SMC-based immunity against extrachromosomal DNA elements

Liu, Hon Wing; Roisné-Hamelin, Florian; Gruber, Stephan

doi:10.1042/bst20221395

Cited by 6 publications

(6 citation statements)

References 97 publications

(184 reference statements)

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“…The SMC homologs can be activated by specific signatures in incoming DNA elements. Depending on the system, they either degrade foreign DNA (WadJet) or induce abortive infection (Lamassu) upon detecting invasive elements ( 5 , 6 , 51 ) (Robins WP, et al, 2023). It is thus possible that the ribonuclease activity in Class 14 SMC-HicA proteins might similarly be triggered by foreign DNA or RNA, potentially playing a role in abortive infection or degradation of invasive elements.…”

Section: Resultsmentioning

confidence: 99%

Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense

Gerdes

2024

mBio

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Toxin–antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, the Mycobacterium tuberculosis genome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands has unveiled a wide array of systems, including TAs that serve in anti-phage defense. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involve hicA adjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles. IMPORTANCE Prokaryotic organisms harbor a multitude of toxin–antitoxin (TA) systems, which have long puzzled scientists as “genes in search for a function.” Recent scientific advancements have shed light on the primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This article describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world.

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Section: Resultsmentioning

confidence: 99%

Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense

Gerdes

2024

mBio

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“…200 µL of culture was harvested and serially diluted sevenfold (from 10 - 1 to 10 - 7 ) in PBS. For total cell number count, 5 µL of the dilutions from 10 - 4 to 10 - 7 were spotted onto nutrient agar plates in duplicate. For pBAD-containing cells, the same amount of all dilutions was spotted onto nutrient agar plates supplemented with ampicillin (100 µg/mL final).…”

Section: Methodsmentioning

confidence: 99%

“…They play crucial roles in various cellular processes, including chromosome segregation during cell division (condensin and cohesin in eukaryotes, Smc-ScpAB, MukBEF, and MksBEF in prokaryotes), the regulation of gene expression, DNA repair, and recombination (cohesin and Smc5/6 in eukaryotes) 1–3 . More recently, emerging evidence suggests that SMC-based complexes are also involved in cellular defence against invasive or selfish genetic elements 4 . In prokaryotes, the JET complex (short for Wadjet, JetABCD) is a sequence-independent anti-plasmid nuclease 5–10 , while the human Smc5/6 complex functions as a viral restriction factor 4,11 .…”

Section: Introductionmentioning

confidence: 99%

“…More recently, emerging evidence suggests that SMC-based complexes are also involved in cellular defence against invasive or selfish genetic elements 4 . In prokaryotes, the JET complex (short for Wadjet, JetABCD) is a sequence-independent anti-plasmid nuclease 5–10 , while the human Smc5/6 complex functions as a viral restriction factor 4,11 . Nevertheless, the role of loop extrusion in DNA immune sensing remains unclear 8,9 .…”

Section: Introductionmentioning

confidence: 99%

“…(A) Schematic representation of E. coli GF4-3 (Type I) JET nuclease dimer-of-pentamers (d-o-p) in the resting state 4,8 . (B) Left: Schematic depicting DNA end masking and pseudo-circularization when streptavidin tetramer is added to biotinylated linear DNA.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for plasmid restriction by SMC JET nuclease

Roisné-Hamelin,

Liu,

Taschner

et al. 2023

Preprint

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SummaryDNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of circular plasmids through DNA cleavage; yet the mechanisms for target recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage implying that residual unextruded DNA is cleaved. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as principle for non-self DNA recognition and molecular signature for plasmid cleavage. We elucidate key elements of SMC loop extrusion including motor directionality and the structure of a DNA-holding state.

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