Luis E. Valentin-Alvarado

Our work on bacterial Schlafens in phage defense is out today @natmicrobiol.nature.com!

Check out the final version here:
rdcu.be/e7Bmz

We are looking for postdocs and students to expand our team! Official postings are coming soon.

Please reach out if you're interested!
#phage #phagesky #microsky

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Diversity, ecology, cell biology and evolution of the Asgard archaea www.nature.com/articles/s41... #jcampubs

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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...

Jennifer Doudna’s $1 Billion Plan To Bring Gene Editing To The Masses Crispr’s ability to cut genetic code like scissors has just started to turn into medicines. Now, gene editing pioneer Jennifer Doudna wants to build an entire ecosystem to bring these treatments mains...

“The best that I can do in terms of making the next breakthrough or discovery is not to do it by myself, but to enable other scientists to do it”
— Jennifer Doudna

www.forbes.com/sites/amyfel...

Understanding how enzymes work: the journey to ensemble–function studies
febs.onlinelibrary.wiley.com/doi/10.1111/...

This is an exceptionally well written review on how enzymes work. Rather than the structure-function relationship, Herschlag & Du analyse the ensemble-function relationship

Structure and mechanism of antiphage retron Eco2 Nature Structural & Molecular Biology - This study shows how the bacterial retron Eco2 defends against viruses. Phage nucleases trigger activation of Eco2, which cuts RNAs, shuts down protein...

1/6) Hot off the press @natsmb.nature.com 🔥! Jasnauskaite et al. reveal how the minimal bacterial retron Eco2 defends against #phage 🛡️. Phage nucleases trigger Eco2, which cuts RNA, shuts down protein production and stops phage replication 🦠🚫. #phagesky #immunity #microbiology #cryo-em rdcu.be/e4AyH

Totally understand this feeling!

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

Eukaryogenesis in light of an expanded catalogue of Asgard genomes. a, Simplified, scaled timeline spanning from before the Last Asgard archaea Common Ancestor (LAsCA) to today. Thin bands mark predicted time ranges of relevant events (for example, GOE), thicker bands represent processes (for example, eukaryogenesis), and brackets indicate the period shown in b. The timeline further highlights milestones, including potential early eukaryotic fossils60 and the modern-day co-occurrence of Heimdallarchaeia and Alphaproteobacteria observed in this study (interaction likely originated earlier).

Fig. 1 | Expanded genomic diversity of Asgard archaea. a, Maximum-likelihood phylogeny based on 47 non-ribosomal markers (NM47)using the WAG + C10 + R4 model with 100 nonparametric bootstrap pseudoreplicates, including 869 Asgardarchaeota MAGs and 309 outgroup genomes. The blue branches (lower right) indicate the new Asgardarchaeota classes, Ranarchaeia, and the recently proposed Asgardarchaeia4. The concentric rings denote (in to out): the predicted genome size, metabolic guilds based on Pfam clustering, sampling locations, and black stars on the outside mark MAGs added by this study. Asgard, Asgardarchaeia; Atabey, Atabeyarchaeia; Baldr, Baldrarchaeia; Frey/Jord, Frey/Jordarchaeia; Gerd, Gerdarchaeales; Heimdall, Heimdallarchaeaceae; Hel, Helarchaeales; Hermod, Hermodarchaeia; Hod, Hodarchaeales; Kari, Kariarchaeaceae; Loki, Lokiarchaeales; Njord, Njordarchaeales; Odin, Odinarchaeia; Ran, Ranarchaeia; Sif, Sifarchaeia; Thor, Thorarchaeia; Wukong, Wukongarchaeia. b, SR4-recoded phylogeny of the same genome set inferred with the model GTR + C60 + G and 100 nonparametric bootstrap pseudoreplicates (Methods). This updated catalogue constitutes a large increase in the medium- to high-quality publicly available genomes (completeness >50% and contamination and redundancy <10%) with 65.3% from the Guaymas Basin and 34.7% from the Bohai Sea. The encircled numbers represent MAGS added by this study. The scale bars in bothsubpanels represent the average number of substitutions per site.Map created in BioRender; Appler, K. https://biorender.com/147ieoc(2025).

Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬

Links: www.nature.com/articles/s41...
www.nature.com/articles/s41...

😍😍😍

New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...

Beyond thrilled to share that our study has been published!
This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and
@texasscience.bsky.social!!!
#MicroSky #ArchaeaSky 1/12

Jennifer Doudna’s $1 Billion Plan To Bring Gene Editing To The Masses Crispr’s ability to cut genetic code like scissors has just started to turn into medicines. Now, gene editing pioneer Jennifer Doudna wants to build an entire ecosystem to bring these treatments mains...

NEW for @forbes.com: Nobel Prize winner Jennifer Doudna’s plan to create a gene editing ecosystem to solve major problems in medicine, agriculture and climate.

“I don’t want it to be a curio, a topic of academic interest,” she says.

www.forbes.com/sites/amyfel...

Excited to share our discovery of archaeal circular, jumbo extrachromosomal elements (up to ~535 kb genomes). One related, 409-kb genome is integrated in CH4-eating Methanoperedens, representing the largest integrative element in Archaea so far! Curious about what they are doing? See the paper

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Systematic discovery of TIR-based immune signaling systems in bacteria Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.

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

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.

🔥 Apply by Jan 8, 2026

Details: phd.pages.ista.ac.at

Happy December!

Join #MVIF 44 – we will discuss diverse #microbiome topics:
human urinary, gut, oral and nasal microbiomes,
extreme environments, and
a new sequence alignment tool.

Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Officially out!

Structural basis of T-loop–independent recognition and activation of CDKs by the CDK-activating kinase Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation o...

Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...

omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.

Check out this work co-led with @benadler.bsky.social here:

www.nature.com/articles/s41...

New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !

The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...