Hoong Chuin Lim

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...

On this fabulous day celebrating André Citroën's birthday 🥖🚗, I’m happy to share my main paper from my postdoc in @jrpenades.bsky.social Lab.
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!

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

Looking for a breakthrough in #bacteriophage engineering? NEB and Yale University researchers used HC-GGA to engineer a fully synthetic P. aeruginosa phage, paving the way for faster, simpler and safer therapeutic development: https://nebiolabs.com/3O1DacT

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification Author summary Our study focuses on Diversity-Generating Retroelements (DGRs), a biological “evolution engine” that microbes and viruses use to rapidly develop new functions within specific genes. DGR...

Published version of our work on diversity-generating retroelements!

We reconstituted a phage DGR in E. coli and deployed high-throughput methods to identify factors influencing the activity of this system. #microsky

journals.plos.org/plosgenetics...

Hi Aude,
Could you please add my lab (www.neb.com/en-us/research-labs/lim-lab)?

Thanks!

Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!

For more information and how to apply, see below 👇

Please RT!

One week left to apply!!

Proteolytically activated antibacterial toxins inhibit the growth of diverse Gram-positive bacteria Many species of bacteria produce small-molecule antibiotics that enter and kill a wide range of competitor microbes. However, diffusible antibacterial proteins that share this broad-spectrum activity ...

A recent cool preprint by John Whitney's lab on a new family of antibacterial proteins secreted by Gram-positive bacteria that enter and kill a broad spectrum of bacteria. Cell entry is receptor-independent and relies on cleavage by a co-secreted protease and the PMF.
www.biorxiv.org/content/10.1...

This is insanely cool!!

A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry Many antibiotics are ineffective against Gram-negative pathogens such as Pseudomonas aeruginosa because they cannot penetrate the bacterial outer membrane. Here, we show that protein antibiotics calle...

The outer membrane of Gram-negative bacteria blocks many antibiotics. Our latest work reveals that L-type pyocins bypass this barrier by inactivating the BAM complex, killing Pseudomonas aeruginosa without entering the cell, providing a new blueprint for beating antibiotic resistance.

Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli Certain phages and microbes use Diversity-Generating Retroelements (DGRs) for rapid, targeted adaptation. This process, called mutagenic retrohoming, uses a reverse transcriptase to specifically intro...

Diversity-generating retroelements are a fascinating class of targeted gene editing system. How DGRs function within cells remains incompletely understood. In this preprint (www.biorxiv.org/content/10.1...
), we report identification of factors influencing DGR activity in E. coli.
#MicroSky

🚨👉 Please check our recent work on bacterial cell division. In situ Cryo-ET reveals the cellular function of the penicillin binding protein 1b supported by AFM, live-cell imaging, in silico AlphaFold proteome screen and TIRFM. Hope you enjoy the read! #teamtomo #cryo-ET ❄️🔬🐎 big thanks to the team!

Expanding the genetic toolbox of the obligate predatory bacterium Bdellovibrio bacteriovorus with inducible gene expression and CRISPR interference Inducible gene expression and CRISPR interference-mediated depletion in the predatory bacterium Bdellovibrio bacteriovorus.

🚨New paper out! #MicroSky
Studying obligate predators like Bdellovibrio bacteriovorus is tricky—essential genes for predation are also essential for survival.
We expanded its genetic toolbox:
🧬promoters to fine-tune expression
🧬IPTG-inducible system
🧬CRISPRi for rapid knockdown
bit.ly/46GUn2c
1/4

Molecular basis of polyadenylated RNA fate determination in the nucleus Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs, that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, including prote...

How do cells sort which RNAs to keep or destroy? New preprint from THJ, Brenneke and Plaschka labs shows that export and decay machineries (TREX2/PAXT) both recognise UAP56-bound RNAs. Whether they’re exported or degraded depends on where in the nucleus this happens.
www.biorxiv.org/content/10.1...

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...

Congrats to Apurva, Brian and Irem and a big thank you to our collaborators:
• Brooke of the Kim lab (UIUC) for microscopy
• Molly of the Helaine lab (Harvard Med) for tRNA-seq
• Eric of the Corrêa lab (NEB) for cleavage site mapping by mass spec

Key highlights:
• A phage-inspired genetic screen to identify the targets of tRNA nucleases.
• OLD severs the anticodon stem with a one-base staggered cut.
• tRNAs destroyed by OLD are irreparable by T4 RNA ligase. • Both cuts occur after the first cytosine within a paired CNG pseudo-palindrome.

First paper from my lab is now published! academic.oup.com/nar/article-... P2-lambda interference was first reported in the 1950's, but how a P2 lysogen restricts lambda replication has remained murky. We uncovered tRNA cleavage by P2-OLD as a key mechanism behind this interference.

We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded.

Link to the job emploi.pasteur.fr/offre-de-emp...
Thx for sharing!

Congrats!!

Bacterial cell wall & periplasm paradigm shift - important read #MicroSky

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