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Chapter 13 : The DNA Damage Response
Category: Microbial Genetics and Molecular Biology
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This chapter reviews the current knowledge about the mechanism of the LexA/RecA regulated response and its output in Escherichia coli, stressing newly emerging areas such as regulation of RecA filament formation and management of specialized DNA repair polymerases. It also talks about the SOS response in other bacterial species and its implications for the evolution and treatment of bacterial pathogens, and further discusses the more poorly understood LexA/ RecA-independent damage response in several model organisms and a potentially larger network of the response to DNA damage. ATP binding, but not hydrolysis, is required for DNA binding; DNA binding greatly stimulates ATP hydrolysis, which in turn promotes RecA’s release from DNA. The current widespread use of fluoroquinolone antibiotics, which, as topoisomerase II poisons, are potent SOS inducers, has potentially serious clinical consequences and influence on evolution of pathogens. In E. coli, Bacillus subtilis, and Mycobacterium tuberculosis there is increasing evidence of LexA/RecA independent modes of DNA damage response, including genes involved in DNA replication and repair. The majority of DNA damage inducible genes are not controlled by LexA or RecA . The DNA damage response has important implications for the evolution and treatment of bacterial pathogens because of its ability to promote genetic change through mutation and induction of mobile genetic elements, potentially induced by the very agents used to treat bacterial infections.
Basic mechanics of the SOS response. In the repressed state, LexA binds to multiple genes, including itself, RecA, and other genes involved in DNA repair and cell division inhibition (the “output”), repressing transcription. When ssDNA accumulates, RecA forms a filament (“the signal”) that cleaves and inactivates LexA, turning on the output genes. Note that the increase of LexA expression will drive back repression quickly in the absence of “signal.”
RecA loading pathways. Single-strand DNA that accumulates during blocks to replication or after UV irradiation becomes bound by SSB. The RecFOR proteins promote removal of SSB and replacement with a RecA filament. Double-strand breaks, such as those produced by ionizing radiation or topoisomerase poisons, are resected by RecBCD exonuclease, which loads RecA onto the emergent single-strand. Note that some gaps may be converted to breaks.
Circuitry of the SOS response. LexA represses itself, RecA, and several other genes that modulate the RecA:ssDNA filament (“RecA*”), including DinI (a positive regulator of RecA filament) and RecX and UvrD (negative regulators of the RecA filament). RecA* inhibits LexA by promoting its cleavage.
Polymerase switching during translesion DNA synthesis. The beta clamp (dark donut shape) binds the replicative DNA polymerase III core (dark oval) during normal processive DNA synthesis. A second translesion polymerase (light gray oval) is bound in reserve on the beta clamp “tool belt.” Upon encounter of a template lesion (black hexagon), polymerase III will stall. The translesion polymerase is then engaged with the primer terminus, which promotes brief, distributive synthesis past the lesion. (Polymerase III core may or may not be released from the clamp on this step, although the latter is shown here.) Because of the limited processivity of the translesion polymerase, polymerase III is reengaged to continue DNA replication shortly after bypass.