Table 1. Examples of conflict systems containing RNA-targeting effector domains.

Conflict system class	RNA toxin effector examples	Targets	Phyletic distribution	Comments
Yeast killer toxin	Zymocin, PaT	Modified U34 (wobble uridine) base-containing tRNA. In Pichia acaciae, predominantly tRNAGln.	Yeast	Toxin domain fused to N-terminal secreted chitinase domain which might breach fungal cell wall
α-Sarcin-like	BECR fold domains (sarcin, restrictocin, hirsutellin, mitogillin, etc.)	Backbone cleavage in rRNA sarcin-ricin loop	Filamentous fungi	Several such RNases with 1–3 BECR domains are found across fungi
Ricin-like	Ricin, saporin, pokeweed antiviral protein, Shiga	N-glycoside hydrolysis of rRNA sarcin-ricin loop base	plants, ciliates, bacteria	Found in a class of ciliate toxin with architectural parallels to bacterial polymorphic toxins
Toxin-antitoxin (T-A)	BECR fold domains (Barnase, EndoU, Colicin-like, RelE-like) MazF/PemK/EndoA, PIN (VapC, etc.) domains, HEPN domains	mRNA (BECR, MazF/PemK/EndoA, RNase LS and RNase LsoA: HEPN), tRNAMet (VapC: PIN), tRNA (BECR), rRNA sarcin-ricin loop (PIN), rRNA S16 (Colicin E3, E4, E6: Colicin E3-like)	Bacteria, archaea	Widespread intra-genomic conflict systems
Polymorphic toxins	Various BECR fold domains, deaminase	tRNA, likely other targets	Bacteria, archaea	The toxin domains typical vary via replacement by alternative cassettes
Colicin-like	BECR fold domains, colicin E3-like	Probably tRNA (BECR), rRNA S16 (Colicin E3, E4, E6: Colicin E3-like)	Bacteria	Differ from above in being secreted by lysis of the producing cell and being encoded on plasmids
CRISPR/Cas	Cas2, HEPN, active RAMPs and Csx3. Cmr and Cas9 in some subtypes	mRNAs, Csx3 exonucleolytically targets terminal polyA tails	Bacteria, archaea	A wide range of actions which are both directed by complementary CRISPR spacer RNAs and independently of them
Restriction-modification systems	HEPN (PrrC-like RNases)	tRNALys	Bacteria	inactivation of R-M system by phage leads to activation of PrrC, which targets endogenous tRNA
Abortive infection (Abi)	HEPN (AbiA-CTD, AbiD, AbiF, AbiJ, AbiU2, AbiV)	Unknown	Bacteria	Part of an extensive antiphage defense which might also directly target phage components
Phage growth limitation (Pgl)	HEPN (RloC-like, pEK499_p136-like families), SNase	Unknown	Bacteria	Sporadic coupling to RNases could cleave phage RNAs in attacks complementary to Pgl DNA modification
Ter-dependent anti-phage system	HEPN (DUF4145-like)	Unknown	Bacteria	Sporadic coupling to HEPN domain could work with core system
Prokaryotic nucleotide or nucleotide-derived secondary messenger-based systems	HEPN	Unknown	Bacteria	Combines with CARF sensor and mCpol nucleotide secondary messenger synthetase
prokaryotic PIWI-based systems	PIWI/argonaute, HEPN	Unknown	Bacteria	In bacteria, pPIWI is adjacent to effector RNAse domains
Animal innate immunity	RNaseL – permuted version of HEPN domain	Viral RNA	Eukaryotes	Activated in vertebrates by oligoadenylate (OA) linear secondary messenger nucleotide