New publication: Inducible #CRISPRi enables efficient and high-fidelity #genome editing in #Streptomyces, by @gillesvanwezel.bsky.social and others. #antibiotics doi.org/10.1093/nar/...
Gilles van Wezel
@gillesvanwezel.bsky.social
Infectious diseases & antibiotics; https://C4D-global.org; Microbial life; Leiden University; NIOO-KNAW; Imagine; Scientific account; Opinions are my own.
Just submitted a huge systems biology paper we worked on for years, on in vitro binding of all transcription factors of Streptomyces coelicolor and across Actinobacteria. With Hannah Augustijn, Hiroshi Otani, @marnixmedema.bsky.social @nigelmouncey.bsky.social. Deserves a special beer #Hellekapelle
New publication: PARAS: High-Accuracy Machine Learning of Substrate Specificities in Nonribosomal Peptide Synthetases, by @gillesvanwezel.bsky.social and others. #bacteria #fungi #antibiotics doi.org/10.1021/jacs...
We invented “triplet tumbling microscopy” (TTM) to track protein-protein interactions in living cells! Tag your protein with GFP and see it interact with *untagged* binding partners www.biorxiv.org/content/10.6...
all credits to @sebarigali.bsky.social and Silvia Ribeiro Monteiro for this great tool to predict regulation of biosynthetic gene clusters.
Ákos T Kovács@evolvedbiofilm.bsky.social · 4mo agoCOMMBAT: a web platform for exploring expression control of biosynthetic gene clusters @narjournal.bsky.social from @sebarigali.bsky.social With @gillesvanwezel.bsky.social @marnixmedema.bsky.social academic.oup.com/nar/advance-...
Chemical dialogues at the crossroads of host–bacteria interactions @cp-trendsplantsci.bsky.social by Emtinan Diab, Nicola Thome, Somayah Elsayed, @raaijmakersjm.bsky.social and @gillesvanwezel.bsky.social www.cell.com/trends/micro...
Chemical dialogues at the crossroads of host–bacteria interactions
Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is...
cell.com
Now out in @acs.org JACS Au, the manuscript by #BarbaraTerlouw et al. describing PARAS, a high-accuracy machine-learning algorithm to predict substrate specificities of nonribosomal peptide synthetase (NRPS) adenylation domains, key for estimating natural product structures from BGC sequence. 1/n
New publication: Plant Coumarins #Modulate Natural Product #Biosynthesis in a #Streptomyces #Root #Endophyte, by @gillesvanwezel.bsky.social and others. doi.org/10.1021/acs....
Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte Journal of Natural Products by Emtinan Diab, Chao Du, Wendalina Tigani, Somayah Elsayed and @gillesvanwezel.bsky.social #LeidenBiology pubs.acs.org/doi/10.1021/...
Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte
The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.
pubs.acs.org
Genes for the biosynthesis of plant natural products are clustered on plants, as discussrd (and published) by @anneosbourn.bsky.social
looking forward to the talk by @anneosbourn.bsky.social on Plant Natural Products and esp triterpenes. Anne is todays speaker in the @led3hub.bsky.social seminar series.
2025 was a year full of great scientific discoveries and breakthroughs. Here, I want to highlight 10 papers that got me really excited. Of course, this is a highly subjective selection and I am sure I am forgetting some papers that I would love to include, but here it goes: (1/12)
New publication: Disentangling the molecular mechanisms of disease suppression by endophytic #Flavobacterium sp. 98, by @xinyapan.bsky.social @gillesvanwezel.bsky.social @raaijmakersjm.bsky.social and others. #plantmicrobiome #plantgrowth doi.org/10.1016/j.mi...
Kudos to #yijunzhu #hannahaugustijn and #victoriapascal for getting this out, and thanks to @gillesvanwezel.bsky.social #dylandodd and #michaelfischbach for the collaboration! Try it out now on gutsmash.bioinformatics.nl
gutSMASH
gutsmash.bioinformatics.nl
academic.oup.com/ismej/advanc... Endophytic adaptation in Flavobacterium sp. 98 @xinyapan.bsky.social @vcarryon.bsky.social @gillesvanwezel.bsky.social ✌🏽 lysoPE story could be cool
Hypoxia Induces Phenotypic and Metabolic Shifts in Endophytic Flavobacterium sp. 98
Abstract. Oxygen plays a crucial role in shaping microbial physiology, functions, and behavior. Endophytic bacteria, residing within plant tissues, inhabit
academic.oup.com
Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth journals.plos.org/plosbiology/...
Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth
Understanding how root microbes respond to drought is crucial for improving crop resilience. This study finds that Streptomyces responses are strain-specific and functionally diverse, with traits and ...
journals.plos.org
GlcNAc build-up acts as a key metabolic signal in #Streptomyces, but how does it triggers developmental responses? @gillesvanwezel.bsky.social &co show that the enzyme NagS dehydrates GlcNAc-6P into a reactive intermediate, triggering a toxicity-based checkpoint @plosbiology.org 🧪 plos.io/44pE08I
thanks @angelahuttner.bsky.social for a very inspiring talk LUMC Leiden. The house in the image you showex was built in 1612, and Rembrandt van Rhijn was 6 years old by then and lived at the bridge in the back, 200 m away. Always when I see the house I think of how Rembrandt will have painted it!
GlcNAc build-up acts as a key metabolic signal in #Streptomyces, but how does it triggers developmental responses? @gillesvanwezel.bsky.social &co show that the enzyme NagS dehydrates GlcNAc-6P into a reactive intermediate, triggering a toxicity-based checkpoint @plosbiology.org 🧪 plos.io/44pE08I
New publication: #Serotonin modulation of #metabolism and #stress response in Pseudomonas fluorescens, by @gillesvanwezel.bsky.social and others. doi.org/10.1186/s129...
@widdowquinn.bsky.social Sandra and I just booked Marillion in Pompeii on 26 July. are you guys going?
Switzerland is joining Horizon Europe! We are uniting two research powerhouses. For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more. Today is a good day for science, and for our EU-Switzerland partnership.
in Cordoba, Spain after the excellent #PMS2025 meeting in Antequera. Used a parking app but with wrong (NL) numberplate. We got a fine but amazingly could pay it off by paying 6 euros att the vending machine. Attached some photos from the beautiful Mezquita.
time for another pint at the Eagle in Cambridge. RIP James Watson and thanks for your inspiration that changed the life of so many scientists.
