To test our method, we focused on DmdR1, which regulates iron-starvation response and has a strong relationship with siderophore BGCs. When we used TFBSs and co-expression patterns to find the DmdR1 regulon, we discovered an unknown locus seemingly linked to desferrioxamines
This shows that even in a well-studied model organism like Streptomyces coelicolor and a well-known pathway like desferrioxamines, we could still discover something new by considering regulation‼️
To infer BGC function using regulation, we focused on experimentally validated transcription factor binding sites (TFBSs) of S. coelicolor. You can explore this collection of TFBSs in our LogoMotif database 🚂 https://t.co/P9Nc4Dg9LF
I’m so proud to present a key story of my PhD project! 🦠🧫Together with @ZachReitzPhD, we developed a regulation-based strategy to predict gene cluster function and used it to discover a new BGC in Streptomyces coelicolor.
Check out our preprint here: https://t.co/avxGEeOnsX
At the @WUR Dies Natalis, @HannahAugustijn just gave a fantastic short research talk about how to unlock the chemical potential of the microbiome by understanding the way their biosynthetic gene clusters are regulated. @WURplant@LeidenBiology@GillesvanWezel
Excited to share our new preprint on LogoMotif! 🚂 We've created a database dedicated to transcription factor binding sites of Actinobacteria for regulatory network exploration 🧬🔍 Thanks to @marnixmedema@GillesvanWezel and all others! Read more at: https://t.co/TbHncFGiW6
And that’s a wrap! Thank you to everyone who attended the #CBNP16 at @uniofwarwick, @UKRI_News and @RSC_CBBG for funding, @pnleao and @ZachReitzPhD for fantastic closing lectures, and all other speakers and poster presenters for their wonderful contribution!
I am a speaker at @PGPRworkshop 2023! Beautiful, sunny Toulouse and really nice crowd of plant-microbes interactions enthusiast experts... what else? 😊
I feel honored to receive the first place poster prize at #NWOlife for a poster about my PhD project on bacterial regulation 🦠🧬 Huge thanks to everyone involved in the different projects and of course my supervisors @marnixmedema and @GillesvanWezel
We've released version 7.0.0 of antiSMASH.
This version adds 10 BGC types, RiPP precursor comparisons, transcription factor binding site preds, and new viz. It also updates A domain substrate predictions and cluster comparison DBs. See https://t.co/3hDHkAni3m for more details