The E. coli Whole-Cell Modeling Project

EcoSal Plus ◽  
2021 ◽  
Author(s):  
Gwanggyu Sun ◽  
Travis A. Ahn-Horst ◽  
Markus W. Covert
Keyword(s):  
Computational Model ◽  
Model Organism ◽  
Current Version ◽  
Whole Cell ◽  
Content Type ◽  
E Coli ◽  
Cell Modeling

The Escherichia coli whole-cell modeling project seeks to create the most detailed computational model of an E. coli cell in order to better understand and predict the behavior of this model organism. Details about the approach, framework, and current version of the model are discussed.

scholarly journals Droplet- Rather than Aerosol-Mediated Dispersion Is the Primary Mechanism of Bacterial Transmission from Contaminated Hand-Washing Sink Traps

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Shireen M. Kotay ◽  
Rodney M. Donlan ◽  
Christine Ganim ◽  
Katie Barry ◽  
Bryan E. Christensen ◽  
...  
Keyword(s):  
Patient Care ◽  
Sampling Methods ◽  
Fluorescent Protein ◽  
Model Organism ◽  
Air Sampling ◽  
Multidrug Resistant ◽  
Hand Washing ◽  
Content Type ◽  
E Coli ◽  
Green Fluorescent

ABSTRACT An alarming rise in hospital outbreaks implicating hand-washing sinks has led to widespread acknowledgment that sinks are a major reservoir of antibiotic-resistant pathogens in patient care areas. An earlier study using green fluorescent protein (GFP)-expressing Escherichia coli (GFP-E. coli) as a model organism demonstrated dispersal from drain biofilms in contaminated sinks. The present study further characterizes the dispersal of microorganisms from contaminated sinks. Replicate hand-washing sinks were inoculated with GFP-E. coli, and dispersion was measured using qualitative (settle plates) and quantitative (air sampling) methods. Dispersal caused by faucet water was captured with settle plates and air sampling methods when bacteria were present on the drain. In contrast, no dispersal was captured without or in between faucet events, amending an earlier theory that bacteria aerosolize from the P-trap and disperse. Numbers of dispersed GFP-E. coli cells diminished substantially within 30 minutes after faucet usage, suggesting that the organisms were associated with larger droplet-sized particles that are not suspended in the air for long periods. IMPORTANCE Among the possible environmental reservoirs in a patient care environment, sink drains are increasingly recognized as a potential reservoir to hospitalized patients of multidrug-resistant health care-associated pathogens. With increasing antimicrobial resistance limiting therapeutic options for patients, a better understanding of how pathogens disseminate from sink drains is urgently needed. Once this knowledge gap has decreased, interventions can be engineered to decrease or eliminate transmission from hospital sink drains to patients. The current study further defines the mechanisms of transmission for bacteria that colonize sink drains.

scholarly journals Dissection of the Hydrogen Metabolism of the EnterobacteriumTrabulsiella guamensis: Identification of a Formate-Dependent and Essential Formate Hydrogenlyase Complex Exhibiting Phylogenetic Similarity to Complex I

2019 ◽  
Vol 201 (12) ◽  
Author(s):  
Ute Lindenstrauß ◽  
Constanze Pinske
Keyword(s):  
Fossil Fuels ◽  
Biochemical Characterization ◽  
Model Organism ◽  
Attractive Alternative ◽  
Hydrogen Metabolism ◽  
Content Type ◽  
E Coli ◽  
Formate Hydrogenlyase ◽  
Alternative Carbon Source

ABSTRACTTrabulsiella guamensisis a nonpathogenic enterobacterium that was isolated from a vacuum cleaner on the island of Guam. It has one H2-oxidizing Hyd-2-type hydrogenase (Hyd) and encodes an H2-evolving Hyd that is most similar to the uncharacterizedEscherichia coliformate hydrogenlyase (FHL-2Ec) complex. TheT. guamensisFHL-2 (FHL-2Tg) complex is predicted to have 5 membrane-integral and between 4 and 5 cytoplasmic subunits. We showed that the FHL-2Tgcomplex catalyzes the disproportionation of formate to CO2and H2. FHL-2Tghas activity similar to that of theE. coliFHL-1Eccomplex in H2evolution from formate, but the complex appears to be more labile upon cell lysis. Cloning of the entire 13-kbp FHL-2Tgoperon in the heterologousE. colihost has now enabled us to unambiguously prove FHL-2Tgactivity, and it allowed us to characterize the FHL-2Tgcomplex biochemically. Although the formate dehydrogenase (FdhH) genefdhFis not contained in the operon, the FdhH is part of the complex, and FHL-2Tgactivity was dependent on the presence ofE. coliFdhH. Also, in contrast toE. coli,T. guamensiscan ferment the alternative carbon source cellobiose, and we further investigated the participation of both the H2-oxidizing Hyd-2Tgand the H2-forming FHL-2Tgunder these conditions.IMPORTANCEBiological H2production presents an attractive alternative for fossil fuels. However, in order to compete with conventional H2production methods, the process requires our understanding on a molecular level. FHL complexes are efficient H2producers, and the prototype FHL-1Eccomplex inE. coliis well studied. This paper presents the first biochemical characterization of an FHL-2-type complex. The data presented here will enable us to solve the long-standing mystery of the FHL-2Eccomplex, allow a first biochemical characterization ofT. guamensis’s fermentative metabolism, and establish this enterobacterium as a model organism for FHL-dependent energy conservation.

scholarly journals Impact of Ralstonia eutropha's Poly(3-Hydroxybutyrate) (PHB) Depolymerases and Phasins on PHB Storage in Recombinant Escherichia coli

2014 ◽  
Vol 80 (24) ◽  
pp. 7702-7709 ◽  
Author(s):  
Jessica Eggers ◽  
Alexander Steinbüchel
Keyword(s):  
Escherichia Coli ◽  
Ralstonia Eutropha ◽  
Model Organism ◽  
Dry Weight ◽  
Growth Behavior ◽  
Carbon Limitation ◽  
Content Type ◽  
Phb Depolymerase ◽  
E Coli ◽  
The Impact

ABSTRACTThe model organism for polyhydroxybutyrate (PHB) biosynthesis,Ralstonia eutrophaH16, possesses multiple isoenzymes of granules coating phasins as well as of PHB depolymerases, which degrade accumulated PHB under conditions of carbon limitation. In this study, recombinantEscherichia coliBL21(DE3) strains were used to study the impact of selected PHB depolymerases ofR. eutrophaH16 on the growth behavior and on the amount of accumulated PHB in the absence or presence of phasins. For this purpose, 20 recombinantE. coliBL21(DE3) strains were constructed, which harbored a plasmid carrying thephaCABoperon fromR. eutrophaH16 to ensure PHB synthesis and a second plasmid carrying different combinations of the genes encoding a phasin and a PHB depolymerase fromR. eutrophaH16. It is shown in this study that the growth behavior of the respective recombinantE. colistrains was barely affected by the overexpression of the phasin and PHB depolymerase genes. However, the impact on the PHB contents was significantly greater. The strains expressing the genes of the PHB depolymerases PhaZ1, PhaZ2, PhaZ3, and PhaZ7 showed 35% to 94% lower PHB contents after 30 h of cultivation than the control strain. The strain harboringphaZ7reached by far the lowest content of accumulated PHB (only 2.0% [wt/wt] PHB of cell dry weight). Furthermore, coexpression of phasins in addition to the PHB depolymerases influenced the amount of PHB stored in cells of the respective strains. It was shown that the phasins PhaP1, PhaP2, and PhaP4 are not substitutable without an impact on the amount of stored PHB. In particular, the phasins PhaP2 and PhaP4 seemed to limit the degradation of PHB by the PHB depolymerases PhaZ2, PhaZ3, and PhaZ7, whereas almost no influence of the different phasins was observed ifphaZ1was coexpressed. This study represents an extensive analysis of the impact of PHB depolymerases and phasins on PHB accumulation and provides a deeper insight into the complex interplay of these enzymes.

scholarly journals Whole yeast model: what and why

2018 ◽  
Author(s):  
Pasquale Palumbo ◽  
Marco Vanoni ◽  
Federico Papa ◽  
Stefano Busti ◽  
Lilia Alberghina
Keyword(s):  
Life Science ◽  
Cell Model ◽  
Model Organism ◽  
Science Research ◽  
Cellular Functions ◽  
Cellular Division ◽  
Whole Cell ◽  
Proposed Model ◽  
Cell Modeling ◽  
Single Input

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.

scholarly journals Whole yeast model: what and why

2018 ◽  
Author(s):  
Pasquale Palumbo ◽  
Marco Vanoni ◽  
Federico Papa ◽  
Stefano Busti ◽  
Lilia Alberghina
Keyword(s):  
Life Science ◽  
Cell Model ◽  
Model Organism ◽  
Science Research ◽  
Cellular Functions ◽  
Cellular Division ◽  
Whole Cell ◽  
Proposed Model ◽  
Cell Modeling ◽  
Single Input

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.

scholarly journals Engineered Escherichia coli with Periplasmic Carbonic Anhydrase as a Biocatalyst for CO2Sequestration

2013 ◽  
Vol 79 (21) ◽  
pp. 6697-6705 ◽  
Author(s):  
Byung Hoon Jo ◽  
Im Gyu Kim ◽  
Jeong Hyun Seo ◽  
Dong Gyun Kang ◽  
Hyung Joon Cha
Keyword(s):  
Escherichia Coli ◽  
Carbonic Anhydrase ◽  
Bacterial Cell ◽  
Soluble Form ◽  
Promising Alternative ◽  
Whole Cell ◽  
Content Type ◽  
E Coli ◽  
Thermal Stability Of ◽  
Periplasmic Enzyme

ABSTRACTCarbonic anhydrase is an enzyme that reversibly catalyzes the hydration of carbon dioxide (CO2). It has been suggested recently that this remarkably fast enzyme can be used for sequestration of CO2, a major greenhouse gas, making this a promising alternative for chemical CO2mitigation. To promote the economical use of enzymes, we engineered the carbonic anhydrase fromNeisseria gonorrhoeae(ngCA) in the periplasm ofEscherichia coli, thereby creating a bacterial whole-cell catalyst. We then investigated the application of this system to CO2sequestration by mineral carbonation, a process with the potential to store large quantities of CO2.ngCA was highly expressed in the periplasm ofE. coliin a soluble form, and the recombinant bacterial cell displayed the distinct ability to hydrate CO2compared with its cytoplasmicngCA counterpart and previously reported whole-cell CA systems. The expression ofngCA in the periplasm ofE. coligreatly accelerated the rate of calcium carbonate (CaCO3) formation and exerted a striking impact on the maximal amount of CaCO3produced under conditions of relatively low pH. It was also shown that the thermal stability of the periplasmic enzyme was significantly improved. These results demonstrate that the engineered bacterial cell with periplasmicngCA can successfully serve as an efficient biocatalyst for CO2sequestration.

scholarly journals Development of a Continuous Bioconversion System Using a Thermophilic Whole-Cell Biocatalyst

2013 ◽  
Vol 79 (6) ◽  
pp. 1996-2001 ◽  
Author(s):  
Pham Huynh Ninh ◽  
Kohsuke Honda ◽  
Yukako Yokohigashi ◽  
Kenji Okano ◽  
Takeshi Omasa ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Membrane Filter ◽  
Host Cells ◽  
Continuous Reactor ◽  
Side Reactions ◽  
Electron Microscopic ◽  
Whole Cell ◽  
Content Type ◽  
Thermophilic Enzymes ◽  
E Coli

ABSTRACTThe heat treatment of recombinant mesophilic cells having heterologous thermophilic enzymes results in the denaturation of indigenous mesophilic enzymes and the elimination of undesired side reactions; therefore, highly selective whole-cell catalysts comparable to purified enzymes can be readily prepared. However, the thermolysis of host cells leads to the heat-induced leakage of thermophilic enzymes, which are produced as soluble proteins, limiting the exploitation of their excellent stability in repeated and continuous reactions. In this study,Escherichia colicells having the thermophilic fumarase fromThermus thermophilus(TtFTA) were treated with glutaraldehyde to prevent the heat-induced leakage of the enzyme, and the resulting cells were used as a whole-cell catalyst in repeated and continuous reactions. Interestingly, although electron microscopic observations revealed that the cellular structure of glutaraldehyde-treatedE. coliwas not apparently changed by the heat treatment, the membrane permeability of the heated cells to relatively small molecules (up to at least 3 kDa) was significantly improved. By applying the glutaraldehyde-treatedE. colihavingTtFTA to a continuous reactor equipped with a cell-separation membrane filter, the enzymatic hydration of fumarate to malate could be operated for more than 600 min with a molar conversion yield of 60% or higher.

scholarly journals Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

2014 ◽  
Vol 197 (1) ◽  
pp. 18-28 ◽  
Author(s):  
Maureen K. Thomason ◽  
Thorsten Bischler ◽  
Sara K. Eisenbart ◽  
Konrad U. Förstner ◽  
Aixia Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Sequencing ◽  
Transcriptional Start Site ◽  
Model Organism ◽  
Prediction Algorithm ◽  
Northern Analysis ◽  
Start Site ◽  
Content Type ◽  
E Coli ◽  
Antisense Rnas

While the model organismEscherichia colihas been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of theE. colitranscriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-typeE. coliand from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by therncandrnemutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts inE. coliand is easily accessible, together with the cDNA coverage plots, in an online genome browser.

scholarly journals Whole-Colony Modeling of Escherichia coli

2021 ◽  
Author(s):  
Christopher J. Skalnik ◽  
Eran Agmon ◽  
Ryan K. Spangler ◽  
Lee Talman ◽  
Jerry H. Morrison ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Molecular Diffusion ◽  
Efflux Pump ◽  
Current Source ◽  
Population Level ◽  
Whole Cell ◽  
Agent Based ◽  
E Coli ◽  
Cell Modeling

AbstractBacterial behavior is the outcome of both molecular mechanisms within each cell and interactions between cells in the context of their environment. Whereas whole-cell models simulate a single cell’s behavior using molecular mechanisms, agent-based models simulate many agents independently acting and interacting to generate complex collective phenomena. To synthesize agent-based and whole-cell modeling, we used a novel model integration software, called Vivarium, to construct an agent-based model of E. coli colonies where each agent is represented by a current source code snapshot from the E. coli Whole-Cell Modeling Project and interacts with other cells in a shared spatial environment. The result is the first “whole-colony” computational model that mechanistically links expression of individual proteins to a population-level phenotype. Simulated colonies exhibit heterogeneous effects on their environments, heterogeneous gene expression, and media-dependent growth. Extending the cellular model with mechanisms of antibiotic susceptibility and resistance, our model also suggested that variation in the expression level of the betalactamase AmpC, and not of the multi-drug efflux pump AcrAB-TolC, was the key mechanistic driver of survival in the presence of nitrocefin. We see this as a significant step forward in the creation of more comprehensive multi-scale models, and it broadens the range of phenomena that can be modeled in mechanistic terms.Author summaryThis work combines several models of molecular and physical processes that impact the physiology and behavior of the common microbe Escherichia coli into a multiscale model. Colonies comprised of multiple individual cells are simulated as they grow and divide—each with complex internal mechanisms, and with physical interactions and molecular diffusion in their environments. The integrative modeling methodology supports the addition of new submodels. The flexibility of this methodology is demonstrated by adding models of antibiotic resistance and simulating the colony’s response to antibiotic treatment.

scholarly journals Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris

2015 ◽  
Vol 198 (5) ◽  
pp. 867-876 ◽  
Author(s):  
Kieran B. Pechter ◽  
Larry Gallagher ◽  
Harley Pyles ◽  
Colin S. Manoil ◽  
Caroline S. Harwood
Keyword(s):  
Nitrogen Fixation ◽  
Caulobacter Crescentus ◽  
Essential Gene ◽  
Rhodopseudomonas Palustris ◽  
Model Organism ◽  
Growth Conditions ◽  
Essential Genes ◽  
Content Type ◽  
E Coli ◽  
Production Of Hydrogen

ABSTRACTRhodopseudomonas palustrisis an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility ofR. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacteriumCaulobacter crescentus, and 187 have essential gene homologs inEscherichia coli. There were 24R. palustrisgenes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essentialE. coligenes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism.R. palustriscells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in bothC. crescentusandR. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria likeE. coli.IMPORTANCEEssential genes in bacteria and other organisms are those absolutely required for viability.Rhodopseudomonas palustrishas served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes ofR. palustrisgrown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identifyR. palustrisgenes essential for viability under specialized growth conditions and also for survival under conditions of stress.

Sign in / Sign up

Export Citation Format

Share Document