Lorenzo Olivi

science.orgEstablishment of titration-based control of DNA replication in Escherichia coliEscherichia coli couples the initiation of DNA replication with cell size by modulating the activity of the replication initiator protein DnaA. The activity of DnaA is regulated both by its interconve...

So happy to finally see my last work from my time at @mib-wur.bsky.social out! Big thanks to @nicoc-micsynmet.bsky.social, @hohlbeinlab.bsky.social and all other co-authors for their invaluable support throughout the whole process!

Laboratory of Microbiology@mib-wur.bsky.social

A basic control processes of microbial life, the control system of genome replication can be made simpler in E. coli, giving insights for synthetic cells! Work by @loreoliv.bsky.social, Belen Adiego-Perez and others. Now in Science Advances: www.science.org/doi/10.1126/...

11 May

🧵 New pre-print out from my time at @mib-wur.bsky.social showing how the titration of the initiator protein DnaA on the chromosome of E. coli can generate stable DNA replication @hohlbeinlab.bsky.social @nicoc-micsynmet.bsky.social doi.org/10.64898/202...

11 May

Controlling the expression of an always-active DnaA mutant and using the native titration power of the chromosome, we show strengths and limits of titration-based control of replication. What we saw tells us about the evolution of E. coli, but also informs design for such systems in synthetic cells!

doi.orgThe Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature CommunicationsA DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...

🧵 Our study on the elusive titration control mechanism of the replication initiator DnaA in Escherichia coli is now out on @natcomms.nature.com‬! @stephkoe.bsky.social @hohlbeinlab.bsky.social‬ @nicoc-micsynmet.bsky.social @ettema.bsky.social‬ @mib-wur.bsky.social doi.org/10.1038/s414...

11 There is still a long road ahead in characterizing the role of initiator titration in controlling DNA replication. Still, it's exciting how cutting-edge microscopy techniques allow us to tackle decades-old biological problems! Read more at: doi.org/10.1038/s414...

12 Bonus! DnaA is also a transcription factor, so together with @baybioms.bsky.social we also investigated how changes in its regulation alter E. coli proteome! Surprisingly, impacting titration or switch alone seems to have no impact on the genes known to be regulated by DnaA...

9 We then deleted known DnaA control loci and measured the DNA content of cells through flow cytometry, while we used microscopy 🔬 to measure their size and to determine the bound fraction of DnaA. We could then suggest a role of titration in stabilizing DNA replication in slow-growing E. coli.

10 More active DnaA in the cell? The chromosome titrates DnaA more, minimizing re-initiations. Less active DnaA? More DnaA is free, mitigating delays in replication. Even more interestingly, severely hampering titration leads to frequent re-initiation events!

7 We started by checking the distribution of DnaA boxes on the chromosome of E. coli. Glad to say that @stephkoe.bsky.social‬ totally knocked it out of the park with this analysis! He showed that DnaA boxes tend to be enriched around oriC, a favorable feature for initiator titration.

8 Next, using single-particle tracking 🔬, we observed the binding state of DnaA in live E. coli cells during steady-state growth at different growth rates. Consistent with previous modelling, we observed that the chromosome of E. coli controls DnaA bound fraction in a growth rate-dependent fashion!

5 We now know that DnaA exists in two forms: DnaA-ATP, competent in unwinding oriC and DnaA-ADP, inactive in oriC unwinding. In this switch model, it is the accumulation of DnaA-ATP that determines replication initiation. As a result, the switch model almost replaced initiator titration.

6 However, recent experimental and modelling efforts suggest that only a concerted action of switch and titration can generate stable cell cycles. Still, to date there is no direct evidence of DnaA being titrated on the chromosome of E. coli. We decided to try to tackle this gap.

3 DnaA binds DNA in specific 9 bp motifs called DnaA boxes. These boxes can have high or low affinity, depending on how well they match a specific consensus sequence. There are hundreds of high affinity boxes spread across the chromosome of E. coli. However, oriC mostly contains low-affinity motifs.

4 During early days of characterization of DNA replication control, it was hypothesized that the chromosome could act as a sponge 🧽 for DnaA, retarding DnaA binding to oriC by first titrating it on the high affinity boxes. This form of control is what is known as initiator titration model.

2 In E. coli, DNA replication starts when DnaA binds to the origin of replication oriC and unwinds it, allowing for the rest of the DNA polymerase to assemble. This initiation step must be finely regulated to ensure that DNA replication happens timely and only once per cell cycle.

16 Aug 2025

Definitely an experience to say the least, but stoked to see it in its final form! Can't wait to share more

Johannes Hohlbein@hohlbeinlab.bsky.social

Heroic effort by @loreoliv.bsky.social to wrap that one up! Reviewers' comments: similar number of words as in the manuscript... More soon.

21 July 2025

I'm beyond excited to share that I've been awarded an @embo.org Postdoctoral Fellowship to join the lab of prof. Johan Elf at Uppsala University @uu.se! Can't wait to dive even deeper in the fascinating world of bacterial physiology!

@wiringthebrain.bsky.social

5 Jan 2025

This is the science that really matters

Giacomo Bartolucci (he)@gbart.bsky.social

1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce". Prepare to get cheesy, I'm glad to share the Cacio e paper preprint: arxiv.org/abs/2501.00536

Lorenzo Olivi reposted

Kevin Mitchell

12 Dec 2024

The tech bro fascination with eugenics is so on brand. The idea that you could make accurate, actionable predictions from individual genotypes (with all their complex, non-linear interactions) from averaged, linearly modeled population-level genomic statistics is just another big data fantasy

Lorenzo Olivi reposted

Johannes Hohlbein

@hohlbeinlab.bsky.social

10 Dec 2024

In the spirit of which, here some new filter wheels designed by Ian Kercher with more info available here: www.printables.com/model/110377... #OpenMicroscopy

Johannes Hohlbein@hohlbeinlab.bsky.social

Non-comprehensive list of projects, hardware, software, and people related to #OpenMicroscopy. List could do with some updates, so please share and suggest additions! github.com/HohlbeinLab/...

github.comGitHub - HohlbeinLab/OpenMicroscopy: Non-comprehensive list of projects and resources related to open microscopy.Non-comprehensive list of projects and resources related to open microscopy. - HohlbeinLab/OpenMicroscopy

Lorenzo Olivi reposted

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18 Nov 2024

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18 Nov 2024

The best resource for #microscopy is among us on BlueSky! Savior of my #sptPALM designs

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