Rafael Pinilla-Redondo (Rafa)

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process.
www.biorxiv.org/content/10.6...

After >10 years of our lab studying bacterial cGAS-like enzymes, @hobbslabutah.bsky.social finally reconstitutes viral sensing in vitro and discovers how these ancient receptors sense phage protease enzymes to detect virion assembly and activate antiviral immunity

www.biorxiv.org/content/10.6...

@nitzantal.bsky.social @romihadary.bsky.social @soreklab.bsky.social use structure prediction and in silico binding site analysis to discover viral immune evasion proteins! Exciting for our lab @reneechang.bsky.social @riveralopz.bsky.social to help with this project.
www.science.org/doi/10.1126/...

CBASS is a cyclic nucleotide-based antiviral system in bacteria that is related to cGAS-STING signaling in animals. One of the big questions is how CBASS is activated during phage infection? We made some progress on this during my final year in the Kranzusch lab.
www.biorxiv.org/content/10.6...

New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.

Exciting news:
Our RNA community in @uniregensburg.bsky.social is set to grow!

We are opening a Junior Group Leader position in RNA biochemistry / ribonucleases / RNA stability. A great opportunity to start your own team within our collaborative RNA network.

Details & application 👇

Description Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

Please RT:📢We are hiring a Post-Doc in Structural Biology to join our multidisciplinary team.

Project: study molecular mechanisms of horizontal gene transfer using cryo-EM and integrative structural biology.

Apply: shorturl.at/ecrVL

#StructuralBiology #CryoEM #Postdoc

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

In our latest work, we characterise the Tmn defence system. We reveal plasmolysis as a new way to block phage infection, dramatically reducing secondary infections.

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

📢 Opportunity to apply for a PhD fellowship to join our group and work on MGE-MGE interactions and phage defence systems!
@mmsb-lyon.bsky.social

See informations about eligibility and research project on this web page: graduate-plus.fr/immunology-v...

Contact me if you are interested !

Unraveling posttranscriptional regulatory networks in phage infection Phages employ sophisticated transcriptional regulatory networks to optimize replication. Recently, Silverman et al. used RIL-seq (RNA interaction by l…

Like bacteria, phages use sRNAs to regulate gene expression! Out today in @cp-trendsmicrobiol.bsky.social, @mvelascogomariz.bsky.social and I highlight a recent RIL-seq study from the @saharmelamed.bsky.social lab that looked into posttranscriptional regulation of lambda!

tinyurl.com/lambda-RIL-seq

New preprint out on bioRxiv!

www.biorxiv.org/content/10.6...

Can conjugative plasmids be used to control plasmid and pathogen spread?

Follow me down the rabbit hole that led to this story 🧵

CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa https://www.biorxiv.org/content/10.64898/2026.02.24.707611v1

Excited to share our preprint exploring the structural, biochemical and in vivo properties of DRT7/UG10 reverse transcriptases which produce dsDNA using their primase and polymerase activities and provide broad-spectrum antiphage defense! www.biorxiv.org/content/10.6...

Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews on FindAPhD.com PhD Project - Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews, listed on FindAPhD.com

📢 Funded PhD in molecular microbiology & phage biology

How do bacterial stress responses control prophage activation and horizontal gene transfer?

Join us at St Andrews to dissect Clp protease–mediated regulation in Staphylococcus aureus.

Apply:
www.findaphd.com/phds/project...

SNIPE is a widespread bacterial defence system that exploits the spatial organization of phage genome injection to specifically target viral DNA, distinguishing self from non-self in prokaryotic immune systems @nature.com @mitpress.bsky.social
www.nature.com/articles/s41...

A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages https://www.biorxiv.org/content/10.64898/2026.02.25.707755v1

Highly mutagenic continuous evolution in E. coli using a Φ29-based orthogonal replication system - Nature Biotechnology Mutational rates of bacterial evolution are increased using an error-prone orthogonal system.

Highly mutagenic continuous evolution in E. coli using a Φ29-based orthogonal replication system - @mrclmb.bsky.social go.nature.com/46rLLvX

1/5
Happy by a recent biorxiv pre-print about DARNA (PD-T7-3) anti-phage defense system. This system is activated by binding to ssDNA, presented by phage SSB, to cleave tRNA in the anti-codon loop.
www.biorxiv.org/content/10.6...

Structure and mechanism of antiphage retron Eco2 Nature Structural & Molecular Biology, Published online: 18 February 2026; doi:10.1038/s41594-026-01754-2This study shows how the bacterial retron Eco2 defends against viruses. Phage nucleases trigger activation of Eco2, which cuts RNAs, shuts down protein production and stops phage replication.

New online: Structure and mechanism of antiphage retron Eco2

Diversity and distribution of bacterial DNA polymerases Abstract. DNA polymerases are key players in DNA replication, repair, and maintenance. However, the overall abundance, diversity, and distribution of bacte

Check out largest scale analysis of bacterial DNA polymerases! Diversity and distribution of bacterial DNA polymerases url: academic.oup.com/nar/article/...

A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination https://www.biorxiv.org/content/10.64898/2026.02.21.707213v1

I also decided to give it a go to write this up in a way that's accessible without a strict scientific background: davvi36.wordpress.com/2026/02/20/p...

Congrats, David! great to see this out in the wild🔥🥳 can’t wait for the sequels!

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans Benz and Camara-Wilpert et al. reveal that plasmid-encoded type IV-A3 CRISPR-Cas systems rely on host I-E adaptation machinery to acquire spacers and mediate inter-plasmid competition via DinG helicas...

Final nerdy nugget 🤓

Analyses suggest it’s not just TAs in target plasmids that matter. Whether CRISPR actually cuts seems to matter too! ✂️

Might explain why our favorite CRISPR-Cas system, Type IV-A, ditched its nuclease!? @fabbenz.bsky.social 🧬🤔
www.cell.com/cell-host-mi...

CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids Abstract. Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-C

Note we were previously puzzled to find ~3% of plasmids carry CRISPRs 👀🧬
academic.oup.com/nar/article/...

David’s new work investigates the consequences of CRISPR-mediated plasmid conflicts, with implications for understanding plasmid establishment, HGT, and combating AMR 💥💊

To CRISPR or not to CRISPR?🥀
That’s a question plasmids face during competition 🧬⚔️

@davvi36.bsky.social et al. shows it depends on whether targeted plasmids have TAs! ⚖️

Fun to be part of this story w/ @leightonpayne.bsky.social Thanks for pulling us in!