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Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses

TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of...

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Autores principales: Jiang, Kaiyi, Lim, Justin, Sgrizzi, Samantha, Trinh, Michael, Kayabolen, Alisan, Yutin, Natalya, Koonin, Eugene V., Abudayyeh, Omar O., Gootenberg, Jonathan S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312701/
https://www.ncbi.nlm.nih.gov/pubmed/37398409
http://dx.doi.org/10.1101/2023.06.13.544871
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author Jiang, Kaiyi
Lim, Justin
Sgrizzi, Samantha
Trinh, Michael
Kayabolen, Alisan
Yutin, Natalya
Koonin, Eugene V.
Abudayyeh, Omar O.
Gootenberg, Jonathan S.
author_facet Jiang, Kaiyi
Lim, Justin
Sgrizzi, Samantha
Trinh, Michael
Kayabolen, Alisan
Yutin, Natalya
Koonin, Eugene V.
Abudayyeh, Omar O.
Gootenberg, Jonathan S.
author_sort Jiang, Kaiyi
collection PubMed
description TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of diverse eukaryotes and their viruses for TnpB homologs and identified numerous putative RNA-guided nucleases that are often associated with various transposases, suggesting they are encoded in mobile genetic elements. Reconstruction of the evolution of these nucleases, which we rename Horizontally-transferred Eukaryotic RNA-guided Mobile Element Systems (HERMES), revealed multiple acquisitions of TnpBs by eukaryotes and subsequent diversification. In their adaptation and spread in eukaryotes, HERMES proteins acquired nuclear localization signals, and genes captured introns, indicating extensive, long term adaptation to functioning in eukaryotic cells. Biochemical and cellular evidence show that HERMES employ non-coding RNAs encoded adjacent to the nuclease for RNA-guided cleavage of double-stranded DNA. HERMES nucleases contain a re-arranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that HERMES can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.
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spelling pubmed-103127012023-07-01 Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses Jiang, Kaiyi Lim, Justin Sgrizzi, Samantha Trinh, Michael Kayabolen, Alisan Yutin, Natalya Koonin, Eugene V. Abudayyeh, Omar O. Gootenberg, Jonathan S. bioRxiv Article TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of diverse eukaryotes and their viruses for TnpB homologs and identified numerous putative RNA-guided nucleases that are often associated with various transposases, suggesting they are encoded in mobile genetic elements. Reconstruction of the evolution of these nucleases, which we rename Horizontally-transferred Eukaryotic RNA-guided Mobile Element Systems (HERMES), revealed multiple acquisitions of TnpBs by eukaryotes and subsequent diversification. In their adaptation and spread in eukaryotes, HERMES proteins acquired nuclear localization signals, and genes captured introns, indicating extensive, long term adaptation to functioning in eukaryotic cells. Biochemical and cellular evidence show that HERMES employ non-coding RNAs encoded adjacent to the nuclease for RNA-guided cleavage of double-stranded DNA. HERMES nucleases contain a re-arranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that HERMES can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications. Cold Spring Harbor Laboratory 2023-06-14 /pmc/articles/PMC10312701/ /pubmed/37398409 http://dx.doi.org/10.1101/2023.06.13.544871 Text en https://creativecommons.org/licenses/by-nc/4.0/It is made available under aCC-BY-NC 4.0 International license.
spellingShingle Article
Jiang, Kaiyi
Lim, Justin
Sgrizzi, Samantha
Trinh, Michael
Kayabolen, Alisan
Yutin, Natalya
Koonin, Eugene V.
Abudayyeh, Omar O.
Gootenberg, Jonathan S.
Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title_full Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title_fullStr Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title_full_unstemmed Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title_short Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
title_sort programmable rna-guided endonucleases are widespread in eukaryotes and their viruses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312701/
https://www.ncbi.nlm.nih.gov/pubmed/37398409
http://dx.doi.org/10.1101/2023.06.13.544871
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