DNA Repair Systems in Eukaryotes and Prokaryotes: Types, Functions, and Phylogenetic Contexts

Mismatch repair (MMR)

Fixes mispaired bases, usually right after replication; preferentially repairs the newly made daughter strand rather than the parental strand.

Photoreactivation

A light-dependent repair system that directly splits UV-induced pyrimidine dimers; described as nonmutagenic.

Direct reversal

Alkylation damage can be reversed by methyltransferase enzymes in a suicide reaction, meaning the enzyme is used up during repair.

Excision repair

Removes damaged DNA from one strand and then resynthesizes the missing stretch using the opposite strand as template.

Base excision repair (BER)

Repairs single-base damage such as deamination or alkylation; can replace just the base/short region or a 2-10 nucleotide stretch.

Nucleotide excision repair (NER)

Repairs bulky lesions such as UV-induced pyrimidine dimers; has two subpathways in eukaryotes: global genome repair and transcription-coupled repair.

Prokaryotic excision repair (uvr system in E. coli)

Makes incisions on both sides of damage, removes the damaged segment, and replaces it by new synthesis.

Recombination-repair

Uses recombination to replace a damaged region, especially when replication leaves a gap opposite a damaged template.

Double-strand break repair by homologous recombination

In eukaryotes, the RAD52 group, MRX/MRN complex, and Rad51 help process broken ends, find homology, and invade the intact template for repair.

Nonhomologous end joining (NHEJ)

Repairs double-strand breaks when a homologous template is not available; can ligate blunt DNA ends.

SOS response in prokaryotes

DNA damage activates RecA, which promotes LexA autocleavage and induces many repair genes.

Error-prone repair

Occurs when damaged DNA has not been repaired and the normal replicative polymerase stalls; DNA polymerase V or IV can synthesize across the lesion.

Translesion synthesis

The process where DNA made by error-prone polymerases often contains errors.

MMR usage

Used immediately after replication to fix replication mismatches and insertion/deletion-type errors.

Photoreactivation and NER usage

Used after UV damage, especially when pyrimidine dimers form.

BER usage

Used for single-base lesions such as deamination, depurination, and alkylation-related damage.

Direct reversal usage

Used for alkylation damage.

Recombination-repair usage

Used when replication encounters damage and leaves a gap in the newly synthesized strand.

Fork recovery systems

Used when a replication fork stalls at damaged DNA or a nick.

Homologous recombination or NHEJ usage

Used when there is a double-strand break; NHEJ is used specifically when homologous sequence is not available.

Transcription-coupled NER

Used when damage is present in the transcribed strand of active genes.

Global genome repair

Surveys damage throughout the genome.

SOS repair

Induced in bacteria when DNA damage is extensive enough to activate RecA and derepress the SOS genes through LexA cleavage.

Double-strand breaks (DSBs)

Serious lesions repaired either by homologous recombination or NHEJ.

Homologous recombination process

The broken ends are processed to make single-stranded overhangs by the MRX/MRN complex.

Rad51 role

Forms a filament on the single-stranded DNA and promotes homology search and strand invasion into an intact homologous DNA molecule.

Role of homologous chromosomes

Provides the undamaged template needed for accurate recombination-based repair; NHEJ is used when no homologous sequence is available.

Chromatin and repair

Repair happens in chromatin, so histone modification and chromatin remodeling are essential for efficient repair.

γ-H2AX

A DSB-dependent histone modification that helps recruit chromatin-modifying activities and assemble repair factors at the break.

Phylogenetic tree root

The oldest ancestor.

Phylogenetic tree nodes

Inferred common ancestors.

Phylogenetic tree branches

Show lineages.

Phylogenetic tree tips/taxa

The sampled species or genes.

Clade

A common ancestor plus all descendants.

MRCA

The most recent shared ancestor.

Sister groups

Share an immediate common ancestor.

Anagenesis

Evolutionary change along a lineage without splitting.

Cladogenesis

Lineage splitting, which produces new species or branches.

Ancestral/plesiomorphic traits

Older states.

Derived traits

Newer states.

Synapomorphy

A shared derived trait.

Autapomorphy

A unique derived trait.

Homology

Similarity due to common ancestry.

Homoplasy

Similarity not due to common ancestry, often from convergence, parallel evolution, or reversals.

Ingroup

The clade of interest.

Outgroup

A closely related lineage outside that clade; helps root the tree and determine which character states are ancestral versus derived.