Internal initiation of reverse transcription in a Penelope-like retrotransposon

Chris J Frangieh; Max E Wilkinson; Daniel Strebinger; Jonathan Strecker; Michelle L Walsh; Guilhem Faure; Irina A Yushenova; Rhiannon K Macrae; Irina R Arkhipova; Feng Zhang

doi:10.1186/s13100-024-00322-z

Internal initiation of reverse transcription in a Penelope-like retrotransposon

Mob DNA. 2024 Jun 11;15(1):12. doi: 10.1186/s13100-024-00322-z.

Authors

Chris J Frangieh^{1

2

3

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5

6}, Max E Wilkinson^{1

2

3

4

5}, Daniel Strebinger^{1

2

3

4

5}, Jonathan Strecker^{1

2

3

4

5}, Michelle L Walsh^{1

2

3

4

5}, Guilhem Faure^{1

2

3

4

5}, Irina A Yushenova⁷, Rhiannon K Macrae^{1

2

3

4

5}, Irina R Arkhipova⁸, Feng Zhang^{9

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11

12

13}

Affiliations

¹ Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
³ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁴ Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁵ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁶ Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
⁷ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
⁸ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA. iarkhipova@mbl.edu.
⁹ Howard Hughes Medical Institute, Cambridge, MA, 02139, USA. zhang@broadinstitute.org.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. zhang@broadinstitute.org.
¹¹ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. zhang@broadinstitute.org.
¹² Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. zhang@broadinstitute.org.
¹³ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. zhang@broadinstitute.org.

Abstract

Eukaryotic retroelements are generally divided into two classes: long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons. A third class of eukaryotic retroelement, the Penelope-like elements (PLEs), has been well-characterized bioinformatically, but relatively little is known about the transposition mechanism of these elements. PLEs share some features with the R2 retrotransposon from Bombyx mori, which uses a target-primed reverse transcription (TPRT) mechanism, but their distinct phylogeny suggests PLEs may utilize a novel mechanism of mobilization. Using protein purified from E. coli, we report unique in vitro properties of a PLE from the green anole (Anolis carolinensis), revealing mechanistic aspects not shared by other retrotransposons. We found that reverse transcription is initiated at two adjacent sites within the transposon RNA that is not homologous to the cleaved DNA, a feature that is reflected in the genomic "tail" signature shared between and unique to PLEs. Our results for the first active PLE in vitro provide a starting point for understanding PLE mobilization and biology.

Keywords: GIY-YIG endonuclease; Hammerhead ribozyme; Reverse transcriptase.

Grants and funding

NSF MCB-2139001/National Science Foundation