E. coli

Unavoidable Disasters: the Hsp70 Chaperone Can Only Prevent Aggregation Over a Limited Time Span

The paper develops a computational model to show that Hsp70 chaperones only delay, not prevent, protein aggregation, depending on client-specific kinetic and thermodynamic properties.

Elucidation of Sequence Constraints for Protein Folding on the Ribosome

This study investigates how ribosome-mediated protein folding imposes sequence constraints by analyzing mutations in E. coli DHFR using deep mutational scanning and fluorogenic sensors.

Reversible decrease in swimming motility accompanies emergent β-lactam antibiotic resistance in Escherichia coli

This study shows that reduced swimming motility accompanies B-lactam antibiotic resistance in E. coli through efflux mechanisms, with motility recovery after antibiotic removal.

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

Inference of cell division parameters in bacteria under transient growth conditions

The paper infers cell division parameters in E. coli under nonsteady growth conditions using single-cell size trajectories and time-resolved models.

Decoupling Quantification and Identification for Label-Free Top-Down Proteomics Improves Proteome Coverage

This paper introduces a workflow that decouples quantification and identification in label-free top-down proteomics, improving proteome coverage and quantification precision.

Rapid environmental DNA detection with isothermal amplification methods: a comparison with the real-time quantitative PCR in the natterjack toad (Epidalea calamita).

This paper compares isothermal amplification methods (LAMP and RPA) with qPCR for detecting natterjack toad eDNA, finding RPA matches qPCR sensitivity while LAMP is less sensitive.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

Evaluating non-oxidative glycolysis using 13C metabolic flux analysis

This study evaluates the precision of 13C metabolic flux analysis using different glucose tracers to estimate non-oxidative glycolysis fluxes in E. coli.

Bioprocess Modeling Made Easy With Hybrax

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

Genomic features and instability of linezolid resistance in vancomycin-resistant Enterococcus faecalis ST525

This study examines genomic features and resistance mechanisms in vancomycin-resistant Enterococcus faecalis ST525 isolates, revealing variable linezolid resistance despite a single mutational mechanism.

Highly prevalent cargo genes of F plasmids harbored in pathogenic Escherichia coli

The paper identifies two groups of previously uncharacterized cargo genes in F plasmids of pathogenic E. coli, potentially contributing to virulence and antimicrobial targets.

RNA-triggered Cas12a2 antibacterial activity and resistance plasmid degradation

This study demonstrates that an inducible CRISPR/Cas12a2 system can reduce bacterial growth and plasmid DNA in vitro and in vivo by targeting resistance transcripts.

Dynamic allocation of MurJ coordinates bacterial growth and division

The paper shows that MurJ, a Lipid II flippase, dynamically coordinates bacterial growth and division by transiently capturing at division sites during septal synthesis.

Stochastic gene expression drives state switching and phenotypic heterogeneity in RNA repair

The paper shows stochastic RNA repair in E. coli leads to phenotypic heterogeneity and state switching in antibiotic responses.

Phage-Inducible Chromosomal Jumbo Islands (PICJIs) spreading antimicrobial resistance, host-adaptation factors and defense systems, a novel satellite family of nucleus-forming Chimalliviridae

The paper identifies PICJIs as large mobile genetic elements in E. coli and Salmonella that spread antimicrobial resistance and defense systems via a specific bacteriophage.

Massively parallel quantification and prediction of monomeric protein yield in Escherichia coli

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

Intrinsic timekeeping in Escherichia coli

This study shows Escherichia coli has an intrinsic timekeeping system that anticipates daily temperature cycles through rhythmic curli plaque formation.

Structural basis of ribosomal RNA repair by RtcB2

This study presents cryo-EM structures of RtcB2 bound to damaged E. coli 30S subunits, revealing how the enzyme recognizes and repairs ribosomal RNA.

A conserved thermodynamic signature links transcriptome organization to growth state

The paper develops a thermodynamic model linking transcriptome organization to growth state by analyzing RNA folding free energies across cell cycle and stress adaptation.

Functional analysis of small-molecule and protein binding domains using monomeric streptavidin-based two-component biosensors

The paper develops a biosensor platform using monomeric streptavidin to evaluate binding domains for small molecules and proteins, demonstrating ligand-dependent activation with biotinylated targets.

Helicase family proteins promote antiviral ADP-ribosylation of DNA purines

The paper identifies a new DarTG subfamily in E. coli that uses a helicase protein to promote ADP-ribosylation of DNA purines, expanding the known functions of helicases in bacterial immunity.

Chromosomally-Encoded Hok/Sok Toxin/Antitoxin SystemsInhibit Phage Infection

This study investigates the role of chromosomally-encoded Hok/Sok toxin/antitoxin systems in inhibiting phage infection in E. coli, finding that Hok proteins significantly reduce infection by BASEL phages.

Ultrasensitive Regulation in the Tryptophan System in Escherichia coli Provides Effective Noise Mitigation

This study analyzes the tryptophan system in E. coli to show how multiple feedback loops enable rapid response and noise mitigation.

Regulatory plasticity of the rdar biofilm morphotype in clinical uropathogenic Escherichia coli and its modulation by ciprofloxacin

This study identifies rdar biofilm formation in clinical uropathogenic E. coli and shows subinhibitory ciprofloxacin suppresses it in resistant isolates.

Local fractal dimension as an indicator of functional reorganization in molecular interaction networks

The paper introduces DIFFRACT, a framework that uses local fractal dimension changes in protein interaction networks to detect functional reorganization, showing its utility in identifying novel biological roles in RAVER1-deficient cells.

Molecular crowding differentially regulates magnetic field-dependent fluorescence, recovery kinetics, and photostability of the magnetosensitive protein MagLOV2

This study investigates how different molecular crowders affect the magnetic field-dependent fluorescence and recovery kinetics of MagLOV2 in E. coli lysate.

Probing bacterial fitness in virtual chemostats

The paper develops computational algorithms to accurately estimate bacterial population growth rates using single-cell models and applies them to study antibiotic response heterogeneity and chemotaxis effects.

Intra-DNA k-mer Conservation Patterns Encode Evolutionary Selection of Variants

The paper introduces kGain, a metric quantifying k-mer frequency shifts due to mutations, and shows it predicts adaptive potential across species and experimental systems.

YhdP forms an envelope-spanning phospholipid-binding bridge in complex with DedD

This study identifies YhdP as an envelope-spanning phospholipid-binding bridge that interacts with DedD to facilitate phospholipid transport in E. coli.