Table 2.
A selection of predicted new defense and TA systems present in DIs of M. aeruginosa
| System and representative component | No. of homologs in DI (no. in genome) | Detected similarity(ies) | Gene context | Comment |
|---|---|---|---|---|
| Putative ABI or TA system | ||||
| MAE_32580 | 3 (4) | None | COG2442 | The conserved motifs and predicted secondary structure of this family are consistent with PIN nuclease signature, a toxin often associated with COG2442 |
| MAE_49350 | 1 | PD-(D/E)XK family | COG1106 (ATPase; AbiL) | Also associated with another ATPase (COG4938); potential substitution of TOPRIM domain function |
| MAE_28990 | 2 (1) | AbiF-like protein family | No | |
| MAE_24760 | 3 | RHH (C terminus), HTH (N terminus) | COG1403 (McrA/HNH) | Two-component system |
| MAE_09110 | 2 (3) | None | MAE_09120 | Two-component system; both proteins are predicted to be alpha-helical; abundant in cyanobacteria |
| MAE_04340 | 2 | None | MAE_04350 | Two-component system; MAE_04340 family also abundant in Firmicutes (e.g., yozC in Bacillus subtilis) |
| MAE_04400 | 3 | None | MAE_04390 | Two-component system of two small proteins specific for cyanobacteria |
| Putative CRISPR-Cas system (cas gene), MAE_30780 | 1 | Cas5 (COG1688) | Predicted Cas7 (MAE_30770), Cas3 (MAE_30790) | Divergent rare variant of CRISPR-Cas system, so far present only in Cyanothece sp. strain PCC 8802 and two species of Thermus thermophilus |
| Uncharacterized defense system | ||||
| MAE_55110 | 5 | Uncharacterized family COG5428 | COG2929/DUF497, which belongs to RelE toxin family | Often stand-alone gene; fused to Era GTPase in Chloroflexi; COG5428 is similar to N-terminal domains of some OB-fold-containing proteins (e.g., PDB code 3bu2) |
| MAE_01610 | 1 | Plasmid stabilization protein SpbA family | No | SpbA family identified on plasmid pHT1030 of Bacillus thuringiensis and shown to be responsible for plasmid maintenance (50) |
| MAE_11480 | 25 | Uncharacterized family pfam01724 (DUF29) | No | See text |
| MAE_57710 | 5 (14) | PD-(D/E)XK nuclease | No | Distant homologs of COG5493/DUF1626 family for which the nuclease domain was identified before (42); also expanded in Pyrobaculum aerophilum (called paRep7 family) |
| MAE_00370 | 27 (46) | PD-(D/E)XK nuclease; COG5493 | No | Often expanded in genomes with many identical copies, thus considered to be transposable element |
| MAE_11990 | 1 (1) | PD-(D/E)XK nuclease; COG1637 (DUF91) | Encoded in operon with RM systems in many other genomes | N-terminal nuclease is distantly related to NucS endonuclease from archaea, which interacts with the replication clamp PCNA (72) |