Reposted by Luuk LoeffSternberg Lab @sternberglab.bsky.social · 28/09/20261/13 — New pre-print from the Sternberg Lab in collaboration with Leifu Chang's Lab! TnpB nucleases have repeatedly given rise to TldRs, nuclease-dead RNA-guided transcription factors. Here we define the biological role of one TldR clade in its native host. Story: www.biorxiv.org/content/10.6... 14920
Reposted by Luuk LoeffAlexander Harms @aharms485.bsky.social · 25/09/2026The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4 514965
Reposted by Luuk LoeffJonathan Kagan @jkagan1.bsky.social · 23/09/2026Today, the Toll-like Receptors reveal a new mechanism of signal transduction: Receptor-Free Signal Transduction. www.nature.com/articles/s41...nature.comTRAM promotes Toll-like-receptor-free myddosome signal transduction - NatureTRAM is a regulator of myddosome assembly through dissociating MyD88 from the TLR–TIRAP complex to enable myddosome maturation and durable downstream signal transduction. 35217
Reposted by Luuk LoeffDavid Bikard @dbikard.bsky.social · 21/09/2026New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8 311155
Reposted by Luuk LoeffMalcolm White @mfwhite2.bsky.social · 21/09/2026New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6... 03420
Reposted by Luuk LoeffDoudna Lab @doudna-lab.bsky.social · 19/09/2026Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & teamscience.orgA noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-CasCRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst... 217569
Reposted by Luuk LoeffMartin Pacesa @martinpacesa.bsky.social · 21/09/2026ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi... 4292140
Reposted by Luuk LoeffMalcolm White @mfwhite2.bsky.social · 16/09/2026Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour... 14627
Reposted by Luuk LoeffFrançois Rousset @francoisrousset.bsky.social · 08/09/2026🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...biorxiv.orgA widespread NADase domain links bacterial immunity with human TEP1Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ... 49354
Reposted by Luuk LoeffKranzusch Lab @kranzuschlab.bsky.social · 02/09/2026Discovery of chimeric RNAs and thousands of new proteins in mammalian cells – including a new regulator of inflammasome signaling! www.nature.com/articles/s41... www.jacksonimmunology.com 03611
Reposted by Luuk LoeffIrma Querques @irmaquerques.bsky.social · 25/08/2026🎉 Our first paper from the Querques lab is out! We uncover the molecular checkpoints controlling cut-and-paste transposition by CRISPR-associated transposons. Congrats to Mateusz & the whole team! 🧬 www.nature.com/articles/s41... @univie.ac.at @meduniwien.ac.atnature.comTransposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases - Nature CommunicationsCRISPR-associated transposons mediate RNA-guided DNA integration, but the molecular basis of transposase function remains poorly understood. Here, the authors uncover the mechanism of a highly active ... 2409
Reposted by Luuk LoeffStella Hurtley @smhsci.bsky.social · 21/08/2026Out now in @science.org Virome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasion | Science www.science.org/doi/10.1126/...science.orgVirome-wide ubiquitin ligase discovery reveals diverse mechanisms of immune evasionViruses are intracellular parasites that reprogram the host proteome to promote replication and evade immune recognition. We applied a virome-wide library of ~10,000 open reading frames to discover vi... 04015
Reposted by Luuk LoeffSavitski Lab @savitski-lab.bsky.social · 20/08/20261/5 How much phosphorylation can a single kinase deposit? In our new study with @typaslab.bsky.social out in @nature.com, phage T7's kinase (T7K) modifies almost all the E. coli proteome + more densely than all ~500 kinases do our own proteomes 🤯 www.nature.com/articles/s41...nature.comPervasive phosphorylation by phage T7 kinase disarms bacterial defences - NatureThe T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection. 58733
Reposted by Luuk LoeffAdy Ragucci @aragucci.bsky.social · 12/08/2026Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social www.biorxiv.org/content/10.6...biorxiv.orgBacterial diadenylate cyclase domains synthesize diverse nucleotide signals in anti-phage defenseBacterial diadenylate cyclase (DAC) enzymes synthesize the nucleotide signal 3′3′ cyclic di-AMP (3′3′-c-di-AMP) to control osmoregulation, cell-wall homeostasis, and DNA-damage responses. Here we disc... 13720
Reposted by Luuk LoeffKranzusch Lab @kranzuschlab.bsky.social · 12/08/2026The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyBnature.comShared principles of human and bacterial antiviral immunity - NatureThe Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector... 513161
Reposted by Luuk LoeffSofia Luengo-Woods @sluengo.bsky.social · 30/07/2026We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6) 37534
Reposted by Luuk LoeffAude Bernheim @audeber.bsky.social · 21/07/2026Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...sciencedirect.comA family of lanthipeptides with anti-phage functionBacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat… 18444
Reposted by Luuk LoeffJonathan Kagan @jkagan1.bsky.social · 17/07/2026A new PAMP, a new innate immunity principle and a new preclinical application. I am so pleased to share our study on STING activation mechanisms in health and disease. Led by the fantastic Stephanie Ragland, follow the link below for a summary of all we learned. www.cell.com/immunity/ful...cell.comPurine and pyrimidine-based bacterial cyclic dinucleotides egress the phagosome and activate the innate immune sensor STINGInnate immune recognition of bacteria is thought to center on cell-surface or endosomal pattern recognition receptors such as TLRs. Ragland et al. identify an intraphagosomal cyclic dinucleotide (CDN)... 14918
Reposted by Luuk LoeffArturo Carabias @arturocdr.bsky.social · 16/07/2026 🧬 Thrilled to share our latest @biorxiv-microbiol.bsky.social preprint! Here we find that Retron-IX build crazy supramolecular rings scaffolded by DNA molecules that sense phage infection! www.biorxiv.org/content/10.6... Read more below🧵! (1/X) 37128
Reposted by Luuk LoeffRafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/20261/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6... 411857
Reposted by Luuk LoeffOsterman Ilya @ostermanilya.bsky.social · 13/07/2026🚨 We're hiring! My new lab at EMBL Hamburg is looking for a Research Technician. I'm looking for someone excited by phages, metabolism, enzymes, structural biology and bacterial immunity—if you know the right person, please share this post!🧵⬇️ Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...embl.wd103.myworkdayjobs.comResearch Technician (Osterman Group – Metabolism-driven immunity)EMBL Hamburg / CSSB The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organization, with more than 110 independent research groups across Heidelberg, Hamburg, Grenobl... 32940
Reposted by Luuk LoeffSternberg Lab @sternberglab.bsky.social · 09/07/20261/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...biorxiv.orgMechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptaseDefense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a... 16123
Reposted by Luuk LoeffSorek Lab @soreklab.bsky.social · 09/07/2026Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!science.orgBacteria sense virus-induced genome degradation via methylated mononucleotidesPhages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis... 410353
Reposted by Luuk LoeffKevin Forsberg @kvnforsberg.bsky.social · 02/07/2026Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...biorxiv.orgBacterial and human exonucleases mediate interkingdom antiviral immunityAll kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo... 511950
Reposted by Luuk LoeffWaggoner Lab @labwaggoner.bsky.social · 24/06/2026The mutational landscape of STING-induced immunity www.nature.com/articles/s41... @nature.com 0208
Reposted by Luuk LoeffPablo Alcón @palconh.bsky.social · 23/06/2026Join us! Postdoc position (2-3 years) in our lab @molbiolau.bsky.social Looking for candidates with experience in cell culture, genome editing, biochemistry, and/or structural biology. Application opens in August via AU's system but informal enquiries by email are welcome from now. (1/2) 11112
Reposted by Luuk LoeffMolecular Cell @cp-molcell.bsky.social · 19/06/2026The DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavagedlvr.itThe DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavageYang et al. reveal a dynamic DdmDE-mediated plasmid clearance pathway. Transient DNA bubbles permit promiscuous DdmE binding, while target specificity arises from slower dissociation at matched sites. DdmE then recruits a DdmD dimer to drive target-centered, bidirectional dsDNA unwinding. Free DdmD subsequently coats extruded ssDNA to enable site-specific endonucleolytic cleavage. 02814
Reposted by Luuk LoeffOhad Roth @ohadroth.bsky.social · 16/06/2026How do pathogens disarm plant immunity? We discovered a widespread strategy used by plant bacterial pathogens: they directly cleave a conserved immune signaling molecule produced by plant immune receptors. www.biorxiv.org/content/10.6...biorxiv.org 26634
Reposted by Luuk LoeffKranzusch Lab @kranzuschlab.bsky.social · 12/06/2026How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6... 311565
Reposted by Luuk LoeffRafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 02/06/2026Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold! 15624
Reposted by Luuk LoeffKranzusch Lab @kranzuschlab.bsky.social · 02/06/2026@romihadary.bsky.social and @soreklab.bsky.social 's discovery that sponge proteins constitute enormous families of viral immune evasion factors is now out in @natmicrobiol.nature.com @reneechang.bsky.social and our lab were happy to help with this story! www.nature.com/articles/s41...nature.comFunctional diversity of phage sponge proteins that sequester host immune signals - Nature MicrobiologyA functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity. 14820
Reposted by Luuk LoeffOsterman Ilya @ostermanilya.bsky.social · 30/05/2026Our aRES story is finally out 😀 Beyond what was reported in the preprint, we found that aRES is activated by direct binding of the phage DNA polymerase. Another NAD-degrading defense system — and multiple phage strategies to overcome it. www.sciencedirect.com/science/arti...sciencedirect.comBacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatasesMany bacterial defense systems restrict phage infection by breaking down the molecule nicotinamide (Nam) adenine dinucleotide (NAD+) into adenosine di… 14121
Reposted by Luuk LoeffMiguel López Rivera @riveralopz.bsky.social · 29/05/2026(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202... 17332
Reposted by Luuk LoeffKranzusch Lab @kranzuschlab.bsky.social · 21/05/2026Amazing piece from @science.org and @richardastone.bsky.social on our field and the growing connection between human and bacterial immunity! #microsky #virosky #immunosky www.science.org/content/arti...science.orgAncient wars between microbes gave us key immune defensesA better understanding of battles between bacteria and viruses could inspire new medicines 13611
Reposted by Luuk LoeffSternberg Lab @sternberglab.bsky.social · 21/05/20261/8 🚨 New preprint from the @sternberglab.bsky.social & @martinjinek.bsky.social labs! CRISPR-associated transposases (CASTs) insert large DNA cargoes at precise genomic locations — no double-strand breaks needed. 47928
Reposted by Luuk LoeffJakob T Rostøl @jakob-tr.bsky.social · 20/05/2026Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...nature.comRevisiting the life cycle of temperate phages - Nature Reviews MicrobiologyThe life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ... 07234
Reposted by Luuk LoeffAlexander Harms @aharms485.bsky.social · 20/05/2026Some phages are named after gods or rivers, this one was named by journalist Thilo Mischke @thilomischke.bsky.social after his grandma ("Oma Karin") while filming in our lab. It's a cool phage that should be temperate but became virulent due to a transposon at its lysogeny control! ⛓️💥💪🏼 3316
Luuk Loeff @lloeff.bsky.social · 19/05/2026Excited to see this online! The structure of the CAST type I holo-complex. Congrats to all involved! By the labs of @martinjinek.bsky.social & @sternberglab.bsky.social. 052
Reposted by Luuk LoeffDarren Obbard @darrenobbard.bsky.social · 18/05/2026Exciting paper! - www.researchsquare.com/article/rs-8...researchsquare.comCyclic dinucleotides induce chromatin remodeling associated with long-lasting antiviral protection in flies and beescGAS-like receptors (cGLRs) are an important family of nucleic acid-sensing pattern recognition receptors in innate immunity, which produce cyclic dinucleotides (CDNs) to activate STING signaling and ... 084
Reposted by Luuk LoeffAritz Roa-Eguiara @aritz-roa.bsky.social · 14/05/2026And another preprint about the Druantia defense system 👏🏻👏🏻 in case you were missing some reading for the weekend, here we go bsky.app/profile/lloe... 031
Reposted by Luuk LoeffFranklin Nobrega @fnobrega.bsky.social · 14/05/2026www.biorxiv.org/content/10.64898/2026.05.13.724313v1 www.biorxiv.org/content/10.64898/2026.05.12.722862v1 www.biorxiv.org/content/10.64898/2026.05.13.724758v1biorxiv.org 051
Reposted by Luuk LoeffFranklin Nobrega @fnobrega.bsky.social · 14/05/2026Very happy to share our Druantia III–Zorya II synergy story, now on bioRxiv: www.biorxiv.org/cgi/content/short/2026.05.12.724681v1 It appears alongside several Druantia III papers from excellent colleagues, each telling a different part of the story. (links below)biorxiv.org 13313
Luuk Loeff @lloeff.bsky.social · 14/05/2026Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵biorxiv.org 55329
Reposted by Luuk LoeffEllinor Alseth @ellinoralseth.bsky.social · 13/05/2026When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So @brownlab.bsky.social and I wrote this, and I'm happy to share the preprint!ecoevorxiv.orgThe bacterial immune system: identifying evolved defense adaptations 15326
Reposted by Luuk LoeffMarvin Tanenbaum @marvintanenbaum.bsky.social · 13/05/2026For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...biorxiv.org 317878
Reposted by Luuk LoeffSternberg Lab @sternberglab.bsky.social · 12/05/20261/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202... 27028
Reposted by Luuk LoeffcryoEM papers @cryoempapers.bsky.social · 08/05/2026Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases www.biorxiv.org/content/10.64898/2026.05.05.722991v1 #cryoEM 011
Reposted by Luuk LoeffDimitry Tegunov @dtegunov.bsky.social · 03/05/2026We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread: 6313118
Reposted by Luuk LoeffCress Lab @cresslab.bsky.social · 30/04/2026Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer. 69851
Reposted by Luuk LoeffKenneth Loi @kenjmloi.bsky.social · 27/04/2026Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below. 7448197