Hachiman
Description
Hachiman Type 1 systems were the first discovered and can be found in 3.4% of microbial genomes (N/A) . Hachiman Type 1 systems are encoded by two genes, hamA (annotated as a Domain of Unknown Function, DUF) and hamB (annotated as a helicase) (N/A) .
More recently, Hachiman Type 2 systems were discovered and appeared to include a third gene, encoded for a DUF protein (HamC) (N/A) .
Hachiman is an anti-phage defense system based on a HamAB protein complex consisting of two components:
- HamA, which is a nuclease (cuts DNA)
- HamB, which is a helicase (unwinds DNA) This system is encoded by a bicistronic locus.This system acts as a genome integrity sensor, monitoring the condition of double-stranded DNA and activating in the event of damage (N/A) .
Molecular mechanism
As far as we are aware, the molecular mechanism is unknown.
In the absence of damage, HamB binds to HamA and represses its activity. HamB interacts with intact DNA via its RecA1, RecA2, NAH, CAH, WH+, and OB domains. When damage is detected, HamB hydrolyzes ATP, which induces a conformational change in HamB and disrupts its interaction with HamA. This disruption releases HamA, which then becomes active and cleaves the DNA, destroying the genome of the phage and the host cell (N/A) .
Example of genomic structure
The Hachiman is composed of 2 proteins: HamA and HamB.
Here is an example found in the RefSeq database:
The Hachiman system in Vibrio metschnikovii (GCF_009763925.1, NZ_CP046822) is composed of 2 proteins HamA_1 (WP_158137983.1) HamB (WP_158137986.1)
HamB has a complex organization in several domains:
- a RecA1 and RecA2 domain corresponding to the helicase core (ATP hydrolysis),
- a WH* domain, which is a DNA-binding domain,
- a NAH domain, which is an interface domain with HamA,
- a CAH domain for stabilizing the structure,
- an OB domain that interacts with single-stranded DNA (N/A) .
Regarding the HamA nuclease, it has a single domain (DUF1837), whose function is unknown. It also has a D-E(X)K catalytic motif, characteristic of metal ion-dependent endonucleases (N/A) .
Distribution of the system among prokaryotes
This system is present in >5% of prokaryotic genomes and capable of robust protection against phylogenetically distinct phages (N/A) .