Yasuo Yoshikuni

CRISPRi-assisted E. coli strains increase success rate of burdensome construct cloning

The paper introduces CRISPRi-assisted E. coli strains to improve cloning success for burdensome genetic constructs by reducing metabolic burden during cloning.

A pooled screening approach reveals bacterial chemoreceptors for short-chain carboxylic acids

The paper identifies bacterial chemoreceptors for short-chain carboxylic acids using a pooled screening assay and structural analysis.

Crystal Structure of 3-Hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus

The paper reports the crystal structure of 3-Hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus, revealing its subdomain organization and substrate-binding state.

CRAGE-RB-PI-seq enables transcriptional profiling of rhizobacteria during plant-root colonization

The paper develops CRAGE-RB-PI-seq to profile rhizobacterial transcription during plant root colonization, revealing key transcriptional changes involved in immune evasion and colonization success.

A Novel Unorthodox Dimeric Primary Enoyl-CoA Reductase Structure

The paper presents the first dimeric ECR structure from Mesorhizobium metallidurans, revealing structural differences that may impact catalytic activity compared to tetrameric ECRs.

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy

This study uses third-harmonic generation microscopy to image plant roots and microbes in their natural environment without labels.

MAESTRO uncovers tandem paralog dynamics as a core driver of fungal stress adaptation

MAESTRO identifies tandem paralog copy number variation as a key mechanism for stress adaptation in Pichia kudriavzevii, linking it to drug resistance and environmental tolerance.

Deciphering the altered conformational states of bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

The paper determines ambient temperature structures of the bifunctional Nmar_1308 enzyme from Nitrosopumilus maritimus, revealing new conformational dynamics relevant to synthetic biology.

Multi-substrate specificity shaped the complex evolution of the aminotransferase family across the tree of life

The paper traces the evolutionary history of aminotransferases across species, revealing their substrate promiscuity and how it shaped nitrogen metabolic networks.

Synthetic genomes unveil the effects of synonymous recoding

This study uses synthetic genomes to investigate how synonymous codon recoding affects organismal fitness and develops a workflow to overcome lethal effects of codon swaps.

Functional plasticity of HCO3- uptake and CO2 fixation in Cupriavidus necator H16

This study investigates the functional plasticity of HCO3- uptake and CO2 fixation in C. necator H16 by testing endogenous and heterologous genes, showing that DIC transporters can support autotrophic growth and higher cell densities.

Proteome capacity constraints favor respiratory ATP generation

The paper shows mitochondrial respiration is more proteome-efficient than aerobic glycolysis in yeast and mammals, with flexibility arising from maintaining a fermentation-capable proteome.

Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica

The paper validates genome-wide CRISPR-Cas9 function in Yarrowia lipolytica by quantifying sgRNA efficiency and identifying high-efficiency guides for 94% of genes.