M. Krupovic

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.

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.

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.

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.

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.

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.

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.

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.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

The paper identifies 56 metagenome-assembled genomes of Bathyarchaeia viruses and describes their CRISPR system components, revealing potential counter-defense mechanisms.

DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution

The paper identifies Polinton diversity in nematode genomes, showing ancient and recent integrations and horizontal gene transfer of distinct DNA polymerases across phyla.

Two dramatically distinct archaeal type IV pili structures formed by the same pilin

The paper determines the atomic structures of two distinct archaeal type IV pili formed by the same pilin under different growth conditions, revealing structural flexibility and conformational diversity.

Distinct groups of RNA viruses associated with thermoacidophilic bacteria

The paper identifies two new groups of RNA viruses associated with thermoacidophilic bacteria in acidic hot springs and other environments.

Two-million-year-old microbial communities from the Kap Kobenhavn Formation in North Greenland

This paper reconstructs microbial communities from 2-million-year-old permafrost in Greenland, finding similarities to modern thawing permafrost microbes and suggesting microbial communities may signal climate change impacts before plants and animals.

Widespread PRC barrel proteins play critical roles in archaeal cell division

This study identifies three PRC barrel proteins in Haloferax volcanii essential for archaeal cell division, showing their conservation and role in division across haloarchaea.

Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from leader- over cryptic promoters

The paper shows that Cbp1-Cren7 chromatinization suppresses cryptic promoter activity and enhances transcription from leader promoters in CRISPR arrays.

Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth

The paper tests DNA Stable Isotope Probing on bacteriophage T4 and Escherichia coli, showing a correlation between substrate isotopic composition and virion isotopic signature.

DNA-binding mechanism and evolution of Replication Protein A

This study characterizes the DNA-binding mechanism of RPA from Pyrococcus abyssi using crystal and cryo-EM structures, revealing conserved features and a novel archaeal-specific domain.

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

The paper identifies 11,420 viroid-like circular RNAs across 5,131 metatranscriptomes and 1,344 plant transcriptomes, revealing a five-fold increase in known viroid-like agents and novel ribozyme combinations.

Varidnaviruses in the human gut: a major expansion of the order Vinavirales

This study identifies and characterizes varidnaviruses in the human gut virome, revealing their prevalence as prophages and suggesting limited active infections.

A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea

This study identifies aCcr1, an archaeal transcription factor, and its viral homologs as regulators of cell cycle progression, showing they control cell division by repressing cdvA expression.

Evolutionary Diversification of Methanotrophic Ca. Methanophagales (ANME-1) and Their Expansive Virome

The paper expands the phylogenetic diversity of ANME-1 archaea and discovers new virus families specific to their virome, revealing evolutionary links and gene displacement mechanisms.

DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps

DeepTracer-ID identifies proteins from cryo-EM maps without additional sequence information by combining DeepTracer modeling with AlphaFold2 predictions.

Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms

This study determines the atomic structure of archaeal bundling pili from Pyrobaculum calidifontis, revealing structural and mechanistic similarities to bacterial biofilm components.

Viral origin of eukaryotic type IIA DNA topoisomerases

This study investigates the origin of eukaryotic type IIA DNA topoisomerases by analyzing phylogenetic relationships between viral and cellular homologs, finding that they likely originated from Nucleocytoviricota viruses.

Identification of a new Inovirus in the absence of bacterial infection in the human virome

The paper identifies a new Inovirus, RIP1, in the human virome without bacterial infection, showing its presence in multiple body sites.

Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses

The paper identifies plankton-infecting herpesvirus relatives in marine environments, revealing a new viral phylum with evolutionary links to both herpesviruses and giant viruses.

A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses

The paper reports a closed genome of Ca. Odinarchaeum and identifies related viruses, providing insights into Asgard archaea's virome and ecology.

Viruses of Asgard archaea

This study identifies three new viral families associated with Asgard archaea in deep-sea sediments, showing they are prokaryotic-like viruses with no clear evolutionary link to eukaryotic viruses.

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes

The paper presents 37 new genomes of haloarchaeal tailed viruses, expands their classification into 14 families, and explores their evolution and ecological distribution.

Metagenome-derived virus-microbe ratios across ecosystems

The paper estimates virus-to-microbe ratios using metagenomic data across ecosystems, finding viruses outnumber cells by ~13x in freshwater and ~2-4x in marine/saline plankton, but only ~2x in non-aquatic environments.