Kira S. Makarova

Diverse bacterial pattern recognition receptors sense the core phage proteome

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

Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses

This study identifies novel viruses from Hawaiian fumaroles using metagenomics, revealing new viral clades and ecological patterns.

YprA family helicases provide the missing link between diverse prokaryotic immune systems

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.

Ecological Determinants of Altruism in Prokaryote Antivirus Defense

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.

Beyond bacterial paradigms: uncovering the functional significance and first biogenesis machinery of archaeal lipoproteins

The paper identifies and characterizes archaeal lipoprotein biogenesis components, showing their essential role in archaeal cell physiology and revealing distinct enzymatic activities.

END nucleases: Antiphage defense systems targeting multiple hypermodified phage genomes

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.

Long range segmentation of prokaryotic genomes by gene age and functionality

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.

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.

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail

The paper identifies and characterizes two RNA polymerases in a thermophilic virus, showing their structural and functional differences and evolutionary origin.

Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems

The paper identifies CRISPR repeat-like RNA elements in CRISPR-Cas systems that function as regulatory guides, showing their prevalence in type I and V-A systems.

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

This study characterizes the RNA-guided nuclease-protease complex Cas7-11-Csx29, showing target RNA binding activates Csx29 to cleave Csx30, leading to cell death.

Structure and function of virion RNA polymerase of crAss-like phage

The paper characterizes the structure and function of a novel DNA-dependent RNA polymerase from a crAss-like phage, showing its role in phage gene transcription and structural similarity to eukaryotic RNA interference polymerases.

CRISPRIdentify: Identification of CRISPR arrays using machine learning approach

CRISPRIdentify uses machine learning to detect CRISPR arrays with reduced false positives and provides certainty scores for identified regions.

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

The paper expands the phylogenetic and metabolic diversity of Asgard archaea and suggests eukaryotes may have originated from an unknown ancestral lineage outside extant archaea.

Towards comprehensive characterization of CRISPR-linked genes

The paper develops a computational method to identify genes likely functionally linked to CRISPR-Cas systems, identifying 80 previously undetected candidate genes, many associated with membrane and signal transduction.