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Hoong Chuin Lim

@hclim.bsky.social
53 followers 154 following 14 posts
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Reposted by Hoong Chuin Lim
Xavier Charpentier @labxc.bsky.social · 07/10/2026
Very happy that this work found a good home at @pnas.org Thanks to the reviewers for their constructive comments. www.pnas.org/doi/10.1073/...
pnas.org
Two D-loop resolution systems enable natural genetic transformation in bacteria | PNAS
Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released ...
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Reposted by Hoong Chuin Lim
Vincent Burrus 🇨🇦💙💛 @vincentburrus.bsky.social · 05/10/2026
#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...
academic.oup.com
Conjugative transfer inhibition of IncA and IncC plasmids by SGI1-like elements via relaxosome assembly interference
Abstract. Broad-host-range IncA and IncC (A/C) conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands,
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
This work is co-led by Apurva Govande (postdoc in my lab) and Brooke Ramsey in Sangjin Kim’s lab at UIUC with contributions from many collaborators, including @aaronwhiteley.bsky.social and Gerry Smith. Check out complementary work from Artem Isaev and colleagues: www.biorxiv.org/content/10.6...
biorxiv.org
OLD sentinel: an abortive tRNase surveys phage replication and DNA defects in RecBCD-compromised cells
OLD, an abortive immunity protein from prophage P2, consists of an ABC ATPase sensor and a TOPRIM nuclease effector — a core architecture shared by a large protein family, including components of anti...
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
Our work highlights the immune threat hidden within essential cellular processes and and reveals a safeguard mechanism analogous to how eukaryotic TREX1 prevents cGAS-STING autoimmunity by clearing cytosolic self-DNA.
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
We show that Ppl, much like OLD and Gabija, is a defense system with an ABC-type ATPase that becomes toxic without RecBCD. Because these ATPases are so common in defense systems, RecBCD dependence is likely widespread.
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
OLD recognizes self-DNA ends that are left uncleared without RecBCD using an ATPase channel. DNA recognition unleashes it toxic tRNA nuclease. Notably, dozens of OLD molecules associate with a single DNA end, explaining how sparse physiological trigger can trigger robust autoimmune response.
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
In 1969, Sironi reported something strange: phage P2’s OLD protein is lethal to RecBCD-deficient hosts. Today, we know many antiviral systems share this toxic phenotype. Our work finally explains why.
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Hoong Chuin Lim @hclim.bsky.social · 02/10/2026
www.biorxiv.org/content/10.6... New preprint from my lab revealing molecular conflicts between host replication and antiviral defense. RecBCD prevents this conflict by clearing immunogenic DNA ends produced during normal replication termination. #MicroSky #PhageSky
biorxiv.org
RecBCD Prevents Bacterial Autoimmunity by Clearing Self-DNA Ends Produced During Replication Termination
Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to ...
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Reposted by Hoong Chuin Lim
New England Biolabs @nebiolabs.bsky.social · 28/09/2026
Earlier this month, NEB hosted the 2026 Boston Phage Symposium on our Ipswich campus! We are thrilled to have supported a shared interest in phage research and great talks from four labs from MIT and @harvard.edu !
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Reposted by Hoong Chuin Lim
New England Biolabs @nebiolabs.bsky.social · 29/06/2026
How do archaeal cells coordinate DNA replication? NEB and Colorado State University scientists tracked DNA polymerase activity in living archaeal cells using genetics, biochemistry, and RADAR-seq to learn more: doi.org/10.1093/nar/gkag395
doi.org
Archaeal family B DNA polymerase facilitates lagging strand DNA replication in the Thermococcales
Abstract. Replicative DNA synthesis is distributed among several DNA polymerases (DNAPs) in both Bacteria and Eukarya. The division of synthesis permits sp
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Reposted by Hoong Chuin Lim
New England Biolabs @nebiolabs.bsky.social · 18/06/2026
In a Molecular Cell paper, NEB scientists describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. doi.org/10.1016/j.molcel.2026.03.027
doi.org
Redirecting
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Reposted by Hoong Chuin Lim
Jesse Shapiro @bjesseshapiro.bsky.social · 05/06/2026
Cheap and easy method for nanopore sequencing phage DNA directly from plaques. Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !! www.nature.com/articles/s41...
nature.com
Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction - Scientific Reports
Scientific Reports - Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction
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Reposted by Hoong Chuin Lim
Seth Shipman @seth-shipman.bsky.social · 23/04/2026
Out now in Nature Biotechnology! Alejandro González-Delgado and a fantastic team of collaborators worked across nine labs to get retron recombineering up-and-running in fifteen bacterial species. Molecular parts on addgene: www.addgene.org/browse/artic... Happy editing!
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Reposted by Hoong Chuin Lim
Kotaro Chihara @kochihara.bsky.social · 20/04/2026
Happy to share our new work on how phages escape bacterial immunity. We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation. www.nature.com/articles/s41... #PhageSky #MicroSky
nature.com
Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications
Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...
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Reposted by Hoong Chuin Lim
Melanie Blokesch @mblokesch.bsky.social · 29/03/2026
Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications. Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101
tiny.cc
Open Positions
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Reposted by Hoong Chuin Lim
Jens Hör @jenshoer.bsky.social · 21/03/2026
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Hoong Chuin Lim
Kranzusch Lab @kranzuschlab.bsky.social · 06/03/2026
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...
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Reposted by Hoong Chuin Lim
Thomas Ipoutcha @tomipou.bsky.social · 05/02/2026
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...
biorxiv.org
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Reposted by Hoong Chuin Lim
New England Biolabs @nebiolabs.bsky.social · 23/01/2026
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: nebiolabs.com/3O1DacT
nebiolabs.com
Golden Gate method enables rapid, fully-synthetic engineering of therapeutically relevant bacteriophages | NEB
Simplified bacteriophage design and synthesis to propel long-obstructed bacteriophage research in new PNAS study from New England Biolabs ® and Yale University Ipswich
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Reposted by Hoong Chuin Lim
Rubin Lab @therubinlab.bsky.social · 12/02/2026
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. 🧵
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Hoong Chuin Lim @hclim.bsky.social · 12/02/2026
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...
journals.plos.org
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...
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Hoong Chuin Lim @hclim.bsky.social · 06/11/2025
Hi Aude, Could you please add my lab (www.neb.com/en-us/research-labs/lim-lab)? Thanks!
neb.com
Lim Lab | NEB
The Lim Lab discovers new enzymes by studying how RNA is used in the battle between phages and bacteria.
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Reposted by Hoong Chuin Lim
Jens Hör @jenshoer.bsky.social · 17/10/2025
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!
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Reposted by Hoong Chuin Lim
Luuk Loeff @lloeff.bsky.social · 10/10/2025
One week left to apply!!
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Reposted by Hoong Chuin Lim
Asaf Levy @asaflevylab.bsky.social · 23/09/2025
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...
biorxiv.org
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 ...
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Hoong Chuin Lim @hclim.bsky.social · 21/09/2025
This is insanely cool!!
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Reposted by Hoong Chuin Lim
Rhys Grinter @rhyswg.bsky.social · 20/09/2025
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.
biorxiv.org
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...
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Hoong Chuin Lim @hclim.bsky.social · 18/09/2025
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
biorxiv.org
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...
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Reposted by Hoong Chuin Lim
Paula Navarro @navarropaula.bsky.social · 03/04/2025
🚨👉 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!
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Reposted by Hoong Chuin Lim
Géraldine Laloux @lalouxlab.bsky.social · 17/09/2025
🚨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
academic.oup.com
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.
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Reposted by Hoong Chuin Lim
William Garland @willgarland.bsky.social · 17/09/2025
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...
biorxiv.org
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...
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Reposted by Hoong Chuin Lim
Julius Brennecke @juliusbrennecke.bsky.social · 17/09/2025
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...
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Hoong Chuin Lim @hclim.bsky.social · 15/09/2025
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
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Hoong Chuin Lim @hclim.bsky.social · 15/09/2025
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.
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Hoong Chuin Lim @hclim.bsky.social · 15/09/2025
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.
academic.oup.com
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Alice Maestri @alicemaestri.bsky.social · 12/09/2025
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!
emploi.pasteur.fr
INSTITUT PASTEUR - Technicien de recherche Microbiologie H/F
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Hoong Chuin Lim @hclim.bsky.social · 30/07/2025
Congrats!!
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Géraldine Laloux @lalouxlab.bsky.social · 29/07/2025
Bacterial cell wall & periplasm paradigm shift - important read #MicroSky www.nature.com/articles/s41...
nature.com
Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology
Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.
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