Yanjie Chao
yjchao.bsky.social
Yanjie Chao
@yjchao.bsky.social
Bacterial RNA Biologist, Group Leader and Professor at Chinese Academy of Sciences, Shanghai Institute of Materia Medica (Formerly Institut Pasteur of Shanghai). Homepage: https://yanjiechao.wordpress.com
Reposted by Yanjie Chao
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇
November 6, 2025 at 10:39 AM
I'm happy to co-organize the 2nd Microbial RNA Symposium in Shanghai! Looking forward to these inspiring talks this weekend! @rnasociety.bsky.social @natmicrobiol.nature.com @cellpress.bsky.social
October 23, 2025 at 3:50 AM
Reposted by Yanjie Chao
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?

Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
Reposted by Yanjie Chao
🚨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
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.
academic.oup.com
September 17, 2025 at 7:27 AM
Reposted by Yanjie Chao
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide

www.nature.com/articles/s41...
Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution
A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...
www.nature.com
August 27, 2025 at 11:04 AM
Reposted by Yanjie Chao
tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa 🦠👏High-throughput tRNA epitranscriptome profiling using mass spec on P. aeruginosa transposon insertion library and links with metabolic networks #microsky #rnasky doi.org/10.1093/nar/...
tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa
Abstract. Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and di
doi.org
July 28, 2025 at 8:28 PM
Reposted by Yanjie Chao
New preprint! We characterise the small, regulatory RNA Arp which controls DNA uptake and twitching motilty in A. baumannii. Led by our Dr Fergal Hamrock @hamrockfergal.bsky.social and in collaboration with @westermannlab.bsky.social and Mike Gebhardt's lab!
DNA uptake and twitching motility are controlled by the small RNA Arp through repression of pilin translation in Acinetobacter baumannii https://www.biorxiv.org/content/10.1101/2025.07.19.665661v1
July 21, 2025 at 2:56 PM
Reposted by Yanjie Chao
Evolution of hunt, kill, devour in a Vibrio ecospecies
Great paper 'Molassodon' - genetically distinct ecospecies from typical V. parahaemolyticus, it has evolved a predatory strategy that devour other bacteria in viscous environments
@campy-bara.bsky.social
www.biorxiv.org/content/10.1...
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...
www.biorxiv.org
July 4, 2025 at 3:15 PM
Reposted by Yanjie Chao
#NatMicroPicks

Vibrio in competition! 🦠💉

An orphan T6SS effector in non-toxigenic Vibrio cholerae targets susceptible strains by disrupting ion balance, shaping Vibrio population dynamics and offering a model for precision antimicrobials.

#MicroSky

www.cell.com/cell-host-mi...
A Vibrio-specific T6SS effector reshapes microbial competition by disrupting Vibrio bioenergetics
Liu et al. report that a Vibrio-specific T6SS effector, TseVs, selectively disrupts Vibrio bioenergetics while sparing non-target microbes via an immunity-independent mechanism. This work reveals how ...
www.cell.com
July 4, 2025 at 1:58 PM
Reposted by Yanjie Chao
Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie!

www.biorxiv.org/content/10.1...
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...
www.biorxiv.org
June 30, 2025 at 7:45 AM
Reposted by Yanjie Chao
3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages https://www.biorxiv.org/content/10.1101/2025.06.06.658255v1
June 7, 2025 at 4:23 AM
Quality over quantity: Small RNA pauses translation elongation to lift protein activity: Molecular Cell www.cell.com/molecular-ce...
Quality over quantity: Small RNA pauses translation elongation to lift protein activity
Small noncoding RNAs typically regulate the translation initiation of target mRNAs and thereby protein production. In this issue of Molecular Cell, Thongdee et al. discovered a novel regulatory mechan...
www.cell.com
May 8, 2025 at 11:01 AM
Reposted by Yanjie Chao
I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies.

#PhageSky

doi.org/10.1093/nar/...
Advancing RNA phage biology through meta-omics
Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i
doi.org
April 23, 2025 at 8:57 AM
Grant opportunity! 200K USD for 3 years from CAS-ANSO program. Apply by May 20th. Details in here: www.anso.org.cn/programmes/S...
April 17, 2025 at 6:12 AM
Reposted by Yanjie Chao
Where science meets culture 🔬🎭
At the Vogel Foundation Dr Eckernkamp’s 25th anniversary gala at the Mainfranken Theater, #HIRI director Jörg Vogel emphasized the vital role of culture for cutting-edge research.
Congrats & thank you for supporting our science!
➡️ www.helmholtz-hiri.de/en/newsroom/...
March 13, 2025 at 3:48 PM
Reposted by Yanjie Chao
📅🖍️ Mark your calendars: The #HIRI & the Shanghai #RNA Club will host @rnasociety.bsky.social’s next RNA Collaborative Seminar on March 12. HIRI group leader @jenshoer.bsky.social will discuss “Insights into the role of RNA in bacterial immunity and phage replication.”
us02web.zoom.us/webinar/regi...
Welcome! You are invited to join a webinar: RNA Collaborative - Helmholtz Institute for RNA-based Infection Research (HIRI) & Shanghai RNA Club. After registering, you will receive a confirmation emai...
Featuring: “Insights into the role of RNA in bacterial immunity and phage replication” Jens Hör, PhD Group Leader, Helmholtz Institute for RNA based Infection Research, Junior Professor, University...
us02web.zoom.us
February 28, 2025 at 12:56 PM
Reposted by Yanjie Chao
It is finally out!

Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!

Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
www.nature.com
February 26, 2025 at 4:43 PM
Reposted by Yanjie Chao
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈

“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
Highly multiplexed spatial transcriptomics in bacteria
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...
www.science.org
January 25, 2025 at 5:33 PM
My collaborators in Shanghai discovered that Within-host evolution of a transcriptional regulator contributes to the establishment of chronic Pseudomonas aeruginosa infection: Cell Reports www.cell.com/cell-reports...
Within-host evolution of a transcriptional regulator contributes to the establishment of chronic Pseudomonas aeruginosa infection
Zhou et al. identify a 9-bp deletion in a putative transcriptional regulator in P. aeruginosa. This mutation is highly associated with chronic P. aeruginosa infection and leads to pyruvate accumulatio...
www.cell.com
January 21, 2025 at 2:36 AM