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Review
. 2018 Dec 4;9(1):5165.
doi: 10.1038/s41467-018-07449-7.

DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins

Lidiya Lisitskaya  1 , Alexei A Aravin  2   3 , Andrey Kulbachinskiy  4
Affiliations
Review

DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins

Lidiya Lisitskaya et al. Nat Commun. .

Abstract

Recognition and repression of RNA targets by Argonaute proteins guided by small RNAs is the essence of RNA interference in eukaryotes. Argonaute proteins with diverse structures are also found in many bacterial and archaeal genomes. Recent studies revealed that, similarly to their eukaryotic counterparts, prokaryotic Argonautes (pAgos) may function in cell defense against foreign genetic elements but, in contrast, preferably act on DNA targets. Many crucial details of the pAgo action, and the roles of a plethora of pAgos with non-conventional architecture remain unknown. Here, we review available structural and biochemical data on pAgos and discuss their possible functions in host defense and other genetic processes in prokaryotic cells.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Structural organization of Ago proteins. The domain architecture of short and long pAgos is schematically illustrated at the top. Short pAgos always contain inactive PIWI domain (PIWI*). The structures of four representative Ago proteins are shown in ternary complexes with guide (“g-”) and target (“t-”) nucleic acids: short inactive AfAgo (PDB: 2W42) and long active TtAgo with g-DNA and t-DNA (PDB: 4NCB), long inactive RsAgo with g-RNA and t-DNA (PDB: 5AWH) and active human Ago2 with g-RNA and t-RNA (PDB: 4W5O). The N-domain is turquoise, L1 is yellow, PAZ is magenta, L2 is gray, MID is orange, PIWI is green. The guide strand is blue, the target strand is black. Metal ions bound in the MID-pocket (5′Me2+) or in the active center (acMe2+) are indicated
Fig. 2
Fig. 2
The catalytic cycle of Ago proteins. Guide-loaded Ago performs search for a complementary target through base-pairing with the seed region of the guide strand, followed by duplex propagation through the central part and the 3′-supplementary site of the guide, thus checking for possible mismatches. Conformational mobility of the PAZ domain (shown by arc-shaped arrows) likely facilitates correct base-pairing, through controlled release of the guide 3′-end and active site closure. Conformational changes in the active site allow binding of catalytic metal ions, followed by cleavage of the target strand and its stepwise release from the complex. The drawings are based on the structures of TtAgo at different steps of its functional cycle (PDBs, from the upper left corner, clockwise: 3DLH, 3F73, 4N41, 4NCB, 4NCA, 4N76, see Supplementary Fig. 2). The guide strand is blue, the target strand is black; only the target strand of DNA substrate is shown (the structure of complexes with double-stranded DNA remains unknown for any pAgo)
Fig. 3
Fig. 3
Conformational changes in the active site of TtAgo during target recognition and catalysis,. The active site residues are shown in red; the glutamate finger is indicated with a red circle. During first steps of guide binding and target recognition, the active site is unplugged (upper raw); duplex propagation is accompanied by changes in the conformations of the PIWI and PAZ domains (indicated with red arrows), plugging-in of the glutamate finger, catalytic metal binding, and activation of catalysis (lower raw). Finally, stepwise target release leads to unplugging of the active site, thus making possible recognition of the next target molecule. The PDB accession numbers (from the upper left corner, clockwise): 3DLH, 3F73, 4N41, 4NCB, 4NCA, 4N76 (see Fig. 2 and Supplementary Fig. 2)
Fig. 4
Fig. 4
Accommodation of helical imperfections in the ternary complexes of pAgo proteins. Structural features of the duplexes formed in the seed region in ternary complexes of TtAgo (upper raw) and RsAgo (bottom) containing bulges or mismatches (shown in red) in the guide or target strand, in comparison with fully double-stranded duplex (“ds”). Only the part of the duplex between the guide 5′-end and the active site in the PIWI domain is shown (guide positions 1 through 10–12 for various complexes); Mg2+ ions bound in the MID-pocket (5′Mg2+) and in the active site (acMg2+) are indicated; some complexes of TtAgo were obtained with a catalytically inactive mutant and thus lack catalytic metal ions. The distortions of the double-helix are shown with red arrowheads; the nucleotide bulges can be either stacked-in (bulges in the guide strand; g-4-A-5 and g-7-T-8 in TtAgo) or flipped-out of the duplex (bulges in the target strand; t-6′-A-7′, t-9′-U-10′ for TtAgo, t-3′-AA-4′ for RsAgo). The ternary complexes were obtained with g-DNA/t-DNA or g-DNA/t-RNA for TtAgo, or g-RNA/t-DNA for RsAgo, as indicated. The PDB accession numbers are (from left to right): TtAgo, 4NCB, 5XP8, 5XOU, 5XOW, 5XPA; RsAgo, 6D8P, 6D8A, 6D92, 6D9L, 6D9K. See Supplementary Table 1 and Supplementary Fig. 3 for full description of each complex
Fig. 5
Fig. 5
Proposed mechanisms of DNA interference by DNA-guided (TtAgo, left) and RNA-guided (RsAgo, right) pAgos. TtAgo was proposed firstly to process invader DNA in a guide-independent manner (“DNA chopping”, a), resulting in slow DNA fragmentation (b) and binding of short DNA duplexes (c), followed by dissociation of the passenger strand (d). Guide-loaded TtAgo can then attack the target DNA with high efficiency (e),. RsAgo was proposed to bind short RNAs processed from mRNAs by Ago-associated or cellular nucleases (a, b), followed by target DNA recognition (c), which can result in DNA degradation by accessory nucleases (d) and/or inhibition of transcription (e)
Fig. 6
Fig. 6
Possible functions of pAgos. In addition to their function in cell defense against invader DNA (or RNA) (a), pAgo proteins might hypothetically be involved in the regulation of gene expression (b), function as suicide systems (c), or participate in the processing of noncanonical DNA structures and DNA repair (d)
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References

    1. Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 2009;10:94–108. doi: 10.1038/nrg2504. - DOI - PMC - PubMed
    1. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science. 2001;293:1146–1150. doi: 10.1126/science.1064023. - DOI - PubMed
    1. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell. 2002;110:563–574. doi: 10.1016/S0092-8674(02)00908-X. - DOI - PubMed
    1. Meister G, et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell. 2004;15:185–197. doi: 10.1016/j.molcel.2004.07.007. - DOI - PubMed
    1. Joshua-Tor L. The Argonautes. Cold Spring Harb. Symp. Quant. Biol. 2006;71:67–72. doi: 10.1101/sqb.2006.71.048. - DOI - PubMed

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