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Thomas Julou @thomasjulou.bsky.social · 16/01/2025

I should also say that we were ready to see much more variability between individual cells (which is also why we used this setup) but it simply turns out not to be the case… Analysed in detail in the article. Of course we needed to have single-cell resolution to be able to come to this conclusion.

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Thomas Julou @thomasjulou.bsky.social · 16/01/2025

Yes, we're very interested in understanding how cells fuel this gene expression response during the first hours of starvation (which is related to ATP levels) and whether dis/aggregation plays an important role in this time window.…This is beyond the scope of this article though!

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Thomas Julou @thomasjulou.bsky.social · 16/01/2025

Interesting question… We have not tried LB, my sense is that the uniform response across cells depends more on the strain than on the media – we have (very) preliminary results indicating that it is a general feature in several natural isolates and media. Stay tuned!

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Thomas Julou @thomasjulou.bsky.social · 15/01/2025

And don't miss the "skeetorial" by @erikvannimwegen.bsky.social: bsky.app/profile/erik...

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Thomas Julou @thomasjulou.bsky.social · 15/01/2025

What does E. coli do when food runs out? We spent years looking at it with our quantitative glasses, and now put the final preprint online: www.biorxiv.org/content/10.1... Congrats to Théo Gervais for the 'tour de force'!

biorxiv.org

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Reposted by Thomas Julou

Erik van Nimwegen @erikvannimwegen.bsky.social · 15/01/2025

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n www.biorxiv.org/content/10.1...

biorxiv.org

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients

It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

Given that this is all in M9 media, using MG1655 (GCSC 6300), the main culprit is the difference in nutrients: 0.4% glucose + 0.2% casamino acids for the 2 published reports vs 0.2% glucose without casamino acids for our preprint. Should I put this in the amino acid supply? Any clue why, anyone? n/n

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

Whether with our much fancier estimation of instantaneous rates (see methods) or with Patange's rather "hacky" filters (used by Proenca too), we never see such pauses of growth nor the anti-correlated oscillations of growth and promoter activity during growth in our experiments 🤯 5/n

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

Theo Gervais and I measured instantaneous growth and gene expression for the bolA reporter (both on plasmid and on the chromosome) in the same genetic background. All described in details in doi.org/10.1101/2024..., although the manuscript does not touch this aspect. 4/n

doi.org

E. coli leverages growth arrest to remodel its proteome upon entry into starvation

It is widely believed that, owing to the limitation of nutrients in natural environments, bacteria spend most of their life in a non-growing state. However, despite its major clinical and ecological i...

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

Note that the y axis do not show the same quantity (promoter activity vs protein concentration). However, Fig S2 of Proenca, et al. indicates that the cross-correlation pattern is seen for activity too. 3/n

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

This negative cross-correlation is reported to happen for promoters driven by RpoS. These plots (first: Patange, et al. using bolA reporter; second: Proenca, et al. using rpoS reporter) are time traces of instantaneous elongation ("growth") and "gene expression". 2/n

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Thomas Julou @thomasjulou.bsky.social · 18/12/2024

I'm puzzled 🤯 By now, we've spent lots of time measuring the effect of growth rate fluctuations on cell-to-cell variability of GFP concentration using various promoters in E. coli. However, we never observed the negative correlation reported by Patange et al. Now reported by Proenca et al too! 1/n

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Thomas Julou @thomasjulou.bsky.social · 11/12/2024

Still have to read the full article - but from the tweetorial and the figures it sounds so cool 🤩

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Thomas Julou @thomasjulou.bsky.social · 11/12/2024

Switzerland!! 🤩 I lost my train card at a gas station last weekend. Went back after realizing one hour later but couldn't find it... Someone had collected it, and send it back by post, without even writing any sender address. Big big thanks to this anonymous person.

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Thomas Julou @thomasjulou.bsky.social · 04/12/2024

Dont miss the great tweetorial by @erikvannimwegen.bsky.social: bsky.app/profile/erik...

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Thomas Julou @thomasjulou.bsky.social · 04/12/2024

The take home is that transcription factors can undergo large transient changes of their level on the same time-scale as their binding and unbinding to DNA. This `non-equilibrium' dynamics enables different target genes to respond differently to the same changes in TF levels. 2/n

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Thomas Julou @thomasjulou.bsky.social · 02/12/2024

Nice!! (link for download: doi.org/10.1016/j.ce...)

doi.org

Redirecting

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Thomas Julou @thomasjulou.bsky.social · 12/11/2024

(in French but auto-subtitles available, or read the transcript in the description)

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Thomas Julou @thomasjulou.bsky.social · 12/11/2024

I can't wait to listen to several of those! This reminds me of this video where Francois Jacob, who coined this concept, gives his take on "night science" - interviewed by the great and only Michel Morange. www.youtube.com/watch?v=p6AH...

youtube.com

François Jacob - Night science (65/77)

YouTube video by Web of Stories - Life Stories of Remarkable People

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