Jonathan Pruneda

UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6 Nature Structural & Molecular Biology - Riechmann et al. uncover structural features governing ubiquitin transfer from ubiquitin-activating E1 enzymes UBA1 and UBA6 to specific E2...

Excited to share our work into ubiquitin E1-E2 specificity mechanisms. CryoEM visualising #ubiquitin transfer,biochemistry,evolution @labhofmann.bsky.social & tissue expression analyses @psarkies.bsky.social Big thanks to the team,reviewers & handling editor @dimitristypas.bsky.social rdcu.be/eTRdR

SAVE THE DATE!
The EMBO workshop "Ubiquitin and Ubiquitin-like proteins in Health and Disease" will be on September 2026.
Exciting line up of talks and an amazing location!
Organised by @kulathu.bsky.social, @merbllab.bsky.social, @simonapolo.bsky.social, Claudio Joazeiro.
Registration open soon.

DUCs are C2 domain containing plant-specific deubiquitinases stabilizing endocytic cargo at the plasma membrane Deubiquitinases (DUBs) remove ubiquitin modifications from proteins in a substrate- or linkage-selective manner and regulate numerous cell-biological processes, including endocytosis. By performing ho...

For all #ubiquitin aficionados out there: Our new study, where we used an #alphafold based screen and found a new class of plant-specific DUBs, which cleave K63 chains and interfere with endocytosis at the plasma membrane. www.biorxiv.org/content/10.6...

UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6 Nature Structural & Molecular Biology, Published online: 05 December 2025; doi:10.1038/s41594-025-01717-zRiechmann et al. uncover structural features governing ubiquitin transfer from ubiquitin-activating E1 enzymes UBA1 and UBA6 to specific E2 ubiquitin-conjugating enzymes, revealing a hierarchy of E2 activity with cognate E1s.

ICYMI: New online: UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6

High-fidelity human chromosome transfer and elimination The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...

A key step towards human genome synthesis. With thanks to @wellcometrust.bsky.social @mrclmb.bsky.social #SynHG doi.org/10.1126/scie...

Differential targeting of human pyroptotic Caspase-5 and Caspase-4 by Shigella OspC2 and OspC3 https://www.biorxiv.org/content/10.64898/2025.12.04.692159v1

Ubiquitin pathway blockade reveals endogenous ADP-ribosylation marking PARP7 and AHR for degradation | The EMBO Journal imageimageDegradation mechanisms of transcriptionally active aryl hydrocarbon receptor (AHR) are unclear. This work reveals that PARP7 ADP-ribosylates itself and ligand-bound AHR, creating a recogniti...

In our latest study we show that ligand-activated transcription factor AHR (environmental sensor) is ADP-ribosylated by PARP7. This ADP-ribose mark is recognised by the E3 ubiquitin ligase DTX2 targeting AHR for proteasomal degradation, enabling cells to rapidly shut down AHR-mediated transcription.

Mono-ADP-ribosylation as a degradation mark?
@andriigorelik.bsky.social, Ivan Ahel et al observe increased ADP-ribosylation of aryl hydrocarbon receptor (AHR) & PARP7 upon ubiquitin-proteasome blockage, crosstalk with DTX2 E3, as rapid AHR-transcription off-switch
www.embopress.org/doi/full/10....

Congrats! Glad to see you’re finally working on ubiquitin! :)

Deubiquitinase USP-14 controls intestinal distension-induced immune activation in Caenorhabditis elegans via Wnt/β-catenin signaling Pathogen infections disrupt multiple host cellular processes, and hosts have consequently evolved mechanisms to detect these perturbations and initiate appropriate immune responses. In Caenorhabditis ...

Pleased to share our latest work by Annesha Ghosh. Using genetic screens, we identify that the deubiquitinase USP-14 regulates innate immunity in C. elegans.

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

We’ve made some new tools to manipulate N-recognins. Check them out in our preprint.
www.biorxiv.org/content/10.1...

Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8

The second part of our (with @origichals.bsky.social and El Hadji) two-part review on non-covalent SUMO interactions is now published, focussing on SUMO-interacting motifs (SIMs), but discussing also other confirmed or potential SUMO-interacting elements.

Well deserved!!

So proud of the lab for its achievements - Thank you to the Pettenkofer foundation for recognising our contributions - here’s to some more bacterial effector related fun in the future! @dunnschool.bsky.social

🚨 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...

Filament formation and NAD processing by noncanonical human FAM118 sirtuins Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...

Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.

⏳Four days to go until #AusUb2025! Check out the video below to hear some conference tips and tricks from our committee chair David Komander (and some potentially controversial interest rankings!?!?).

More interviews to come in the next few days so watch this space 😉

See you there!

The Saccharomyces killer toxin K62 is a protein of the aerolysin family | mBio Pore-forming toxins are potent biological weapons used across nature, from virulence factors to immune defense proteins. This study identifies K62, a little-known antifungal toxin produced by a wild y...

The Rowley/Ytreberg/Patel labs at UI have led a multidisciplinary study to characterize a new yeast toxin! Published in the ASM's flagship Journal - mBio. Eight undergraduate authors contributed to the study, a great team effort! journals.asm.org/doi/10.1128/... @uidaho.bsky.social

Photo of the Baylink lab group that attended ASMNW.

ASM NW was wonderful this year! In addition to the great science, this trainee-focused meeting plays such an important role in providing the next generation of scientists, microbiologists, and clinicians an opportunity to learn, network, and share their own research.

🧪🦠

Targeted recruitment of USP15 enhances CTLA4 surface levels and restricts its degradation. Induced protein proximity offers powerful new routes to modulate protein fate. While proteolysis-targeting chimeras (PROTACs) promote degradation through E3 ligase recruitment, the converse principle-...

Our latest preprint is out!
We developed an inducible “RapTag” system that uses ENTAC to chemically recruit USP15 to the unstable protein CTLA4. This induced proximity stabilises and slows down the rapid lysosomal turnover of CTLA4.
@livuni-ismib.bsky.social
www.biorxiv.org/content/10.1...

Salmonella multimutants enable efficient identification of SPI-2 effector protein function in gut inflammation and systemic colonization - Nature Communications Intracellular Salmonella enterica uses a type III secretion system to secrete more than 30 effector proteins into host cells. Here, Newson et al. generate six mutant strains deficient in different set...

Excited to share our latest work, where we create Salmonella mutants deficient for cohorts of SPI-2 T3SS effectors. These strains can be used to efficiently identify particular effectors that contribute to SPI-2 phenotypes doi.org/10.1038/s414...

Can we improve peer review? We think we can! Check out an experiment I helped with as part of @solvingforsci.bsky.social 's mission to make science better.
And if you don't want to read the whole bioRxiv manuscript, here's an overview of the main findings:
solvingfor.org/news-posts-d...

SUMO interactions: the 1st of two reviews which Aanchal (@origichals.bsky.social), El Hadji, and I have recently written on non-covalent interactions of SUMO is now out. The 1st covers interactions with E1, E2, and deSUMOylating enzymes; the 2nd - on interactions with SIMs etc. - will appear soon.

Have a look at this Tools of the Trade Article I wrote for @natrevmcb.nature.com on decoding #ubiquitin signals inside cells using UbiREAD!
Many thanks to @lisaheinke.bsky.social for the opportunity to write this TotT!

🚨Thrilled to share our latest work, published online today
@nature.com in which we decipher mechanisms underlying the enigmatic VEXAS syndrome - a huge team effort
@mskcancercenter.bsky.social led by superstars Varun Narendra + @tandriladas.bsky.social 1/

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

It's been an amazing year for the new PTM field of #MARUbylation - happy that I could get involved first-hand!

This October I’m drawing 1 molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social

Day 20/31
Prompt RIVALS
Pdb: 8V27 & 8G6S

Two rival histone modifications on a nucleosome. Ubiquitination of H2BK120 activates genes while H2AK119 represses them.

Next: BLAST
Suggestions?