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10.3390/genes14020523
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Article

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

by
Yali Wang
1,
Mengke Guo
1,
Naisu Yang
1,
Zhongxia Guan
1,
Han Wu
2,
Numan Ullah
1,
Emmanuel Asare
1,
Shasha Shi
1,
Bo Gao
1 and
Chengyi Song
1,*
1
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
2
Department of Immunology, School of Medicine, Shenzhen University, Shenzhen 518060, China
*
Author to whom correspondence should be addressed.
Genes 2023, 14(2), 523; https://doi.org/10.3390/genes14020523
Submission received: 22 November 2022 / Revised: 17 February 2023 / Accepted: 17 February 2023 / Published: 19 February 2023
(This article belongs to the Special Issue Co-evolution of Mobilome and Genome)
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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: TnpB; transposable elements; IS605; IS607; IS1341 TnpB; transposable elements; IS605; IS607; IS1341

Share and Cite

MDPI and ACS Style

Wang, Y.; Guo, M.; Yang, N.; Guan, Z.; Wu, H.; Ullah, N.; Asare, E.; Shi, S.; Gao, B.; Song, C. Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes 2023, 14, 523. https://doi.org/10.3390/genes14020523

AMA Style

Wang Y, Guo M, Yang N, Guan Z, Wu H, Ullah N, Asare E, Shi S, Gao B, Song C. Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes. 2023; 14(2):523. https://doi.org/10.3390/genes14020523

Chicago/Turabian Style

Wang, Yali, Mengke Guo, Naisu Yang, Zhongxia Guan, Han Wu, Numan Ullah, Emmanuel Asare, Shasha Shi, Bo Gao, and Chengyi Song. 2023. "Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species" Genes 14, no. 2: 523. https://doi.org/10.3390/genes14020523

APA Style

Wang, Y., Guo, M., Yang, N., Guan, Z., Wu, H., Ullah, N., Asare, E., Shi, S., Gao, B., & Song, C. (2023). Phylogenetic Relationships among TnpB-Containing Mobile Elements in Six Bacterial Species. Genes, 14(2), 523. https://doi.org/10.3390/genes14020523

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