Biology subjects

Okura, R.

Publications and source records attributed to Okura, R..

6 recordsLinked to original sources

bioRxiv2026

Rapid enhancement of antibiotic resistance and divergent remodeling of gene expression in single cells of bacteria

Exposing bacterial cell populations to antibiotics often results in the emergence of descendants with enhanced resistance. Phenotypic heterogeneity and global physiological responses are thought to contribute to resistance evolution. However, identifying the specific stages of drug exposure where phenotypic heterogeneity and physiological responses play critical roles remains elusive. Using long-term single-cell lineage tracking of an Escherichia coli resistance model, here we reveal that resistance-enhanced cells emerge rapidly within a few generations in a clonal bacterial cell population under chloramphenicol (Cp) exposure and stably transmit the enhanced resistance for hundreds of generations in the presence of Cp. High expression of a resistance protein was advantageous during the initial period of drug exposure, but conferred only a marginal fitness advantage during the period of resistance enhancement. Transcriptomic profiles of resistance-enhanced cell populations were lineage-specific, suggesting that multiple gene expression states can support enhanced resistance. Altogether, these results suggest that an interplay between initial phenotypic heterogeneity and divergent remodeling of gene expression drives the rapid acquisition of enhanced antibiotic resistance.

microbiology↗

bioRxiv2024

Raman spectra identify heterogeneous vancomycin resistance and transcriptomes of Staphylococcus aureus

Staphylococcus aureus is a pathogenic bacterium that has caused multiple epidemics linked with the emergence of new antibiotic resistance. Vancomycin is the first-line antibiotic to treat methicillin-resistant S. aureus (MRSA) infections. However, several types of vancomycin-non-susceptible MRSA strains have been isolated from patients to date. Rapid assessment of their resistance levels and underlying molecular profiles is crucial for preventing their spread and counteracting resistance; however, the broad resistance spectrum and the diversity of genetic changes have impeded this practice. Here, we demonstrate that the vancomycin resistance levels of various MRSA strains can be determined using dimension-reduced Raman spectra obtained from single cells. The transcriptome profiles of the different strains can also be predicted from their dimensionally reduced Raman spectra by simple linear regression. This Raman-transcriptome correspondence allows us to map the transcriptome components onto dimension-reduced Raman space and characterize groups of genes associated with different phenotypes. Furthermore, single-cell Raman spectra predicted a cell strain with greater phenotypic heterogeneity, which was confirmed by single-cell growth analysis. Overall, our results demonstrate the efficacy of Raman spectroscopy in identifying resistant phenotypes, their associated gene expression features, and intrapopulation phenotypic heterogeneity.

microbiology↗

bioRxiv2022

Single mutation makes Escherichia coli an insect mutualist

We report an experimental system in which Escherichia coli evolves into an insect mutualist. When the essential gut symbiont of the stinkbug Plautia stali was replaced by E. coli, a few survivor insects exhibited specific localization and vertical transmission of E. coli. Through trans-generational maintenance with P. stali, several hyper-mutating E. coli lines independently evolved hosts high adult emergence and improved body color. Such "mutualistic" E. coli lines exhibited independent mutations disrupting the carbon catabolite repression (CCR) global transcriptional regulator. Each of the mutations reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that the single CCR mutations instantly make E. coli an insect mutualist. Our discovery uncovers that evolution of elaborate mutualism can proceed more easily and rapidly than conventionally envisaged.

evolutionary biology↗

bioRxiv2021

Actively growing cells are the predominant persisters in exponential phase of Escherichia coli

Bacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. Although the refractoriness of persistent cell populations has classically been attributed to growth-inactive cells generated before drug exposure, evidence is accumulating that actively growing cell fractions can also generate persister cells. However, single-cell characterization of persister cell history remains limited due to the extremely low frequencies of persisters. Here, we visualize the responses of over one million individual cells of wildtype Escherichia coli to lethal doses of antibiotics, sampling cells from different growth phases and culture media into a microfluidic device. We show that when cells sampled from exponentially growing populations were treated with ampicillin or ciprofloxacin, most persisters were growing before antibiotic treatment. Growing persisters exhibited heterogeneous survival dynamics, including continuous growth and fission with L-form-like morphologies, responsive growth arrest, or post-exposure filamentation. Incubating cells under stationary phase conditions increased both the frequency and the probability of survival of non-growing cells to ampicillin. Under ciprofloxacin, however, all persisters identified were growing before the antibiotic treatment, including samples from post-stationary phase culture. These results reveal diverse persister cell dynamics that depend on antibiotic types and pre-exposure history.

microbiology↗

bioRxiv2021

A unified framework for measuring selection on cellular lineages and traits

Intracellular states probed by gene expression profiles and metabolic activities are intrinsically noisy, causing phenotypic variations among cellular lineages. Understanding the adaptive and evolutionary roles of such variations requires clarifying their linkage to population growth rates. Extending a cell lineage statistics framework, here we show that a populations growth rate can be expanded by fitness cumulants of any cell lineage trait. The expansion enables quantifying the contribution of each fitness cumulant, such as variance and skewness, to population growth. We introduce a function that contains all the essential information of cell lineage statistics, including mean lineage fitness and selection strength. We reveal a relation between fitness heterogeneity and population growth rate response to perturbation. We apply the framework to experimental cell lineage data from bacteria to mammalian cells, revealing that third or higher-order cumulants contributions are negligible under constant growth conditions but could be significant in regrowing processes from growth-arrested conditions. Furthermore, we identify cellular populations in which selection leads to an increase of fitness variance among lineages. The framework assumes no particular growth models or environmental conditions, and is thus applicable to various biological phenomena for which phenotypic heterogeneity and cellular proliferation are important.

systems biology↗

bioRxiv2020

Scale invariance during bacterial reductive division observed by an extensive microperfusion system

In stable environments, cell size fluctuations are thought to be governed by simple physical principles, as suggested by recent finding of scaling properties. Here we show, using E. coli, that the scaling concept also rules cell size fluctuations under time-dependent conditions, even though the distribution changes with time. We develop a microfluidic device for observing dense and large bacterial populations, under uniform and switchable conditions. Triggering bacterial reductive division by switching to non-nutritious medium, we find that the cell size distribution changes in a specific manner that keeps its normalized form unchanged; in other words, scale invariance holds. This finding is underpinned by simulations of a model based on cell growth and intracellular replication. We also formulate the problem theoretically and propose a sufficient condition for the scale invariance. Our results emphasize the importance of intrinsic cellular replication processes in this problem, suggesting different distribution trends for bacteria and eukaryotes.

cell biology↗