Harbinger Transposons and an Ancient HARBI1 Gene Derived from a Transposase
Abstract
In this study we report main properties of Harbinger DNA transposons identified in protists, plants, insects, worms, and vertebrates. This is the first superfamily of eukaryotic DNA transposons where all autonomous transposons, even those that are hosted by species from different kingdoms, encode two proteins: a superfamily-specific transposase and a DNA-binding protein characterized by the presence of the conserved SANT/myb/trihelix motif. The last motif is known to be important for the DNA binding by different transcription regulators. Therefore, we suggest that this protein is necessary for coordinated expression of the Harbinger transposase. Although mammalian genomes are free of recognizable remnants of Harbingers, we identified a widely expressed HARBI1 gene encoding a 350-aa protein entirely derived from a Harbinger transposase some 450-500 million years ago. The HARBI1 proteins are conserved in humans, rats, mice, cows, pigs, chickens, frogs, and various bony fish, as well as other extremely important proteins, including RAG1 and RAG2. Conserved motifs detected in the Harbinger transposases are also well preserved in the HARBI1 proteins. Therefore, the HARBI1 proteins are expected to be nucleases important for functioning of bony vertebrates. We also found that the protein most similar to HARBI1 is encoded by an autonomous Harbinger 3_DR transposon that was transpositionally active in the zebrafish genome a few million years ago. Nonautonomous transposons derived from Harbinger3_DR are characterized by a striking preference for a 17-bp target site never seen previously in any other DNA transposon. Based on this observation, we suggest that the hypothetical HARBI1 nucleases are also characterized by a strong DNA-target specificity.
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The distances between the second D and E residues are much longer in Transib transposons (206-214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies.
“This includes the distances between the second D and E residues, which are much longer in Transib transposons (206–214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies (e.g., approximately 35-aa in Mariner/Tc1 [23], 2-aa in P [23], approximately 35-aa in Harbinger [24], with hAT as an exception (325-aa, [25]).”
From RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons (2005) · cites this paper as [24]
Transib transposons belong to the only superfamily of eukaryotic DNA transposons with 5-bp TSDs generated upon insertions into the genome.
“Given the predominance of 5-bp TSDs, it is striking that Transib transposons belong to the only superfamily of eukaryotic DNA transposons with 5-bp TSDs generated upon insertions into the genome [17,24].”
From RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons (2005) · cites this paper as [24]
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RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
Kapitonov, V. V., & Jurka, J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030181 · Cited by 521 · see citing works
Self-citation
- Authors
- Kapitonov, V. V., & Jurka, J.
- Affiliations
- Genetic Information Research Institute (US)
- Venue
- DNA and Cell Biology
- Publisher
- SAGE Publications
- Published
- 2004-05
- Volume
- 23
- Issue
- 5
- Pages
- 311-324
- ISSN
- 1044-5498 (ISSN-L)
- 1557-7430
- OpenAlex
- W1980996964
- Cited by
- 128
- References
- 55
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 8 · 2023: 6 · 2022: 5 · 2021: 23 · 2020: 5 · 2019: 5 · 2018: 5 · 2017: 5 · 2016: 4 · 2015: 3 · 2014: 2 · 2013: 4 · 2012: 6
- FWCI
- 5.89
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- DNA and Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- U.S. National Library of Medicine (P41LM006252, 2 P41 LM 06252-04A1)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- DNA transposons, transposase, DNA-binding proteins, zebrafish genome, transposon evolution, vertebrate genomes
- MeSH terms
- Amino Acid Sequence, Animals, Anopheles, DNA Transposable Elements, Humans, Insecta, Molecular Sequence Data, Vertebrates, Zebrafish, Conserved Sequence, Diatoms, Gene Expression Regulation, Developmental, Evolution, Molecular, Transposases, Amino Acid Motifs, Takifugu, Mice, Rats
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