Nucleic acid mediated activation of a short prokaryotic Argonaute immune system

• Published in: Nature communications Vol. 15; no. 1; pp. 4852 - 12
• Main Authors: Kottur, Jithesh, Malik, Radhika, Aggarwal, Aneel K.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06-06-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/326/41/2533; 631/45/173; 631/535/1258/1259; 631/535/1266; 82/80; Argonaute Proteins - chemistry; Argonaute Proteins - genetics; Argonaute Proteins - metabolism; Assembly; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding; Catalysis; Cryoelectron Microscopy; Crystal structure; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - metabolism; Humanities and Social Sciences; Hydrolysis; Immune system; Models, Molecular; multidisciplinary; Nucleic acids; Nucleic Acids - chemistry; Nucleic Acids - metabolism; Protein Binding; Protein Domains; Ribonucleic acid; RNA; RNA, Guide, CRISPR-Cas Systems - metabolism; Science; Science & Technology - Other Topics; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49271-4

A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P)
+
hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15–3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.
The SPARTA defense system, activated by invading DNA for NAD(P)+ hydrolysis, was recently identified in bacteria. Here, authors visualize SPARTA before and after nucleic acid binding and uncover the basis of its active assembly leading to abortive infection.