DNA translocases are molecular motors that move rapidly along DNA using adenosine triphosphate as the source of energy. We directly observed the movement of purified FtsK, an Escherichia coli translocase, on single DNA molecules. The protein moves at 5 kilobases per second and against forces up to 60 piconewtons, and locally reverses direction without dissociation. On three natural substrates, independent of its initial binding position, FtsK efficiently translocates over long distances to the terminal region of the E. coli chromosome, as it does in vivo. Our results imply that FtsK is a bidirectional motor that changes direction in response to short, asymmetric directing DNA sequences.

The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer in trans. This intersubunit interaction allows primase to select initiation sites on template DNA and implicates the regulatory domain as a "molecular brake" that restricts primer length. Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis.

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 ...