Archaeal DNA Repair Mechanisms

Abstract

Archaea often thrive in environmental extremes, enduring levels of heat, pressure, salinity, pH, and radiation that prove intolerable to most life. Many environmental extremes raise the propensity for DNA damaging events and thus, impact DNA stability, placing greater reliance on molecular mechanisms that recognize DNA damage and initiate accurate repair. Archaea can presumably prosper in harsh and DNA-damaging environments in part due to robust DNA repair pathways but surprisingly, no DNA repair pathways unique to Archaea have been described. Here, we review the most recent advances in our understanding of archaeal DNA repair. We summarize DNA damage types and their consequences, their recognition by host enzymes, and how the collective activities of many DNA repair pathways maintain archaeal genomic integrity.

Keywords: DNA damage; DNA metabolism; DNA modifications; DNA repair; archaea; double-strand breaks; genomic integrity.

Figure 1

Predicted distribution of pathway-specific archaeal DNA repair proteins by clade [10], according to KEGG (Kyoto Encyclopedia of Genes and Genomes) orthologies. Many pathways appear conserved, with most variation found in distribution of mismatch repair (MMR) and nucleotide excision repair (NER) proteins.

Figure 2

Archaeal DNA repair pathways follow similar generalized steps: (i) Recognition of DNA damage by pathway-specific enzymes. (ii) Initiation of repair by conversion of DNA damage into appropriate and repairable substrate. (iii) Conclusion of repair by resynthesis of damaged DNA from a complementary undamaged strand, degradation of damaged strand by flap endonuclease of intrinsic DNA polymerase exonuclease activity, and nick ligation by DNA ligase.

Figure 3

“Error-prone” double-strand break (DSB) repair pathways in Archaea: (a) In microhomology-mediated end joining (MMEJ), small regions of microhomology (yellow) are revealed by exonuclease activity; annealing and subsequent processing by flap endonuclease and DNA ligase often results in the loss of genetic information. (b) Non-homologous end joining (NHEJ) in some archaeal species relies on recognition of broken ends by Ku which brings broken ends together, where exonuclease activity produces complementary ends for conclusion of DNA repair. The proteins that mediate NHEJ in many archaeal clades have not yet been defined.

Figure 4

Homologous recombination-based DSB repair in Archaea. Broken end recognition by the Mre11/Rad50 complex allows formation of 3′ overhangs by the HerA hexamer. RadA forms a nucleoprotein filament on the 3′overhangs and facilitates initiated homologous recombination through strand invasion. In the case of just one strand invasion event, synthesis-dependent strand annealing (SDSA) can occur before repair conclusion, a non-crossover event. If both strands are involved in local strand invasion events, a Holliday junction may form, the resolution of which may lead to crossover events.

Figure 5

Potential mismatch repair pathways through NucS/EndoMS. NucS/EndoMS may surveil newly synthesized areas of the genome for mismatch incorporations. If a dual cut is made as in vitro, a DSB-like substrate would be formed, requiring DSB repair pathways or more immediate repair conclusion by DNA Polymerase, Flap endonuclease, and DNA ligase.

Figure 6

Archaeal ribonucleotide excision repair. Embedded ribonucleotide monophosphates (rNMPs) are recognized and specifically excised by RNaseH2, resulting in one nucleotide gap with 3′-hydroxyl. Repair is concluded when DNA polymerase performs strand-displacement synthesis and the activities of flap endonuclease and DNA ligase remove the original strand and seal the resulting nick.

Figure 7

Reconstituted archaeal base excision repair from Thermococcus kodakarensis. AGOG recognizes 8-oxo-G modifications and acts as a bifunctional glycosylase, both excising the damaged base and cleaving the DNA backbone at the site of damage. The resulting substrate contains a 3′ unsaturated aldehyde (UA) and 5′ dRP. Damage repair is initiated by the activity of Endonuclease IV, which converts the 3′-UA to an extendable 3′-hydroxyl group. In long-patch base excision repair (BER), strand displacement activity of DNA polymerase during synthesis is used in tandem with flap endonuclease and DNA ligase to conclude repair. In short-patch BER, dRP lyase activity intrinsic to DNA polymerase simply removes the dRP moiety while synthesizing the correct base from the undamaged strand, and DNA ligase seals the nick.

Figure 8

Eukaryotic global genomic nucleotide excision repair. DNA damages which distort the DNA double helix are recognized by XPC, which recruits the damage recognition XPA and TFIIH complex. Components of the TFIIH complex melt strands of DNA around a verified DNA lesion, allowing cuts of the damaged strand by XPG and XPF. The TFIIH complex uses helicase activity to “excise” the damaged strand, allowing conclusion of repair by DNA polymerase and DNA ligase I.

Figure 9

Current eukaryotic and bacterial models of transcription coupled nucleotide excision repair (TC-NER) and a hypothetical archaeal model. In all cases, RNA polymerase (RNAP) is arrested at template-strand DNA damage and recognized by the TRCF-CSB in Eukarya, Mfd in Bacteria, and potentially Eta in Archaea. The TRCF either backtracks RNAP or terminates transcription while recruiting NER enzymes directly to the site of damage. Homologs of the eukaryotic XP proteins found in many Archaea act in our archaeal model.