Constantinos Patinios

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1/4 Excited to share our new preprint on phage genome editing: Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes Preprint: lnkd.in/dv4g5kW6

4/4 We then used this library to isolate T7 variants capable of infecting otherwise resistant, LPS-deficient E. coli hosts, showing how scalable phage genome editing can be used to expand host range.

Many thanks to Frank Englert, Sarshad K. Valappil, Jonas Kubilius, @drjonesky.bsky.social , @vivekmutalik.bsky.social , and Chase Beisel. #Bacteriophage #PhageEngineering #GenomeEditing #CRISPR #PhageTherapy

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2/4 We unexpectedly found that Cas9 nickase, which introduces only a single-strand DNA break, can edit selected phage genomes with remarkably high efficiency while preserving phage titers. Unlike many existing approaches, this avoids multi-step workflows, counterselection, and extensive screening.

3/4 Maintaining high phage titers also makes the method well suited for large-scale mutagenesis. Using nCas9, we generated a library of more than 440,000 T7 tail-fiber variants in a single editing step.

🚀 Excited to share that I’ve been awarded an EMBO Installation Grant to establish my research group at the EMBL Partnership Institute, Vilnius University Life Sciences Center! The grant provides €50,000/year for 5 years to build an internationally competitive lab and advance genome editing research.

This work will drive new genome editing technologies and uncover fundamental DNA repair mechanisms, with impact across microbiome research, synthetic biology, industrial biotechnology, and healthcare.

bit.lyDr C. Patinios Awarded EMBO Installation Grant to Advance Genome Editing Research in LithuaniaVilnius University is a prestigious institution of science and studies in Lithuania, which develops world-class science and develops science-based international studies.

🔗 Discover more: bit.ly/3LUzM2U #EMBO #GenomeEditing #CRISPR #SyntheticBiology #Microbiology #Biotechnology #Vilnius #LifeSciences

nature.comRNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity - NatureCas12a3 nucleases constitute a distinct clade of type V CRISPR–Cas bacterial immune systems that preferentially cleave the 3′ tails of tRNAs after recognition of target RNA to induce growth arres...

🧬 My project, “Pause-Repair-Edit,” aims to move beyond current CRISPR tools by developing safer genome editing approaches that pause DNA replication to activate natural repair pathways—opening genome editing to many microorganisms that are currently hard to engineer.

Constantinos Patinios reposted

Oleg Dmytrenko

@olehdmy.bsky.social

7 Jan

Our paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...

Constantinos Patinios reposted

eLife

@elife.bsky.social

24 Sept 2025

Openness means more than access. We’re pleased to announce that we now publish Replication Studies, helping make science more reliable, transparent, and trustworthy. buff.ly/Gebypvq

Constantinos Patinios reposted

Nature Biotechnology

@natbiotech.nature.com

go.nature.comTargeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature BiotechnologyAppend editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - @helmholtz-hiri.bsky.social go.nature.com/4n7zDpG

doi.orgTargeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature BiotechnologyAppend editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.

🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...

This opens up brand-new possibilities for precision editing and studying DNA repair!

Big shout-out to first authors Darshana Gupta, (myself :) ) & Harris V. Bassett, senior author Chase L. Beisel, and project initiator Scott P. Collins 🙌

We developed append editing, a genome-editing strategy that installs ADP-ribose groups onto DNA to unlock new repair outcomes: 🔹 In bacteria → precise, scar-free edits via homologous recombination 🔹 In eukaryotes → unique T→A or T→C base substitutions not possible with current editors

🚀 Join the Patinios Lab at the VU LSC - EMBL Partnership Institute for Genome Editing Technologies! We are looking for a Postdoctoral Researcher to join our growing team! 🔎

Deadline: Open until a suitable candidate is found. 📧 Send your CV + Motivation Letter to: constantinos.patinios@gmc.vu.lt

gmc.vu.ltThe Laboratory of Dr. Constantinos PatiniosVU Gyvybės mokslų centras jungia tris VU padalinius – Biomokslų, Biotechnologijos ir Biochemijos institutus. Centras įkurtas vystant integruotą mokslo, studijų ir verslo centrą (slėnį) „Saulėtekis“.

Learn more ➡️ www.gmc.vu.lt/en/lsc-embl/...

🚀 Join the Patinios Lab at the VU LSC - EMBL Partnership Institute for Genome Editing Technologies! We are looking for a Postdoctoral Researcher to join our growing team! 🔎

🌍 Based in beautiful Vilnius, Lithuania 🔬 Access to state-of-the-art equipment and facilities 💼 Competitive salary, personalized mentorship, and cutting-edge research!

🧬 Our work focuses on next-generation genome editing tools for bacteria, yeasts, and phages — with a special focus on DNA replication stalling and repair!

🚀 Join the Patinios Lab at the VU LSC - EMBL Partnership Institute for Genome Editing Technologies! We are looking for a Postdoctoral Researcher to join our growing team! 🔎

European Research Council (ERC)

If you’re passionate about genome editing or synthetic biology… If you want tailored mentorship to drive independent research and launch your career… This is the place for you! ✨

Constantinos Patinios reposted

@erc.europa.eu

11 Mar 2025

Good news on this 35th anniversary of the #Restoration of #Independence in #Lithuania! A new ERC project from a Lithuanian researcher can now go ahead, as they were able to secure alternative EU funding for her ERC Consolidator Grant. How did this happen? Find out in the thread 🧵👇

14 Mar 2025

Excited to see our SIBR work out in Trends in Biotechnology :) doi.org/10.1016/j.ti... This is the first study I have coordinated from start to finish, and it brings me immense satisfaction to see it published. For a brilliant description of the tech check this: www.linkedin.com/feed/update/...

doi.orgRedirecting

doi.orgStreamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas systemCupriavidus necator H16 is a promising microbial platform strain for CO2 valorisation. While C. necator is amenable to genome editing, existing tools are often inefficient or rely on lengthy protocols...

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

colab.research.google.comGoogle Colab

If you want to use SIBR2.0 for your gene/protein of interest, you can visit the SIBR Site Finder site: colab.research.google.com/drive/162gIZ...

Huge thanks to Simona Della Valle, Enrico Orsi and Sjoerd Creutzburg for driving this work. Happy editing :)

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

By using SIBR2.0-Cas12a we achieved ~70% editing efficiency, in just 48h after electroporation

SIBR2.0 can virtually control the expression of any gene/protein of interest, in a wide range of (if not all) mesophilic prokaryotes

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

his means that even with the alternative translation site present in the SIBR sequence, a non-functional and split protein will be produced

We show that SIBR2.0 is great for inhibiting the translation of the T7 RNAP in E. coli and then we used it to tightly and inducibly express the Cas12a protein in C. necator

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

The alternative site for translation appeared to be gene- and organism- specific

This is where magic happened!! We developed SIBR2.0 :) SIBR2.0 includes the introduction of SIBR within the coding sequence of the gene of interest, splitting it into 2 distinct exons

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

Initially, we used the previously developed SIBR system (check here: doi.org/10.1093/nar/...) to tightly control and delay Cas9-based counterselection. This setup resulted in >80% editing efficiency in C. necator, in just 48 hours after electroporation, outcompeting any other method out there

doi.orgValidate User

Then, we attempted to do the same for Cas12a but were unsuccessful. Surprisingly, we discovered an alternative translation initiation site within the SIBR sequence, which allowed for the translation of fully functional Cas12a proteins

SIBR2.0 is now out in a preprint!! doi.org/10.1101/2024...

I am happy to announce our preprint for building a streamlined and efficient genome editing pipeline in the industrially relevant Cupriavidus necator H16 using -MY FAVOURITE- SIBR-Cas system

doi.orgTargeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotesBase editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains ...

How about a new genome editing tool?? #Append Editing, #ADPr-TAE, #Homologous recombination, #Base mutagenesis. doi.org/10.1101/2024... Thread: 🧵

Altogether, our approach, leverages the addition of a chemical moiety to DNA to expand current modalities for precision gene editing

Huge thanks to all authors and collaborators, especially to Darshana Gupta, Harris Bassett and Chase Beisel for leading this study, and to Scott Collins for initiating this study

How about a new genome editing tool?? #Append Editing, #ADPr-TAE, #Homologous recombination, #Base mutagenesis. doi.org/10.1101/2024... Thread: 🧵

ADP-ribosylation of bacterial genomes drives efficient homologous recombination, offering flexible and scar-free genome editing without base replacement nor counter-selection

In contrast, ADP-ribosylation of eukaryotic genomes, drives substitution of the ADPr-thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions

How about a new genome editing tool?? #Append Editing, #ADPr-TAE, #Homologous recombination, #Base mutagenesis. doi.org/10.1101/2024... Thread: 🧵

In our work, we harness the bacterial anti-phage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes

Using a DarT2-nCas9 fusion protein, we program site-specific ADP-ribosylation of thymines within a target DNA sequence

How about a new genome editing tool?? #Append Editing, #ADPr-TAE, #Homologous recombination, #Base mutagenesis. doi.org/10.1101/2024... Thread: 🧵

I am proud to present the latest work from my PostDoc research @Beisel lab @HIRI @HZI. In this work we present a novel type of genome editors which we call Append Editors (AE)