Targeting of human mitochondrial DNA with programmable pAgo nuclease

Rimskaya, B.; Kropocheva, E.; Shchukina, E.; Ulaschik, E.; Gelgenbein, D.; Lisitskaya, L.; Shmanai, V.; Smirnikhina, S.; Kulbachiskiy, A.; Mazunin, I.

doi:10.1101/2025.11.20.689640

bioRxiv · 10.1101/2025.11.20.689640

Targeting of human mitochondrial DNA with programmable pAgo nuclease

Rimskaya, B.·Kropocheva, E.·Shchukina, E.·Ulaschik, E.·Gelgenbein, D.·Lisitskaya, L.·Shmanai, V.·Smirnikhina, S.·Kulbachiskiy, A.·Mazunin, I.

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Abstract

Manipulating the mitochondrial genome remains a major challenge in genetic engineering, largely due to the mitochondrial double-membrane structure. While recent advances have expanded the genetic toolkit for nuclear and cytoplasmic targets, precise editing of mtDNA has remained elusive. Here we report the first successful mitochondrial import of a functional RNA-guided prokaryotic Argonaute protein from the mesophilic bacterium Alteromonas macleodii (AmAgo). By directing AmAgo to the single-stranded D- or R-loop region of mtDNA using synthetic RNA guides, we observed a nearly threefold reduction in mtDNA copy number in human cell lines. This proof of concept study demonstrates that a bacterial Argonaute can remain active within the mitochondrial environment and influence mtDNA levels. These findings lay the groundwork for further development of programmable systems for mitochondrial genome manipulation. HighlightsAmAgo targeted to mitochondria significantly reduces human mtDNA copy number Mitochondrial localization of AmAgo is essential for changes in the mtDNA content AmAgo effects on mtDNA are modulated by exogenous guide RNAs Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/689640v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@ddd069org.highwire.dtl.DTLVardef@9db9a3org.highwire.dtl.DTLVardef@1068b02org.highwire.dtl.DTLVardef@904c87_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Rimskaya, B., Kropocheva, E., Shchukina, E., Ulaschik, E., Gelgenbein, D., Lisitskaya, L., Shmanai, V., Smirnikhina, S., Kulbachiskiy, A., Mazunin, I.. 2025-11-21. Targeting of human mitochondrial DNA with programmable pAgo nuclease. https://doi.org/10.1101/2025.11.20.689640

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