John Helmann

CuiT is a Cu importer required for metal homeostasis in Salmonella enterica https://www.biorxiv.org/content/10.64898/2026.01.22.701185v1

Congrats @regolab.bsky.social! www.pnas.org/doi/10.1073/...

Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota https://www.biorxiv.org/content/10.64898/2026.01.14.699351v1

The Bacillus subtilis class A penicillin-binding protein 4 (PBP4) requires an accessory protein RpdA Peptidoglycan (PG) synthesis is essential to maintain cell integrity during bacterial growth and division. In Bacillus subtilis, PG synthesis involves class A PBPs that act independently and class B P...

The Bacillus subtilis class A penicillin-binding protein 4 (PBP4) requires an accessory protein RpdA www.biorxiv.org/content/10.6...

A mechanotransduction mechanism for antibiotic defense in Gram-positive bacteria In this issue of Structure, Yu et al. show that the Bacillus subtilis ytr operon encodes two distinct ABC transporters. The authors present the cryo-EM structures of YtrEF in the apo and ADP-vanadate-...

🫴 A mechanotransduction mechanism for antibiotic defense in Gram-positive bacteria (Bacillus subtilis, with some interesting suppressor mutants):

In

Structure www.cell.com/structure/fu...

#subtiWiki #subtilis

Membrane editing with proximity labeling reveals regulators of lipid homeostasis - Nature Chemical Biology Coupling an optogenetic lipid-modifying enzyme with proximity labeling reveals protein networks and mechanisms regulating lipid homeostasis in the membranes of target organelles.

Thrilled to share our latest study, led by @reikatei.bsky.social, in @natchembio.nature.com! We began by asking a simple question—how do cells know if they have too much of a lipid in a particular membrane, and how do they respond to rectify this imbalance?
www.nature.com/articles/s41...
More info 👇

Registration is open for the 2026 Gordon Research Conference on Microbial Stress Response to be held on July 19-24 2026!! Submit your abstract by February 15th to be considered for a short talk. Apply now before it fills up!! Hope to see you there!! www.grc.org/microbial-st...

The Taste of Carbonation The enzyme carbonic anhydrase mediates the taste sensation of carbonated drinks.

🧪HAPPY 2026 EVERYONE!!!! 🥂🍾🥳

When you enjoy your bubbly this evening, do spare a thought about carbonic anhydrase - it's an amazing enzyme (almost as fast as 2025 felt! 😜), and it turns out, it's also responsible for tasting CO2's "fizziness"!!! 🍾

www.science.org/doi/10.1126/...

This work was also our first time doing membrane localization (way to go Cassidy)! And so proud of Bella’s gorgeous Paenibacillus tree showing the distribution of the transmembrane containing Spo0B! Also it’s the lab’s first paper without ribosomes 🫨, but don’t worry - the ribosomes made the Spo0B!

The Mannose Phosphotransferase System in Enterococcus lactis Is Essential for Gastrointestinal Colonization Enterococcus lactis, a recently established species that was previously classified as Enterococcus faecium clade B. Given its recent taxonomic classification, studies on this bacterium are scarce, an...

Interesting new paper on Enterococcus lactis (the species formerly known as Clade B E. faecium)

'The Mannose Phosphotransferase System in Enterococcus lactis Is Essential for Gastrointestinal Colonization'

onlinelibrary.wiley.com/doi/abs/10.1...

Predicting drug inactivation by changes in bacterial growth dynamics - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Predicting drug inactivation by changes in bacterial growth dynamics

Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪
www.nature.com/articles/s44...

Mycobacterium tuberculosis overcomes phosphate starvation by extensively remodelling its lipidome with phosphorus-free lipids - Nature Communications Here, the authors show that Mycobacterium tuberculosis manipulates lipid metabolism to overcome host restriction, by remodelling its lipidome and utilising host lipids as an alternative phosphate sour...

We’re excited to share our latest study that reshapes our understanding of Mycobacterium tuberculosis (Mtb) lipid composition, with major implications for drug discovery, immunity, and vaccine development.

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

A thread.

The FsrA‐Mediated Iron‐Sparing Response Regulates the Biosynthesis of the Epipeptide EPE in Bacillus subtilis Under iron-limited conditions, FsrA base-pairs with the intergenic region between epeX and epeE, enhancing epeE translation and triggering EPE production. Toxin-mediated cell lysis releases nutrients....

The FsrA-Mediated Iron-Sparing Response Regulates the Biosynthesis of the Epipeptide EPE in Bacillus subtilis

#MolMicrobiol by Sarah Miercke, Rabea Ghandour, Kai Papenfort and Thorsten Mascher

onlinelibrary.wiley.com/doi/10.1111/...

Contribution of the Bacillus subtilis ytrGABCDEF operon to antibiotic stress adaptation | Microbiology Spectrum The Bacillus subtilis ytrGABCDEF operon is a reliable and specific marker for the inhibition of cell wall biosynthesis by antibiotics. It has therefore advanced as a common reporter in transcriptomic,...

Contribution of the Bacillus subtilis ytrGABCDEF operon to antibiotic stress adaptation

Microbiology Spectrum from from Michaela Wenzel at Chalmer University of Technology, Gothenburg

journals.asm.org/doi/10.1128/...

Spx inhibits expression of the SwrA•DegU master flagellar activator in Bacillus subtilis | Journal of Bacteriology Bacterial flagella are elaborate machines that are inserted through the bacterial cell envelope. The regulation of flagellar gene expression is organized in hierarchical tiers that largely correlate w...

Spx inhibits expression of the SwrA•DegU master flagellar activator in Bacillus subtilis

-in JBacteriol

journals.asm.org/doi/10.1128/...

The molecular basis of the synergistic toxicity of nickel and copper, common environmental co-contaminants | Applied and Environmental Microbiology Many environments are contaminated by metals. These metals are toxic to the microorganisms that inhabit these environments and carry out important ecosystem services. While much is known about bacteri...

journals.asm.org/doi/10.1128/...

We have a new paper out, led by my PhD student Linda! Ni and Cu are common co-occurring contaminants. They are also synergistic in their toxicity. We examined the mechanisms of this synergism, finding that sulfur assimilation and Fe-S cluster biogenesis are targets.

Structural analysis of a Gram-positive type VII ABC transporter induced by cell wall-targeting antibiotics Bacteria utilize a variety of mechanisms to remodel the cell wall in response to environmental and antimicrobial stress. In the model organism Bacillu…

Cool new paper on the structure and possible function of the type VII ABC transporter YtrEF in cell wall remodeling in Bacillus subtilis!
#SubtiWiki

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

For those interested in further reading, the studies establishing the triplet nature of the genetic code were also reviewed by both Benzer and Crick in two 1962 Scientific American articles -- both worth a read!
www.jstor.org/stable/24937...
www.jstor.org/stable/24936...

See our @natmicrobiol.nature.com News&Views on the publication from Yun Chen laboratory

A rapid writing exercise for María Negre Rodríguez, a PhD student in my group

Ecological function of phenazine in soil
www.nature.com/articles/s41...

#MicrobiomeEcology at #LeidenBiology

🚨 New Preprint Alert 🚨

Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄

Check it out here: www.biorxiv.org/content/10.1...

Monitoring single cell bioenergetic status and cell lysis in dense and differentiating Bacillus subtilis cultures Bacillus subtilis is a major model organism for studying population heterogeneity in clonal bacterial cultures due to its high genetic tractability and ability to differentiate into subpopulations wit...

A new methods paper from us, this time with a focus on reliable monitoring membrane potential and cell lysis at different growth stages and cell densities. Also, note the surprisingly high level of background lysis in seemingly healthy B. subtilis cultures.
www.biorxiv.org/content/10.1...

RagB stimulates the activity of the peptidoglycan polymerase RodA in Bacillus subtilis | EMBO reports imageimageRagB regulates the SEDS protein RodA in Bacillus subtilis, by interacting with RodA and by stimulating its activity. This regulation is essential for cell wall synthesis, especially when Cla...

RagB stimulates the activity of the peptidoglycan polymerase RodA in Bacillus subtilis

[RagB = YrrS]

@emboreports.org by Frédérique Pompeo et al

www.embopress.org/doi/full/10....

A ptsH mutation suppresses growth defects and antibiotic sensitivity in a cpgA mutant defective in metabolite proofreading | Journal of Bacteriology Metabolism relies on the concerted action of hundreds of enzymes, many of which have some activity with non-canonical substrates. The resulting reactions constitute an often-ignored underground metabolism. Glyceraldehyde-3-phosphate dehydrogenase ...

A ptsH mutation (encoding the HPr-G54D variant) suppresses growth defects and antibiotic sensitivity in a Bacillus subtilis cpgA mutant defective in metabolite proofreading!

Where? In Journal of Bacteriology!

🫳 journals.asm.org/doi/10.1128/...

#subtiwiki #subtilis #CCR

Elio Schaechter was one of my heroes. His 1958 paper with Ole Maaløe and Niels Kjeldgaard (fondly known as “SMK”) is a North Star for so much work in my group. A wonderful scientist, great communicator, and a very kind person. May his memory be a blessing.

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 ...

This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to @ahocher.bsky.social‬, @valeriesoo.bsky.social‬, Pauline Misson, @tobiaswarnecke.bsky.social‬ and MRC LMS Proteomics. A thread 🔽
journals.plos.org/plosbiology/...

Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome Abstract. Recent evidence indicates that the bacterial Rho helicase regulates Bacillus subtilis gene expression in a growth-dependent manner. This regulati

New cool work from French friends and colleagues: identification of Rho termination sites in B. subtilis! academic.oup.com/nar/article/...

#SubtiWiki @narjournal.bsky.social @inrae-france.bsky.social

This paper was led by Dr. Ankita Sachla with contributions from current sr. res. assoc. Ahmed Gaballa and former undergraduate student Diana Herrera (Cornell '19; yes.... this took a while).

A metabolic diagram illustrating various ways the HPr protein interacts with other proteins to affect metabolism.

The B. subtilis histidine-containing phosphocarrier protein (HPr) supports PTS-sugar import, interacts with GAPDH, and helps mediate carbon catabolite repression (CCR). Here, a mutant HPr protein is shown to alleviate metabolic intoxication in a cpgA mutant.
journals.asm.org/doi/10.1128/...

Thanks Christoph!

Thanks Peter!