Publications by authors named "Namiko Mitarai"

56 Publications

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

PLoS Comput Biol 2021 02 11;17(2):e1008655. Epub 2021 Feb 11.

The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1008655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904209PMC
February 2021

On Phage Adsorption to Bacterial Chains.

Biophys J 2020 11 29;119(9):1896-1904. Epub 2020 Sep 29.

Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Bacteria often arrange themselves in various spatial configurations, which changes how they interact with their surroundings. In this work, we investigate 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2020.09.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677248PMC
November 2020

Valine-Induced Isoleucine Starvation in K-12 Studied by Spike-In Normalized RNA Sequencing.

Front Genet 2020 5;11:144. Epub 2020 Mar 5.

Department of Biology, University of Copenhagen, Copenhagen, Denmark.

cells respond to a period of famine by globally reorganizing their gene expression. The changes are known as the stringent response, which is orchestrated by the alarmone ppGpp that binds directly to RNA polymerase. The resulting changes in gene expression are particularly well studied in the case of amino acid starvation. We used deep RNA sequencing in combination with spike-in cells to measure global changes in the transcriptome after valine-induced isoleucine starvation of a standard K12 strain. Owing to the whole-cell spike-in method that eliminates variations in RNA extraction efficiency between samples, we show that ribosomal RNA levels are reduced during isoleucine starvation and we quantify how the change in cellular RNA content affects estimates of gene regulation. Specifically, we show that standard data normalization relying on sample sequencing depth underestimates the number of down-regulated genes in the stringent response and overestimates the number of up-regulated genes by approximately 40%. The whole-cell spike-in method also made it possible to quantify how rapidly the pool of total messenger RNA (mRNA) decreases upon amino acid starvation. A principal component analysis showed that the first two components together described 69% of the variability of the data, underlining that large and highly coordinated regulons are at play in the stringent response. The induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS, and Lrp regulons. This underlines the notion that with the high resolution possible in deep RNA sequencing analysis, any different starvation method (e.g., nitrogen-deprivation, removal of an amino acid from an auxotroph strain, or valine addition to K12 strains) will produce measurable variations in the stress response produced by the cells to cope with the specific treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.00144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066862PMC
March 2020

Sustainability of spatially distributed bacteria-phage systems.

Sci Rep 2020 02 21;10(1):3154. Epub 2020 Feb 21.

Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

Virulent phages can expose their bacterial hosts to devastating epidemics, in principle leading to complete elimination of their hosts. Although experiments indeed confirm a large reduction of susceptible bacteria, there are 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 modelling the transient dynamics of bacteria and phages when they are introduced into an environment with finite resources, we quantify how time delayed lysis, the spatial separation of initial bacterial positions, and the self-protection of bacteria growing in spherical colonies favour bacterial survival. Our results suggest that spatial structures on the millimetre and submillimetre scale play an important role in maintaining microbial diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-59635-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035299PMC
February 2020

How pirate phage interferes with helper phage: Comparison of the two distinct strategies.

Authors:
Namiko Mitarai

J Theor Biol 2020 02 29;486:110096. Epub 2019 Nov 29.

The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, 2100-DK, Denmark. Electronic address:

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 SaPI's strategy interferes with the helper phage spreading significantly more than the P4's strategy, because SaPI interferes with the helper phage's 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtbi.2019.110096DOI Listing
February 2020

Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells.

Sci Rep 2019 04 15;9(1):6056. Epub 2019 Apr 15.

Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, København, Denmark.

Transient antibiotic treatment typically eradicates most sensitive bacteria except a few survivors called persisters. The second messenger (p)ppGpp plays a key role in persister formation in Escherichia coli populations but the underlying mechanisms have remained elusive. In this study we induced (p)ppGpp synthesis by modulating tRNA charging and then directly observed the stochastic appearance, antibiotic tolerance, and resuscitation of persister cells using live microscopy. Different physiological parameters of persister cells as well as their regularly growing ancestors and sisters were continuously monitored using fluorescent reporters. Our results confirmed previous findings that high (p)ppGpp levels are critical for persister formation, but the phenomenon remained strikingly stochastic without any correlation between (p)ppGpp levels and antibiotic tolerance on the single-cell level. We could not confirm previous notions that persisters exhibit markedly low concentrations of intracellular ATP or were linked to post-transcriptional effects of (p)ppGpp through the activation of small genetic elements known as toxin-antitoxin (TA) modules. Instead, we suggest that persister cell formation under regular conditions is driven by the transcriptional response to increased (p)ppGpp levels.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-42403-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465370PMC
April 2019

Gene Expression Changes with Minor Effects on the Population Average Have Major Effects on the Occurrence of Cells with Extreme Protein Concentrations.

mSphere 2019 01 30;4(1). Epub 2019 Jan 30.

The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark

The cell-to-cell heterogeneity in a bacterial population provides a rich response to environmental changes and robust survival of an isogenic population. Especially, the rare, extreme phenotypes can be important for survival under transient lethal conditions. We analyze the probability of having an extremely high or low protein level in a stochastic model of gene expression. The fraction of rare state cells defined as the cells in the tails of distributions is found to be highly sensitive to small changes of the mean protein level. The result highlights the importance of relatively weak changes to the mean for the occurrence of rare phenotypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00575-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354807PMC
January 2019

Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli.

J Mol Biol 2019 03 25;431(6):1088-1097. Epub 2019 Jan 25.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark. Electronic address:

We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The only difference between the two inserts was that the first base in one was moved to become the last base in the other, providing a difference in the reading frame, one of which had the biased codons typical for ribosomal protein genes and which previously was shown to be faster translated than average. This insert reduced the mRNA stability and increased premature transcription termination and together resulted in a hundred-fold difference in lacZ expression. We next generated lacZ variants with 7, 14 or 21 fast translated, ribosomal-type codons inserted into codon 13 of lacZ. This gave progressively more unstable mRNAs and also progressively increased transcription termination up to 90%. By modeling, based on estimates of the translation rate of individual codons, we can explain these observations by an increased susceptibility of the mRNA to degradation, determined by the length and degree of the early mRNA being uncovered by ribosomes. Thus, we suggest that the translation rate differences among the synonymous codons early in a gene enable a "velocity code" within the amino acid coding ability, where the translation rate differences encode the mRNA stability and the premature termination of the RNA polymerase.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2019.01.026DOI Listing
March 2019

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

Phys Biol 2019 01 4;16(2):026001. Epub 2019 Jan 4.

The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, 2100-DK, Denmark.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1478-3975/aaf3e3DOI Listing
January 2019

Dynamic Modeling of Indole Glucosinolate Hydrolysis and Its Impact on Auxin Signaling.

Front Plant Sci 2018 26;9:550. Epub 2018 Apr 26.

DynaMo Center, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.

Plants release chemicals to deter attackers. relies on multiple defense compounds, including indol-3-ylmethyl glucosinolate (I3G), which upon hydrolysis initiated by myrosinase enzymes releases a multitude of bioactive compounds, among others, indole-3-acetonitrile and indole-3-acetoisothiocyanate. The highly unstable isothiocyanate rapidly reacts with other molecules. One of the products, indole-3-carbinol, was reported to inhibit auxin signaling through binding to the TIR1 auxin receptor. On the contrary, the nitrile product of I3G hydrolysis can be converted by nitrilase enzymes to form the primary auxin molecule, indole-3-acetic acid, which activates TIR1. This suggests that auxin signaling is subject to both antagonistic and protagonistic effects of I3G hydrolysis upon attack. We hypothesize that I3G hydrolysis and auxin signaling form an incoherent feedforward loop and we build a mathematical model to examine the regulatory network dynamics. We use molecular docking to investigate the possible antagonistic properties of different I3G hydrolysis products by competitive binding to the TIR1 receptor. Our simulations reveal an uncoupling of auxin concentration and signaling, and we determine that enzyme activity and antagonist binding affinity are key parameters for this uncoupling. The molecular docking predicts that several I3G hydrolysis products strongly antagonize auxin signaling. By comparing a tissue disrupting attack - e.g., by chewing insects or necrotrophic pathogens that causes rapid release of I3G hydrolysis products - to sustained cell-autonomous I3G hydrolysis, e.g., upon infection by biotrophic pathogens, we find that each scenario gives rise to distinct auxin signaling dynamics. This suggests that plants have different defense versus growth strategies depending on the nature of the attack.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2018.00550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932361PMC
April 2018

Theory of invasion extinction dynamics in minimal food webs.

Phys Rev E 2018 Feb;97(2-1):022404

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts extinctions in terms of an alternating sequence of two basic processes: resource depletion by or competitive exclusion between consumers. We first propose a conceptual invasion extinction model (IEM) involving random fitness coefficients. We bolster this IEM by an analytical, recursive procedure for calculating idealized extinction cascades after any species addition and simulate the long-time evolution. Our procedure describes minimal food webs where each species interacts with only a single resource through the generalized Lotka-Volterra equations. For such food webs ex- tinction cascades are determined uniquely and the system always relaxes to a stable steady state. The dynamics and scale invariant species life time resemble the behavior of the IEM, and correctly predict an upper limit for trophic levels as observed in the field.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.97.022404DOI Listing
February 2018

Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology.

Mol Cell 2018 06 3;70(5):768-784. Epub 2018 Feb 3.

Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Electronic address:

Bacterial toxin-antitoxin (TA) modules are abundant genetic elements that encode a toxin protein capable of inhibiting cell growth and an antitoxin that counteracts the toxin. The majority of toxins are enzymes that interfere with translation or DNA replication, but a wide variety of molecular activities and cellular targets have been described. Antitoxins are proteins or RNAs that often control their cognate toxins through direct interactions and, in conjunction with other signaling elements, through transcriptional and translational regulation of TA module expression. Three major biological functions of TA modules have been discovered, post-segregational killing ("plasmid addiction"), abortive infection (bacteriophage immunity through altruistic suicide), and persister formation (antibiotic tolerance through dormancy). In this review, we summarize the current state of the field and highlight how multiple levels of regulation shape the conditions of toxin activation to achieve the different biological functions of TA modules.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2018.01.003DOI Listing
June 2018

Existence and construction of large stable food webs.

Phys Rev E 2017 Sep 8;96(3-1):032406. Epub 2017 Sep 8.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

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 return instead here 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 the sequential addition of species. The resulting food webs can reach dozens of species and generally yield nonrandom degree distributions in accordance with the constraints imposed through the assembly process. Our model thus serves as a formal starting point for the study of sustainable interaction patterns between species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.96.032406DOI Listing
September 2017

A growing microcolony can survive and support persistent propagation of virulent phages.

Proc Natl Acad Sci U S A 2018 01 19;115(2):337-342. Epub 2017 Dec 19.

Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen, Denmark;

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 to a virulent mutant of phage P1. When the colony consists of less than [Formula: see text]50,000 members it is eliminated, while larger initial colonies allow long-term survival of both phage-resistant mutants and, importantly, colonies of mostly phage-sensitive members. A mathematical model predicts that colonies formed solely by phage-sensitive bacteria can survive because the growth of bacteria throughout the colony exceeds the killing of bacteria on the surface and pinpoints how the critical colony size depends on key parameters in the phage infection cycle.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1708954115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777033PMC
January 2018

Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation.

Nucleic Acids Res 2017 Aug;45(14):8180-8189

Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark.

Toxin-antitoxin (TA) loci are widespread in bacteria including important pathogenic species. Recent studies suggest that TA systems play a key role in persister formation. However, the persistence phenotype shows only weak dependence on the number of TA systems, i.e. they are functionally redundant. We use a mathematical model to investigate the interaction of multiple TA systems in the switching between growth and persistence. We explore two scenarios: (i) TA systems are bistable and each TA system experiences its own noise and (ii) the noise in the level of common stress signal (e.g. (p)ppGpp) coordinates all TA systems simultaneously. We find that in the first scenario the exit from the persister state strongly depends on the number of TA systems. However in the second case, we could reproduce the weak dependence. The duration of the high (p)ppGpp state was found to be the key parameter for persistence. The (p)ppGpp-driven synchronized transition of all TA systems results in the redundancy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737467PMC
August 2017

Deterministic extinction by mixing in cyclically competing species.

Phys Rev E 2017 Mar 20;95(3-1):032318. Epub 2017 Mar 20.

Niels Bohr International Academy/Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.

We consider a cyclically competing species model on a ring with global mixing at finite rate, which corresponds to the well-known Lotka-Volterra equation in the limit of infinite mixing rate. Within a perturbation analysis of the model from the infinite mixing rate, we provide analytical evidence that extinction occurs deterministically at sufficiently large but finite values of the mixing rate for any species number N≥3. Further, by focusing on the cases of rather small species numbers, we discuss numerical results concerning the trajectories toward such deterministic extinction, including global bifurcations caused by changing the mixing rate.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.95.032318DOI Listing
March 2017

Characterization of phase transitions in a model ecosystem of sessile species.

Phys Rev E 2017 Mar 13;95(3-1):032409. Epub 2017 Mar 13.

Niels Bohr Institute, Copenhagen University, Blegdamsvej 17, 2100 Copenhagen, Denmark.

We consider a model ecosystem of sessile species competing for space. In particular, we consider the system introduced by Mathiesen et al. [J. Mathiesen, N. Mitarai, K. Sneppen, and A. Trusina, Phys. Rev. Lett. 107, 188101 (2011)PRLTAO0031-900710.1103/PhysRevLett.107.188101] where species compete according to a fixed interaction network with links determined by a Bernoulli process. In the limit of a small introduction rate of new species, the model exhibits a discontinuous transition from a high-diversity state to a low-diversity state as the interaction probability between species, γ, is increased from zero. Here we explore the effects of finite introduction rates and system size on the phase transition by utilizing efficient parallel computing. We find that the low state appears for γ>γ_{c}. As γ is increased further, the high state approaches the low state, suggesting the possibility that the two states merge at a high γ. We find that the fraction of time spent in the high state becomes longer with higher introduction rates, but the availability of the two states is rather insensitive to the value of the introduction rate. Furthermore, we establish a relation between the introduction rate and the system size, which preserves the probability for the system to remain in the high-diversity state.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.95.032409DOI Listing
March 2017

Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination.

Front Microbiol 2017 14;8:362. Epub 2017 Mar 14.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen Copenhagen, Denmark.

Protein production is controlled by ribosome binding to the messenger RNA (mRNA), quantified in part by the binding affinity between the ribosome and the ribosome binding sequence on the mRNA. Using the operon as model, Ringquist et al. (1992) found a more than 1,000-fold difference in protein yield when varying the Shine-Dalgarno sequence and its distance to the translation start site. Their proposed model accounted for this large variation by only a variation in the binding affinity and the subsequent initiation rate. Here we demonstrate that the decrease in protein yield with weaker ribosome binding sites in addition is caused by a decreased mRNA stability, and by an increased rate of premature transcription termination. Using different ribosome binding site sequences of the gene, we found that an approximately 100-fold span in protein expression could be subdivided into three mechanisms that each affected expression 3- to 6-fold. Our experiments is consistent with a two-step ribosome initiation model, in which occlusion of the initial part of the mRNA by a ribosome simultaneously protects the mRNA from both premature transcription termination and degradation: The premature termination we suggest is coupled to the absence of occlusion that allows binding of transcription termination factor, possibly Rho. The mRNA stability is explained by occlusion that prevents binding of the degrading enzymes. In our proposed scenario, a mRNA with lower translation initiation rate would at the same time be "hit" by an increased premature termination and a shorter life-time. Our model further suggests that the transcription from most if not all natural promoters is substantially influenced by premature termination.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2017.00362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5361652PMC
March 2017

Bifurcation of transition paths induced by coupled bistable systems.

J Chem Phys 2016 Jun;144(21):215102

Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example and show that its transition paths are bifurcating. We then derive a criterion to predict the bifurcation of transition paths in a generalized coupled bistable system. We confirm the validity of the theory for the example system by numerical simulation. We also demonstrate in the example system that, if the steady states of individual gene circuits are not changed by the coupling, the bifurcation pattern is not dependent on the number of gene circuits. We further show that the transition rate exponentially decreases with the number of gene circuits when the transition path does not bifurcate, while a bifurcation facilitates the transition by lowering the quasi-potential energy barrier.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.4953242DOI Listing
June 2016

Three is much more than two in coarsening dynamics of cyclic competitions.

Phys Rev E 2016 04 12;93:042408. Epub 2016 Apr 12.

Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.

The classical game of rock-paper-scissors has inspired experiments and spatial model systems that address the robustness of biological diversity. In particular, the game nicely illustrates that cyclic interactions allow multiple strategies to coexist for long-time intervals. When formulated in terms of a one-dimensional cellular automata, the spatial distribution of strategies exhibits coarsening with algebraically growing domain size over time, while the two-dimensional version allows domains to break and thereby opens the possibility for long-time coexistence. We consider a quasi-one-dimensional implementation of the cyclic competition, and study the long-term dynamics as a function of rare invasions between parallel linear ecosystems. We find that increasing the complexity from two to three parallel subsystems allows a transition from complete coarsening to an active steady state where the domain size stays finite. We further find that this transition happens irrespective of whether the update is done in parallel for all sites simultaneously or done randomly in sequential order. In both cases, the active state is characterized by localized bursts of dislocations, followed by longer periods of coarsening. In the case of the parallel dynamics, we find that there is another phase transition between the active steady state and the coarsening state within the three-line system when the invasion rate between the subsystems is varied. We identify the critical parameter for this transition and show that the density of active boundaries has critical exponents that are consistent with the directed percolation universality class. On the other hand, numerical simulations with the random sequential dynamics suggest that the system may exhibit an active steady state as long as the invasion rate is finite.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.93.042408DOI Listing
April 2016

Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases.

J Bacteriol 2016 07 27;198(14):1918-1926. Epub 2016 Jun 27.

Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark

Unlabelled: Escherichia coli regulates its metabolism to adapt to changes in the environment, in particular to stressful downshifts in nutrient quality. Such shifts elicit the so-called stringent response, coordinated by the alarmone guanosine tetra- and pentaphosphate [(p)ppGpp]. On sudden amino acid (aa) starvation, RelA [(p)ppGpp synthetase I] activity is stimulated by binding of uncharged tRNAs to a vacant ribosomal site; the (p)ppGpp level increases dramatically and peaks within the time scale of a few minutes. The decrease of the (p)ppGpp level after the peak is mediated by the decreased production of mRNA by (p)ppGpp-associated transcriptional regulation, which reduces the vacant ribosomal A site and thus constitutes negative feedback to the RelA-dependent (p)ppGpp synthesis. Here we showed that on sudden isoleucine starvation, this peak was higher in an E. coli strain that lacks the 10 known mRNase-encoding toxin-antitoxin (TA) modules present in the wild-type (wt) strain. This observation suggested that toxins are part of the negative-feedback mechanism to control the (p)ppGpp level during the early stringent response. We built a ribosome trafficking model to evaluate the fold increase in RelA activity just after the onset of aa starvation. Combining this with a feedback model between the (p)ppGpp level and the mRNA level, we obtained reasonable fits to the experimental data for both strains. The analysis revealed that toxins are activated rapidly, within a minute after the onset of starvation, reducing the mRNA half-life by ∼30%.

Importance: The early stringent response elicited by amino acid starvation is controlled by a sharp increase of the cellular (p)ppGpp level. Toxin-antitoxin module-encoded mRNases are activated by (p)ppGpp through enhanced degradation of antitoxins. The present work shows that this activation happens over a very short time scale and that the activated mRNases negatively affect the (p)ppGpp level. The proposed mathematical model of (p)ppGpp regulation through the mRNA level highlights the importance of several feedback loops in early (p)ppGpp regulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JB.00062-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936095PMC
July 2016

Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli.

J Bacteriol 2016 06 27;198(12):1783-93. Epub 2016 May 27.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University.

Unlabelled: Bacteria living in physically structured habitats are exposed heterogeneously to both resources and different types of phages. While there have been numerous experimental approaches to examine spatially distributed bacteria exposed to phages, there is little theory to guide the design of these experiments, interpret their results, or expand the inferences drawn to a broader ecological and evolutionary context. Plaque formation provides a window into understanding phage-bacterium interactions in physically structured populations, including surfaces, semisolids, and biofilms. We develop models to address the plaque dynamics for a temperate phage and its virulent mutants. The models are compared with phage λ-Escherichia coli system to quantify their applicability. We found that temperate phages gave an increasing number of gradually smaller colonies as the distance increased from the plaque center. For low-lysogen frequency this resulted in plaques with most of the visible colonies at an intermediate distance between the center and periphery. Using spot inoculation, where phages in excess of bacteria were inoculated in a circular area, we measured the frequency and spatial distribution of lysogens. The spot morphology of cII-negative (cII(-)) and cIII(-) mutants of phage λ displays concentric rings of high-density lysogenic colonies. The simplest of these ring morphologies was reproduced by including multiplicity of infection (MOI) sensitivity in lysis-lysogeny decisions, but its failure to explain the occasional observation of multiple rings in cIII(-) mutant phages highlights unknown features of this phage. Our findings demonstrated advantages of temperate phages over virulent phages in exploiting limited resources in spatially distributed microbial populations.

Importance: Phages are the most abundant organisms on earth, and yet little is known about how phages and bacterial hosts are influencing each other in density and evolution. Phages can be either virulent or temperate, a difference that is highlighted when a spatially structured bacterial population is infected. Phage λ is a temperate phage, with a capacity for dormancy that can be modified by single gene knockouts. The stochastic bias in the lysis-lysogeny decision's probability is reflected in plaque morphologies on bacterial lawns. We present a model for plaque morphology of both virulent and temperate phages, taking into account the underlying survival of bacterial microcolonies. It reproduces known plaque morphologies and speaks to advantages of temperate phages in a spatially structured environment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JB.00965-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886755PMC
June 2016

Food Web Assembly Rules for Generalized Lotka-Volterra Equations.

PLoS Comput Biol 2016 Feb 1;12(2):e1004727. Epub 2016 Feb 1.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734619PMC
February 2016

Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity.

Phys Rev E Stat Nonlin Soft Matter Phys 2015 Aug 13;92(2):022710. Epub 2015 Aug 13.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.

Transcriptional repression may cause transcriptional noise by a competition between repressor and RNA polymerase binding. Although promoter activity is often governed by a single limiting step, we argue here that the size of the noise strongly depends on whether this step is the initial equilibrium binding or one of the subsequent unidirectional steps. Overall, we show that nonequilibrium steps of transcription initiation systematically increase the cell-to-cell heterogeneity in bacterial populations. In particular, this allows also weak promoters to give substantial transcriptional noise.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.92.022710DOI Listing
August 2015

Coupled positive and negative feedbacks produce diverse gene expression patterns in colonies.

mBio 2015 Apr 7;6(2). Epub 2015 Apr 7.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark

Unlabelled: Formation of patterns is a common feature in the development of multicellular organism as well as of microbial communities. To investigate the formation of gene expression patterns in colonies, we build a mathematical model of two-dimensional colony growth, where cells carry a coupled positive-and-negative-feedback circuit. We demonstrate that the model can produce sectored, target (concentric), uniform, and scattered expression patterns of regulators, depending on gene expression dynamics and nutrient diffusion. We reconstructed the same regulatory structure in Escherichia coli cells and found gene expression patterns on the surface of colonies similar to the ones produced by the computer simulations. By comparing computer simulations and experimental results, we observed that very simple rules of gene expression can yield a spectrum of well-defined patterns in a growing colony. Our results suggest that variations of the protein content among cells lead to a high level of heterogeneity in colonies.

Importance: Formation of patterns is a common feature in the development of microbial communities. In this work, we show that a simple genetic circuit composed of a positive-feedback loop and a negative-feedback loop can produce diverse expression patterns in colonies. We obtained similar sets of gene expression patterns in the simulations and in the experiments. Because the combination of positive feedback and negative feedback is common in intracellular molecular networks, our results suggest that the protein content of cells is highly diversified in colonies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00059-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453545PMC
April 2015

Disturbance accelerates the transition from low- to high-diversity state in a model ecosystem.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Feb 4;89(2):022704. Epub 2014 Feb 4.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.

The effect of disturbance on a model ecosystem of sessile and mutually competitive species [Mathiesen et al., Phys. Rev. Lett. 107, 188101 (2011); Mitarai et al., Phys. Rev. E 86, 011929 (2012)] is studied. The disturbance stochastically removes individuals from the system, and the created empty sites are recolonized by neighboring species. We show that the stable high-diversity state, maintained by occasional cyclic species interactions that create isolated patches of metapopulations, is robust against small disturbance. We further demonstrate that finite disturbance can accelerate the transition from the low- to high-diversity state by helping the creation of small patches through diffusion of boundaries between species with standoff relations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.89.022704DOI Listing
February 2014

Phage and bacteria support mutual diversity in a narrowing staircase of coexistence.

ISME J 2014 Nov 23;8(11):2317-26. Epub 2014 May 23.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

The competitive exclusion principle states that phage diversity M should not exceed bacterial diversity N. By analyzing the steady-state solutions of multistrain equations, we find a new constraint: the diversity N of bacteria living on the same resources is constrained to be M or M+1 in terms of the diversity of their phage predators. We quantify how the parameter space of coexistence exponentially decreases with diversity. For diversity to grow, an open or evolving ecosystem needs to climb a narrowing 'diversity staircase' by alternatingly adding new bacteria and phages. The unfolding coevolutionary arms race will typically favor high growth rate, but a phage that infects two bacterial strains differently can occasionally eliminate the fastest growing bacteria. This context-dependent fitness allows abrupt resetting of the 'Red-Queen's race' and constrains the local diversity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2014.80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4992086PMC
November 2014

Speciation, diversification, and coexistence of sessile species that compete for space.

PLoS One 2014 12;9(5):e96665. Epub 2014 May 12.

Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.

Speciation, diversification, and competition between species challenge the stability of complex ecosystems. Laboratory experiments often focus on one or two species competing under conditions where they may grow exponentially. Field studies, in contrast, emphasize multi-species communities characterized by many types of ecological interactions. A general problem is to understand conditions that support a dynamically maintained coexistence of many species in an ecosystem over a long time span. In the present paper we propose a lattice model of multiple competing and evolving sessile species. When allowing the interspecies interactions to mutate, we obtain coexistence of many species in a complex ecosystem, provided that there is a cost for each interaction. The diversity reached by the model incorporating speciation is found to be substantially higher than in the case when entirely new species appear due to immigration from outside of the considered ecosystem. The species self-organize their spatial distribution through competitive interactions to create many patches, implicitly protecting each other from competitively superior species, and speciation in each patch leads the system to high diversity. We also show that species that exist a long time tend to have a relatively small population, as this allows them to avoid encounter with competitive invaders.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096665PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018333PMC
January 2015

Control of ribosome traffic by position-dependent choice of synonymous codons.

Phys Biol 2013 Oct 8;10(5):056011. Epub 2013 Oct 8.

Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark.

Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/1478-3975/10/5/056011DOI Listing
October 2013

Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy.

PLoS Comput Biol 2013 29;9(8):e1003174. Epub 2013 Aug 29.

Niels Bohr Institute/CMOL, University of Copenhagen, Copenhagen, Denmark.

Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined "conditional cooperativity". Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxin level, and then again transcription at high toxin level. Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for a wide range of parameters. We then demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757081PMC
February 2014
-->