Jachowski, T. J. | Search bioRxiv

bioRxiv2023

Short oligomers rather than rings of human RAD52 promote single-strand annealing

Genome maintenance and stability rely on the repair of DNA double-strand breaks. The break repair can be mediated by the single-strand annealing protein RAD52. RAD52 forms rings that are thought to promote annealing. However, RAD52s annealing activity decreases with increasing concentrations that favor ring formation. Thus, which oligomeric form and how RAD52 anneals DNA strands and detects sequence homology is unclear. We combine mass photometry with biochemical assays to quantify oligomeric states of human RAD52 with and without DNA and put forward an alternative mechanism illustrating the critical role of short oligomers for single-stranded DNA annealing. We found that while truncated RAD52 formed undecameric rings at nanomolar concentrations, full-length RAD52 was mostly monomeric at lower nanomolar, physiological concentrations. At higher concentrations, it formed rings with a variable stoichiometry from heptamers to tridecamers. At low concentrations, with hardly any rings present, RAD52 already promoted single-strand annealing. Rings and short oligomers could bind at least two single DNA strands, but if complementary strands were both bound to rings annealing was inhibited. Our findings suggest that single-strand annealing and homology detection is mediated by short oligomers of RAD52 instead of rings.

molecular biology↗

bioRxiv2020

Germanium nanospheres for ultraresolution picotensiometry of kinesin motors

Kinesin motors are essential for transport of cellular cargo along cytoskeletal microtubule filaments. How motors step, detach, and cooperate is still unclear. To dissect the molecular motion of kinesin-1, we have developed germanium nanospheres as ultraresolution optical trapping probes. We found that single motors took 4-nm-center-of-mass steps. Furthermore, motors never detached from microtubules under native hindering load conditions. Instead, motors slid on microtubules with microsecond-long, 8-nm steps and remained in this slip state before detaching or reengaging in directed motion. Surprisingly, reengagement and, thus, rescue of directed motion was prevailing. We argue that teams of motors may be synchronized through this slip state and rescues need to be accounted for to understand long-range transport. One Sentence SummaryOptical trapping of high-refractive-index semiconductor nanoparticles shows how motors detach and walk with 4-nm steps.

biophysics↗

bioRxiv2019

The kinesin-8 Kip3 depolymerizes microtubules with a collective force-dependent mechanism

Microtubules are highly dynamic filaments with dramatic structural rearrangements and length changes during the cell cycle. An accurate control of the microtubule length is essential for many cellular processes in particular, during cell division. Motor proteins from the kinesin-8 family depolymerize microtubules by interacting with their ends in a collective and length-dependent manner. However, it is still unclear how kinesin-8 depolymerizes microtubules. Here, we tracked the microtubule end-binding activity of yeast kinesin-8, Kip3, under varying loads and nucleotide conditions using high-precision optical tweezers. We found that single Kip3 motors spent up to 200 s at the microtubule end and were not stationary there but took several 8-nm forward and backward steps that were suppressed by loads. Interestingly, increased loads, similar to increased motor concentrations, also exponentially decreased the motors residence time at the microtubule end. On the microtubule lattice, loads also exponentially decreased the run length and time. However, for the same load, lattice run times were significantly longer compared to end residence times suggesting the presence of a distinct force-dependent detachment mechanism at the microtubule end. The force dependence of the end residence time enabled us to estimate what force must act on a single motor to achieve the microtubule depolymerization speed of a motor ensemble. This force is higher than the stall force of a single Kip3 motor, supporting a collective force-dependent depolymerization mechanism that unifies the so-called "bump-off" and "switching" models. Understanding the mechanics of kinesin-8s microtubule end activity will provide important insights into cell division with implications for cancer research. STATEMENT OF SIGNIFICANCEKinesin-8 motors are important for microtubule length regulation and are over-expressed in different types of cancer. Yet, on the molecular level, it is unclear how these motors depolymerize microtubules. Using high-precision optical tweezers, we measured how single yeast kinesin-8 motors, Kip3, interacted with the microtubule end. Interestingly, we found that single Kip3 motors were still motile at the microtubule end. The force dependence of how long single motors were associated with the microtubule end enabled us to estimate what force motors must exert onto each other to achieve the collective microtubule depolymerization speed of many motors. Our data support a collective force-dependent depolymerization mechanism. A better understanding of Kip3s microtubule end activity has implications for cell division and associated diseases.

biophysics↗