NER in E. coli

It is also thought that one of the functions of UvrB is in lesion verification. A region of UvrB, a flexible p-hairpin structure, is inserted into the DNA helix to verify that the distortion represents bona fide DNA damage and to determine which strand contains the damage. Atomic force microscopy has revealed that the DNA is actually wound around the UvrB protein, and it has been suggested that the 

UvrD protein, also called helicase II, is another helicase involved in NER. It unwinds and releases the damaged oligonucleotide produced by the incisions. In addition it releases UvrC from the postincision complex. After displacement of the damaged oligo and displacement of UvrC, UvrB protein remains bound to the gap. DNA polymerase I displaces UvrB and synthesizes new DNA to fill in the gap. After the repair patch is synthesized, DNA ligase seals the nick. The size of the repair patch is 12 nucleotides approximately 90% of the time. 

Clearly, the process of NER is very complex even in a simpler organism such as E. coli. While much is known about the process, there is still a great deal to be learned. In particular, it is not completely clear how the damage recognition complex discriminates the particular class of substrates it efficiently recognizes from those lesions that it does not recognize and undamaged DNA. 

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Damaged bases in DNA that arise from ROS or by the deamination of cytosine to uracil are usually removed by BER however, there is no evidence for the existence ofTC-BER that would be analogous to TC-NER [11, 32]. Some oxidized bases may be repaired by TC-NER when they interfere with transcription elongation. In any case, oxidized bases that alter base incorporation events in nascent RNA could contribute significantly to the pool of altered proteins in cells. In fact, 8-oxo-G has been shown to be subject to TC-NER in E. coli and to induce altered proteins via transcriptional mutagenesis [62]. Furthermore, in a recent publication, Saxowsky et al. report that 8-oxo-G induces a change in the activity of the Ras protein in mammalian cells via transcriptional mutagenesis and that downstream phosphorylation events are dependent on Ras [117]. 

Excision repair. The E. coli mismatch repair is a type of excision repair. However, a different nucleotide excision repair system (NER) is utilized by all organisms from bacteria to human to remove a variety of defects. These include thymine dimers, photohydrates, oxidized bases, adducts of cisplatin (Box 5-B), mutagens derived from polycyclic aromatic compounds,683 and poorly recognized OC mismatched pairs.692 In E. coli this excision repair process depends upon proteins encoded by genes UvrA, B, C, and D and also DNA polymerase I and DNA ligase.693 695a A dimer of protein UvrA forms a complex with helicase UvrB (Eq. 27-22).696 696a... 

NER in bacteria involves only three proteins to carry out the complete process of damage recognition and excision UvrA, UvrB, and UvrC. Owing to its relative simplicity, the UvrABC system has been studied extensively, particularly in E. coli, and serves as a model system for NER [20, 21]. 

The solution structures of DNA duplexes containing the mutagenic lesions of benzo [a] pyrene-dtrihydroxybenz[a] anthracene, aminopyrene-dG, aminofluorene-dG and malondialdehyde-dG derivatives have been reported. In each case the lesion was shown to intercalate into the duplex causing only minimal disruption to the duplex structure. These structures have been used to study the nucleotide excision repair (NER) by the UvrABC nuclease system from E. coli of the bulky purine lesions. ... 

Psoralen interstrand cross-links pose strong blocks to T7 RNA polymerase, E. coli RNA polymerase, and RNA Pol II [54, 65, 81], which is to be expected since the double helix cannot unwind in the vicinity of the adduct. Psoralen monoadducts on the transcribed strand of DNA pose blocks to transcription as well. Historically, psoralen adducts are of great interest since they were among the first chemically induced lesions to be investigated for TC-NER. Interestingly, psoralen interstrand cross-links are subject to TC-NER, but the monoadducts are not [82]. 

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