Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease

Kim, Seung-Yoon; Jung, Yuna; Lim, Dongbin

doi:10.1016/j.bbrc.2020.02.145

Cited by 23 publications

(20 citation statements)

References 20 publications

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“…Here, we show that the APAZ-containing Sir2 and short pAgo proteins form a heterodimeric complex (Fig. 3) similarly as in the case of a short pAgo and a Mrr nuclease domain-containing protein 25 . Furthermore, our structure modelling results show that the APAZ region of Sir2 proteins shares similarity with the N, L1 and L2 domains of canonical Agos substantiating previous sequence-based predictions 11,19 At the same time, Sir2 proteins entirely lack the PAZ domain (Fig.…”

Section: Discussionsupporting

confidence: 60%

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion

Zaremba

Dakineviciene

Golovinas

et al. 2021

Preprint

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Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID, and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). Intriguingly, the majority (~60%) of prokaryotic Agos (pAgos) identified bioinformatically are shorter (comprised of only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here, we show that short pAgos from Geobacter sulfurreducens, Caballeronia cordobensis and Paraburkholderia graminis, together with the NAD+-bound Sir2-proteins form a stable heterodimeric Sir2/Ago complex that recognizes invading plasmid or phage DNA through the pAgos subunit and activates Sir2 subunit triggering the endogenous NAD+ depletion and cell death thus preventing the propagation of invading DNA. This is the first demonstration that short Sir2-associated pAgos provide defence against phages and plasmids and underscores the diversity of mechanisms of prokaryotic Agos.

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Section: Discussionsupporting

confidence: 60%

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion

Zaremba

Dakineviciene

Golovinas

et al. 2021

Preprint

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“…APAZ domains are commonly fused to SIR2, Toll/interleukin-1 receptor (TIR)-like, or DUF4365 domains ( Ryazansky et al., 2018 ; Swarts et al, 2014b ). It was predicted that these domains are nucleases that compensate for the loss of catalytic activity of the associated short pAgos ( Hegge et al., 2018 ), and it was recently proposed that a short pAgo complexed with a DUF4365-APAZ domain mediates RNA-guided DNA cleavage ( Kim et al., 2020 ). However, most short pAgo-associated domains are fused to a SIR2 or TIR domain.…”

Section: Introductionmentioning

confidence: 99%

Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

Koopal

Potocnik

Mutte

et al. 2022

Cell

134

164

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“…To date, only a few pAgos derived from thermophilic archaea and mesophilic bacteria have been well characterized ( Swarts et al, 2014a , 2015 ; Kaya et al, 2016 ; Zander et al, 2017 ; Cao et al, 2019 ; Chong et al, 2019 ; Hegge et al, 2019 ; Kuzmenko et al, 2019 ; Kim et al, 2020 ; Olina et al, 2020 ; Liu et al, 2021b ). Some Agos can act as programmable endonucleases to cleave targets between nucleotides 10 and 11 using a divalent cation to catalyze the hydrolysis of the phosphodiester bond that lies across nucleotides 10 and 11 of the base-pairing guide ( Swarts et al, 2015 ; Jolly et al, 2020 ; Kuzmenko et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern

et al. 2021

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Argonaute proteins (Agos) from thermophilic archaea are involved in several important processes, such as host defense and DNA replication. The catalytic mechanism of Ago from different microbes with great diversity and genome editing potential is attracting increasing attention. Here, we describe an Argonaute from hyperthermophilic Ferroglobus placidus (FpAgo), with a typical DNA-guided DNA endonuclease activity but adopted with only a short guide 15–20 nt length rather than a broad guide selectivity for reported Agos. FpAgo performed the precise cleavage of phosphodiester bonds between 10 and 11 nt on the target strand (counting from the guide strand) guided strictly by 5′-phosphorylated DNA at temperatures ranging from 75 to 99°C. The cleavage activity was regulated by the divalent cations Mn2+, Mg2+, Co2+, and Ni2+. In addition, FpAgo possesses guide/target mismatch tolerance in the seed region but is sensitive to mismatches in the 3′-guide region. Notably, the EMSA assay revealed that the FpAgo-guide-target ternary complex exhibited a stronger binding affinity for short 15 and 16 nt guide DNAs than longer guides. Moreover, we performed structural modeling analyses that implied the unique PAZ domain of FpAgo for 3′-guide recognition and binding to affect guide length specificity. This study broadens our understanding of thermophilic Agos and paves the way for their use in DNA manipulation.

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Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease

Cited by 23 publications

References 20 publications

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion

Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern

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Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease

Cited by 23 publications

References 20 publications

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern

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Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion

Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD⁺ depletion