R. Miyazaki

Structure and function of bacterial YeeE-YeeD complex in thiosulfate uptake pathway

This study investigates the YeeE-YeeD complex in thiosulfate uptake, showing YeeD's role in transport and decomposition, and presents their structural interactions.

Critical residues of the antibiotic peptide LysM that inhibits lipid II flipping

This study identifies critical residues in the LysM protein that inhibit lipid II flipping by MurJ, using alanine-scanning mutagenesis.

The architecture of metabolic networks constrains the evolution of microbial resource hierarchies

This study uses genome-scale metabolic modeling to show that microbial metabolic hierarchies are constrained by central metabolism, limiting their evolutionary diversity.

Edge strand of Escherichia coli BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways

This study identifies how BepA interacts with immature LptD on the BAM complex to direct it to assembly or degradation pathways.

Fine interaction profiling of VemP and mechanisms responsible for its translocation-coupled arrest-cancelation

This study identifies interacting partners and mechanisms of VemP's translocation-coupled arrest-cancelation in Vibrio alginolyticus.

Reversible auto-inhibitory regulation of Escherichia coli metallopeptidase BepA for selective β-barrel protein degradation

This study investigates how the α9/H246 loop in BepA regulates its protease activity, revealing a histidine switch mechanism that controls degradation of misassembled LptD.

Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species

This study compares strain-level diversity in the gut microbiota of two closely related honey bee species, finding significant differences in functional gene content and diversity despite similar 16S rRNA phylotype overlap.

Transcriptome signature in E. coli under a prolonged starvation environment

This study identifies transcriptome changes in E. coli during long-term starvation, revealing common and distinct gene expression patterns compared to short-term stationary phase.

Dynamics of bacterial cell proliferation inhibited by specific proteins for effective horizontal transmission of the integrative and conjugative element ICEclc

The paper investigates how ParA and Shi proteins from ICEclc inhibit bacterial cell proliferation to facilitate horizontal gene transfer, revealing their mechanism and conservation across proteobacteria.