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Liu, Jie

Biochemistry

2006

Ph. D.

Genetic recombination between homologous DNA molecules is very common among organisms and plays important roles in DNA replication and repair. Biochemical studies have revealed a conserved macromolecular structure responsible for catalyzing homologous recombination in organisms as diverse as phage, bacteria, and eukaryotes: the presynaptic filament, consisting of single-stranded DNA (ssDNA) coated with recombination proteins. One of the best-studied presynaptic filaments is that of bacteriophage T4, which provides an excellent model for the structure and function of filaments from higher organisms. Phageencoded recombination proteins Gp32 (SSB), UvsX (recombinase), and UvsY (Recombination Mediator Protein or RMP) take part in the correct assembly of the filament, and then start strand invasion that is the first step of recombination-dependent replication. In the biochemical model of UvsY-dependent nucleation of the T4 presynaptic filament assembly, Gp32 binds to the ssDNA in a sequence-nonspecific and highly cooperative manner to remove secondary structure and induces a favorable conformation for recognition by T4 recombination proteins. UvsY hexamers can bind ssDNA coated with Gp32, causing a conformation change which weakens Gp32-ssDNA. Recruitment of UvsX to this site displaces Gp32. UvsY helps UvsX to displace Gp32 from ssDNA and stabilizes UvsX-ssDNA complexes to form the presynaptic filament, a prerequisite to homologous pairing and strand transfer. Since the functions of Gp32, UvsX, and UvsY, are strongly conserved in other recombination systems, e.g. the RPA, Rad51, and Rad52 proteins, respectively, of yeast/humans, and the SSB, RecA, and RecO/R respectively, of E. coli, the T4 presynaptic filament model informs the entire debate on recombination mechanisms.