Table 5C-2. Exaptation of transposases to regulatory and other protein functions


New Protein Function(s)


Budding yeast (Kluyveromyces lactis)

Mating-type switch specific endonuclease

(Rusche and Rine 2010)

Fission yeast (Schizosaccharomyces pombe)

Retrotransposon silencing

(Cam, Noma et al. 2008)

Fission yeast and mammals

Domestication of pogo-like transposases into centromere-binding proteins

(Casola, Hucks et al. 2008)

Ciliate protozoa

DNA cleavage for macronuclear development

(Nowacki, Higgins et al. 2009)


DAYSLEEPER from hAT transposase essential for normal plant growth; binds motif (Kubox1) upstream region of Ku70 DNA repair locus

(Bundock and Hooykaas 2005)


Transcription factors regulating light signalling

(Lin, Ding et al. 2007)


Maverick transposon-derived Mustang (MUG) family – essential for normal vigor and development

(Cowan, Hoen et al. 2005; Joly-Lopez, Forczek et al. 2012)

Sugarcane, rice, maize (Zea mays) and Sorghum bicolor

Mustang (MUG) family – highly conserved in grasses; ubiquitously transcribed, downregulated by phytohormones; possible involvement in hormonal homeostasis

 (Kajihara, de Godoy et al. 2012)


FHY3 and FAR1 transcriptional regulatory proteins involved in phytochrome A-signaling pathway

(Hudson, Lisch et al. 2003)

Cereal grasses (wheat, barley, rice, oat, rye, maize, sorghum and sugarcane)

Gary protein from hAT transposase, shows conservation and positive selection across grasses but function unknown

(Muehlbauer, Bhau et al. 2006)

Drosophila and other animals

Minos/Tc1 transposase related to paired DNA-binding domain and Pax family of transcription factors

(Franz, Loukeris et al. 1994; Breitling and Gerber 2000)


PIF transposons protein containing a Myb/SANT domain, closely related to MADF DNA-binding domain in several Drosophila transcription factors

(Casola, Lawing et al. 2007)

Drosophila and other animals

Pipsqueak (Psq) DNA binding domain family proteins related to CENP-B/transposase subgroup

(Siegmund and Lehmann 2002)


HARBI1, conserved protein for vertebrate development predicted nuclease, from Harbinger transposon

(Kapitonov and Jurka 2004)


Adaptive immune system endonuclease for VDJ joining activity in antigen receptor diversification

(Brandt and Roth 2004; Kapitonov and Jurka 2005)

Homo sapiens

Chimeric SETMAR chromatin remodeling function from Hsmar1 transposase

(Cordaux, Udit et al. 2006)

Homo sapiens

PogZ derived from lentivirus (retrovirus) integrase; interacts with lens epithelium-derived growth factor/p75 (LEDGF/p75)

(Bartholomeeusen, Christ et al. 2009)

Homo sapiens

Metnase/SETMAR – chromatin formatting, suppresses chromosome rearrangements, enhances DNA repair, replication, and decatenation

(Shaheen, Williamson et al. 2010; Fnu, Williamson et al. 2011)

Drosophila and humans

THAP apoptosis protein DNA-binding domain related to P factor transposase

(Roussigne, Kossida et al. 2003; Quesneville, Nouaud et al. 2005)

Many eukaryotes

WRKY-GCM1 Zn-finger DNA binding domain from MULE transposases

(Babu, Iyer et al. 2006)

Many eukaryotes

BED finger DNA-binding domain in chromatin insulator-binding proteins

(Aravind 2000)




Aravind, L. (2000). "The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases." Trends Biochem Sci 25(9): 421-423.

Babu, M. M., L. M. Iyer, et al. (2006). "The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons." Nucleic Acids Res 34(22): 6505-6520.

Bartholomeeusen, K., F. Christ, et al. (2009). "Lens epithelium-derived growth factor/p75 interacts with the transposase-derived DDE domain of PogZ." J Biol Chem 284(17): 11467-11477.

Brandt, V. L. and D. B. Roth (2004). "V(D)J recombination: how to tame a transposase." Immunol Rev 200: 249-260.

Breitling, R. and J. K. Gerber (2000). "Origin of the paired domain." Dev Genes Evol 210(12): 644-650.

Bundock, P. and P. Hooykaas (2005). "An Arabidopsis hAT-like transposase is essential for plant development." Nature 436(7048): 282-284.

Cam, H. P., K. Noma, et al. (2008). "Host genome surveillance for retrotransposons by transposon-derived proteins." Nature\ 451\(7177\): 431-436\.

Casola, C., D. Hucks, et al. (2008). "Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals." Mol Biol Evol 25(1): 29-41.

Casola, C., A. M. Lawing, et al. (2007). "PIF-like transposons are common in drosophila and have been repeatedly domesticated to generate new host genes." Mol Biol Evol 24(8): 1872-1888.

Cordaux, R., S. Udit, et al. (2006). "Birth of a chimeric primate gene by capture of the transposase gene from a mobile element." Proc Natl Acad Sci U S A 103(21): 8101-8106.

Cowan, R. K., D. R. Hoen, et al. (2005). "MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms." Mol Biol Evol 22(10): 2084-2089.

Fnu, S., E. A. Williamson, et al. (2011). "Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining." Proc Natl Acad Sci U S A 108(2): 540-545.

Franz, G., T. G. Loukeris, et al. (1994). "Mobile Minos elements from Drosophila hydei encode a two-exon transposase with similarity to the paired DNA-binding domain." Proc Natl Acad Sci U S A 91(11): 4746-4750.

Hudson, M. E., D. R. Lisch, et al. (2003). "The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway." Plant J 34(4): 453-471.

Joly-Lopez, Z., E. Forczek, et al. (2012). "A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana." PLoS Genet 8(9): e1002931.

Kajihara, D., F. de Godoy, et al. (2012). "Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum." Genet Mol Biol 35(3): 632-639.

Kapitonov, V. V. and J. Jurka (2004). "Harbinger transposons and an ancient HARBI1 gene derived from a transposase." DNA Cell Biol 23(5): 311-324.

Kapitonov, V. V. and J. Jurka (2005). "RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons." PLoS Biol 3(6): e181.

Lin, R., L. Ding, et al. (2007). "Transposase-derived transcription factors regulate light signaling in Arabidopsis." Science 318(5854): 1302-1305.

Muehlbauer, G. J., B. S. Bhau, et al. (2006). "A hAT superfamily transposase recruited by the cereal grass genome." Mol Genet Genomics 275(6): 553-563.

Nowacki, M., B. P. Higgins, et al. (2009). "A functional role for transposases in a large eukaryotic genome." Science 324(5929): 935-938.

Quesneville, H., D. Nouaud, et al. (2005). "Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element." Mol Biol Evol 22(3): 741-746.

Roussigne, M., S. Kossida, et al. (2003). "The THAP domain: a novel protein motif with similarity to the DNA-binding domain of P element transposase." Trends Biochem Sci 28(2): 66-69.

Rusche, L. N. and J. Rine (2010). "Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonuclease." Genes Dev 24(1): 10-14.

Shaheen, M., E. Williamson, et al. (2010). "Metnase/SETMAR: a domesticated primate transposase that enhances DNA repair, replication, and decatenation." Genetica 138(5): 559-566.

Siegmund, T. and M. Lehmann (2002). "The Drosophila Pipsqueak protein defines a new family of helix-turn-helix DNA-binding proteins." Dev Genes Evol 212(3): 152-157.