Miloš Tišma
@tismaa
Biology is life 🌱 Biophysics is a tool Postdoc at Harvard Medical School Joe Loparo + TJ Ha Lab PhD at TU Delft | Cees Dekker Lab
I just still cannot help myself from looking that these beautiful real-time dynamics videos from @anjbadri.bsky.social lab! thanks to all the authors from @joeloparo.bsky.social / @anjbadri.bsky.social and TJ Ha labs.
Our model is that RecA explores the chromosome through filament movement and extension, while local negative supercoiling enables productive strand engagement and stabilization. Chromosome topology is therefore an active regulator of homology search - not passive DNA packaging !! 10/10
But this faster search was completely unproductive: we observed 0/100 homology-resolution events over 2 h !!! Drug washout restored normal dynamics and resolution. Mobility can solve the encounter problem; DNA topology solves the commitment problem. 9/10
We then tested the model in living Caulobacter cells. Removing negative supercoiling with novobiocin (blocking the gyrase) did not prevent RecA filament formation or pole-to-pole search. Instead, filaments traversed the cells ~45% faster and paused less. 8/10
This topological preference was broadly conserved in bacteria! RecA orthologs from E. coli, Caulobacter, Bacillus, Streptomyces, and Staphylococcus all strongly favored negatively supercoiled targets, despite their evolutionary and chromosomal diversity. 7/10
Real-time imaging revealed the step controlled by topology: commitment. Transient sampling occurred on both DNA states, but we saw no transient-to-stable transitions on relaxed targets. On supercoiled DNA, stable capture also pinned a plectoneme at the homologous site. 6/10
This was not simply an effect of DNA compaction. Binding was essentially unchanged from highly compacted targets to DNA stretched beyond 90% of its contour length. Artificially compacting relaxed DNA with PEG also failed to rescue binding. Topology-not compaction-was key. 5/10
The effect was striking. Within 15 min, 85/85 negatively supercoiled DNA molecules were stably bound, versus 5/543 relaxed molecules. Even after 1 h, <3% of relaxed targets bound. The kinetic preference for negative supercoiling was ~100-fold. 4/10
We used a single-molecule assay that lets us tune the topology to precise supercoiling levels of DNA targets while watching RecA-ssDNA filaments search and bind in real time. 2/10
So thankful for winning the Poster Prize at @fusionconf.bsky.social in Prokaryotic Cell Biology for my research on the effects of chromosome topology on DNA repair! Looking forward to developing the work further and sharing more soon !! 🤩🤩
In the last steps of the manuscript writing and I just ran the full document through the new @qedscience.bsky.social "Meet the 1%" manuscript comparison... I am beyond excited to share my postdoc work from @joeloparo.bsky.social lab in the next few weeks! 🤩🤩
Wrapped up a GRC on Bacterial Cell Biology and Development last week in SNHU, New Hampshire. A full week of talks on novel bacterial systems and new mechanistic details on eastablished systems. Great chance to learn, connect with peers and enjoy science!
A lovely visit to Yale School of Medicine to see @leoschaerfen.bsky.social graduate with a spectacular PhD work. 🤩
This is so real 🤣🤣 I do not know the explanation of this but definitely resonates very well…
Glad to receive the trust and recognition in being awarded a Dutch NWO Rubicon Fellowship for important work on antibiotic resistance. I will be tackling this problem using a combination of biophysics, biochemistry and microbiology in Joe Loparo lab at Harvard Medical School (Dept. of BCMP).
Out today in Nucleic Acids Research! My final publication from @ceesdekker.bsky.social lab together with A.M. Gonzalez ! Together with @gruberlab.bsky.social in Lausanne, we show the interaction between supercoiled DNA and partitioning protein ParB. Read full: doi.org/10.1093/nar/...