Michele Partipilo

New preprint from our group! When we first started working with affordable, continuous-culture mini-bioreactors a few years ago, we realized they offered a unique solution for CRISPRi experiments, which rely on cell growth to dilute targeted proteins.

www.biorxiv.org/content/10.6...

🧬 Can ancient Arctic genes help today’s crops survive climate extremes?
In #TOLERATE , scientists engineer root-friendly microbes with resilience traits found in ancient soils, boosting water retention, nutrient uptake & heat/drought tolerance.

Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation Biological carbon fixation is currently limited to seven naturally occurring pathways. Synthetic carbon fixation pathways have the potential to surpass aerobic natural pathways in efficiency, but none...

Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...

Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes Redox homeostasis is central to microbial physiology and stress adaptation, yet the functional roles of transhydrogenases remain poorly understood beyond a few organisms. In this study, we systematica...

How does Pseudomonas putida keep its redox balance steady across different metabolic states?

Our new preprint shows that two transhydrogenases -membrane-bound PntAB and soluble SthA - act together as a flexible, reversible system to control NAD(H)/NADP(H) ratios.

www.biorxiv.org/content/10.1...

250,000 people took part in the NO KINGS march in Chicago, with more than 7m marching in 2,700 locations US-wide, according to organisers @indivisible.org, as Americans increasingly resist Trump's authoritarianism.

A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.

🚀 Thrilled to share our new Nature Communications article:
“A blueprint for designing the next-generation of synthetic C1 microbes”
We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts.
🔗 www.nature.com/articles/s41... A short 🧵1/4

Synthetic C1 metabolism in Pseudomonas putida enables strict formatotrophy and methylotrophy via the reductive glycine pathway | mBio Soluble C1 feedstocks, such as formate and methanol, have gained attention as sustainable substrates for biotechnology, with the potential to reduce greenhouse gas emissions and reliance on sugar-based resources. Despite their promise, the metabolic ...

🚨 New paper in mBio!
We established strict formatotrophic & methylotrophic growth in engineered Pseudomonas putida via the reductive glycine pathway (rGlyP). journals.asm.org/doi/full/10....
Here’s a teaser of how we did it 🧵👇1/5

A Robust Isotope Ratio LC-MS/MS Workflow for High-Throughput Metabolic Profiling of Bacteria Stable isotope dilution mass spectrometry (IDMS) has become a cornerstone of quantitative metabolomics, enabling accurate intracellular metabolite quantification across a range of biological systems. ...

1/ 🚨 New preprint!
We've developed a robust IDMS-based LC-MS/MS workflow for high-throughput intracellular metabolomics in diverse bacteria. www.biorxiv.org/content/10.1...
#Metabolomics #MassSpec #SystemsBiology

Now published in Microbial Biotechnology! enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10....

The 5th edition of the #Pseudomonas grass roots meeting will take place on the 27th/28th of October 2025 in Denmark. This year, our group at DTU Biosustain will host 2 exciting days of networking, exchanging ideas and learning for early career-stage scientists working with Pseudomonas. 👇

Great work by @oscarpuiggene.bsky.social from our @labnikel.bsky.social showing methanol assimilation in P. Putida via enhanced serine–threonine cycle, do not miss this read!

Back from an inspiring week at #ME16 in our home #Copenhagen! 🌍

Engaging talks, exciting science, and amazing connections — we’re full of new ideas!

🎉 Big congrats to @giusifav.bsky.social for winning a poster award 🏆
🙌 And proud to have our PI @pabnik.bsky.social as co-chair of the event!

A promiscuous Bcd amino acid dehydrogenase promotes biofilm development in Bacillus subtilis

-in NPJ Biofilms and Microbiomes by David Ranava et al from Northwestern University / Mee-Ngan Yap, Arthur Prindle

www.nature.com/articles/s41...

The TOLERATE team met at DTU (Denmark) for a productive General Assembly.

New coordinator Pablo Ivan Nikel opened the meeting, presenting the transition and confirming that the project continues full speed ahead.

More info 👉 tolerate-eu-project.com
Subscribe 👉 eepurl.com/i6uufM

#EUProjects

Designed bacteria can detect specific molecules Researchers have developed a computer-guided method for designing and engineering bacteria that can detect the presence of specific molecules in the environment. This method will advance the use...

www.sciencenews.dk/en/designed-...

Piece from ScienceNews.dk on our glyoxylate and glycolate sensor strains

Single-molecule visualization of ATP-induced dynamics of the subunit composition of an ECF transporter complex under turnover conditions Nature Communications - The association and dissociation dynamics of the ECF transporter complex for vitamin B12 are visualized by single-molecule FRET, highlighting the original transport...

Solène’s 4.5 years of postdoctoral work in our lab (she started just before the corona pandemic) has now been published. A heroic effort that revealed -at the single molecule level- that ATP drives the dissociation of an ECF transporter complex under turnover conditions. See rdcu.be/elTKc

Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions Abstract. Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementatio

Interested in engineering bacteria to turn #C1feedstocks into high-value chemicals for #bioproduction? Here is a thread summarizing our latest review on the roadblocks and how we might bio-hack our way past them 🧵 1/n academic.oup.com/femsre/advan...

One‐pot dual protein labeling for simultaneous mechanical and fluorescent readouts in optical tweezers Optical tweezers are widely used in the study of biological macromolecules but are limited by their one-directional probing capability, potentially missing critical conformational changes. Combining ...

Out now! Our latest paper where we show a "one-pot" labelling technique which allows for simultaneous mechanical and fluorescent readouts from a protein (Hsp90):
onlinelibrary.wiley.com/doi/10.1002/...
Congratulations to everyone who worked on this, especially Laura!

Microbes like Cupriavidus necator naturally grow on #renewable feedstocks ♻️🧫 (CO₂, formate, hydrogen), yet their potential remains untapped due to the lack of efficient genetic tools... 1/2

www.cell.com/trends/biote...

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system This study developed two simple, efficient, and rapid genome editing tools termed Self-splicing Intron-Based Riboswitch-Cas9 (SIBR-Cas9) and SIBR2.0-Cas12a, for editing the genome of the industrially ...

Our brand new CRISPR/Cas toolkit for genome editing of Cupriavidus necator is out🦠🧬
A joint effort w/ @dellavallesimo.bsky.social and Costas (and many more!)
Check 🧵 our long journey for developing a new state-of-the-art for the manipulation of this promising bug 1/n

www.cell.com/trends/biote...

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation The urgent need for a circular carbon economy has driven research into sustainable substrates, including one-carbon (C1) compounds. The non-pathogenic soil bacterium Pseudomonas putida is a promising ...

The utilization of #C1-feedstocks, such as methanol, by non-model bacteria demands an in-depth analysis of design alternatives, a modular strategy to identify bottlenecks and efficient solutions within the host #metabolism of the chosen host...
www.biorxiv.org/content/10.1...

With great collaborations come great outcomes! A fine example from @eorsi.bsky.social from @pabnik.bsky.social's lab et collaborators of how to design, build and develop cell biosensors for value-added chemicals (related to synthetic C1 assimilation, of course)! 🧪

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...

Computation-aided designs enable developing auxotrophic #metabolic #sensors for wide-range glyoxylate and glycolate detection—spearheaded by Enrico Orsi w/a choral assembly of cool collaborators @naturecomms.bsky.social #SynBio #OpenAccess
www.nature.com/articles/s41...

Preprint alert🚨Systematic #engineering of synthetic serine cycles in #Pseudomonas putida uncovers emergent topologies for #methanol assimilation · @biorxivpreprint.bsky.social led by Òscar Puiggené #SynBio #Methylotrophy #CircularEconomy
www.biorxiv.org/content/10.1...

One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle - Nature Microbiology An engineered one-carbon-fixation pathway increases biomass yields of Cupriavidus necator compared with the Calvin cycle and can support future, sustainable bio-based production.

Super excited to see my main PhD project finally out in @naturemicrobiol.bsky.social www.nature.com/articles/s41.... We show for the first time that a synthetic and engineered pathway can indeed exceed nature at one-carbon fixation.

One-carbon fixation at the next level! A piece of work that opens up new scenarios for engineering bacteria for sustainable biomanufacturing! ⚗️🦠♻️

New: Using F-tractin to visualize #actin in living cells? Dmitry Shatskiy, Athul Sivan, Roland Wedlich-Söldner, and Alexander Belyy @alexanderbelyy.bsky.social determined the F-tractin-F-actin structure and showed that this probe is nearly identical to #Lifeact. https://buff.ly/3EIqAur
#cytoskeleton

A tuneable minimal cell membrane reveals that two lipid species suffice for life - Nature Communications All cells are encapsulated by a membrane of complex lipidic composition, and understanding the roles of different lipids in membrane function is experimentally challenging to address. Here, Justice et...

great title!! And the paper is cool too.

www.nature.com/articles/s41...

Microbes Saving Lives and Reducing Suffering Click on the article title to read more.

#Microbes Saving Lives & Reducing Suffering—led by KenTimmis, this is a call to action for understanding and exploiting microbes & their role in helping humans at the face of current challenges as a global society @microbiotech.bsky.social
enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....