Mart Krupovic

A giant virus with a 4-megabase genome and a vastly expanded repeatome.

The paper describes Sissivirus, a giant virus with a 4-megabase genome and a large repeatome, identifying repeat accumulation as a key driver of its genome expansion.

Loss of replication and transcription systems accompanying transition to nucleus-dependent replication in Ariadnavirales, a proposed new order in nucleocytoviricot class Megaviricetes

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.

Molecular architecture of colossal surface layers from hyperthermophilic archaea

This study determines the structure of a large S-layer protein from Pyrobaculum arsenaticum using cryo-EM and AlphaFold, revealing its unique multidomain architecture and evolutionary conservation.

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Virus-host interactions on volcanic ash from Mount Etna

This study examines viral and bacterial diversity in volcanic ash from Mount Etna, revealing novel species and active virus-host interactions.

Transcription factor CCTF1 plays a decisive role in regulating the proteasome activity during archaeal cell division

The paper identifies CCTF1 as a key regulator of proteasome activity during archaeal cell division by controlling PAN expression through promoter binding.

A Pair of DNA Glucosyltransferases Elevate Counter-defense in Bacteriophage T4

This study shows that bacteriophage T4 uses two glucosyltransferases to modify its DNA, helping it evade bacterial defense systems, with redundancy providing an evolutionary advantage.

Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host and their phages

The paper describes a tripartite interaction between a patescibacterial epibiont, its gammaproteobacterial host, and their phages, revealing host specificity and genetic adaptations.

A single-stranded DNA virus replicates in the mitochondria of a marine oomycete

This study identifies a single-stranded DNA virus replicating in oomycete mitochondria, expands DNA virus diversity, and highlights marine environments as underexplored virus reservoirs.

Nested parasitism in hypersaline environments: viruses and virus satellites of haloarchaea and their nanosized cellular symbionts

The paper investigates hyperparasitism in hypersaline environments by analyzing viruses and virus satellites associated with haloarchaea and nanohaloarchaea, revealing new viral families and gene transfers.

Three transcription factors coordinate the archaeal cell cycle progression through a regulatory braking point mechanism

This study identifies three transcription factors that regulate the archaeal cell cycle in Saccharolobus islandicus through a braking point mechanism, differing from eukaryotic regulation.

Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily

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.

Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes

This study analyzes the cell cycle of Saccharolobus islandicus and finds that transcriptional patterns are conserved with eukaryotes, showing phase-specific gene expression for metabolism, protein synthesis, and chromatinization.

Biogenesis of DNA-carrying extracellular vesicles by the dominant human gut methanogenic archaeon

This study characterizes DNA-carrying extracellular vesicles (EVs) from Methanobrevibacter smithii, revealing their role in DNA and protein export in the gut.

A new class of OLD family ATPases Cran1 functions in cell cycle progression in an archaeon

This study identifies a new class of OLD family ATPases in archaea, showing Cran1 is essential for cell cycle progression rather than antiviral defense.

"Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes

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

Cryo-EM analysis of the Bacillus thuringiensis extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum

The paper identifies F-ENA as a widespread family of endospore appendages in Firmicutes using cryo-EM, revealing their structure and role in spore clustering.

Episomal virus maintenance enables bacterial population recovery from infection and virus-bacterial coexistence

This study shows that episomal virus maintenance in Salinibacter ruber allows population recovery from infection and supports virus-bacterial coexistence under high MOI.

The protein structurome of Orthornavirae and its dark matter

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

Structural diversity and clustering of bacterial flagellar outer domains

The paper analyzes flagellar outer domains in bacterial species, revealing structural diversity and identifying new clusters of flagellin structures.

Jumping DNA polymerases in bacteriophages

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

Mriyaviruses: Small Relatives of Giant Viruses

The paper identifies a new class of viruses, Mriyaviricetes, with small genomes related to giant Nucleocytoviricota viruses, suggesting they are close relatives of their ancestors and use a unique rolling circle replication mechanism.

Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins

The paper uses protein structure modeling to analyze the evolutionary relationships and functional domains of eukaryotic DNA viruses with double jelly-roll capsids, revealing their origin and evolution.

Closest relatives of poxviruses replicate in the digestive system of humans and animals worldwide

The paper discovers a new group of DNA viruses, egoviruses, found in the digestive systems of humans and animals, closely related to poxviruses and suggesting an evolutionary link between gut-infecting viruses and animal pathogens.

Diversity, Origin and Evolution of the ESCRT Systems

This paper reconstructs the evolution of ESCRT systems in archaea, identifying homologs in Asgardarchaeota and other groups, suggesting an early origin of ESCRT components and their connection to the ubiquitin system.

Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence

This study uses long-read transcriptomics to analyze OsHV-1, revealing conserved capsid maturation gene expression and a mechanism to evade ADAR-based antiviral defense.

Gene sharing networks to automate genome-based prokaryotic viral taxonomy

This paper introduces vConTACT 2.0, a network-based tool for prokaryotic virus taxonomy that scales to large datasets and achieves high accuracy in taxonomic assignments.