scholarly journals Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

2008 ◽  
Vol 24 (18) ◽  
pp. 2044-2050 ◽  
Author(s):  
Markus W. Covert ◽  
Nan Xiao ◽  
Tiffany J. Chen ◽  
Jonathan R. Karr
Keyword(s):  
Escherichia Coli ◽  
Differential Equations ◽  
Ordinary Differential Equations ◽  
Single Gene ◽  
Supplementary Information ◽  
Wild Type ◽  
Flux Balance ◽  
Transcriptional Regulatory ◽  
The Individual ◽  
Gene Perturbation

AbstractMotivation: The effort to build a whole-cell model requires the development of new modeling approaches, and in particular, the integration of models for different types of processes, each of which may be best described using different representation. Flux-balance analysis (FBA) has been useful for large-scale analysis of metabolic networks, and methods have been developed to incorporate transcriptional regulation (regulatory FBA, or rFBA). Of current interest is the integration of these approaches with detailed models based on ordinary differential equations (ODEs).Results: We developed an approach to modeling the dynamic behavior of metabolic, regulatory and signaling networks by combining FBA with regulatory Boolean logic, and ordinary differential equations. We use this approach (called integrated FBA, or iFBA) to create an integrated model of Escherichia coli which combines a flux-balance-based, central carbon metabolic and transcriptional regulatory model with an ODE-based, detailed model of carbohydrate uptake control. We compare the predicted Escherichia coli wild-type and single gene perturbation phenotypes for diauxic growth on glucose/lactose and glucose/glucose-6-phosphate with that of the individual models. We find that iFBA encapsulates the dynamics of three internal metabolites and three transporters inadequately predicted by rFBA. Furthermore, we find that iFBA predicts different and more accurate phenotypes than the ODE model for 85 of 334 single gene perturbation simulations, as well for the wild-type simulations. We conclude that iFBA is a significant improvement over the individual rFBA and ODE modeling paradigms.Availability: All MATLAB files used in this study are available at http://www.simtk.org/home/ifba/.Contact: [email protected] information: Supplementary data are available at Bioinformatics online.

scholarly journals 3-Point Block Methods for Direct Integration of General Second-Order Ordinary Differential Equations

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
J. O. Ehigie ◽  
S. A. Okunuga ◽  
A. B. Sofoluwe
Keyword(s):  
Differential Equations ◽  
Ordinary Differential Equations ◽  
Absolute Stability ◽  
Second Order ◽  
Stability And Convergence ◽  
Block Methods ◽  
Good Region ◽  
The Stability ◽  
The Individual ◽  
Region Of Absolute Stability

A Multistep collocation techniques is used in this paper to develop a 3-point explicit and implicit block methods, which are suitable for generating solutions of the general second-order ordinary differential equations of the form . The derivation of both explicit and implicit block schemes is given for the purpose of comparison of results. The Stability and Convergence of the individual methods of the block schemes are investigated, and the methods are found to be 0-stable with good region of absolute stability. The 3-point block schemes derived are tested on standard mechanical problems, and it is shown that the implicit block methods are superior to the explicit ones in terms of accuracy.

scholarly journals Transmission Ratio Distortion Due to the bl Gene in Table Beet

2001 ◽  
Vol 126 (3) ◽  
pp. 340-343 ◽  
Author(s):  
Diane Austin ◽  
I.L. Goldman
Keyword(s):  
Single Gene ◽  
Recessive Gene ◽  
Segregation Ratio ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Wild Type ◽  
Gene Model ◽  
Male Gametes ◽  
Ratio Distortion ◽  
The Individual

The bl gene conditions a blotchy phenotype (irregular sectors of red and white root color) in table beet (Beta vulgaris ssp. vulgaris). Segregation of the bl gene was found to be consistent with a single recessive gene, however, some evidence for a departure from a single gene model was observed when blbl plants were used as females. In this report, segregation of the bl gene was examined in greater detail in 10 F2 populations derived from crosses of red blotchy-rooted females (genotype blbl, denoted blotchy) with red-rooted males (BlBl, denoted red,), and 10 F2 populations derived from the reciprocal cross. In blbl × BlBl crosses, the proportion of red-rooted progeny was greater than 0.75 in seven of the crosses, and was significantly greater (P = 0.005) in three crosses. A test for heterogeneity was significant, indicating that the proportion of red-rooted progeny differed significantly in these 10 crosses. In BlBl × blbl crosses, the proportion of red-rooted progeny was <0.75 in seven of the crosses and there were no significant departures from the expected 3:1 ratio in any of the individual crosses. However, a pooled estimate of the segregation ratio showed a significant (P < 0.01) departure from the 3:1 ratio (pooled estimate = 0.71). These data demonstrate transmission ratio distortion at the bl locus when blbl plants are used as both females and males in matings with wild type plants, but the degree of distortion is greater when blbl plants are used as females. Ratio distortion in such crosses may be due to a variety of factors, including increased transmission of the bl gene through female or male gametes depending on the direction of the cross, reduced fitness of maternally derived blbl progeny, epigenetic phenomena, increased fitness of paternally derived blbl progeny, or linkage of the bl gene to viability genes.

scholarly journals A palette of fluorophores that are differentially accumulated by wild-type and mutant strains of Escherichia coli: surrogate ligands for profiling bacterial membrane transporters

Microbiology ◽  
2021 ◽  
Author(s):  
Jesus Enrique Salcedo-Sora ◽  
Srijan Jindal ◽  
Steve O'Hagan ◽  
Douglas B. Kell
Keyword(s):  
Escherichia Coli ◽  
Fluorescent Dyes ◽  
Efflux Pump ◽  
Gene Knockout ◽  
Single Gene ◽  
Wild Type ◽  
Efflux Pump Inhibitor ◽  
Content Type ◽  
Effects Of Ph ◽  
Small Collection

Our previous work demonstrated that two commonly used fluorescent dyes that were accumulated by wild-type Escherichia coli MG1655 were differentially transported in single-gene knockout strains, and also that they might be used as surrogates in flow cytometric transporter assays. We summarize the desirable properties of such stains, and here survey 143 candidate dyes. We eventually triage them (on the basis of signal, accumulation levels and cost) to a palette of 39 commercially available and affordable fluorophores that are accumulated significantly by wild-type cells of the ‘Keio’ strain BW25113, as measured flow cytometrically. Cheminformatic analyses indicate both their similarities and their (much more considerable) structural differences. We describe the effects of pH and of the efflux pump inhibitor chlorpromazine on the accumulation of the dyes. Even the ‘wild-type’ MG1655 and BW25113 strains can differ significantly in their ability to take up such dyes. We illustrate the highly differential uptake of our dyes into strains with particular lesions in, or overexpressed levels of, three particular transporters or transporter components (yhjV, yihN and tolC). The relatively small collection of dyes described offers a rapid, inexpensive, convenient and informative approach to the assessment of microbial physiology and phenotyping of membrane transporter function.

ISOLEMENT ET CHARACTÉRISATION DE MUTANTS SENSIBLES OU RÉSISTANTS À L'OZONE CHEZESCHERICHIA COLIB

1982 ◽  
Vol 24 (5) ◽  
pp. 593-600 ◽  
Author(s):  
L. Poliquin ◽  
C. Hamelin ◽  
Y. S. Chung
Keyword(s):  
Escherichia Coli ◽  
Single Gene ◽  
Dna Lesions ◽  
The Other ◽  
Wild Type ◽  
Ozone Sensitivity ◽  
Other Hand ◽  
Radio Sensitivity ◽  
Escherichia Coli B

Escherichia coli B strains, either more sensitive or resistant to ozone than wild-type (OZsor OZr), were obtained after mutagenesis. OZsstrains carrying a mutation in ozrA or orzB, two genes located on both sides of malB, appeared as phenotypically different with regards to radio-sensitivity and cellular filamentation. OZrstrains, on the other hand, probably carry an allele of ozrA but were radioresistant and divided normally even with induction. A single gene (ozrA) thus seems to determine three levels of sensitivity to ozone, sensitivity to radiation and cellular filamentation in this organism. The possible involvement of a specific endonuclease in the repair of ozone-induced DNA lesions is considered.

Phenotypic characterization of overexpression or deletion of the Escherichia coli crcA, cspE and crcB genes

Microbiology ◽  
2003 ◽  
Vol 149 (8) ◽  
pp. 2107-2117 ◽  
Author(s):  
Olivier Sand ◽  
Monica Gingras ◽  
Nancy Beck ◽  
Christine Hall ◽  
Nancy Trun
Keyword(s):  
Escherichia Coli ◽  
Phenotypic Characterization ◽  
Temperature Sensitive ◽  
Wild Type ◽  
Topoisomerase Iv ◽  
Fold Induction ◽  
The Individual ◽  
K 12 ◽  
Fold Activation

The authors have previously shown that overexpression of the Escherichia coli K-12 crcA, cspE and crcB genes protects the chromosome from decondensation by camphor. In this study they examine the phenotypic consequences of deleting or overexpressing crcA, cspE and crcB. Overexpressing crcA, cspE and crcB increases supercoiling levels of plasmids in wild-type cells and in temperature-sensitive (Ts) gyrase mutants, suppresses the sensitivity of gyrase and topoisomerase IV (topo IV) Ts mutants to nalidixic acid, makes gyrase and topo IV Ts mutants more resistant to camphor and corrects the nucleoid morphology defects in topo IV Ts mutants. Overexpression of crcA, cspE and crcB results in a slight (2·2-fold) activation of the rcsA gene. Deleting crcA, cspE and crcB is not lethal to cells but results in an increase in sensitivity to camphor. Deletion of crcA, cspE and crcB exacerbates the nucleoid morphology defects of the topo IV Ts mutants. When the individual crcA, cspE or crcB genes were tested for their effects on camphor resistance and regulation of rcsA, cspE alone conferred 10-fold camphor resistance and 1·7-fold activation of rcsA. These activities were augmented when crcB was overexpressed with cspE (100-fold camphor resistance and 2·1-fold induction of rcsA).

scholarly journals Effects of bfp Mutations on Biogenesis of Functional Enteropathogenic Escherichia coli Type IV Pili

2000 ◽  
Vol 182 (9) ◽  
pp. 2498-2506 ◽  
Author(s):  
Ravi P. Anantha ◽  
Kelly D. Stone ◽  
Michael S. Donnenberg
Keyword(s):  
Escherichia Coli ◽  
Outer Membrane ◽  
Signal Sequence ◽  
Outer Membrane Proteins ◽  
Laboratory Strain ◽  
Type Iv Pili ◽  
Host Cells ◽  
Wild Type ◽  
Type Iv ◽  
The Individual

ABSTRACT Enteropathogenic Escherichia coli expresses a type IV fimbria known as the bundle-forming pilus (BFP) that is required for autoaggregation and localized adherence (LA) to host cells. A cluster of 14 genes is sufficient to reconstitute BFP biogenesis in a laboratory strain of E. coli. We have undertaken a systematic mutagenesis of the individual genes to determine the effect of each mutation on BFP biogenesis and LA. Here we report the construction and analysis of nonpolar mutations in six genes of thebfp cluster, bfpG, bfpB,bfpC, bfpD, bfpP, andbfpH, as well as the further analysis of a previously described bfpA mutant strain that is unable to express bundlin, the pilin protein. We found that mutations inbfpB, which encodes an outer membrane protein;bfpD, which encodes a putative nucleotide-binding protein; and bfpG and bfpC, which do not have sequence homologues in other type IV pilus systems, do not affect prebundlin expression or processing but block both BFP biogenesis and LA. The mutation in bfpP, the prepilin peptidase gene, does not affect prebundlin expression but blocks signal sequence cleavage of prebundlin, BFP biogenesis, and LA. The mutation in bfpH, which is predicted to encode a lytic transglycosylase, has no effect on prebundlin expression, prebundlin processing, BFP biogenesis, or LA. For each mutant for which altered phenotypes were detected, complementation with a plasmid containing the corresponding wild-type allele restored the wild-type phenotypes. We also found that association of prebundlin or bundlin with sucrose density flotation gradient fractions containing both inner and outer membrane proteins does not require any accessory proteins. These studies indicate that many bfp gene products are required for biogenesis of functional type IV pili but that mutations in the individual genes do not lead to the identification of new phases of pilus assembly.

scholarly journals CRYPTIC OPERON FOR β-GLUCOSIDE METABOLISM IN ESCHERICHIA COLI K12: GENETIC EVIDENCE FOR A REGULATORY PROTEIN

Genetics ◽  
1981 ◽  
Vol 97 (1) ◽  
pp. 11-25
Author(s):  
Roberto Defez ◽  
Maurilio De Felice
Keyword(s):  
Escherichia Coli ◽  
Cyclic Amp ◽  
Single Gene ◽  
Regulatory Protein ◽  
Regulatory Site ◽  
Structural Genes ◽  
Wild Type ◽  
Cis Acting ◽  
E Coli ◽  
Escherichia Coli K12

ABSTRACT Escherichia coli K12 does not metabolize β-glucosides such as arbutin and salicin because of lack of expression of the bglBSRC operon, which contains structural genes for transport (bglC) and hydrolysis (bglB) of phospho-β-glucosides. Mutants carrying lesions in the cis-acting regulatory site bglR metabolize β-glucosides as a consequence of expression of this cryptic operon (Prasad and Schaefler 1974). We isolated mutations promoting β-glucoside metabolism that were unlinked to bglR; some of these mutations were shown to be amber. All of them were mapped at 27 min on the E. coli K12 linkage map and appeared to define a single gene, for which we propose the designation bglY. Utilization of β-glucosides in bglY mutants appeared to be a consequence of expression of the bglBSRC operon, since bglB bglR and bglB bglY double mutants had the same phenotype. All bglY mutations analyzed were recessive to the wild-type bglY  + allele. Phospho-β-glucosidase B and β-glucoside transport activities are inducible in bglY mutants, as they are in bglR mutants. Metabolism of β-glucosides in both bglR and bglY mutants required cyclic AMP. We propose that bglY encodes a protein acting as a repressor of the bglBSRC operon, active in both the presence and absence of β-glucosides, whose recognition site would be within the bglR locus.

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