Biology subjects

Mitarai, N.

Publications and source records attributed to Mitarai, N..

28 records · Page 2Linked to original sources

bioRxiv2021

Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism

Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes falls into a dormant state where the growth rates slow down by orders of magnitude. The dormant cells have unique characteristics: The metabolic activity is quite slow, and the dormant cells typically exhibit a high tolerance for a range of stresses, such as antibiotics applications. To reveal the origins of such heterogeneity of timescales, we constructed a kinetic model of Escherichia coli central carbon metabolism, including the dynamics of the energy currency molecules, and asked if perturbations of the metabolites concentrations lead to the distinct metabolic states. By numerically studying the relaxation dynamics, we found that the model robustly exhibits two qualitatively distinct relaxation dynamics depending on the initial conditions generated by the perturbations. In the first type, the concentrations of metabolites reach the steady-state quickly, resembling the growing dynamics. On the other hand, the other type of dynamics takes a much longer time to reach the steady-state, and during the relaxation, cell growth almost halts, reminding us of the dormant cells. In order to unveil the mechanism of distinct behaviors, we reduced the metabolic network model into a minimal model without losing the emergence of distinct dynamics. Analytical and numerical studies of the 2-variable minimal model revealed the necessary conditions for the distinct behavior, namely, the depletion of energy due to the futile cycle and its non-uniform impact on the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network. The result is consistent with the experimental reports that the dormant cells commonly exhibit low ATP levels and provides a possible explanation for the appearance of dormant cells that causes antibiotic persistence.

systems biology↗

bioRxiv2020

Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse

The vast majority of a bacterial population is quickly killed when treated with a lethal concentration of antibiotics. The time scale of this killing is often comparable with the bacterial generation time before addition of antibiotics. Yet, a small subpopulation typically survives for an extended period. However, the long-term killing dynamics of bacterial cells has not been fully quantified even in well-controlled laboratory conditions. We constructed a week-long killing assay and followed the survival fraction of Escherichia coli K12 exposed to a high concentration of ciprofloxacin. We found that long-term survivors were formed during exponential growth, with some cells surviving at least 7 days. The long-term dynamics contained at least three timescales, which greatly enhances predictions of the population survival time compared to the biphasic extrapolation from the short term behavior. Furthermore, we observed a surprisingly long memory effect of a brief carbon starvation pulse, which was dependent on the (p)ppGpp synthase relA. Specifically, one hour of carbon starvation prior to antibiotics exposure increased the surviving fraction by nearly 100-fold even after 4 days of ciprofloxacin treatment.

microbiology↗

bioRxiv2020

Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate

Stationary phase is the general term for the state a bacterial culture reaches when no further increase in cell number occurs due to the exhaustion of nutrients in the growth medium. Depending on the type of nutrient that is first depleted, the metabolic state of the stationary phase cells may vary greatly, and the subsistence strategies that best support cell survival may differ. As ribosomes play a central role in bacterial growth and energy expenditure, ribosome preservation is a key element of such strategies. To investigate the degree of ribosome preservation during long-term starvation, we compared the dynamics of ribosomal RNA (rRNA) levels of carbon-starved and phosphorus-starved Escherichia coli cultures for up to 28 days. The starved cultures contents of full-length 16S and 23S rRNA decreased exponentially and phosphorus starvation resulted in much more rapid rRNA degradation than carbon starvation. Bacterial survival kinetics were also quantified over the starvation period. Upon replenishment of the nutrient in question, carbon-starved cells resumed growth faster than cells starved for phosphate for the equivalent amount of time, and for both conditions, the lag time increased with the starvation time. While these results are in accordance with the hypothesis that cells with a larger ribosome pool recover more readily upon replenishment of nutrients, we also observed that the lag time kept increasing with increasing starvation time, also when the amount of rRNA per viable cell remained constant. ImportanceBacteria grow exponentially consuming nutrients, and then starve until the next nutrient is added. To elucidate the survival kinetics of the cells under starvation, we performed month-long, carbon and phosphorus starvation experiments of Escherichia coli monitoring ribosomal RNA levels and survival of the cells. The starved cultures concentration of ribosomal RNA dropped exponentially with time, and the speed of degradation was much quicker under the phosphorus starvation than the carbon starvation. We have also quantified the lag time, i.e., the time needed to resume growth when the starved cells are transferred into fresh media. The observation revealed that the lag time increases with starvation time and the phosphorus starvation has a greater impact on the increase of the lag time.

microbiology↗

bioRxiv2020

On phage adsorption to bacterial chains

Bacteria often arrange themselves in various spatial configurations which changes how they interact with their surroundings. In this paper, we investigate in silico how the structure of the bacterial arrangements influences the adsorption of bacteriophages. We quantify how the adsorption rate scales with the number of bacteria in the arrangement, and show that the adsorption rates for microcolonies (increasing with exponent [~]1/3) and bacterial chains (increasing with exponent [~]0.5 - 0.8) are substantially lower than for well-mixed bacteria (increasing with exponent 1). We further show that, after infection, the spatially clustered arrangements reduce the effective burst size by more than 50 % and cause substantial superinfections in a very short time interval after phage lysis. SIGNIFICANCEWhen bacteria forms clusters they substantially change their exposure to invading phages and other external agents from the well-mixed scenario. Despite this fact, much research has focused on and is focusing on using well-mixed bacteria. Understanding the kinetics of the spatial structures is paramount to developing robust analyses and theories of experimental results. We carefully investigate how the clusters lower the adsorption rate of external phages and how the clustering modifies the hit probabilities for the bacteria.

biophysics↗

bioRxiv2019

When to wake up? The optimal waking-up strategies for starvation-induced persistence

Prolonged lag time can be induced by starvation contributing to the antibiotic tolerance of bacteria. We analyze the optimal lag time to survive and grow the iterative and stochastic application of antibiotics. A simple model shows that the optimal lag time can exhibit a discontinuous transition when the severeness of the antibiotic application, such as the probability to be exposed the antibiotic, the death rate under the exposure, and the duration of the exposure, is increased. This suggests the possibility of reducing tolerant bacteria by controlled usage of antibiotics application. When the bacterial populations are able to have two phenotypes with different lag times, the fraction of the second phenotype that has different lag time shows a continuous transition. We then present a generic framework to investigate the optimal lag time distribution for total population fitness for a given distribution of the antibiotic application duration. The obtained optimal distributions have multiple peaks for a wide range of the antibiotic application duration distributions, including the case where the latter is monotonically decreasing. The analysis supports the advantage in evolving multiple, possibly discrete phenotypes in lag time for bacterial long-term fitness. Author summaryBacteria grow exponentially consuming nutrients, and then starve until the next nutrient is added. During the starvation, the cells enter dormancy and the cells become tolerant not only to starvation but also to other stressors. When nutrients are given to the starved cells, it takes some time before the cells fully "wake-up" and proliferate again. At first sight, it appears that the shorter this lag time the better for the bacteria. However, if the environment may contain another deadly stressor such as antibiotics, it may be better to "over-sleep" until the stressor is gone. Thus, they need to evolve to optimize their waking up strategy in the fluctuating environment. Here we have developed a theory for the optimal strategy for the repeated grow-and-starvation cycles with a fluctuating application of antibiotics. The optimal lag time exhibits a steep transition from immediate wake-up to over-sleep when the severeness of the antibiotics exceeds the threshold. The proposed general framework provides a way to predict the optimal distribution of lag time for various environmental fluctuation, and it may open for possible applications in administrating drug usage for interventions of pathogenic bacteria as well as cancer therapies where drug tolerance of dormant cells are observed.

systems biology↗

bioRxiv2019

Optimal strategies for pirate phage spreading

Pirate phages use the structural proteins encoded by unrelated helper phages to propagate. The best-studied example is the pirate P4 and helper P2 of coliphages, and it has been known that the Staphylococcus aureus pathogenicity islands (SaPIs) that can encode virulence factors act as pirate phages, too. When alone in the host, the pirate phages act as a prophage, but when the helper phage gene is also in the same host cell, the pirate phage has ability to exploit the helper phages structural proteins to produce pirate phage particles and spread, interfering with the helper phage production. The known helper phages in these systems are temperate phages. Interestingly, the interference of the pirate phage to the helper phage occurs in a different manner between the SaPI-helper system and the P4-P2 system. SaPIs cannot lyse a helper lysogen upon infection, while when a helper phage lyse a SaPI lysogen, most of the phage particles produced are the SaPI particles. On the contrary, in the P4-P2 system, a pirate phage P4 can lyse a helper P2 lysogen to produce mostly the P4 particles, while when P2 phage lyses a P4 lysogen, most of the produced phages are the P2 particles. Here, the consequences of these different strategies in the pirate and helper phage spreading among uninfected host is analyzed by using mathematical models. It is found that SaPIs strategy interferes with the helper phage spreading significantly more than the P4s strategy, because SaPI interferes with the helper phages main reproduction step, while P4 interferes only by forcing the helper lysogens to lyse. However, the interference is found to be weaker in the spatially structured environment than in the well-mixed environment. This is because, in the spatial setting, the system tends to self-organize so that the helper phages take over the front of propagation due to the need of helper phage for the pirate phage spreading. Competing interestsThe author declares no competing interest.

ecology↗

bioRxiv2018

Sustainability of spatially distributed bacteria-phage systems

Virulent phages can expose their bacterial hosts to devastating epidemics, in principle opening for a complete elimination of their hosts. Although experiments indeed confirm large reduction of susceptible bacteria, there is no reports of complete extinctions. We here address this phenomenon from the perspective of spatial organization of bacteria and how this can influence the final survival of them. By modeling the transient dynamics of bacteria and phages when they are introduced into an environment with finite resources, we quantify how the spatial separation of initial bacterial positions and the self-protection of bacteria growing in spherical colonies favor bacterial survival. This suggest that spatial structures on the millimeter scale plays an important role in maintaining microbial diversity.

ecology↗

bioRxiv2018

Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering

In type-I toxin-antitoxin (TA) systems, the action of growth-inhibiting toxin proteins is counteracted by the antitoxin small RNAs (sRNAs) that prevent the translation of toxin messenger RNAs (mRNAs). When a TA module is encoded on a plasmid, the short lifetime of antitoxin sRNA compared to toxin mRNAs mediates post-segregational killing (PSK) that contribute the plasmid maintenance, while some of the chromosomal encoded TA loci have been reported to contribute to persister formation in response to a specific upstream signal. Some of the well studied type-I TA systems such as hok/sok are known to have a rather complex regulatory mechanism. Transcribed full-length toxin mRNAs fold such that the ribosome binding site is not accessible and hence cannot be translated. The mRNAs are slowly processed by RNases, and the truncated mRNAs can be either translated or bound by antitoxin sRNA to be quickly degraded. We analyze the role of this extra processing by a mathematical model. We first consider the PSK scenario, and demonstrate that the extra processing compatibly ensures the high toxin expression upon complete plasmid loss, without inducing toxin expression upon acquisition of a plasmid or decrease of plasmid number to a non-zero number. We further show that the extra processing help filtering the transcription noise, avoiding random activation of toxins in transcriptionally regulated TA systems as seen in chromosomal ones. The present model highlights impacts of the slow processing reaction, offering insights on why the slow processing reactions are commonly identified in multiple type-I TA systems.

systems biology↗

bioRxiv2017

A Growing Microcolony can Survive and Support Persistent Propagation of Virulent Phages

Bacteria form colonies and secrete extracellular polymeric substances that surround the individual cells. These spatial structures are often associated with collaboration and quorum sensing between the bacteria. Here we investigate the mutual protection provided by spherical growth of a monoclonal colony during exposure to phages that proliferate on its surface. As a proof of concept we exposed growing colonies of Escherichia coli to a virulent mutant of phage P1. When the colony consists of less than ~ 50000 members it is eliminated, while larger initial colonies allow long-term survival because the growth of bacteria throughout the spherical colony exceeds the killing of bacteria on the surface. A mathematical model pinpoints how this critical colony size depends on key parameters in the phage infection cycle. Surprisingly, we predict that a higher phage adsorption rate would allow substantially smaller colonies to survive a virulent phage.\n\nSignificance StatementBacteria are repeatedly exposed to an excess of phages, and carry evidence of this in terms of multiple defense mechanisms encoded in their genome. In addition to molecular mechanisms, bacteria may exploit the defense of spatial refuges. Here we demonstrate how bacteria can limit the impact of a virulent phage attack by growing as a colony which only exposes its surface to phages. We identify a critical size of the initial colony, below which the phages entirely eliminates the colony, and above which the colony continues to grow despite the presence of phages. Our study suggests that coexistence of phages and bacteria is strongly influenced by the spatial composition of microcolonies of susceptible bacteria.

microbiology↗

bioRxiv2017

Existence and construction of large stable food webs

Ecological diversity is ubiquitous despite the restrictions imposed by competitive exclusion and apparent competition. To explain the observed richness of species in a given habitat, food web theory has explored nonlinear functional responses, self-interaction or spatial structure and dispersal -- model ingredients that have proven to promote stability and diversity. We here instead return to classical Lotka-Volterra equations, where species-species interaction is characterized by a simple product and spatial restrictions are ignored. We quantify how this idealization imposes constraints on coexistence and diversity for many species. To this end, we introduce the concept of free and controlled species and use this to demonstrate how stable food webs can be constructed by sequential addition of species. When we augment the resulting network by additional weak interactions we are able to show that it is possible to construct large food webs of arbitrary connectivity. Our model thus serves as a formal starting point for the study of sustainable interaction patterns between species.

ecology↗