Table 1.
Retron system classification
| RT-Cladea | Structured RNA familya | Retron Type/Subtype/ varianta | Clusterb | Sub-clusterb | Description of domainsc | Described Retronsd |
|---|---|---|---|---|---|---|
| 1 | IA1/IIA1 | I-A | 22 | 1 | N-terminal ATPase module containing Walker A and Walker B motifs of P-loop NTPases (ABC ATPase) | Retron-Eco7 (Ec78); Retron-Eco4 (Ec83); Retron-Vpa1 (Vp96); Retron-Vch1 (Vc95) |
| 39 | 1 | N-terminal HNH endonuclease | ||||
| 1 | IB1 | I-B1 | 22 | 2 | N-terminal ATPase module containing Walker A and Walker B motifs of P-loop NTPases (ABC ATPase) + TOPRIM domain (Motif IV: EDxxL; Motif V: DxD) | |
| 3 | IB2 (Proteobacteria/Firmicutes) | I-B2 | 159 | 1 | N-terminal ATPase module containing Walker A and Walker B motifs of P-loop NTPases (ABC ATPase) + TOPRIM domain (Motif IV: EGxxE; Motif V: DxD) | |
| 8 | IC | I-C1 | NC | RT fused at the C-termini with a TOPRIM domain (Motif IV: EGxxD; Motif V: DxD) | Retron-Eco2 (Ec67) | |
| 8 | IC | I-C2 | NC | RT fused at the C-termini with a TOPRIM domain (Motif IV: EGxxD; Motif V: DxE) | ||
| 8 | Nd | I-C3 | NC | RT fused at the C-termini with a TOPRIM domain (Motif IV: EGxxD; Motif V: DxD) | ||
| 1 | IA1/IIA1 | II-A1 | 42 | 2 | N-terminal Nucleoside deoxyribosyltransferase-like (NDT) + C-terminal DNA binding domain | Retron-Sen2 (St85); Retron-Vch2 (Vc81); Retron-Eco3 (Ec73) |
| 1 | IIA2 | II-A2 | 42 | 3 | N-terminal Nucleoside deoxyribosyltransferase-like (NDT). Some members carries an N-terminal Tryipsine-like serine protease domain; frameshift separating the C-terminal DNA binding domain | |
| 9 | IIA3 (Proteobacteria/Firmicutes) | II-A3 | 42 | 1 | N-terminal Nucleoside deoxyribosyltransferase-like (NDT) + C-terminal DNA binding domain | Retron-Eco1 (Ec86); Retron-Vch3 (Vc137)e |
| 2 | IIIA1 | III-A1 | 113 | 1 | PRTase-like | |
| 742 | 1 | C-terminal winged helix DNA binding domain | ||||
| 9 | IIIA2 | III-A2 | 113 | 4 | PRTase-like | |
| 1121 | 1 | C-terminal winged helix DNA binding domain | ||||
| 9 | IIIA3 | III-A3 | 67 | 3 | N-terminal PRTase-like and RuvB C-terminal winged helix DNA binding domain | |
| 9 | Nd | III-A4 | 67 | 2b | N-terminal PRTase-like and RuvB C-terminal winged helix DNA binding domain | |
| 5,6,9 | nd | III-A5 | 67 | 2a | N-terminal PRTase-like and C-terminal winged helix DNA binding domain | |
| 67 | 1 | PRTase-like | ||||
| 113 | 2 | PRTase-like | ||||
| 113 | 3 | PRTase-like | ||||
| 1689 | 1 | C-terminal winged helix DNA binding domain | ||||
| 3 | IV | IV | 826 | 1 | Integral membrane protein: N-terminal signal peptide and two TM helices | Retron-Eco6 (Ec48) |
| 3 | V | V | 85 | 1 | ‘Cold-Shock’ DNA binding domain | Retron-Sen1 (Se72) |
| 3 | nd | VI | 2 | 1 | Cro/C1-type HTH domain | |
| 2075 | 1 | Accesory protein of unknown function | ||||
| 3272 | 1 | Accesory protein of unknown function | ||||
| 2760 | 1 | Accesory protein of unknown function | ||||
| 4 | nd | VII-A1 | NC | RT fused to DUF3800 at the C-terminus | ||
| 4 | nd | VII-A2 | 2165 | 1 | DUF3800 (Structural homology to RNaseH2) | |
| 4 | nd | VIII | 2446 | 1 | Putative serine esterase (DUF626) | |
| 7 | IX | IX | 1740 | 1 | HEPN domain | |
| 1093 | 1 | C-terminal HTH12; “Winged helix" DNA-binding domain | ||||
| 7 | nd | X | 2273 | 1 | IHF-like DNA-binding proteins and C-terminal VHL-like domain | |
| 8 | nd | XI | NC | RT fused at the C-termini with a Peptidase (Trypsin-like Serine protease) domain | ||
| 8 | nd | XII | NC | RT fused at the C-termini with a C-terminal TIR_2 domain | ||
| 10 | XIII (Firmicutes/Mx162/Mx65/Ne144) | XIII | 114 | 1 | DEDE motif, winged helix domain and C-terminal SWIM Zn-finger domain (CxCx12CxH) | Retron-Nex2 (Ne144); Retron-Mxa1 (Mx162); Retron-Mxa2 (Mx65); Retron-Sau1 (Sa163) |
| 216 | 1 | WGR-like domain and C-terminal HEAT/ARM-like repeat containing protein | ||||
| 259 | 1 | HEAT/ARM-repeat containing protein | ||||
| 1688 | 1 | HEAT/ARM-repeat containing protein | ||||
| 3262 | 1 | HEAT/ARM-repeat containing protein | ||||
| 216 | 2 | HEAT/ARM-repeat containing protein |
aRetron Classification based on RT phylogeny (Clades)/RNA structure/Retron system as specified on Figures 2 and 5.
bSpecific cluster (subcluster) numbers (as specified on Supplementary Table S2) characteristic of every Retron System.
cDescription of protein domains of the associated gene/fusion.
dRetron described in Simon et al. (2019) as ‘experimentally validated retrons’.
eRetron described in Inouye et al. 2011.