Our latest publication uses gene deletions to shed light on the specificity of bacterial nitroreductases and reports engineered strains that unlock new applications in whole-cell #biocatalysis, #metabolic_engineering, and #genetic_code_expansion www.nature.com/articles/s41... (1/3)

Retention and biosynthesis of diverse nitroarenes in Escherichia coli after combinatorial nitroreductase gene deletions - Nature Chemistry

Nitroarenes are unstable in microbial cultures, limiting the biomanufacturing of these industrially and pharmaceutically important chemicals. Genome engineering of nitroreductase-deficient E. coli str...

nature.com

We have to stop using "paper count" as a useful scientific metric. More writing output no longer means more knowledge gained www.washingtonpost.com/education/20...

One professor’s AI-assisted output: 200 papers and 14 books this year

An online platform removed 257 papers written or co-written by the University of Chicago’s Nicholas Polson after other academics raised questions.

washingtonpost.com

From our FY26 Functional Genomics call: Speciality chemicals like non-standard amino acids could be made more efficiently in microbes with hardier enzymes. @kunjapur.bsky.social will use biodesign to make pathway enzymes more thermostable. Full portfolio: https://jointgeno.me/FGFY26

New PET upcycling work in Science Advances: BHET/MHET readily enter E. coli, letting us directly couple PET glycolysis to whole-cell biocatalysis. Fun collaboration with Dion Vlachos, and congrats to first author Roman Dickey! www.science.org/doi/10.1126/...

Robust cellular transformations of PET deconstruction products by import of glycol esters

Efforts to transform polyethylene terephthalate (PET) deconstruction products using live cells have been limited by terephthalic acid (TPA) uptake. Here, we used an intracellular carboxylate reduction...

science.org

Consider checking out our latest review article if you're interested in how a wave of efforts in amino acid biosynthesis are creating new opportunities in genetic code expansion

Annual Reviews@annualreviews.bsky.social · 3mo ago

The 2026 Annual Review of Chemical and Biomolecular Engineering is now online! Most read article is "Advancing Genetic Code Expansion in Live Cells Through Metabolic Engineering" by @kunjapur.bsky.social, D'Jana Wyllis, Saloni Gupta, and Shelby Anderson bit.ly/4p7mkbf

Our latest paper describes a single bacterial strain that can make different Phe derivatives from supplemented aromatic aldehydes or carboxylic acids and incorporate them into target proteins via genetic code expansion Congrats to Shelby Anderson and co-authors www.nature.com/articles/s41...

Excited to share our new preprint "Genetic code expansion enables plant-directed control of bacterial activity", a fantastic collaboration with @kunjapur.bsky.social lab! www.biorxiv.org/content/10.6...

Thank Bob Langer & AIChE again for this honor and featuring us: César de la Fuente, Aditya Kunjapur, Albert Keung & Ashish Kulkarni @delafuentelab.bsky.social @kunjapur.bsky.social giving.aiche.org/impact/stori...

I had an amazing time yesterday visiting @vdlorenzo.bsky.social and hearing about the many exciting projects underway in his lab. Our evening stroll through the heart of Madrid and dinner of tapas made for an unforgettable experience

It's an honor to visit @vdlorenzo.bsky.social and colleagues at El Centro Nacional de Biotecnología in beautiful Madrid, España. Me alegra estar aquí

Victor de Lorenzo (CNB, Madrid)@vdlorenzo.bsky.social · 11mo ago

Glad to welcome @kunjapur.bsky.social to the @cnb-csic.bsky.social to enjoy his seminar on his latest research in Synthetic Biology!

Interested in using microbes to degrade plastics? We made the discovery that two breakdown products of PET, MHET and BHET, are readily taken up by E. coli cells Our latest preprint exploits this surprise to realize improvements in cell-based upcycling www.biorxiv.org/content/10.1...

Robust cellular transformations of PET deconstruction products by import of glycol esters

Efforts to transform polyethylene terephthalate (PET) deconstruction products using live cells have been limited by terephthalic acid (TPA) uptake. Here, we used an intracellular carboxylate reduction...

biorxiv.org

My students have become very good at cloning. Now I can be in two continents at once this fall

Excited to announce our new methods paper in Methods in Enzymology! We share our pipeline for building high-diversity DNA libraries & exploring protein stability in E. coli. Free access until Sept 4: authors.elsevier.com/a/1lRkeHRzCX... Updated, companion preprint: www.biorxiv.org/content/10.1...

Exciting to see this collaborative work about modeling soil microbiomes from the Kuehn, Mani, and Tikhonov labs published today Also delighted to have lead author Kiseok Lee start his postdoc in our lab Check out the paper below!

Kiseok (Keith) Lee@kiseokmicro.bsky.social · last yr.

Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change. www.nature.com/articles/s41...

Looking forward to the amazing program & making new connections at the 17th International Symposium on Biocatalysis and Biotransformations (Biotrans 2025) starting today in Basel I'm honored to present our work on Tuesday at 15:15 in the non-canonical amino acids session #biocatalysis

Wrapping up a fantastic #ME16 #Copenhagen — a success by all measures! Honored to co-chair the meeting w/I. Borodina, M. Chang, A. Mirończuk, C. Vickers, V. Šťovíček, Y. Zhou, M. Köpke & M. Herrgård & to work w/an outstanding team of colleagues, engaging communities & topics all around the world

Congrats on completing your PhD @kiseokmicro.bsky.social! And welcome to our lab - very excited to work with you

Kiseok (Keith) Lee@kiseokmicro.bsky.social · last yr.

<End of the PhD chapter> Graduation happened last week! So grateful for all the relationships I nurtured at uchicago. I will miss this place! Thank you Cathy for hooding me! Also, I am very excited to start postdoc tomorrow in Aditya Kunjapur @kunjapur.bsky.social lab in University of Delaware!

I'm enjoying the start of the International Metabolic Engineering 16 #ME16 meeting in Copenhagen this week Thanks to the organizers for providing a chance to share our work Thanks to my students for taking these pics Looking forward to meeting other attendees

Today in Nature we report a systematic strategy to activate & identify gene sets in plants. We identify 8 new genes from the yew tree's Taxol biosynthetic pathway, enabling us to engineer tobacco with 17- & 20-gene pathways to Taxol precursors baccatin III & deBz-deoxy-Taxol #SingleCell #secmet 🧬🧪🌾

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III - Nature

An approach that combines single-nucleus RNA sequencing and multiplexed perturbation identifies genes that enable the biosynthesis of direct precursors of the anti-cancer drug Taxol, whose&nbsp;curren...

nature.com

It is a real honor and delight to be hosted by @pabnik.bsky.social at DTU Biosustain! Looking forward to meeting folks & sharing info/ideas

Pablo Ivan Nikel@pabnik.bsky.social · last yr.

Happy to host @kunjapur.bsky.social as a sabbatical #professor at DTU Biosustain, supported by Otto Mønsteds Fond! We share a passion for using #SynBio to engineer #microbes with non-natural building blocks for advanced #biotechology. He’s in #Europe — drop a line to connect & discuss cool #Science!

Trump Has Cut Science Funding to Its Lowest Level in Decades www.nytimes.com/interactive/... ^ Useful info in this article about the level of funding of various NSF directorates/programs relative to the 10Y avg by this time of year

Trump Has Cut Science Funding to Its Lowest Level in Decades

The lag in funding extends far beyond D.E.I. initiatives, affecting almost every area of science: chemistry, computing, engineering, materials and more.

nytimes.com

With the state of US scientific funding it seems like an inappropriate time to celebrate anything But in the last week thanks to years of dedication from my students we were recognized through the Roberta Colman and Gerard Mangone awards, & tenure. Thank you to those who made it possible (1/3)

If you're curious how the first 5 amino acids of newly generated protein N-termini can affect protein stability in E. coli, then check out our latest preprint We find new patterns of exceptions to the usual N-end rule Kudos to Sunny Sen & co-authors #synbio #protein_degradation

Thomas Arnesen@natmachinery.bsky.social · last yr.

Protein degradation in E. coli via N-terminal degradation signals (degrons) defined by the @kunjapur.bsky.social lab. @ispt-proteinterm.bsky.social www.biorxiv.org/content/10.1...

Protein degradation in E. coli via N-terminal degradation signals (degrons) defined by the @kunjapur.bsky.social lab. @ispt-proteinterm.bsky.social www.biorxiv.org/content/10.1...

Combinatorial mutagenesis of N-terminal sequences reveals unexpected and expanded stability determinants of the Escherichia coli N-degron pathway

Although it is known that penultimate N-terminal residues can influence protein stability by the N-degron pathway, there has not been a comprehensive effort to document nor predict these effects for n...

biorxiv.org

🚨OUT NOW Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid by @kunjapur.bsky.social et al. #MicroSky 🦠🔧 www.nature.com/articles/s41...

Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid - Nature Microbiology

A genetically engineered microbial symbiosis based on synthetic auxotrophy is created, with potential implications as a biocontainment strategy.

nature.com

A more accurate statement than my original post: It seems there may be few known pairs of microbial species, outside of obligate intracellular symbionts/parasites, where one relies exclusively on another. Using a blend of synthetic and chemical biology, we designed such an interaction

Aditya Kunjapur@kunjapur.bsky.social · last yr.

It seems there are no free-living organisms known to rely exclusively on one other organism for their survival Until perhaps now Check out our latest publication in @natmicrobiol.nature.com to see how we designed an exclusive microbial reliance using GCE rdcu.be/ekepI 1/2

It seems there are no free-living organisms known to rely exclusively on one other organism for their survival Until perhaps now Check out our latest publication in @natmicrobiol.nature.com to see how we designed an exclusive microbial reliance using GCE rdcu.be/ekepI 1/2

Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid

Nature Microbiology - A genetically engineered microbial symbiosis based on synthetic auxotrophy is created, with potential implications as a biocontainment strategy.

rdcu.be

This move could singlehandedly dismantle American leadership in science and technology innovation. It goes into effect on Monday. How will universities adjust their budgets to support critical ongoing research?

Carl T. Bergstrom@carlbergstrom.com · 2y ago

6. The policy does not just affect funding going forward. All existing NIH grants will have their indirect rates cut to 15% as of today, the date of issuance. For a large university, this creates a sudden and catastrophic shortfall of hundreds of millions of dollars against already budgeted funds.

See here for an exciting development in genome engineering for genetic code expansion and for understanding the pliability of components involved in protein translational termination - from the Isaacs Lab www.nature.com/articles/s41...

Engineering a genomically recoded organism with one stop codon - Nature

Ochre, a strain of Escherichia coli engineered to have a single stop codon, enables reassignment of four codons for non-degenerate functions, such as incorporation of non-standard amino acids into pro...

nature.com

2025-01-12 Issue of #engineeredlivingmaterials feed biomed.news/bims-enlima/... h/t @biomednews.bsky.social includes @kunjapur.bsky.social lab's preprint @biorxivpreprint.bsky.social on combined biosynthesis and site-specific incorporation of phenylalanine derivatives in engineered bacteria