Rune Busk Damgaard

M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress
#Drosophila

Tomato? or tomahto?

A tale of two tags: UFMylation counters ubiquitination for ciliary homeostasis - Cell Death & Differentiation Cell Death & Differentiation - A tale of two tags: UFMylation counters ubiquitination for ciliary homeostasis

Interesting article and accompanying spotlight on the cross-talk between ciliary homeostasis and ubiquitination (written by Jonathan Pruneda and @rbdamgaard.bsky.social).

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

💡 Ciliary homeostasis turns out to depend on an unexpected tug-of-war between UFMylation and ubiquitination.

In a recent editorial in Cell Death & Differentiation,
@jnpruneda.bsky.social and I highlight new work from Wang et al. 🧵👇

A tale of two tags: UFMylation counters ubiquitination for ciliary homeostasis - Cell Death & Differentiation Cell Death & Differentiation - A tale of two tags: UFMylation counters ubiquitination for ciliary homeostasis

This work expands the landscape of PTM crosstalk and raises the possibility that ciliary dysfunction contributes to neurological and developmental disorders linked to the UFM1 pathway.

🔗 www.nature.com/articles/s41...

Mechanistically, UFMylation and ubiquitination compete for the same lysine on IFT88, forming a mutually exclusive modification switch that controls protein stability and ciliary integrity across tissues.

While ubiquitination is a well-known regulator of protein stability, the roles of many ubiquitin-like modifiers remain unclear. Here, UFL1-mediated UFMylation emerges as a protective signal for the ciliary protein IFT88.

💡 Ciliary homeostasis turns out to depend on an unexpected tug-of-war between UFMylation and ubiquitination.

In a recent editorial in Cell Death & Differentiation,
@jnpruneda.bsky.social and I highlight new work from Wang et al. 🧵👇

🚨 Postdoc position in my lab!

A project on protein binder discovery for K6-linked #ubiquitin to investigate their role in infection is available.

📍 DTU, Copenhagen, Denmark
⏰ Deadline: 18 December 2025

Apply here: efzu.fa.em2.oraclecloud.com/hcmUI/Candid...

🚨 Postdoc position in my lab!

A project on protein binder discovery for K6-linked #ubiquitin to investigate their role in infection is available.

📍 DTU, Copenhagen, Denmark
⏰ Deadline: 18 December 2025

Apply here: efzu.fa.em2.oraclecloud.com/hcmUI/Candid...

A #postdoc position in atypical #ubiquitin signalling and protein binder engineering is opening soon in my lab at DTU Bioengineering! Get in touch if you are interested.

🚀 Off to our Research Retreat with the Section for Medical Biotechnology, DTU Biotechnology and Biomedicine.

Two days of science, ideas & innovation 🧬💡
12 faculty pitches, 30+ PhDs & postdocs, and endless opportunities for new collaborations 🔬🤝✨

A few months ago, our review “The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling” 🧬🧰🛠️ came out in ChemBioChem. Time to give it a spotlight!

chemistry-europe.onlinelibrary.wiley.com/doi/full/10....

Hope this serves as a useful overview for anyone working on ubiquitin signalling or PTMs. Big thanks to those who did the heavy lifting in the writing process: Julian Koch, Camilla Reiter Elbæk & @dompri.bsky.social 🙌😊

We also highlight:
✅ Trade-offs between specificity, throughput, & sensitivity
✅ Gaps in the current toolbox where innovation is needed
✅ The value of combining orthogonal methods for robust insight

…alongside analytical platforms such as:
✅ Immunoblotting 🧫📊
✅ Fluorescence microscopy 🔬🌈
✅ Enzymatic assays 🧪⏱️
✅ Mass spectrometry ⚡📈

In the review, we summarise state-of-the-art tools for probing linkage-type specificity:
🎯 Antibodies & antibody-like molecules
🎯 Affimers
🎯 Engineered Ub-binding domains
🎯 Catalytically inactive deubiquitinases
🎯 Macrocyclic peptides

Why this matters ⬇️
Ubiquitin chain diversity, i.e. different linkage types, mixed or branched chains, is central to cell signalling.
But analysing these chain types specifically remains a big challenge.

A few months ago, our review “The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling” 🧬🧰🛠️ came out in ChemBioChem. Time to give it a spotlight!

chemistry-europe.onlinelibrary.wiley.com/doi/full/10....

Is it still useful to insist that authors spell out every protein name in research papers? Many names are long, obscure, and say nothing about function... we might as well call them James, Joan, and John.

The goal of a PhD is not to learn some facts or read a few papers or learn a bunch of techniques. The goal of a PhD is to learn independence, problem solving, how to finish things you start, resilience, & gain the ability to adapt & think creatively. Learning these things is hard.

Regeringens sult efter at afskaffe bureaukratiet er gået for vidt, når den nu rammer forskerne Regeringen hævder, at der med de nye besparelser på universiteterne ikke vil gå midler fra forskning. Men forskere arbejder ikke i et vakuum. Når administrationen fjernes, ryger tiden fra forskningen

Jeg er godt træt af måden regeringens spareplan rammer universiteterne.

the really key number to remember is that biorxiv serves the entire global science community, posting thousands of papers per month for millions of readers, and it's entire running costs ( a few $M/year) are less than some single labs....

it’s a global contest, whether we want to compete or watch from the sidelines

Special day for our group @cbmr.science as we celebrate the successful defense of our (first) freshly minted PhD, Dr. Conchita Bringas 🥳 Her thesis was based on characterizing novel #AMPK inhibitors. Special thanks to the great committee @rbdamgaard.bsky.social ,Dave Carling & Lykke Sylow.

Postdoc Position (f/m/x) We are looking to support our rapidly growing team as soon as possible:

We have a 4-year postdoc position open in our Research Unit on proteostasis!
The project explores inter-tissue regulation using advanced proteomics approaches.
Collaborative & interdisciplinary environment. More details & application here:
jobs-uk-koeln.onlyfy.jobs/job/pktg6ivj...

ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213 - Nature Communications RNF213 is an E3 ligase with ATPase activity. Here, the authors show that RNF213 is activated by ATP binding and senses cellular energy states, and reveal a transthiolation mechanism induced by immune ...

Great to see this out. A story that spanned continents, cities and budget codes…

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

Big thanks to all the teams involved!

@clausenlab.bsky.social @e3chembio.bsky.social

Congrats!!

Haven’t shared this in a while. But the #ubiquitin and #ubl Starter Pack now includes 116 profiles to follow if you’re interested in the field: signalling, structure and biochemistry, biology, mechanisms, proteostasis, TPD, chemical biology… Check out the list and let me know if you are missing.

Happy to see our review out in ChemBioChem @chemistryeurope.bsky.social in which we describe the tools and strategies for deciphering linkage type-specific #ubiquitin signalling: doi.org/10.1002/cbic.... Thanks to Julian for spearheading this, and to Camilla and Dominik for important contributions.