@NobregaFL

bsky:fnobrega | Phages, Bacterial defense systems, CRISPR, Microbial communities, Mucus interactions | https://xitter.cf/t.co/NFQGR1sc7h | https://xitter.cf/t.co/BOBOTcpNQR

 Southampton, UK
fnobregalab.org
Joined December 2017
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In a collaboration between the Patel, Aravind, and my group, we asked how far cyclic nucleotide signalling in bacterial antiviral immunity can diversify. Pycsar systems use cyclic pyrimidines. Can related systems also use cyclic purines?
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The Institute for Protein Design is hiring postdocs! 🧬 We design new proteins to tackle big challenges in medicine, sustainability & technology. Interested in joining our interdisciplinary environment? Learn more here: ipd.uw.edu/join-us/
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Tominaga K. (tomiken)@pacyc1841Sep 24
Self-organized division of labor and selection for long-term antiviral defense in CRISPR arrays. | bioRxiv biorxiv.org/content/10.64898…
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Vivek Mutalik@vivek_mutalikSep 19
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them....Our new preprint takes this on 🧵👇
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Kenneth Loi
@kenjmloiSep 17
VIPR is now out in @ScienceMagazine! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
Kenneth Loi
@kenjmloiApr 27
Excited 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.
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Sergey Ovchinnikov@sokryptonSep 17
Also a highly experimental port of these models into WebGPU, allowing direct prediction on your 💻: localfold.org WARNING: will drain battery🪫, overheat 🔥💻 & eat your data plan 📱 Started by Martin Steinegger as AF2 port to WebGPU martin-steinegger.github.io/… (3/3)
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Tominaga K. (tomiken)@pacyc1841Sep 4
High-throughput recovery of integron cassettes for gene discovery screens | Nature Microbiology nature.com/articles/s41564-0…

High-throughput recovery of integron cassettes for gene discovery screens

Nature Microbiology - Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria...

nature.com
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Tominaga K. (tomiken)@pacyc1841Aug 27
Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling | Nature Microbiology nature.com/articles/s41564-0…

Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling

Nature Microbiology - A genomic screen reveals homologues of ESCRT components in mirusviruses that infect unicellular aquatic eukaryotes.

nature.com
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biorxiv.org/content/10.64898… Mo' evidence 'differential RNA decay' (term coined 2011 in doi:10.1128/AEM.05068-11 for MqsR), here, by toxin MazF, showing no cell death but instead a nice stationary-phase stress response.

Highly specific mRNA cleavage by the MazF endoribonuclease orchestrates stationary transcriptome...

Bacterial toxin-antitoxin (TA) systems are classically viewed as stress-activated toxic switches. Specifically, ribonucleolytic toxins are thought to indiscriminately cleave RNA to halt cellular...

biorxiv.org
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Tominaga K. (tomiken)@pacyc1841Aug 13
Plasmid biology is compressed in host chromosomal architecture | bioRxiv biorxiv.org/content/10.64898…

Plasmid biology is compressed in host chromosomal architecture

Plasmids drive horizontal gene transfer and the spread of antibiotic resistance, yet their distribution across microbial genomes is highly uneven and often viewed as environmentally driven, leaving...

biorxiv.org
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In our preprint, we identify Pucsar, a Pycsar-related family that generates 3’,5’-cGMP to activate different antiviral effectors.
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In PucsarTIR, cGMP progressively converts a self-sequestered inactive effector into a filament, where TIR assembly creates the NADase-active conformation. Great work by shared first authors Arpita, Yi, and Maxwell Burroughs! biorxiv.org/content/10.64898…

Cyclase-generated 3’,5’-cGMP activates PucsarTIR antiphage defense through a stepwise zig-zag...

Bacteria use nucleotide second messengers to couple phage recognition to antiviral effector activation. Here, we identify Pucsar, an ofshoot of the Pycsar-related antiphage family, whose cyclases...

biorxiv.org
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Franklin Nobrega retweeted
Tominaga K. (tomiken)@pacyc1841Aug 13
Genomic catalogue of giant viruses reveals expanded diversity and functional potential | Nature Microbiology nature.com/articles/s41564-0…

Genomic catalogue of giant viruses reveals expanded diversity and functional potential

Nature Microbiology - This curated genome-resolved, metagenomic resource expands the known diversity of Nucleocytoviricota and Mirusviricota lineages.

nature.com
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Tominaga K. (tomiken)@pacyc1841Aug 14
Structural mechanism governing the directionality of bridge recombination | Nature nature.com/articles/s41586-0…

Structural mechanism governing the directionality of bridge recombination

Nature - Cryo-electron microscopy structures show how IS621 bridge recombinase mediates DNA excision, explaining its natural preference for insertion and informing the design of programmable...

nature.com
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Gina El Nesr
@ginaelnesrAug 10
Today in @Nature we are excited to share the final version of Dyna-1 and *all* of the datasets we curated! New to the manuscript is prospective experimental validation. Congrats to @HWaymentSteele @DorotheeKern @sokrypton and team!!! 🔗nature.com/articles/s41586-0… 📑rdcu.be/fy2Ax
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Jakob T Rostøl@jakob_trAug 12
If you missed it before, check out Xu’s great work here science.org/doi/10.1126/scia… It answers an important question in the anti-phage field, namely how defence genes not encoded by MGEs are mobilised between bacteria 🧫

Bacteriophages mobilize bacterial defense systems via lateral transduction

Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.

science.org
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David Taylor@davidwtaylorjrAug 12
Check out our exciting new work on TasA and TasH structures! Great work by @KGuan7 and Nathan Appleby. Another fun collaboration with @PiyushGoyal! biorxiv.org/content/10.64898…
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Xianghua (Cici) Li@XianghuaLi2Aug 3
1/6 🧬 Big news in genomics & synthetic biology! We @huijin6418 @BenLehner present the complete mutagenesis of both the genome and proteome of the bacteriophage ΦX174! 📖 Read the full preprint on @bioRxiv here: doi.org/10.64898/2026.07.25.…
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Tominaga K. (tomiken)@pacyc1841Jul 23
Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield? | bioRxiv biorxiv.org/content/10.64898…

Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield?

The Candidate Phyla Radiation (CPR) consists of microorganisms with highly reduced genomes and limited metabolic capabilities, including the inability to synthesize nucleotides and amino acids....

biorxiv.org
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James Chen@JamesChenPhDJul 17
New preprint! We combined pooled-AlphaFold3 with functional genomics to map ~1.3M protein interactions across a mycobacterial proteome, revealing functions for dozens of essential genes and providing a scalable framework to decode bacterial biology. biorxiv.org/cgi/content/shor…
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