Table 1.
DNA exonucleases of E. coli
| Enzyme | Gene(s) | Preferred substrate | Polarity | Other features | Biological role in DNA metabolism |
|---|---|---|---|---|---|
| ExoI | xonA (=sbcB) | ssDNA | 3′ -5′ | processive; stimulated by SSB | recombination, damage repair, mutation avoidance, MMR |
| ExoIII | xthA (=xth) | dsDNA | 3′ - 5′ | acts at nicks and ends, abasic endonuclease; 3′ phosphatase; can remove damaged 3′ residues | base excision repair, repair of oxidative and ionizing radiation damage |
| ExoIV | orn?2 | Olignucleo- tides | 3′ -5′ | may be identical to RNA oligoribonuclease2 | ? nucleotide recycling? |
| ExoVII | xseA, xseB | ssDNA | 3′ - 5′, 5′ - 3′’ | heterodimer, processive, oligonucleotide products, metal cofactor-independent | damage repair, mutation avoidance, MMR |
| ExoVIII | recE | dsDNA | 5′ - 3′ | processive, encoded by cryptic Rac prophage | recombination, damage repair |
| ExoIX | ygdG (=xni) | ? | ? | in 5′ nuclease/FEN-1 family3 | ? |
| ExoX | exoX | ssDNA, dsDNA | 3′ - 5′ | distributive | mutation avoidance, MMR |
| DNA polI 5′ Exo (ExoVI) | polA | ssDNA | 5′ - 3′ | flap endonuclease | replication (Okazaki fragment maturation) |
| DNA Pol I 3′ Exo (ExoII) | polA | ssDNA | 3′ - 5′ | proofreading | |
| DNA Pol II 3′ Exo | polB | ssDNA | 3′ - 5′ | proofreading | |
| DNA Pol III 3′ Exo | dnaQ (=mutD) | ssDNA | 3′ - 5′ | subunit | proofreading |
| RecBCD | recB, recC, recD | dsDNA, ssDNA | 3′ - 5′, 5′ - 3′ | ExoV, highly processive, ATP-dependent, oligonucleotide products, helicase activity; Chi recognition | recombination, DSB repair, restriction of bacteriophage |
| RecJ | recJ | ssDNA | 5′ - 3′ | processive; stimulated by SSB | recombination, damage repair, mutation avoidance, MMR |
| RNase T (Exo T) | rnt | ssDNA | 3′ - 5′ | activity on DNA > RNA, homodimer, distributive | repair?3 |
| SbcCD | sbcC, sbcD | dsDNA | 3′ - 5′ > 5′ - 3′ | ATP-dependent, processive | repair |
| Endonucleas e IV exonuclease activity | nfo | dsDNA | 3′ -5′ | Zn2+ enzyme; can digest damaged 3′ residues; also possesses endonuclease 5′ to AP sites and other damaged residues | BER, NIR, repair of oxidative and ionizing radiation damage |
| TatD (Exonuclease XI) | tatD | dsDNA > ssDNA | 3′ - 5′ | Mg2+ dependent DNase, unclear whether endonuclease or exonuclease activity | ?, E. coli YcfH and YjjV are paralogs; yeast Tat-D is orthologous, with 3′ to 5′ Exo/Endo activity. |
1
Abbreviations: Pol, polymerase; Exo, exonuclease, dsDNA, double-strand DNA; ssDNA single-strand DNA; MMR, mismatch repair; DSB, double-strand break; BER, base excision repair; NIR, nucleotide incision repair
2
Eukaryotic oligoribonuclease has activity on oligodeoxynucleotides making it likely that E. coli oligoribonuclease is identical to exonuclease IV.
3
RNase T can act as a high-copy suppressor of some DNA repair defects of RecJ− ExoI− ExoVII− strains, has potent DNase activity and so could play a redundant function in DNA metabolism.