Osterman Ilya
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ostermanilya.bsky.social
Osterman Ilya
@ostermanilya.bsky.social
Senior Research Associate, microbiologist, biochemist, The Sorek lab, Weizmann Institute of Science
Pinned
🧬 Metabolic arms race continues!
We discovered a new NAD⁺-depleting bacterial immune system aRES and phage enzymes that overcome it.
Our preprint is out: www.biorxiv.org/content/10.6...
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program
www.biorxiv.org
Reposted by Osterman Ilya
Molecular basis for anti-jumbo phage #immunity by AVAST type 5.

Avs5 detects an early jumbo‑phage activator and halts infection by rapidly hydrolyzing NAD+.

www.sciencedirect.com/science/arti... #phage #bacteriophage #MicroSky
February 7, 2026 at 7:26 PM
Reposted by Osterman Ilya
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

www.nature.com/articles/s41...
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
www.nature.com
February 6, 2026 at 3:15 PM
Reposted by Osterman Ilya
BackToBack #PhageSky in @nature.com

A pore-forming antiphage defence is activated by oligomeric phage proteins
-from Maxwell & Norris
www.nature.com/articles/s41...

Bacterial immune activation via supramolecular assembly with phage triggers
-from Laub & Ghanbarpour
www.nature.com/articles/s41...
February 4, 2026 at 10:42 PM
Reposted by Osterman Ilya
Chemical inhibition of a bacterial immune system

Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. One compound, IP6C, improves phage-therapy against P. aeruginosa & is effective against Thoeris in polymicrobial communities
www.cell.com/cell-host-mi...
Chemical inhibition of a bacterial immune system
Bacteriophages are promising alternatives to antibiotics for treating bacterial infections. However, bacteria possess immune systems that neutralize bacteriophages. Zang et al. discover small molecule...
www.cell.com
January 30, 2026 at 5:20 PM
Reposted by Osterman Ilya
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
🧬 Metabolic arms race continues!
We discovered a new NAD⁺-depleting bacterial immune system aRES and phage enzymes that overcome it.
Our preprint is out: www.biorxiv.org/content/10.6...
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program
www.biorxiv.org
January 29, 2026 at 11:20 AM
Reposted by Osterman Ilya
A prophage-encoded abortive infection protein preserves host and prophage spread www.nature.com/articles/s41...
A prophage-encoded abortive infection protein preserves host and prophage spread - Nature
A Gifsy-1 prophage–encoded higher eukaryotes and prokaryotes nucleotide-binding protein, HepS, senses Siphoviridae infection, activates abortive defence by cleaving host transfer RNAs, blocks rival ph...
www.nature.com
January 28, 2026 at 7:13 PM
Reposted by Osterman Ilya
Our latest CRISPR ring nuclease paper focusses on Csx15 - which seems to act as of a sponge as well as a canonical phosphodiesterase. Great work led by @haotianchi.bsky.social

www.biorxiv.org/content/10.6...
www.biorxiv.org
January 22, 2026 at 8:57 AM
Reposted by Osterman Ilya
A bacterial defense system targeting modified cytosine of phage genomic DNA | Nature Communications https://www.nature.com/articles/s41467-026-68792-8
January 22, 2026 at 10:33 PM
Reposted by Osterman Ilya
#NatMicroPicks

Asgard archaea and the origin of eukaryotes! 🦠

Eukaryotic cellular complexity evolved largely within the Asgard lineage before mitochondrial endosymbiosis and later bacterial gene acquisitions

#MicroSky

www.nature.com/articles/s41...
Dominant contribution of Asgard archaea to eukaryogenesis - Nature
A survey of the reconstructed gene set of the last eukaryotic common ancestor shows a consistent link between Asgard archaea and the origin of numerous, functionally diverse eukaryotic genes, dem...
www.nature.com
January 16, 2026 at 2:56 PM
Reposted by Osterman Ilya
Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky
A phage protein screen identifies triggers of the bacterial innate immune system
Nature Microbiology, Published online: 16 January 2026; doi:10.1038/s41564-025-02239-6A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.
go.nature.com
January 16, 2026 at 4:53 PM
Reposted by Osterman Ilya
NLR-like immunity in bacteria

A new study from the Alex Gao lab. The scope of this work is incredible!!!

www.biorxiv.org/content/10.6...
Diverse bacterial pattern recognition receptors sense the conserved phage proteome
Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...
www.biorxiv.org
January 5, 2026 at 1:59 PM
Potential metabolic symbiosis between bacteria and phages — very inspiring!
journals.asm.org/doi/10.1128/...
Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems | mSystems
Here, we sought phages that were capable of infecting Patescibacteriota metagenome-assembled genomes (MAGs), and further explored the diversity and novelty of Patescibacteriota phages, as well as the mechanisms underlying phage-Patescibacteriota interactions in groundwater ecosystems. The abundance profiles of phage-Patescibacteriota interactions suggested that lysogenic infection may represent a mutually adapted strategy between Patescibacteriota and their phages in groundwater ecosystems. Furthermore, the groundwater Patescibacteriota phages possessed diverse auxiliary metabolic genes which might facilitate the symbiotic associations and metabolic exchange between host Patescibacteriota MAGs and other free-living microbes and expand the metabolic capabilities of host Patescibacteriota MAGs. This study elucidated the mechanisms of phage-Patescibacteriota interactions and the potential roles of phages in modulating the physiology and ecology of Patescibacteriota within groundwater ecosystems.
journals.asm.org
December 24, 2025 at 5:33 PM
Reposted by Osterman Ilya
Looking for a POSTDOC to work on jumbo phages (those with large genomes and fascinating cell biology), using our latest ASO technology (Gerovac M et al. 2025 Nature) to define RNA export mechanisms as well as to help to advance phage therapy. Here's the job ad.
December 19, 2025 at 10:51 PM
Reposted by Osterman Ilya
Microbes weaponizing secondary metabolites to make rivals vulnerable to phage attack 🧪🦠

www.nature.com/articles/s41...
Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection - Nature Microbiology
A secondary metabolite sensitizes competitor Bacillus subtilis to a wide panel of lytic phages by sequestering iron and preventing the activation of Spo0A.
www.nature.com
December 19, 2025 at 3:03 PM
Reposted by Osterman Ilya
Preprint alert📢! 
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host?
➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied

Here is what we found. 
www.biorxiv.org/content/10.6...
#MicroSky #PhageSky
🧵
Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community
Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, partic...
www.biorxiv.org
December 18, 2025 at 2:11 PM
Reposted by Osterman Ilya
AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription [new]
Phage proteins inhibit bacterial transcription. Novel inhibitors binding RNA polymerase discovered via structural predictions.
December 18, 2025 at 3:33 PM
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle: Molecular Cell www.cell.com/molecular-ce...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings re...
www.cell.com
December 18, 2025 at 6:44 PM
Reposted by Osterman Ilya
💥 alert article 💥
New preprint from the lab !!! 🥳
In this work, we explore the 3D genome architecture of the virulent phage PAK_P3 during its infection cycle in P. Aeruginosa. We unveil a highly dynamic structuration as well as specific interactions patterns.

www.biorxiv.org/content/bior...
www.biorxiv.org
December 17, 2025 at 7:14 AM
Reposted by Osterman Ilya
Closing the Loop on Phage-bacteria Coevolution https://www.biorxiv.org/content/10.64898/2025.12.15.694372v1
December 16, 2025 at 11:01 PM
Reposted by Osterman Ilya
A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti https://www.biorxiv.org/content/10.64898/2025.12.16.694600v1
December 17, 2025 at 3:18 AM
Reposted by Osterman Ilya
A synthetic cell phage cycle | Nature Communications https://www.nature.com/articles/s41467-025-67249-8
December 16, 2025 at 1:06 AM
Reposted by Osterman Ilya
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.

In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
www.biorxiv.org
December 15, 2025 at 9:49 PM
De novo origin of numerous microproteins in enterobacteria

Igor Fesenko, Svetlana A Shabalina, Gisela Storz, Eugene V Koonin.
Nucleic Acids Research, Volume 53, Issue 22, 11 December 2025
doi.org/10.1093/nar/...
December 15, 2025 at 8:49 PM
Reposted by Osterman Ilya
Durham University (@durham.ac.uk) and NEB scientists described the first biochemical characterization of GmrSD Type IV restriction enzyme substrate specificity and inhibition by phage protein IP1*. https://royalsocietypublishing.org/doi/10.1098/rstb.2024.0072
Modified DNA substrate selectivity by GmrSD-family Type IV restriction enzyme BrxU
Abstract. Bacteriophages (phages), viral predators of bacteria, generate selection pressure that causes bacteria to evolve defence systems. Type I, II and
royalsocietypublishing.org
December 15, 2025 at 5:50 PM