Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

Peter H Yoon; Petr Skopintsev; Honglue Shi; LinXing Chen; Benjamin A Adler; Muntathar Al-Shimary; Rory J Craig; Kenneth J Loi; Evan C DeTurk; Zheng Li; Jasmine Amerasekera; Marena Trinidad; Hunter Nisonoff; Kai Chen; Arushi Lahiri; Ron Boger; Steve Jacobsen; Jillian F Banfield; Jennifer A Doudna

doi:10.1093/nar/gkad1053

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

Nucleic Acids Res. 2023 Dec 11;51(22):12414-12427. doi: 10.1093/nar/gkad1053.

Authors

Peter H Yoon^{1

2}, Petr Skopintsev^{2

3}, Honglue Shi^{2

4}, LinXing Chen^{2

5}, Benjamin A Adler^{2

3}, Muntathar Al-Shimary^{1

2}, Rory J Craig³, Kenneth J Loi^{1

2}, Evan C DeTurk^{2

3}, Zheng Li⁶, Jasmine Amerasekera⁷, Marena Trinidad^{2

4}, Hunter Nisonoff⁸, Kai Chen^{1

2}, Arushi Lahiri^{1

2}, Ron Boger^{2

3}, Steve Jacobsen^{6

9}, Jillian F Banfield^{2

5}, Jennifer A Doudna^{1

2

3

4

10

11

12

13}

Affiliations

¹ Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA.
² Innovative Genomics Institute; University of California, Berkeley, CA, USA.
³ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
⁴ Howard Hughes Medical Institute, University of California, Berkeley; Berkeley, CA, USA.
⁵ Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
⁶ Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
⁷ Department of Human Genetics, University of California, Los Angeles, CA, USA.
⁸ Center for Computational Biology, University of California, Berkeley; Berkeley, CA, USA.
⁹ Howard Hughes Medical Institute, University of California, Los Angeles CA, USA.
¹⁰ Gladstone Institutes; San Francisco, CA, USA.
¹¹ Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA.
¹² Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA, USA.
¹³ Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA.

Abstract

RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.

MeSH terms

Bacteria* / enzymology
Bacteria* / genetics
DNA Transposable Elements
Endonucleases* / genetics
Endonucleases* / metabolism
Eukaryotic Cells / enzymology
Evolution, Molecular*
Prokaryotic Cells / enzymology
Transposases / metabolism

Substances

DNA Transposable Elements
Endonucleases
Transposases

Grants and funding

U01 AI142817/AI/NIAID NIH HHS/United States