The maintenance of DNA integrity is a crucial task for the proper functioning of the cell. However, the physicochemical constitution of DNA is constantly assaulted by a perplexing diversity of lesions that arise from physical or chemical attacks from the environment, byproducts of normal cellular metabolism, and errors during replication (Figure 1). These damaging agents produce lesions such as modified nucleotides, bulky adducts on nucleotides, single- and double-strand breaks, inter- or intra-strand crosslinks, apurinic or apyrimidinic base free sites, mismatches, deletions, and insertions (Figure 1). If left unrepaired, these lesions ultimately lead to genomic/gene instability, compromise cellular growth or replication, and various diseases like cancer, neurological disorders, immunodeficiency, Fanconi anemia in humans, premature aging, etc.
Evolution has invested significantly by implementing an intricate network of DNA repair systems in every organism — from bacteria to humans —to circumvent the diverse and generally adverse outcome(s) of DNA damage. These different DNA repair systems can be classified on the basis of the type of lesion being processed and protein components or mechanisms involved in the repair pathway. In other words, a cell deploys an arsenal of complementary protein molecular machinery that recognizes a class of DNA lesions and targets them for removal from the DNA. In the Escherichia coli paradigm, these include direct reversal of damage, nucleotide excision repair (NER), mismatch repair (MMR), base excision repair (BER), homologous recombination (HR) mediated repair, and non-homologous end joining (NHEJ) (Figure 1). These studies had also been recognized with “Nobel Prize in Chemistry 2015” to Tomas Lindahl, Paul Modrich, and Aziz Sancar highlighting the significance of DNA damage and repair systems in all three domains of life.
NER system is a multi-step, ATP-dependent process and catalytically versatile because of its capacity to remove myriad types of chemically and structurally diverse DNA lesions. Albeit with variable efficiencies, NER is critical for the removal of UV-induced photoproducts (cyclobutane dimers, 6–4 photoproducts, and thymine glycol), bulky adducts, apurinic or apyrimidinic (AP) sites, nicks, gaps, and cross-links. NER pathway has been characterized to an unprecedented level in bacteria, yeast, and humans and these studies envisage six discrete steps: DNA scanning, damage detection, damage verification, incision, removal of damage, DNA synthesis, and ligation as depicted in Figure 1. In the eubacterial domain, the pathway commences when the UvrA2B2 heterotetrameric complex bound to ATP scans the DNA for lesions by utilizing energy from ATP hydrolysis. After the damage is recognized by the UvrA component, the lesion is then occupied by UvrB for damage verification and UvrA gets evicted in an ATP hydrolysis dependent manner. Specifically, UvrA detects damage-induced structural distortions in the DNA, and then the lesion-containing strand is transferred to the active site of UvrB whereby it is embraced by the beta-hairpin motif for damage verification, resulting in a tight UvrB-preincision complex. While doing so, UvrB arrives at the damaged site by virtue of its ability to translocate on single-stranded DNA (ss-DNA) and unwind double-stranded DNA (dsDNA). Thus, UvrC is recruited by UvrB-preincision complex precisely on the damaged strand, where it specifically cleaves at 4-5 nucleotides 3ʹ and 8 nucleotides 5ʹ to the damage site in a concerted manner. Subsequently, the UvrD helicase removes the lesion-containing short oligonucleotide while UvrB remains bound to the gapped DNA until it is displaced by the DNA PolI mediated non-conservative DNA synthesis. Finally, the reaction is faithfully completed by DNA LigA that seals the nick, and the damaged site is restored back to the undamaged state.
