Structural analysis of the ParR/parC plasmid partition complex

Abstract

Accurate DNA partition at cell division is vital to all living organisms. In bacteria, this process can involve partition loci, which are found on both chromosomes and plasmids. The initial step in Escherichia coli plasmid R1 partition involves the formation of a partition complex between the DNA-binding protein ParR and its cognate centromere site parC on the DNA. The partition complex is recognized by a second partition protein, the actin-like ATPase ParM, which forms filaments required for the active bidirectional movement of DNA replicates. Here, we present the 2.8 Å crystal structure of ParR from E. coli plasmid pB171. ParR forms a tight dimer resembling a large family of dimeric ribbon-helix-helix (RHH) 2 site-specific DNA-binding proteins. Crystallographic and electron microscopic data further indicate that ParR dimers assemble into a helix structure with DNA-binding sites facing outward. Genetic and biochemical experiments support a structural arrangement in which the centromere-like parC DNA is wrapped around a ParR protein scaffold. This structure holds implications for how ParM polymerization drives active DNA transport during plasmid partition.

Superstructure of the centromeric complex of TubZR C plasmid partitioning systems

“…The superstructure this complex forms is helical, right-handed, and places the parC DNA on the exterior of the helix and ParR on the interior (18,19). This arrangement clusters the interaction surfaces between ParM and ParR, which are located at the tip of the ParM filament and within the last few residues of ParR (18,19).…”

“…Type I plasmid partitioning systems (4, 5) are based on deviant Walker A ATPases (6, 7), type II (8) on actin-like proteins (9), and type III (10-12) on tubulin/FtsZ-like proteins (13,14). Although the structure of the filament implicated in segregation has been determined for all three systems (9, 14-16), only examples of type I and II centromeric complexes have so far been resolved (17)(18)(19).The centromeric complex of the type II (actin-like) ParMRC plasmid partitioning system is formed by the binding of adapter protein ParR to parC, a series of parallel (direct), 11-base pair (bp) repeats (20). The superstructure this complex forms is helical, right-handed, and places the parC DNA on the exterior of the helix and ParR on the interior (18,19).…”

“…Type I plasmid partitioning systems (4, 5) are based on deviant Walker A ATPases (6, 7), type II (8) on actin-like proteins (9), and type III (10-12) on tubulin/FtsZ-like proteins (13,14). Although the structure of the filament implicated in segregation has been determined for all three systems (9, 14-16), only examples of type I and II centromeric complexes have so far been resolved (17)(18)(19).…”

“…The rough disposition of four of the repeats making up Bacillus thuringiensis serovar israelensis pBtoxis (Bt) tubC, but not the TubR binding site or register, has been assigned by Tang and colleagues who demonstrated binding by Bt TubR to this region of pBtoxis (10, 21). Furthermore, the structure of the TubR adapter protein has been determined in the absence of DNA (13), revealing that it forms a recognitionhelix dimer with a potential DNA binding surface and demonstrating that it is unrelated to type II ParR (18,19). Finally, it has been shown that the TubRC complex is capable of recruiting TubZ (13,21).…”

“…Although the structure of the filament implicated in segregation has been determined for all three systems (9, 14-16), only examples of type I and II centromeric complexes have so far been resolved (17)(18)(19).…”