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Sternberg Lab @sternberglab.bsky.social · Jul 24

16/16 This work was a big team effort and fun collaboration! Thanks to everyone: Matt, Egill, Tanner, Jing, Zaofeng, Americo, Florian, Hamna, Ryan, Nick, Israel and our stellar mentor Sam for making this project possible!

Sternberg Lab @sternberglab.bsky.social · Jul 24

15/16 In summary, we shed light on the biological role of a naturally occurring version of CRISPR interference (CRISPRi), that emerged in gut-associated bacteria to benefit multiple aspects of their lifestyle.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

14/16 The repeated exaptation of TnpB to regulate flagellin suggests strong evolutionary pressure favoring RNA-guided control of flagellin expression, particularly in gut-associated bacterial species.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

13/16 In other key members of the human gut microbiome, flagellin-regulating TldRs can be found additionally associated with the translational repressor CsrA. The coordinated action of TldR and CsrA suggests a dual mode of both transcriptional and post-transcriptional gene regulation.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

12/16 The extra domain stabilizes the filament by increasing inter-subunit contacts. Structure-guided mutagenesis confirmed that this domain is essential to improve motility of the lysogen. We believe it could similarly explain the decreased activation of TLR5.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

11/16 We found that both flagellar filaments have a drastically different structure. The prophage flagellar filament is significantly thicker and presents a surprising mesh-like structure. This is due to the presence of an extra domain in the prophage flagellin.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

10/16 To try to link these phenotypic observations, we teamed up once again with @piratefernandez.bsky.social‬ and decided to inspect the structures of the prophage flagellin in comparison to their host counterpart.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

9/16 The phenotypic effects of lysogenization result in a consequential ecological outcome: enhanced colonization of the murine gut, illustrating the advantage of flagellar remodeling in a host-associated environment.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

8/16 We also find that lysogenic conversion by FRφ reduces activation of TLR5, a receptor that detects flagellin to initiate the immune response, suggesting that lysogenization may facilitate immune evasion.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

7/16 We find that lysogenic conversion by FRφ leads to increased motility of the host. Essentially, Enterobacter (and even E. coli actually) swims faster when expressing FliCp instead of FliCh.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

6/16 To tackle this question we focused on a clinical isolate of Enterobacter, that natively contains what we now call a Flagellin Remodeling prophage (FRφ), and started our detective work to uncover the potential advantage(s) conferred by the acquisition of this prophage.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

5/16 Prophages sometimes provide new traits to their bacterial host, that is called “lysogenic conversion”. Now, why would a phage manipulate the flagellar apparatus of their host? That question is the focus of our new study.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

4/16 Strikingly, FliC-associated TldRs are found in prophages and target the promoter of host-encoded FliC. Basically, TldR silences the host FliC (FliCh) and the prophage copy (FliCp) takes over, effectively leading to a remodeling of the host flagellar apparatus.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

3/16 Unlike TnpB, which can be found in transposons and in association with transposases, TldR is often found in association with FliC (flagellin), the main subunit of flagellar filaments. Flagella are large appendages used by bacteria for motility.

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Sternberg Lab @sternberglab.bsky.social · Jul 24

2/16 Last year we reported the discovery of RNA-guided transcriptional repressors, derived from the Cas12 ancestor TnpB. We called it TldR for “TnpB-like nuclease dead repressors”. Yet, we did not address their actual biological role.
More details here: tinyurl.com/2camf88e

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Sternberg Lab @sternberglab.bsky.social · Jul 24

1/16 New pre-print from the Sternberg Lab!
We uncover how temperate phages can use RNA-guided transcription factors to remodel the flagellar composition of their bacterial host and enhance their fitness.
Find the preprint and full story here: tinyurl.com/mshwjd77

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Reposted by Sternberg Lab

Broad Institute @broadinstitute.org · Jun 24

Gene editing pioneer David Liu discusses baby K.J. Muldoon, the first person treated with a customized gene editing therapy, what made K.J.'s treatment possible, and how on-demand treatments for rare genetic diseases could one day become routine. #GeneEditing #Science

Q&A: One scientist’s bold vision to make on-demand treatments routine for life-threatening rare genetic diseases

Broad core member and gene editing pioneer David Liu describes a framework that could enable the treatment of 1,000 patients with personalized gene editing therapies by 2030.

www.broadinstitute.org

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Reposted by Sternberg Lab

Molly Gale (Gale-Hammell Lab) @mollygale.bsky.social · Jun 16

🧬🌽 Happy Transposon Day! 🌽🧬

Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

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Reposted by Sternberg Lab

François Rousset @francoisrousset.bsky.social · Jun 12

Nature invented CRISPRa way before scientists did 🤩

Awesome work by the @sternberglab.bsky.social

Looking forward to seeing cool applications coming out of this !

Sternberg Lab @sternberglab.bsky.social · Jun 11

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs.
Full story here:
www.biorxiv.org/content/10.1...

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Reposted by Sternberg Lab

Gianluca Prezza @gprezza.bsky.social · Jun 12

Did you think you needed a promoter for CRISPRa? Think again!

Sternberg Lab @sternberglab.bsky.social · Jun 11

6/10 dCas12f-Sigma factors are able to recruit their native RNA polymerase (RNAP) to drive RNA-guided transcription at programmable sites. Remarkably, we were able to generate RNA (see RNA-seq) without relying on promoters in intergenic sequences, even within genes, and on either DNA strand.

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Sternberg Lab @sternberglab.bsky.social · Jun 11

10/10 This work was a big team effort and fun collaboration! Thanks to everyone: Florian, Tanner, Adriana, Juniper, Renjian, ‪@stephentang23.bsky.social‬, Henry, Chance, George, and our stellar mentors Sam and Leifu for making these projects possible!

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Sternberg Lab @sternberglab.bsky.social · Jun 11

9/10 In summary, we discovered an RNA-guided system that programmably creates de novo transcription start sites in bacteria. It represents a naturally occurring version of CRISPR activation (CRISPRa) but does not rely on targeting pre-existing promoters.

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Sternberg Lab @sternberglab.bsky.social · Jun 11

8/10 We teamed up with the Chang Lab who determined the beautiful structures of the RNA-guided transcription initiation complex (and more!) which feature dCas12f, Sigma and the native RNA polymerase. Be sure to check out their thread on the structural findings! www.biorxiv.org/content/10.1...

Structural basis of RNA-guided transcription by a dCas12f-σE-RNAP complex

RNA-guided proteins have emerged as critical transcriptional regulators in both natural and engineered biological systems by modulating RNA polymerase (RNAP) and its associated factors(1-5). In bacter...

www.biorxiv.org

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Sternberg Lab @sternberglab.bsky.social · Jun 11

7/10 Transcription initiates in a tight ~45-48 bp window downstream of the PAM/TAM flanking the target site. All sequence specificity is imparted by Cas12f. The associated Sigma factor is recruited without imposing any of the typical -35 and -10 promoter DNA sequence requirements.

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Sternberg Lab @sternberglab.bsky.social · Jun 11

6/10 dCas12f-Sigma factors are able to recruit their native RNA polymerase (RNAP) to drive RNA-guided transcription at programmable sites. Remarkably, we were able to generate RNA (see RNA-seq) without relying on promoters in intergenic sequences, even within genes, and on either DNA strand.

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