The mechanism of bacterial defense system DdmDE fromLactobacillus casei DOI Creative Commons
Pingping Huang, P. S. Yan, Lijie Guo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 9, 2024

Abstract Bacteria has developed a diverse array of defense mechanisms to protect against invasion by mobile genetic elements. Recent study identified bacterial module DdmDE system which encodes helicase-nuclease fusion protein DdmD and putative prokaryotic Argonaute-like DdmE, imposing fitness advantages the bacteria eliminating invasive plasmids. However, mechanistic basis how detects degrades plasmids is not fully understood. Here, studying from Lactobacillus casei (LcDdmDE), we found that LcDdmD able degrade ssDNA nick in presence Mn 2+ , it exhibits 5’-3’ DNA helicase activity length-dependent mechanism. Meanwhile, serves as sensor utilizes guide recognize target DNA. We determined cryo-EM structures dimer bound with fork DNA, guide/target DNA-bound LcDdmE, complex LcDdmDE-bubble intermediate state well active state. Together functional analysis, revealed working mechanism LcDdmDE system. In such scenario, guided ssDNA, LcDdmE recruits auto-inhibited loading onto target. Through substantial conformational changes, dissociates into monomer unwind duplex for plasmid degradation. Our provides structural insights DdmDE, presenting pAgo-directed degradation allosterically regulated helicase-nuclease.

Language: Английский

Structure and Activation Mechanism of a Lamassu Phage Defence System DOI Creative Commons
Yan Li, David W. Adams, Hon Wing Liu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 15, 2025

Summary Lamassu is a diverse family of defence systems that protect bacteria, including pandemic strains Vibrio cholerae , against phage infection. They target essential cellular processes, aborting infection and preventing propagation by terminating the infected host. The mechanisms which efectors are activated when needed otherwise suppressed unknown. Here, we present structures system from Salmonella enterica . We show an oligomerization domain nuclease efector, LmuA, sequestered two tightly-folded SMC-like LmuB protomers LmuC. Upon activation, liberated LmuA proteins assemble into cyclic homo-tetramer, in four domains brought proximity to create active site capable cleaving DNA. propose tetramer formation likely one-way switch establishes threshold limit potential spontaneous activation cell death. Our findings reveal mechanism defence, involving liberation immune efectors, shed light on how balance potent responses with self-preservation.

Language: Английский

Citations

1
DdmDE eliminates plasmid invasion by DNA-guided DNA targeting DOI
Xiaoyuan Yang, Zhangfei Shen, Chen Wang

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5253 - 5266.e16

Published: Aug. 22, 2024

Language: Английский

Citations

7
Nucleic acid recognition during prokaryotic immunity DOI Creative Commons
Christian F. Baca, Luciano A. Marraffini

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(2), P. 309 - 322

Published: Jan. 1, 2025

Language: Английский

Citations

0
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus DOI Creative Commons
Zhikang Dai, Yu Chen, Zeyuan Guan

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(3)

Published: Jan. 24, 2025

Abstract Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting acids. However, activation mechanism of SiAgo system, comprising a short from archaeon Sulfolobus islandicus its associated SiAga1 SiAga2, remains largely unknown. Here, we determined cryo-electron microscopy structures SiAgo–Aga1 apo complex RNA–DNA-bound at resolutions 2.7 3.0 Å, respectively. Our results revealed that positively charged pocket is generated interaction between SiAga1, exhibiting an architecture similar to APAZ-pAgo accommodating Further investigation elucidated conserved acid recognition SiAgo–Aga1. Both are essential for antiviral defense. Biochemical structural analyses demonstrated undergoes extensive conformational changes binding RNA–DNA duplex, thereby licensing with effector SiAga2 trigger immune response. Overall, our findings highlight evolutionary conservation Agos across phylogenetic clades provide insights into system.

Language: Английский

Citations

0
A gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense DOI Creative Commons
Ruoyu Li, Yusong Liu, Haishan Gao

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(3)

Published: Jan. 24, 2025

Abstract The DdmDE antiplasmid system, consisting of the helicase-nuclease DdmD and prokaryotic Argonaute (pAgo) protein DdmE, plays a crucial role in defending Vibrio cholerae against plasmids. Guided by DNA, DdmE specifically targets plasmids, disassembles dimer, forms DdmD–DdmE handover complex to facilitate plasmid degradation. However, precise ATP-dependent DNA translocation mechanism has remained unclear. Here, we present cryo-EM structures bound single-stranded (ssDNA) nucleotide-free, ATPγS-bound, ADP-bound states. These structures, combined with biochemical analysis, reveal unique “gate-clamp” for ssDNA DdmD. Upon ATP binding, arginine finger residues R855 R858 reorient interact γ-phosphate, triggering HD2 domain movement. This shift repositions gate residue Q781, causing flip 3′ flank base, which is then clamped F639. After hydrolysis, releases nucleotide, inducing return its open state. conformational change enables translocate along one nucleotide 5′ direction. study provides new insights into contributes understanding mechanistic diversity within SF2 helicases.

Language: Английский

Citations

0
Bacterial Hachiman complex executes DNA cleavage for antiphage defense DOI Creative Commons

Yongqing Cui,

Zhikang Dai, Yifang Ouyang

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 17, 2025

Bacteria have developed a variety of immune systems to combat phage infections. The Hachiman system is novel prokaryotic antiphage defense comprising HamA and HamB proteins, which contains the DUF1837 helicase domains, respectively. However, mechanism remains only partially understood. Here, we present cryo-electron microscopy (cryo-EM) structure featuring fusion Cap4 nuclease domain within HamA. Further analysis indicates that on resembles PD-(D/E)XK but lacks active sites. Bioinformatics reveals catalytically inactive domains often recruit other functional fulfill anti-phage defense. interacts with form heterodimer HamAB mediate ATP hydrolysis execute DNA cleavage, thus implementing Our findings elucidate structural basis complex, highlighting critical roles in immunity. bacterial system. authors demonstrate type I-B functions as heterodimeric cooperate counteract infection.

Language: Английский

Citations

0
Target DNA-induced filament formation and nuclease activation of SPARDA complex DOI Creative Commons
Feng Wang,

Haijiang Xu,

Chendi Zhang

et al.

Cell Research, Journal Year: 2025, Volume and Issue: unknown

Published: March 24, 2025

Abstract The short Argonaute-based bacterial defense system, SPARDA ( S hort P rokaryotic Ar gonaute and D Nase/RNase- A PAZ), utilizes guide RNA to target invading complementary DNA exhibits collateral nuclease activity, leading cell death or dormancy. However, its detailed mechanisms remain poorly understood. In this study, we investigated the system from Novosphingopyxis baekryungensis Nba SPARDA) discovered an unexpected filament configuration upon binding, which strongly correlated with activity. Filament formation activation require a guide–target heteroduplex of sufficient length perfect complementarity at central region. series cryo-EM structures complexes, loaded RNA, varying lengths, substrate ssDNA, were determined ~3.0 Å resolution. Structural analyses indicated that binding induces dimerization complex, while engagement disrupts dimerization. Further propagation triggers through checkpoint mechanism. consists backbone formed by interlocking Argonaute proteins, inner layer composed DREN domains. leads tetramerization monomeric domain, activating activity against environmental nucleic acids — feature leveraged for molecular diagnostics. For bacteria heterologously expressing bacteriophages plasmids relies on formation. Collectively, these findings illustrate working mechanism complex highlight importance in host defense.

Language: Английский

Citations

0
The mechanism of bacterial defense system DdmDE from Lactobacillus casei DOI
Pingping Huang, P. S. Yan, Lijie Guo

et al.

Cell Research, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 24, 2024

Language: Английский

Citations

2
DdmDE eliminates plasmid invasion by DNA-guided DNA targeting DOI
Xiaoyuan Yang, Zhangfei Shen, Chen Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 20, 2024

Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA efense M odule DdmDE system. Through biochemical analysis, structural determination,

Language: Английский

Citations

0
Anti-plasmid immunity: a key to pathogen success? DOI
Jack P. K. Bravo

Future Microbiology, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 4

Published: Sept. 4, 2024

Language: Английский

Citations

0