Yanrui Ye

Overflow metabolism in bacterial, yeast, and mammalian cells: different names, same game
doi.org/10.1038/s443...

Glad to contribute to this collaborative community platform.
A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!

No paywall:
www.cell.com/action/show...

Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation - Nature Communications Genetic code expansion (GCE) enables the incorporation of new amino acids into proteins. Here, authors demonstrate the rapid OrthoRep-driven evolution of aminoacyl-tRNA synthetases for GCE, increasing...

Happy to share the peer-reviewed and updated version of our work on OrthoRep-driven evolution of aaRSs for genetic code expansion with unnatural amino acids. Congrats to Yuichi Furuhata, a true master bioengineer, on leading this excellent work! www.nature.com/articles/s41...

An in vivo target mutagenesis system for multiple hosts This study developed an in vivo targeted mutagenesis system for multiple hosts based on replication elements of broad host-range plasmids. This system is designed to accelerate the rapid evolution of proteins and metabolic pathways, further leveraging the performance advantages of unconventional hosts.

Online now: An in vivo target mutagenesis system for multiple hosts

Renewal of NIH grants linked to more innovative results, study finds Nature - Survey of hundreds of scientists’ work suggests that cutting off funding disrupts focus and reduces the novelty of research.

Innovation takes time

US scientists who received renewals from the NIH over the past four decades produced more novel research than those who didn’t
https://go.nature.com/44s6cc5

Microbe that infests hospitals can digest medical-grade plastic ― a first Nature - The bacterium Pseudomonas aeruginosa produces an enzyme that breaks down biodegradable plastics.

A strain of bacterium that often causes infections in hospital can break down plastic

https://go.nature.com/3SvsiTC

Molecular process control for industrial biotechnology The development of sustainable and economically competitive biotechnological processes is a central challenge of modern industrial biotechnology. Conventional strategies such as macroscopic and molecu...

Molecular process control for industrial biotechnology
www.cell.com/trends/biote...

Modular Engineering of Thermo-Responsive Allosteric Proteins Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membra...

www.biorxiv.org/content/10.1...

New publication! We identify growth coupled sensitivity: a deceivingly simple mechanism that makes E. coli switch to the best sugar. We combined neat theory (due to @erikvannimwegen.bsky.social, and to which I contributed) with clean experiments (due to @thomasjulou.bsky.social and Theo Gervais).

Escherichia coli with a 57-codon genetic code The near-universal genetic code of living organisms uses 64 codons to encode the 20 canonical amino acids in protein synthesis. Here we design and generate a variant of Escherichia coli with a 4 Mb sy...

Check out the pre-print of my main PhD work, Syn57! Together with my incredible co-first authors and a big team we‘ve built a full E. coli genome operating on a 57-codon genetic code!
So much hard work, and so much love for everyone who was involved!

www.biorxiv.org/content/10.1...

ProGen3: scaling protein language model data and parameters improves the quality of generations, especially further away from natural sequences.

@jeffruffolo.bsky.social @thisismadani.bsky.social

www.biorxiv.org/content/10.1...

Enhancing the Cre-loxP system: Two new genetic tools – roxCre and loxCre – can improve the performance of the Cre-loxP system for making genetic modifications in vivo.
elifesciences.org/reviewed-pre...

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection The pre-nuclear stage of Chimalliviridae infection and whether the phage nucleus is essential have remained mysterious. Armbruster and Rani et al. demonstrate that the phage nucleus is required for ph...

#midweekmicro🔬

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection🧬

@cp-cellhostmicrobe.bsky.social #microsky

www.cell.com/cell-host-mi...

Our latest work has been published in Trends in Biotechnology.

A huge thanks to my co-authors for their invaluable contributions!

bsky.app/profile/cp-t...

Expediting genome synthesis of Corynebacterium glutamicum with an artificial chromosome vector We developed an artificial chromosome plasmid (CAC) for large-scale genome replacement of Corynebacterium glutamicum, accelerating the genome synthesis for this organism. This work offers design principles for advancing de novo genome design and synthesis for industrially relevant Gram-positive microbes.

Online now: Expediting genome synthesis of Corynebacterium glutamicum with an artificial chromosome vector

Jason Chin is coming to #SynBioBeta2025!

A pioneer in genome writing and genetic code expansion, his breakthroughs - from virus-resistant organisms to sustainable biomanufacturing - are reshaping biology. Don’t miss his vision for the future! Watch a clip from his TED Talk.

Interactions and evolutionary relationships among bacterial mobile genetic elements Nature Reviews Microbiology, Published online: 11 March 2025; doi:10.1038/s41579-025-01157-yIn this Review, Lang and colleagues present an overview of the current knowledge landscape regarding mobile genetic elements in bacteria, with a focus on their…

New online! Interactions and evolutionary relationships among bacterial mobile genetic elements

A conserved bacterial genetic basis for commensal-host specificity Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are...

Keeping your symbiosis genes on a plasmid is a smart move if you have multiple potential hosts. Here a gut bacterial symbiont, but same is true for N-fixing Rhizobia.
www.science.org/doi/10.1126/...

Heterodimerization of Endolysin Isoforms During Bacterial Infection by Staphylococcal Phage {varphi}2638A https://www.biorxiv.org/content/10.1101/2024.01.16.575832v1 Bacteriophage endolysins targeting Gram-positive bacteria typically feature a modular architecture o

Heterodimerization of Endolysin Isoforms During Bacterial Infection by Staphylococcal Phage {varphi}2638A https://www.biorxiv.org/content/10.1101/2024.01.16.575832v1

Conserved jumbo phage factors required for protein import into a phage nucleus Bacteriophages use diverse mechanisms to evade anti-phage defenses systems. ΦKZ-like jumbo phages assemble a proteinaceous nucleus-like compartment that excludes antagonistic host nucleases, while int...

And see this related preprint www.biorxiv.org/content/10.1...

Conserved jumbo phage factors required for protein import into a phage nucleus

Yup. That does say "phage nucleus" and it really is a nucleus-like compartment.

Optimized directed evolution of E. coli leucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nepsilon-acetyl-methyllysine https://www.biorxiv.org/content/10.1101/2024.11.27.625662v1 Site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in eukaryotes has pred

Optimized directed evolution of E. coli leucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nepsilon-acetyl-methyllysine https://www.biorxiv.org/content/10.1101/2024.11.27.625662v1

Continuous evolution of user-defined genes at 1 million times the genomic mutation rate When nature evolves a gene over eons at scale, it produces a diversity of homologous sequences with patterns of conservation and change that contain rich structural, functional, and historical informa...

This is incredible
www.science.org/doi/10.1126/...

Home - SEVA plasmids - Standard European Vector Architecture Standard European Vector Architecture 4.0 Welcome to the CNB-hosted database and material repository of standard and modular plasmid vectors for (de/re) constructing complex bacterial phenotypes ...

🌐 We just joined Bluesky! SEVA is a free, open-access plasmid repository and an international standard supporting the synthetic biology community. Catch us here! #SynBio ⬇️ seva-plasmids.com