Konstantin Severinov

This paper introduces an active learning method to discover PAMs for uncharacterized CRISPR-Cas9 orthologs without sequencing, reducing data requirements and validating it on known and novel Cas9 variants.

This study shows H-NS silences bacterial antiviral immunity by compacting chromatin, and its deletion enhances phage defense in E. coli.

This paper characterizes OLD, an abortive immunity protein, revealing its structure and activation mechanism in response to phage replication and DNA defects in RecBCD-compromised cells.

The paper identifies phages infecting E. coli HS, shows their resistance to restriction via modifications, and links phage infection to a Klebsiella-like capsule.

This study characterizes a Type V BREX defense system in Haloarcula hispanica and shows that two archaeal viruses evade it via a virion protein.

The paper identifies and characterizes a novel type V CRISPR-Cas system, Cas12r-CRISPR, encoded by Lalka phages in Thermus bacteria, showing its role in targeting mobile genetic elements.

This study characterizes SuCas9, a compact Cas9 ortholog from Streptococcus uberis, showing it can cleave DNA in vitro and function in human cells with a novel PAM sequence.

This study shows that plasmid copy number affects the expression dynamics and phage resistance of the CfrBI R-M system, with medium-copy plasmids providing the highest resistance.

The paper identifies AcrIE9 as an inhibitor of E. coli K12 Type IE CRISPR-Cas system through a census of anti-CRISPR proteins in Enterobacterales.

This study elucidates the molecular mechanism of BREX anti-phage immunity by showing how BrxX methyltransferase recognizes DNA and forms an immune complex to protect against phage infection.

The paper argues that the number of defense and counter-defense systems in the prokaryote-virus arms race is limited to around 10 due to metabolic and autoimmune costs.

The paper isolates and analyzes new phages infecting Thermus thermophilus from diverse hot springs, revealing both known relatives and novel phages with unique genetic features.

This study investigates how pseudoknot base pairing affects cotranscriptional structural switching in fluoride riboswitches, showing a critical wobble base pair is essential for function across different temperatures.

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

The paper shows that viral proteins activate PARIS-mediated tRNA degradation, and viral tRNAs rescue infection by preventing cleavage.

This study investigates the localization dynamics of two phage-encoded RNA polymerases during phiKZ infection, showing vRNAP is injected and excluded from the phage nucleus while nvRNAP is synthesized and localized within the nucleus.

This study benchmarks DNA isolation methods for marine metagenomics by evaluating eight kits across three sample types, focusing on quality, contamination, and community composition.

This study shows that CRISPR-Cas in E. coli is active and suppresses cryptic prophages through RNAi, preventing cell death and persister cell resuscitation.

The paper shows that TopoI interacts with RNA polymerase in E. coli to prevent R-loop formation by relaxing negative supercoiling during transcription.

This study elucidates how the AR9 bacteriophage's non-virion RNA polymerase recognizes uracil-containing promoters in the template strand of dsDNA through a unique structural mechanism.

The paper identifies two distinct transporters, BacA and YejABEF, that mediate the uptake of the peptide antibiotic phazolicin in Sinorhizobium meliloti, reducing resistance acquisition.

The paper develops ONT-cappable-seq to study phage transcription in Pseudomonas aeruginosa, revealing transcription start sites, terminators, and operon structures in LUZ7.

This study shows that AsCas12a can efficiently cleave target DNA using split crRNAs, with residual activity even when only the spacer is present.

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.

The paper discovers a new LAP antibiotic, phazolicin, which inhibits bacterial ribosomes in a species-specific manner by blocking the exit tunnel.

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.

The paper estimates the optimal number of spacers in CRISPR arrays that maximizes bacterial protection against viral attacks by balancing spacer diversity and effectiveness.

The paper demonstrates multiplex gene editing in mammalian cells and mouse brains using a single CRISPR array processed by Cpf1 without requiring additional factors.

This study characterizes C2c2, a CRISPR-Cas effector that uses an RNA guide to target and cleave RNA, showing its potential as a programmable RNA-targeting tool.