, and SR protein sequences. The alignment was performed with MAFFT and drawn by Jalview Version 2. (A) Schematic of TnpB. The key domains include HTH—helix turn helix (blue), WED—wedge domain (grey), RuvC I, II, III (green), HH—arginine rich helix (yellow), ZF—zinc finger (red). (B) The alignment of several sequences was selected from TnpB-B, TnpB-B, TnpB-C and TnpB-D subgroups according to the phylogenetic tree. The HTH, RKrich HH, ZF, and RuvC I, II, and III domains are marked using a red box. (C) The alignments of the Y1 sequence. The HuH, Y and Q residues are indicated. (D) The alignments of SR. The DNA banding, catalytic, and Helix domains are also shown. The active site seine is marked using a black arrow.

Figure 5

The genome number of different TCME groups in six species. The IS607 is shown in grey color, IS605 is shown in orange color, and the color blue represents IS1341.

Figure 6

The average copies number of different subgroups of TCMEs in genomes of six studied bacterial species. The IS605a, IS605b, IS605c, IS607a, IS607b, and IS1341 subgroups were shown in black, orange, grey, green, blue, and red, respectively.