Now online: Pingzhuang Ge's studies on the impact of pH on local chromatin structure and transcriptional activity of the H-NS-regulated hdeAB operon www.biorxiv.org/content/10.6...

PDB101: Molecule of the Month: Histones Across the Tree of Life Uncovering the evolutionary diversity of histones

pdb101.rcsb.org/motm/314

What are the main sources of gene expression noise in bacteria, and why do slower growing bacteria exhibit more expression noise? TLDR: we found growth-rate fluctuations are a key driver of gene expression noise that increase as average growth rate decreases.
www.biorxiv.org/content/10.6...
1/n

I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...

Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious?

Either way, we have good news.
We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July.

Sign up: meetings.embo.org/event/26-arc...

We look forward to seeing you in Cambridge, UK

Please repost!!

Experimental structures provide valuable hypotheses and accelerate but do not replace evolutionary and statistical analyses of protein sequences

Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉

In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria.

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

Localised activity of reverse gyrase at gene regulatory elements DNA topoisomerases are essential enzymes found in all cells, where they regulate DNA supercoiling. Reverse gyrase (RG) is a unique type of topoisomerase that introduces positive supercoils into DNA an...

Delighted to share our new preprint: www.biorxiv.org/content/10.6...
We address a longstanding question about the role of the topoisomerase reverse gyrase in hyperthermophiles. Great collaboration with Baranello and @tobiaswarnecke.bsky.social groups. #Archaeasky #Microsky

Reverse gyrase and 3D genome architecture suppress hyperthermophile genome instability arising from horizontal gene transfer Reverse gyrase (Rgy), a distinctive topoisomerase conserved in all hyperthermophiles, has the unique ability to introduce positive DNA supercoils. It has long been hypothesized that Rgy overwinds geno...

Delighted to share our latest preprint on reverse gyrase, a unique topoisomerase found exclusively in thermophiles!
www.biorxiv.org/content/10.6...

I'm super excited to announce the first preprint of my PhD, together with Chenxi Ou and @sokrypton.org!

ML has revolutionized protein modeling, but crucial challenges remain. For example, we can't reliably predict complicated protein structures without MSAs, which limits what we can design.

Peristaltic waves inside Stylaria lacustris #microscopy

This work would not have been possible without our collaborators @naomichitakemata.bsky.social, who I met during the EMBO Achaea meeting last year, and @vikramalva.bsky.social, Yimin, and Birte.

Ending my PhD with a bang:
Face-to-face histones are important organizers of archaeal chromatin alongside classical histones.

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

Versatile NTP recognition and domain fusions expand the functional repertoire of the ParB-CTPase fold beyond chromosome segregation | PNAS Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...

Now published. Thank you very much to our collaborative team, and very supportive editors and reviewers!!!

www.pnas.org/doi/10.1073/...

Modulation of archaeal hypernucleosome structure and stability by Mg2+ DNA-wrapping histone proteins play a central role in chromatin organization, gene expression and regulation in most eukaryotes and archaea. While the …

New article online: Modulation of archaeal hypernucleosome structure and stability by Mg2+

In this work, we dissect the effects of Mg2+ on hypernucleosomes formed by the canonical histones from M. fervidus (HMfA and HMfB) and T. kodakarensis (HTkA and HTkB).

www.sciencedirect.com/science/arti...

Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.

Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...

📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

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

Screen binders using ipSAE YouTube video by ProteinDesignStudio

pip install ipsae
from www.linkedin.com/in/ullah-sam...

www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...

Archaea produce peptidoglycan hydrolases that kill bacteria Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

Scaling down protein language modeling with MSA Pairformer www.biorxiv.org/content/10.1101/2025.08....

And the story is published now!🍾
www.nature.com/articles/s41...

Open access link: rdcu.be/exnOc

Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social

Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky

Next up from our lab - a ring nuclease with a novel fold which cleaves all cOA species involved in Type III CRISPR defence. It's also found in plasmid and phage genomes, where it presumably functions as an anti-CRISPR.
www.biorxiv.org/content/10.1...

Different Bacterial Genes Have Different Turn-Ons Not all genes respond in the same way to regulation by the same molecule—a property that might enable cells to produce complex genetic responses.

Because of a lack of separation of the time scales for TF binding/unbinding and fluctuations in active TF levels, non-equilibrium gene regulation may be common in bacteria.
Check out this nice piece by ‪@philipcball.bsky.social‬ on our new publication in PRX Life.
physics.aps.org/articles/v18...

The role of nucleoid-associated proteins in mediating responses to environmental changes Bacteria face diverse environmental challenges, such as changes in temperature, pH, and osmolarity, and exposure to antibiotics, which necessitate ada…

I am pleased to share our new review on the role of bacterial nucleoid-aasociated proteins in mediating responses to changes in environment. Important: some NAPs can directly ‘sense’ physico-chemical changes. www.sciencedirect.com/science/arti... @pingzhuangge.bsky.social

Now online - the Review "Histone-mediated chromatin organization in prokaryotes and viruses" from @samuelschwab.bsky.social‬ @vikramalva.bsky.social @damelab.bsky.social‬ and co.

#histones #DNAorganization #chromatin #eukaryogenesis

Read it here 👉 authors.elsevier.com/sd/article/S...

Histone-mediated chromatin organization in prokaryotes and viruses Histones are fundamental chromatin-organizing proteins in eukaryotes and archaea, where they assemble into (hyper)nucleosomes that wrap DNA. Recent studies have expanded the known repertoire of histon...

A must-read for histone afficionados: our new review on 'Histone-mediated chromatin organization in prokaryotes and viruses' www.cell.com/trends/bioch... @samuelschwab.bsky.social @vikramalva.bsky.social

Ready to meet some Nobel Laureates 😄

We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM

Hitomezashi stitch patterns:
samuelschwab.com/hitomezashi-...

A snapshot of the HLp tetramer (purple) wrapping ~60 bp of DNA (green).

Excited to share our new preprint on HLp—a bacterial histone from Leptospira perolatii that forms stable tetramers and wraps ~60 bp of DNA: "DNA Wrapping by a Tetrameric Bacterial Histone" www.biorxiv.org/content/10.1...

@mpi-bio-fml.bsky.social