AbiD/F

Description

AbiD, also known as AbiD1 or AbiF (N/A) , is an antiphage defense system belonging to the family of abortive infection (Abi) systems, discovered in the 90's in research related to the dairy industry (N/A) . These systems allow a bacterium infected by a bacteriophage to interrupt viral replication by triggering growth arrest or cell death, thereby preventing the spread of the phage within the bacterial population.

AbiD is a single gene system discovered in May 1995 in the plasmid pBF61 of Lactococcus lactis (N/A) . An homolog of AbiD, named AbiD1 was discovered in July 1995 (N/A) .

Molecular mechanism

The molecular mechanism of AbiD/AbiF is based on regulated ribonuclease-type toxicity. The AbiF system is a type III Toxin-Antitoxin system operating through direct interaction between antitoxin RNA RCd22 and AbiF which is the toxic protein in dimer form. The rcd22 gene is located immediately upstream of abiF within the same operon (N/A) .

For AbiD1 (N/A) (AAA79209), the expression of the protein is triggered by the orf1 of phage bIL66 which results in inhibition of the phage RuvC-like endonuclease activity and stops phage multiplication.

In Clostridioides difficile, the abiD/F gene encodes a dimeric ribonuclease containing two HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) domains (N/A) .

Structurally and functionally, AbiD/F systems share strong similarities with Cas13 RNA-targeting CRISPR-Cas effectors. Both contain HEPN domains and rely on RNA-mediated regulation, suggesting that AbiF-like systems represent evolutionary precursors of Cas13 and other RNA-targeting CRISPR-Cas defenses. Intermediate forms such as Cas13 exhibit biochemical properties bridging AbiF-type toxin–antitoxin systems and CRISPR-based immunity, supporting the evolutionary link between these mechanisms (N/A) .

Example of genomic structure

The AbiD is composed of 1 protein: AbiD.

Here is an example found in the RefSeq database:

The AbiD system in Idiomarina sp. OT37-5b (GCF_002968395.1, NZ_CP027188) is composed of 1 protein: AbiD (WP_105307479.1)

Distribution of the system among prokaryotes

Structure

Experimental validation

      
graph LR;
    Chopin_2005[Chopin et al., 2005] --> Origin_0
    Origin_0[lactococcal plasmid  
AAA63619.1] --> Expressed_0[lactococci]
    Expressed_0[lactococci] ----> 936 & c2 & P335
    subgraph Title1[Reference]
        Chopin_2005
end
    subgraph Title2[System origin]
        Origin_0
end
    subgraph Title3[Expression species]
        Expressed_0
end
    subgraph Title4[Protects against]
        936
        c2
        P335
end
    style Title1 fill:none,stroke:none,stroke-width:none
    style Title2 fill:none,stroke:none,stroke-width:none
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none