Egill Richard

Excited to share the work that’s been on my mind for the past 2 years, now on bioRxiv! Led with @mattwalkerhi, and my first project in the @SternbergLab . Check it out ⬇️ tinyurl.com/mshwjd77

Ancient wars between microbes gave us key immune defenses | @ScienceMagazine | AAAS science.org/content/articl…

1/8 🚨 New preprint from the @SternbergLab & Jinek labs! CRISPR-associated transposases (CASTs) insert large DNA cargoes at precise genomic locations — no double-strand breaks needed.

Very happy to share our Druantia III–Zorya II synergy story, now on bioRxiv: biorxiv.org/cgi/content/sh… It appears alongside several Druantia III papers from excellent colleagues, each telling a different part of the story (links below).

1/9 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/10.64898/2026.…

Our 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.

I'm excited to share that our work on co-translational degradation of cas12a mRNA is finally out! Many thanks to all the authors who made it happen. nature.com/articles/s4158…

Thrilled to share our review paper on @TrendsBiochem. We summarize the latest breakthroughs in expanding the genetic code beyond single noncanonical amino acids (ncAAs) — from orthogonal translation systems and quadruplet codons to rare codon recoding — enabling the synthesis of sophisticated “new-to-nature” biopolymers with multiple distinct functionalities. authors.elsevier.com/a/1m%7E-z3S6Gf…

@crypticprophage Genuine question: why do you consider cell death necessary for abortive infection? Wouldn’t any system that drives the host into dormancy (for instance) upon phage infection also qualify as abortive, by definition?

Drinking the Kool-Aid: You indicate that ToxIN works by "an abortive infection mechanism" yet Fineran et al. themselves originally published in 2009 that there is no Abi as there was no cell lysis, even with pBAD overexpression (pnas.org/doi/10.1073/pn…).

…icro-journals.onlinelibrary.wiley.com/doi/10.1111/17… More excellent proof that cells are dormant via ribosome dimerization/inactivation in E. coli and EHEC persister cells during various stresses and that resuscitation activates ribosomes.

Bacteria are full of diverse molecular tricks. This Science article reports an interesting one that is being misrepresented by news coverage, including the coverage in Science. The study describes an enzyme complex that synthesizes alternating dinucleotide repeat DNA as part of an immune response. Protein templating DNA is a cool observation, even if the sequence is only a repeating dinucleotide. The headline-grabbing takeaway is the mechanism of the Drt3b subunit. While its partner, Drt3a, uses a canonical RNA template (reverse transcription), Drt3b synthesizes the complementary strand in the absence of a nucleic acid template. Instead, it uses specific amino acid residues (a glutamate and an arginine) to stabilize and "select" the incoming dNTPs. It is tempting to view this as a radical shift in our understanding of information transfer, a "protein-templated" genetic sequence. However, we should be cautious with the "paradigm shift" narrative. Why this isn't "rewriting" the Genetic Code: Despite claims in the news coverage, this finding does not represent a new form of hereditary information transfer. This is not a protein "reading" itself to create a complex message; rather, it is a highly specialized structural constraint. The protein is essentially a "stuttering" machine, physically keyed to produce a simple, repetitive sequence. The "information" is hard-coded into the protein's fold to perform a single, specific defensive task, rather than acting as a general-purpose template for diverse genetic messages. The Parallel to tmRNA: This observation is not entirely unprecedented when we look at how bacteria handle biochemical "dead ends." It reminds me of transfer-messenger RNA (tmRNA). In trans-translation, when a ribosome stalls on a broken mRNA, the tmRNA molecule steps in to provide both the tRNA component and a short mRNA "tag" to rescue the ribosome: - The "Non-Standard" Template: Much like tmRNA provides an external sequence to fix a stalled process, the DRT3 ncRNA and the Drt3b protein provide "internal" instructions to create DNA where no genomic template exists. - Specialized Rescue: Both mechanisms are niche "emergency" responses, one for proteostasis (tmRNA) and one for viral defense (DRT3). In the end, this discovery doesn't replace our understanding of the genetic code; it expands the "toolbox" of how cells can synthesize polynucleotides when the standard rules don't apply. It is a beautiful reminder that in the microbial world, if a chemical shortcut is possible, evolution has likely found it.

モジャオメ science.org/doi/10.1126/sc…

@JakubTomek13 @hhmi_science I used @qedScience to pre-review all of my lab's @biorxivpreprint articles and it provides significantly more detailed, scholarly, and constructive feedback than reviews commissioned by journals. And it takes 15-30 minutes instead of 6 weeks+

Joint effort over four years of EPC Rocha & Fred Le Roux Labs sampling in the wild! nature.com/articles/s4146…

Genomic context and protein sequence can be used together to discover bacterial phage defense systems. @AudeBer

Our paper describing a toolbox of c-di-GMP FRET biosensors and its application to elucidate the interplay between c-di-GMP and bacterial motility just appeared: nature.com/articles/s4146…

We wrote a review on using machine learning to study evolutionary genetics and molecular evolution in Trends in Genetics @TrendsGenetics . It is open access—please read it if you are interested in this topic sciencedirect.com/science/articl…

🚨Please repost!! 🧬We are hiring POSTDOC now!! Fully-funded 5-year position 👩🏻‍🔬👨‍🔬

Check out the structure a DNA-guided Cas12a! It's gnarly and familiar. Great work by graduate student @fregoso_ocampo @TexasScience @ut_mbs. Fun collaboration with Piyush Jain at UF. Architecture of a DNA-guided Cas12a biorxiv.org/content/10.648…

Happy to announce that our paper on orphan genes in bacteria dropped in PNAS yesterday! This is a problem I've been thinking about since the start of my PhD. Grateful for this journey, as well as All The Friends I Made Along the Way. Also, Eid Mubarak to those who celebrate!

Just published! at Nucleic Acids Research. A new example of how gene order in bacterial genomes impacts cell physiology. In this episode we messed up with RNA polymerase genes! academic.oup.com/nar/article/54…