Retrotransposon-like nature of Tp1 elements: implications for the organisation of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum
Open accessAbstract
The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in the hypermethylated (M+) fraction of the genome where they have been found exclusively in scrambled clusters of up to 50kb long. Scrambling is thought to have arisen by insertion of Tp1 into further copies of the same sequence. In the present study, sequence analysis of cloned Tp1 elements has revealed striking homologies of the predicted amino acid sequence to several highly conserved domains characteristic of retrotransposons. The relative order of the predicted coding regions indicates that Tp1 elements are more closely related to copia and Ty than to retroviruses. Self-integration and methylation of Tp1 elements may function to limit transposition frequency. Such mechanisms provide a possible explanation for the origin and organisation of M + DNA in the Physarum genome.
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Some retrotransposons require a tRNA molecule to initiate reverse transcription.
“Some retrotransposons also require a tRNA molecule to initiate reverse transcription (12)(13)(14).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [13]
tRNA i Met-primed reverse transcription is conserved among many LTR retrotransposons, including copia from Drosophila melanogaster, Tp1 and Tp2 from Physarum polycephalum, and Saccharomyces cerevisiae Ty5.
“tRNA i Met -primed reverse transcription is conserved among many LTR retrotransposons, including the copia retrovirus-like particle from Drosophila melanogaster (12), Tp1 and Tp2 from the slime mold Physarum polycephalum (13), and Saccharomyces cerevisiae Ty5 (14).”
From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [13]
Cites
Origins and evolutionary relationships of retroviruses
Doolittle, R. F., Johnson, M. S., & McClure, M. A. (1989) · The Quarterly Review of Biology · doi:10.1086/416128 · Cited by 577 · see citing works
Johnson, M. S., McClure, M. A., Feng, D. F., Gray, J., & Doolittle, R. F. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.20.7648 · Cited by 480 · see citing works
Kikuchi, Y., Ando, Y., & Shiba, T. (1986) · Nature · doi:10.1038/323824a0 · Cited by 90 · see citing works
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Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication
Jin, D., & Musier-Forsyth, K. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev118.002957 · Cited by 67 · see citing works
“tRNAi-primed reverse transcription is conserved among many LTR retrotransposons, including the copia retrovirus-like particle from Drosophila melanogaster (12), Tp1 and Tp2 from the slime mold Physarum polycephalum (13), and Saccharomyces cerevisiae Ty5 (14).”
Background
- Authors
- Rothnie, H. M., McCurrach, K. J., Glover, L. A., Hardman, N., Rothnie, H. M., McCurrach, K. J., Glover, L. A., & Hardman, N.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1991
- Volume
- 19
- Issue
- 2
- Pages
- 279-286
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC333591
- OpenAlex
- W1973735045
- Cited by
- 45
- References
- 3
- Citations by year
- 2019: 1 · 2013: 1
- FWCI
- 8.24
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Physical Sciences › Engineering › Biomedical Engineering › Slime Mold and Myxomycetes Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- retrotransposons, Physarum polycephalum, repetitive DNA, transposable elements, self-integration, DNA methylation, transposition regulation
- MeSH terms
- Amino Acid Sequence, Codon, DNA Transposable Elements, Endonucleases, Methylation, Molecular Sequence Data, Endopeptidases, Physarum, Repetitive Sequences, Nucleic Acid, RNA-Directed DNA Polymerase, Sequence Homology, Nucleic Acid, Genomic Library, Open Reading Frames, Sequence Alignment
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