A5011153767- Microbial Metabolic Engineering and Bioproduction
- Evolution and Genetic Dynamics
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Biofuel production and bioconversion
- Antibiotic Resistance in Bacteria
- Evolutionary Game Theory and Cooperation
- Enzyme Structure and Function
- Microbial Community Ecology and Physiology
- Fungal and yeast genetics research
- Probiotics and Fermented Foods
- Enzyme Catalysis and Immobilization
- Diverse Topics in Contemporary Research
- Marine and Coastal Research
- Bacteriophages and microbial interactions
- GABA and Rice Research
- Gut microbiota and health
- thermodynamics and calorimetric analyses
- Biochemical Acid Research Studies
- Ion channel regulation and function
- Pharmacogenetics and Drug Metabolism
- Educational Systems and Policies
- Mycobacterium research and diagnosis
RIKEN Center for Biosystems Dynamics Research
2018-2024
Hokkaido University
2022-2024
Forschungszentrum Jülich
2021-2022
Tokyo Institute of Technology
2009-2018
Research Institute of Innovative Technology for the Earth
2015-2018
University of Cologne
2012-2014
Abstract Understanding the constraints that shape evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation evolutionary lacking. Here, we perform high-throughput laboratory Escherichia coli under addition 95 antibacterial chemicals quantified transcriptome, resistance, genomic profiles evolved strains. Utilizing machine learning techniques, analyze phenotype–genotype data identified low...
The fitness landscape represents the complex relationship between genotype or phenotype and under a given environment, structure of which allows explanation prediction evolutionary trajectories. Although previous studies have constructed landscapes by comprehensively studying mutations in specific genes, high dimensionality genotypic changes prevents us from developing capable predicting evolution for whole cell. Herein, we address this problem inferring phenotype-based antibiotic resistance...
Targeted gene editing can be achieved using CRISPR/Cas9-assisted recombineering. However, high-efficiency requires careful optimization for each locus to modified which tedious and time-consuming. In this work, we developed a simple, fast cheap method the Editing Assembly of SYnthetic operons recombineering (EASY-CRISPR) in Escherichia coli. Highly efficient different constitutive elements by set optimized guide RNAs single- or double-stranded DNA repair templates carrying relatively short...
The Corynebacterium glutamicum NCgl1221 mechanosensitive channel mediates l-glutamate secretion by sensing changes in membrane tension caused treatments such as biotin limitation and penicillin. protein has an N-terminal domain (1–286 a.a.) homologous to the Escherichia coli MscS a long C-terminal (287–533 of unknown function. In order investigate role secretion, we constructed series C-terminally truncated mutants NCgl1221. We found that domain, E. MscS, retained ability cause response...
We previously reported that the Corynebacterium glutamicum RNase E/G encoded by rneG gene (NCgl2281) is required for 5' maturation of 5S rRNA. In search intracellular target RNAs other than rRNA precursor, we detected amount isocitrate lyase, an enzyme glyoxylate cycle, increased in knockout mutant cells grown on sodium acetate as sole carbon source. Rifampin chase experiments showed half-life aceA mRNA was about 4 times longer wild type. Quantitative real-time PCR analysis also confirmed...
Summary The Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant (Δ rnc mutant) showed elongated cell shape, and presence several lines on surface, indicating a required for maintaining normal morphology in C. . level mraZ mRNA was increased, whereas cgR_1596 encoding putative wall hydrolase ftsEX were decreased Δ mutant. half‐life significantly prolonged pnp strains. This indicated that degradation performed by 3′‐to‐5′...
Abstract Antibiotic treatment generally results in the selection of resistant bacterial strains, and dynamics resistance evolution is dependent on complex interactions between cellular components. To better characterize mechanisms antibiotic evaluate its dependence gene regulatory networks, we performed systematic laboratory Escherichia coli strains with single-gene deletions 173 transcription factors under three different antibiotics. This resulted identification several genes whose...
Abstract Drug-resistant tuberculosis (TB) is a growing public health problem. There an urgent need for information regarding cross-resistance and collateral sensitivity relationships among drugs the genetic determinants of anti-TB drug resistance developing strategies to suppress emergence drug-resistant pathogens. To identify mutations that confer in Mycobacterium species, we performed laboratory evolution nonpathogenic smegmatis , which closely related against ten drugs. Next, whole-genome...
Co-culture is a promising way to alleviate metabolic burden by dividing the pathways into several modules and sharing conversion processes with multiple strains. Since an intermediate passed from donor recipient via extracellular environment, it inevitably diluted. Therefore, enhancing consumption rate important for increasing target productivity. In present study, we demonstrated enhancement of mevalonate in Escherichia coli adaptive laboratory evolution applied evolved strain isoprenol...
The oxidation of NADH with the concomitant reduction a quinone is crucial step in metabolism respiring cells. In this study, we analyzed relevance three different systems actinobacterial model organism Corynebacterium glutamicum by characterizing defined mutants lacking non-proton-pumping dehydrogenase Ndh (Δ ndh ) and/or one alternative NADH-oxidizing enzymes, L -lactate LdhA ldhA and malate Mdh mdh ). Together menaquinone-dependent LldD malate:quinone oxidoreductase Mqo, LdhA-LldD Mdh-Mqo...
has been applied for the industrial production of various metabolites, such as amino acids. To understand biosynthesis membrane protein in this bacterium, we investigated process signal recognition particle (SRP) assembly. SRP is found all three domains life and plays an important role insertion proteins. RNA initially transcribed precursor molecules; however, relatively little known about its maturation. In
Corynebacterium glutamicum is the major host for industrial production of amino acids and has become one best studied model organisms in microbial biotechnology. Rational strain construction led to an improvement producer strains a variety novel with broad substrate product spectrum. A key factor success these approaches detailed knowledge transcriptional regulation C. glutamicum. Here, we present large compendium 927 manually curated microarray-based profiles wild-type engineered detecting...
The Corynebacterium glutamicum NCgl2281 gene encodes an RNase E/G family endoribonuclease having additional N-terminal domain of unknown function. In this study, we constructed plasmids expressing the full length (FL) and N-terminally truncated form (ΔN) examined their complementation ability as to Escherichia coli rng::cat rne-1 mutations. Both FL- ΔN-NCgl2281 rescued defects caused by mutation, i.e., accumulation 16S rRNA precursor, overproduction AdhE protein, growth inhibition on M9...
The Corynebacterium glutamicum R grtA (cgR_2936), grtB (cgR_2934) and grtC (cgR_2933) genes were identified as paralogs encoding glutamine-rich toxic proteins. We also a new antisense small RNA AsgR (antisense sRNA for grtA) that overlaps the 3' end of gene. Single over-expressions grtA, resulted in complete inhibition Escherichia coli cell growth. This growth was rescued by co-expression AsgR. Similar effects observed C. glutamicum, although toxicities these proteins moderate. Inhibition...