Programmable DNA Cleavage by Cyanobacterial Argonaute Proteins

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Yuliya S. Zaitseva^1#, Ekaterina V. Kropocheva^1#, Andrey V. Kulbachinskiy^1,a*, and Daria M. Gelfenbein^1,b*

¹Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia

^* To whom correspondence should be addressed.

^# These authors contributed equally to the work.

Received: August 19, 2025; Revised: September 9, 2025; Accepted: September 15, 2025

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Argonaute proteins are an evolutionarily conserved family of proteins capable of recognizing and cleaving specific nucleic acid sequences using complementary guide molecules. Eukaryotic Argonautes play a key role in RNA interference by utilizing short RNAs of various classes to recognize target mRNAs. Prokaryotic Argonautes are much more diverse and most of them recognize DNA targets. The search for new Argonautes that would be active under varying conditions is important for both understanding their functions and developing new tools for genetic technologies. Many previously studied Argonautes exhibit low activity at low and moderate temperatures. To overcome this limitation, we isolated and studied two Argonaute proteins from psychrotolerant cyanobacteria, CstAgo from Cyanobacterium stanieri and CspAgo from Calothrix sp. Both proteins use short DNA guides to recognize and cleave DNA targets. CstAgo displayed no specificity for the 5′-end structure of the guide, while CspAgo demonstrated a weak preference for the 5′-terminal nucleotide. CstAgo was highly active and capable of cleaving single-stranded DNA at temperatures from 10 to 50°C. CspAgo was more cold-sensitive but cleaved double-stranded plasmid DNA using specific guides. Therefore, the studied proteins can be potentially used for DNA manipulations under a wide range of conditions.

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KEY WORDS: Argonaute, programmable nucleases, DNA cleavage

DOI: 10.1134/S0006297925602680

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