Eugene V. Koonin

The paper identifies and characterizes a new family of prokaryotic defense proteins, WARDs, which are associated with various defense systems and provide phage resistance.

This study uses computational simulations to show that short random peptides enhance RNA evolution and structural diversity, suggesting an RNA-peptide world in early life.

The paper identifies a new viral order, Ariadnavirales, based on genomic analysis of SmDNAV, which lacks key replication and transcription genes, indicating host-dependent replication.

This study shows that tumor cells adapt to changing environments through phenotypic switching, with optimal survival achieved by blocking mesenchymal to epithelial transition.

This study identifies 103 putative families within the Stelpaviricetes class of ribovirians, revealing their evolutionary relationships and suggesting a protist origin for the class and fungal origin for Potyviridae.

The paper identifies 90 structurally distinct STAND NTPase families in bacteria and archaea that recognize phage proteins, revealing their role in antiviral defense.

The paper identifies YprA family helicases as a missing link connecting DISARM and Druantia immune systems in prokaryotes, revealing new defense classes and their antiviral mechanisms.

The paper develops a mathematical model to explore why mobile genetic elements (MGEs) frequently carry defense systems, finding that the strength of inter-MGE interference determines whether these systems are beneficial or costly.

This study investigates how Druantia III and Zorya II antiphage defence systems in bacteria synergize through shared DNA intermediates, showing their coordinated response during phage infection.

The paper examines the relationship between genome size and selection pressure in prokaryotes, revealing heterogeneous selection patterns across bacteria and archaea.

This study identifies Tmn as a bacterial membrane protein that blocks phage spread by inducing plasmolysis and activates synergistic defence responses through ATP depletion.

The paper identifies conjugative megaplasmids in the human gut microbiome that can disseminate prophage genomes across bacterial lineages, explaining their wide distribution.

Constrained-tree hypothesis testing on 4,290 core eukaryotic protein clusters attributes 50% of likelihood weight to Asgard archaea; Alphaproteobacterial ancestry is largely confined to oxidative phosphorylation and iron-sulfur cluster biogenesis.

This paper shows that cheaters can promote cooperation by enabling group survival in a multi-level selection model, challenging the classical view that cheaters destabilize cooperation.

The paper models prokaryotic antivirus defense strategies and finds that immunity is preferred at high viral pressure and PCD at low host population size, with potential antagonism from overinvestment in immunity.

The paper introduces KlebPhaCol, a resource containing 53 phages and 74 Klebsiella isolates, including a novel gut phage order, to advance understanding of Klebsiella-phage interactions.

The paper identifies archaeal microcompartments in Hodarchaeales, showing they enhance energy production and may have contributed to eukaryogenesis.

This study shows that some Asgard archaea use terminal oxidase and globin for oxygen adaptation, suggesting ancient oxygen tolerance and potential role in eukaryogenesis.

This study develops a mathematical model to show that prokaryotes evolve antivirus defense strategies based on environmental virus prevalence, with adaptive immunity optimal in stable environments and HGT dominant in fluctuating ones.

The paper identifies a new family of Obelisk-like cccRNAs in hot springs using FLDS, expanding the Obelisk superfamily with structurally similar but sequence-divergent proteins.

The paper identifies Jug phages as prevalent in human and animal gut microbiomes, showing high transcription activity and potential ecological significance.

This study uses a computational simulator to show how globular protein folds can evolve from random sequences, finding that stable folds emerge with 3-8 amino acid replacements per site.

This study quantifies the contribution of gene gain and loss versus genome rearrangements to gene order evolution in bacteria and archaea, finding gene gain and loss dominate.

Cryo-EM at 2.9-3.1 Å shows bacterial OLE, ROOL and GOLLD RNAs self-assemble without protein into a dimer, an 8-chain nanocage and a 14-chain nanocage.

The paper identifies ENDPaCF1, a novel defense system in Pseudomonas aeruginosa, which targets hypermodified phage DNA through an endonuclease domain fused to an inactive Endonuclease III, revealing its role in antiphage immunity.

The paper identifies a new family of marine bacteriophages with double-stranded RNA genomes, named Paraxenoviridae, based on genomic and structural analyses.

The paper uses protein structure prediction to analyze dark matter proteins in Orthornavirae, identifying new domains and highlighting the prevalence of disordered regions.

The paper identifies viral crlRNAs that suppress bacterial immunity by reprogramming Cas proteins and demonstrates their potential for mammalian genome editing.

The paper identifies instances of DNA polymerase (DNAP) swapping among bacteriophages, showing gene replacements between families and subfamilies without altering surrounding gene organization.

The paper identifies long-range gene clustering in prokaryotic genomes based on gene age and functionality, suggesting it results from genome rearrangement rather than conservation.