Table 2.
DNA repair genes found in Acinetobacter sp. Ver3.
| Repair system | Gene | NCBI accession | Function |
|---|---|---|---|
| Excision repair | |||
| Base excision repair (BER) | mug∗ | EZQ06622 | G:T/U mismatch-specific DNA-glycosylase |
| ung | EZQ12129 | Uracyl-DNA glycosylase | |
| ndk | EZQ11607 | AP endonuclease | |
| mutM | EZQ01011 | (8-oxoG) DNA glycosylase | |
| mutY | EZQ12003 | A/G-specific adenine glycosylase | |
| nth | EZQ02198 | 5′ AP endonuclease – endonuclease III | |
| exoIII | EZQ11928 | Exonuclease III | |
| tag | EZQ12006 | Methyl-A glycosylase I | |
| Nucleotide excision repair (NER) | uvrA | EZQ11284 | DNA binding |
| uvrB | EZQ11685 | Helicase – 3′ incision endonuclease | |
| uvrC | EZQ10970 | 5′ Incision endonuclease | |
| uvrD | EZQ10386 | Excision helicase | |
| mfd | EZQ12414 | Transcription- repair coupling factor | |
| Mismatch repair (MMR) | mutL | EZQ12151 | Binds MutS |
| mutS | EZQ10668 | Binds mismatches and loops | |
| Recombinational repair | |||
| Non-homologous end-joining (NHEJ) | Not present | ||
| Homologous recombination | |||
| Initiation- RecBCD pathway | recA | EZQ12424 | Recombinase |
| recB | EZQ12371 | Exo V helicase | |
| recC | EZQ12370 | Exo V nuclease | |
| recD | EZQ12372 | Exo V helicase | |
| Initiation- RecFOR pathway | recF | EZQ02163 | Assist RecA filamentation |
| recO | EZQ10098 | Binds ssDNA, assists RecF | |
| recR | EZQ10461 | ATP-binding, assists RecF | |
| recN | EZQ10978 | ATP-binding | |
| recJ | EZQ11310 | 5′–3′ ssDNA exonuclease | |
| recQ | Not present | ATP-dependent DNA helicase | |
| Initiation- SbcBCD pathway | sbcB | Not present | |
| sbcC | EZQ09958 | Hypothetical protein CL42_09425 | |
| sbcD | EZQ09959 | ATP-dependent dsDNA exonuclease | |
| ssb | EZQ00997 | Single strand binding protein | |
| Branch migration | ruvA | EZQ11507 | 5′–3′ junction helicase (with RuvB) |
| ruvB | EZQ11506 | 5′–3′ junction helicase (with RuvA) | |
| Resolvases | rucC | EZQ12511 | Junction endonuclease |
| recG | EZQ11853 | Resolvase, 3′–5′ junction helicase | |
| Other systems | |||
| SOS and error prone repair 3 umuDC operons | lexA | Not present | SOS activator |
| umuC | EZQ06645 | Error prone DNA polymerase V subunit C | |
| umuD | EZQ06644 | Error prone DNA polymerase V subunit D | |
| umuC | EZQ01410 | Error prone DNA polymerase V subunit C | |
| umuD | EZQ01411 | Error prone DNA polymerase V subunit D | |
| umuC | EZQ01153 | Error prone DNA polymerase V subunit C | |
| umuD | EZQ01152 | Error prone DNA polymerase V subunit D | |
| ddR | Not present | Regulator in A. baylyi | |
| dinB | EZQ03773 | Error prone DNA polymerase IV | |
| Alkyltransferases | ogt | EZQ02427 | Alkyltransferase with regulatory motif |
| Photolyases | phr | EZQ09984 | Deoxyribodipyrimidine photolyase |
| phlK | EZQ01671 | Photolyase-like |
Comparison with strains A. baumannii DSM 30007, A. johnsonii DSM 6963, and A. lwoffii DSM 2403 showed that the highlighted genes are present only in Ver3.
∗Not homologous to E. coli mug, but belongs to the same family.