Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase

Abstract

FtsK from Escherichia coli is a fast and sequence-directed DNA translocase with roles in chromosome dimer resolution, segregation, and decatenation. From the movement of single FtsK particles on defined DNA substrates and an analysis of skewed DNA sequences in bacteria, we identify GNGNAGGG, its complement, or both as a sequence motif that controls translocation directionality. GNGNAGGG is skewed so that it is predominantly on the leading strand of chromosomal replication. Translocation across this octamer from the 3 side of the G-rich strand causes FtsK to pause, turn around, and translocate in the opposite direction. Only 39 ؎ 4% of the encounters between FtsK and the octamer result in a turnaround, congruent with our optimum turnaround probability prediction of 30%. The probability that the observed skew of GNGNAGGG within 1 megabase of dif occurred by chance in E. coli is 1.7 ؋ 10 ؊57 , and similarly dramatic skews are found in the five other bacterial genomes we examined. The fact that FtsK acts only in the terminus region and the octamer skew extends from origin to terminus implies that this skew is also important in other basic cellular processes that are common among bacteria. Finally, we show that the FtsK translocase is a powerful motor that is able to displace a triplex-forming oligo from a DNA substrate.dimer resolution ͉ sequence-directed translocases ͉ skewed sequences ͉ triplex displacement ͉ single-molecule T he DNA sequence of an organism encodes information on multiple levels. Beyond directly encoding proteins, specific DNA sequences recruit and direct the proteins required for processes such as DNA replication, transcription, and repair. DNA sequence-dependent proteins typically locate their binding site by diffusion where they then carry out a specific action (1). In contrast, the Escherichia coli DNA translocase FtsK uses an ATP-powered search mechanism to reach its target (dif ), the site of chromosome dimer resolution (2-5). During replication, crossing over by homologous recombination can lead to the formation of a chromosome dimer that must be resolved into monomers before segregation (2). FtsK is required to activate the site-specific recombinases XerC and XerD that resolve these dimers at the dif site, which is near the terminus of replication (2, 6). FtsK is anchored in the membrane at the division septum and actively translocates the dif sites into spatial proximity, rather than waiting for dif to diffuse into the septal region (7-9). The overall efficiency of reaching dif by translocation is greatly affected by two factors. First, FtsK must be able to bypass or displace bound proteins or other potential roadblocks it may encounter on the DNA. Second, FtsK must maintain its overall direction of translocation toward dif.Perhaps the simplest mechanism for ensuring that FtsK always translocates toward dif would involve FtsK loading at sequences that point FtsK in the proper direction. However, single-molecule observations of the FtsK motor domain (FtsK 50C ) translocating on DNA showed ...

Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK

“…In addition, several studies have investigated how FtsK is guided toward dif through interactions with KOPS (7-9, 14, 18). Early reports suggested that FtsK could recognize KOPS during translocation, enabling it to reorient while translocating (7,8,14,19). However, other studies have suggested that KOPS acts only as a loading site for FtsK (9,13).…”

“…FtsK 50C is a DNA-dependent ATPase, which can activate XerCDdif recombination (6). Single-molecule studies have shown that FtsK 50C translocates at ≈5 kb s −1 and resists stalling at forces up to 65 pN (8,12,13,17). In addition, several studies have investigated how FtsK is guided toward dif through interactions with KOPS (7-9, 14, 18).…”

“…In vitro work has focused on the C-terminal FtsKαβγ motor domain, referred to as FtsK 50C , or similar constructs (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16). FtsK 50C is a DNA-dependent ATPase, which can activate XerCDdif recombination (6).…”

“…The motor domain has three subdomains, called α, β, and γ. FtsKαβ is a RecA-like ATPase that forms a homohexamer, which encircles DNA and couples the energy derived from ATP hydrolysis to translocation along DNA (5,6). FtsKγ is a winged helix domain that binds to KOPS (FtsK Orienting Polar Sequences), an 8-mer DNA sequence that is overrepresented in the E. coli genome and is preferentially oriented toward dif (7,8). During chromosome segregation, FtsK is guided toward the terminus region by KOPS, and upon reaching dif, FtsKγ activates XerCD.…”

SpoIIIE strips proteins off the DNA during chromosome translocation

“…The pore size of the FtsK hexameric ring in the crystal structure is ∼30 Å. Doublestranded DNA could easily be threaded through this annulus, but proteins associated with the DNA might not be accommodated. In vitro experiments with the cytoplasmic motor domains of FtsK and SpoIIIE indicate that these enzymes can displace ssDNA when it encounters a DNA triplex (Bigot et al 2005;Levy et al 2005;Ptacin et al 2008), suggesting that DNA-binding proteins might also be stripped off. However, some DNA-binding proteins have very high affinity for their cognate binding sites.…”