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Chapter 20 : The RecA Protein

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Abstract:

This chapter focuses on the bacterial RecA proteins, which have at least three major roles. The first function involves a direct participation in the central steps of recombination, via the DNA strand exchange activity. Second, RecA protein has a role in regulation. As a regulatory function, the RecA protein facilitates the autocatalytic cleavage of the LexA repressor and certain other proteins to induce the SOS response to DNA damage. Finally, the RecA protein participates in yet another type of repair process. Late in the SOS response, especially when DNA damage levels are particularly high and nonmutagenic DNA repair is insufficient to get replication restarted, a need arises to restart replication via lesion bypass. The known biochemical activities of the RecA protein parallel these cellular roles. These include binding to DNA, ATP hydrolysis, filament formation, DNA strand exchange, and the coprotease activity. The nucleation of RecA protein on single-stranded DNA (ssDNA) is slowed considerably if the DNA is bound by the single-strand DNA-binding protein SSB. The capacity to promote uniquely unidirectional DNA strand exchange reactions, to bypass significant structural barriers, and to promote four-strand exchange reactions is so far unique to the bacterial RecA proteins, and all of these processes require ATP hydrolysis.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Image of Figure 1
Figure 1

Replication fork demise at the sites of DNA damage. (A) Encounter with a strand break leads to a double-strand break and dissociation of one arm of the fork. (B) Encounter with an unrepaired DNA lesion can result in the creation of a gap at a stalled fork. In either case, repair pathways involve recombination.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Image of Figure 2
Figure 2

RecA protein structure. (A) A RecA filament is shown, with 24 RecA monomers, based on the 1992 structure by Story and Steitz ( ) (see text). One monomer is colored in a darker gray. (B) A RecA monomer, with bound ADP. (C) An electron micrograph of one segment of a RecA filament formed on DNA.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 3

Domain structures of RecA protein and its homologues in and . The open box is the core domain shared by all four proteins. The RecA C-terminal domain is unique to bacterial RecA proteins. Homologies among other domain elements are indicated by shading patterns.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 4

Assembly and disassembly pathways for RecA filaments. After nucleation, filament extension proceeds 5′ to 3′ relative to the ssDNA, and can encompass adjacent duplex regions. RecA dissociation occurs from the opposite filament end, and proceeds also 5′ to 3′.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 5

RecA protein-mediated DNA strand exchange reactions. (A) The most common three-strand reaction used in many studies. (B) The standard four-strand reaction. RecA protein filaments are nucleated in the gap of the circular DNA substrate, and DNA pairing is also initiated in this gap. (C) Initiation of DNA strand exchange at a free duplex DNA end. (D) Initiation of DNA strand exchange at a free single-strand (RecA-bound) DNA end.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 6

Unproductive complexes that can stall DNA strand exchange reactions. The formation of a joint molecule involves the uptake of a duplex DNA into the RecA filament and its alignment with the previously bound single-stranded DNA. Extension of the region of paired DNA requires a continued spooling of the duplex into the filament, as shown in the top panel. This extension can be blocked by a secondary DNA pairing involving another part of the duplex (leaving an external loop of DNA [middle panel]) or any unproductive interaction of the duplex and the filament (bottom panel) that halts the needed spooling process.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 7

Model for RecA protein-mediated rotation of DNA to effect DNA strand exchange. Any duplex DNA external to the filament, perhaps as a result of the formation of external DNA loops as shown in Fig. 6 , would be rotated around the outside of the filament in a reaction coupled to ATP hydrolysis. Rotation in the direction of the curved arrows will result in branch movement in the direction of the black arrows.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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Figure 8

Fork regression as might occur at a stalled replication fork. The product of this reaction is sometimes called a chicken foot.

Citation: Cox M. 2005. The RecA Protein, p 369-388. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch20
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