scholarly journals Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States

Metabolites ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 749
Author(s):  
Wolfram Liebermeister ◽  
Elad Noor
Keyword(s):  
Kinetic Constants ◽  
Omics Data ◽  
Central Metabolism ◽  
E Coli ◽  
Metabolic Fluxes ◽  
Metabolic States ◽  
Wide Range ◽  
Metabolite Concentrations ◽  
Metabolic Models

Enzyme kinetic constants in vivo are largely unknown, which limits the construction of large metabolic models. Given measured metabolic fluxes, metabolite concentrations, and enzyme concentrations, these constants may be inferred by model fitting, but the estimation problems are hard to solve if models are large. Here we show how consistent kinetic constants, metabolite concentrations, and enzyme concentrations can be determined from data if metabolic fluxes are known. The estimation method, called model balancing, can handle models with a wide range of rate laws and accounts for thermodynamic constraints between fluxes, kinetic constants, and metabolite concentrations. It can be used to estimate in-vivo kinetic constants, to complete and adjust available data, and to construct plausible metabolic states with predefined flux distributions. By omitting one term from the log posterior—a term for penalising low enzyme concentrations—we obtain a convex optimality problem with a unique local optimum. As a demonstrative case, we balance a model of E. coli central metabolism with artificial or experimental data and obtain a physically and biologically plausible parameterisation of reaction kinetics in E. coli central metabolism. The example shows what information about kinetic constants can be obtained from omics data and reveals practical limits to estimating in-vivo kinetic constants. While noise-free omics data allow for a reasonable reconstruction of in-vivo kcat and KM values, prediction from noisy omics data are worse. Hence, adjusting kinetic constants and omics data to obtain consistent metabolic models is the main application of model balancing.

scholarly journals Model balancing: consistent in-vivo kinetic constants and metabolic states obtained by convex optimisation

2019 ◽  
Author(s):  
Wolfram Liebermeister
Keyword(s):  
Estimation Method ◽  
Kinetic Constants ◽  
Omics Data ◽  
Posterior Density ◽  
Rate Laws ◽  
Metabolic Fluxes ◽  
Metabolic States ◽  
Wide Range ◽  
Metabolite Concentrations

AbstractEnzyme kinetic constants in vivo are largely unknown, which limits the construction of large metabolic models. In theory, kinetic constants can be fitted to measured metabolic fluxes, metabolite concentrations, and enzyme concentrations, but these estimation problems are typically non-convex. This makes them hard to solve, especially if models are large. Here I assume that the metabolic fluxes are given and show that consistent kinetic constants, metabolite levels, and enzyme levels can then be found by solving a convex optimality problem. If logarithmic kinetic constants and metabolite concentrations are used as free variables and if Gaussian priors are employed, the posterior density is strictly convex. The resulting estimation method, called model balancing, can employ a wide range of rate laws, accounts for thermodynamic constraints on parameters, and considers the dependences between flux directions and metabolite concentrations through thermodynamic forces. It can be used to complete and adjust available data, to estimate in-vivo kinetic constants from omics data, or to construct plausible metabolic states with a predefined flux distribution. To demonstrate model balancing and to assess its practical use, I balance a model of E. coli central metabolism with artificial or experimental data. The tests show what information about kinetic constants can be extracted from omics data and reveal practical limits of estimating kinetic constants in vivo.

scholarly journals Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis

2019 ◽  
Author(s):  
Kanika Verma ◽  
Kanika Saxena ◽  
Rajashekar Donaka ◽  
Aseem Chaphalkar ◽  
Manish Kumar Rai ◽  
...  
Keyword(s):  
Cellular Metabolism ◽  
Negative Regulation ◽  
Metabolic Alterations ◽  
E Coli ◽  
Metabolic States ◽  
Metabolite Concentrations ◽  
A Cell ◽  
Bona Fide

SummaryChanges in metabolism can alter the cellular milieu; can this also change intracellular proteostasis? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change proteostasis, arguably, it should also alter mutational buffering. Building on this, we find that altered cellular metabolic states in E. coli buffer distinct mutations. Buffered-mutants had folding problems in vivo and were differently chaperoned in different metabolic states. Notably, this assistance was dependent upon the metabolites and not on the increase in canonical chaperone machineries. Additionally, we were able to reconstitute the folding assistance afforded by metabolites in vitro and propose that changes in metabolite concentrations have the potential to alter proteostasis. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in the positive or negative regulation of proteostasis.

scholarly journals A Toxic Environment: a Growing Understanding of How Microbial Communities Affect Escherichia coli O157:H7 Shiga Toxin Expression

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Erin M. Nawrocki ◽  
Hillary M. Mosso ◽  
Edward G. Dudley
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Microbial Interactions ◽  
Severe Illness ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Lambdoid Prophage

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) strains, including E. coli O157:H7, cause severe illness in humans due to the production of Shiga toxin (Stx) and other virulence factors. Because Stx is coregulated with lambdoid prophage induction, its expression is especially susceptible to environmental cues. Infections with Stx-producing E. coli can be difficult to model due to the wide range of disease outcomes: some infections are relatively mild, while others have serious complications. Probiotic organisms, members of the gut microbiome, and organic acids can depress Stx production, in many cases by inhibiting the growth of EHEC strains. On the other hand, the factors currently known to amplify Stx act via their effect on the stx-converting phage. Here, we characterize two interactive mechanisms that increase Stx production by O157:H7 strains: first, direct interactions with phage-susceptible E. coli, and second, indirect amplification by secreted factors. Infection of susceptible strains by the stx-converting phage can expand the Stx-producing population in a human or animal host, and phage infection has been shown to modulate virulence in vitro and in vivo. Acellular factors, particularly colicins and microcins, can kill O157:H7 cells but may also trigger Stx expression in the process. Colicins, microcins, and other bacteriocins have diverse cellular targets, and many such molecules remain uncharacterized. The identification of additional Stx-amplifying microbial interactions will improve our understanding of E. coli O157:H7 infections and help elucidate the intricate regulation of pathogenicity in EHEC strains.

scholarly journals Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0139507 ◽  
Author(s):  
Ahmad A. Mannan ◽  
Yoshihiro Toya ◽  
Kazuyuki Shimizu ◽  
Johnjoe McFadden ◽  
Andrzej M. Kierzek ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Open System ◽  
Central Metabolism ◽  
E Coli ◽  
Metabolic Fluxes ◽  
Genome Scale

scholarly journals In Vitro and In Vivo Antibacterial Activities of SM-216601, a New Broad-Spectrum Parenteral Carbapenem

2005 ◽  
Vol 49 (10) ◽  
pp. 4185-4196 ◽  
Author(s):  
Yutaka Ueda ◽  
Katsunori Kanazawa ◽  
Ken Eguchi ◽  
Koji Takemoto ◽  
Yoshiro Eriguchi ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Antibacterial Activities ◽  
Multiresistant Pathogens ◽  
E Coli ◽  
Wide Range ◽  
Agar Dilution ◽  
Resistant Strains ◽  
Mrsa Strains

ABSTRACT SM-216601 is a novel parenteral 1β-methylcarbapenem. In agar dilution susceptibility testing, the MIC of SM-216601 for 90% of the methicillin-resistant Staphylococcus aureus (MRSA) strains tested (MIC90) was 2 μg/ml, which was comparable to those of vancomycin and linezolid. SM-216601 was also very potent against Enterococcus faecium, including vancomycin-resistant strains (MIC90 = 8 μg/ml). SM-216601 exhibited potent activity against penicillin-resistant Streptococcus pneumoniae, ampicillin-resistant Haemophilus influenzae, Moraxella catarrhalis, Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, with MIC90s of less than 0.5 μg/ml, and intermediate activity against Citrobacter freundii, Enterobacter cloacae, Serratia marcescens, and Pseudomonas aeruginosa. The therapeutic efficacy of SM-216601 against experimentally induced infections in mice caused by S. aureus, E. faecium, E. coli, and P. aeruginosa reflected its in vitro activity and plasma level. Thus, SM-216601 is a promising candidate for nosocomial bacterial infections caused by a wide range of gram-positive and gram-negative bacteria, including multiresistant pathogens.

Genome scale metabolic models and analysis for evaluating probiotic potentials

2020 ◽  
Vol 48 (4) ◽  
pp. 1309-1321
Author(s):  
Yoon-Mi Choi ◽  
Yi Qing Lee ◽  
Hyun-Seob Song ◽  
Dong-Yup Lee
Keyword(s):  
In Silico ◽  
Metabolic Characteristics ◽  
Knowledge Based ◽  
Main Challenge ◽  
Metabolic States ◽  
Probiotic Strains ◽  
Metabolic Models ◽  
Genome Scale

Probiotics are live beneficial microorganisms that can be consumed in the form of dairy and food products as well as dietary supplements to promote a healthy balance of gut bacteria in humans. Practically, the main challenge is to identify and select promising strains and formulate multi-strain probiotic blends with consistent efficacy which is highly dependent on individual dietary regimes, gut environments, and health conditions. Limitations of current in vivo and in vitro methods for testing probiotic strains can be overcome by in silico model guided systems biology approaches where genome scale metabolic models (GEMs) can be used to describe their cellular behaviors and metabolic states of probiotic strains under various gut environments. Here, we summarize currently available GEMs of microbial strains with probiotic potentials and propose a knowledge-based framework to evaluate metabolic capabilities on the basis of six probiotic criteria. They include metabolic characteristics, stability, safety, colonization, postbiotics, and interaction with the gut microbiome which can be assessed by in silico approaches. As such, the most suitable strains can be identified to design personalized multi-strain probiotics in the future.

Prospects for the application of lignin containing sorbents in veterinary medicine

2020 ◽  
pp. 29-30
Author(s):  
Anastasiya A. Moroz ◽  
◽  
Svetlana A. Schislenko ◽  
Keyword(s):  
Veterinary Medicine ◽  
Laboratory Animals ◽  
Gastrointestinal Infections ◽  
Animal Products ◽  
High Sorption Capacity ◽  
E Coli ◽  
Wide Range ◽  
High Sorption ◽  
Acute Form

Vaccines against colibacillosis are mainly used, containing only one specific variant of pathogenic E. coli with a preventive purpose among the livestock of stationary dysfunctional farms in conditions of Krasnoyarsk region. For therapeutic purposes, veterinarians usually use wide range of antimicrobial preparations to combat outbreaks of gastrointestinal infections. Many researchers point to the high variability of E. coli bacteria. Use of such preparations, in addition to the formation of high resistance in opportunistic microorganisms to the latter, provoke the accumulation of antibacterial drugs in animal products. Authors conducted studies of the possibility of the practical use of lignin-containing sorbents for therapeutic and prophylactic purposes in field of veterinary medicine in the period from 2001 to 2020. Authors proposed to use the residues after extraction, formed during the complex processing of larch bark, as an enterosorbent. Authors studied the therapeutic and prophylactic effect of enterosorbent from larch bark in case of gastrointestinal infections in experiments in vivo. It was found that the use of the sorbent for therapeutic purposes for 2 days ensured the safety of laboratory animals in the acute form of colibacillosis infection. Preservation was ensured by preventing the penetration of microbial toxins into the tissues of the gastrointestinal tract. The prophylactic and therapeutic efficacy of the investigated type of enterosorbent is associated with angioprotective, antitoxic effects due to the high sorption capacity of the drugs.

scholarly journals Global query on bacterial sirtuin CobB interactants reveals crosstalk with PRPP synthase Prs

2020 ◽  
Author(s):  
Beata M. Walter ◽  
Joanna Morcinek-Orłowska ◽  
Aneta Szulc ◽  
Andrew L. Lovering ◽  
Manuel Banzhaf ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Global Analysis ◽  
Stable Complex ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Nad Metabolism ◽  
E Coli ◽  
Nad Synthesis ◽  
Wide Range

AbstractProtein lysine acetylation regulates a wide range of cellular functions. It is controlled by a family of NAD-dependent protein deacetylases called sirtuins. In eukaryotes, sirtuins activity is coupled to spatiotemporally-controlled NAD+ level, whereas the mechanism of their regulation in bacteria is less clear. E. coli possesses a single sirtuin – CobB. However, it is unclear how CobB activity is coupled to NAD+ metabolism. In this work we show that this coordination is achieved in E. coli cells through a CobB interaction with PRPP synthase Prs, an enzyme necessary for NAD+ synthesis. Employing global analysis of protein-protein interactions formed by CobB, we demonstrate that it forms a stable complex with Prs. This assembly stimulates CobB deacetylase activity and partially protects it from inhibition by nicotinamide. We provide evidence that Prs acetylation is not necessary for CobB binding but affects the global acetylome in vivo. Our results show that CobB ameliorates Prs activity under conditions of Prs cofactors deficiency. Therefore, we propose that CobB-Prs crosstalk orchestrates the NAD+ metabolism and protein acetylation in response to environmental cues.

scholarly journals Analytical kinetic model of native tandem promoters in E. coli

2021 ◽  
Author(s):  
Vatsala Chauhan ◽  
Mohamed Nasurudeen Mohamed Bahrudeen ◽  
Cristina Santos Dias Palma ◽  
Ines S. C. Baptista ◽  
Bilena Lima de Brito Almeida ◽  
...  
Keyword(s):  
Single Cell ◽  
Step Function ◽  
Single Cell Protein ◽  
Linear Functions ◽  
Cell Protein ◽  
Transcription Start Sites ◽  
E Coli ◽  
Wide Range ◽  
Promoter Occupancy

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites 'dTSS', pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs.

scholarly journals Synthesis and Assessment of Antibacterial Activities of Ruthenium(III) Mixed Ligand Complexes Containing 1,10-Phenanthroline and Guanide

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Atakilt Abebe ◽  
Tizazu Hailemariam
Keyword(s):  
Staphylococcus Aureus ◽  
Antibacterial Activities ◽  
Drug Resistant ◽  
E Coli ◽  
Antibiotic Drugs ◽  
Wide Range ◽  
In Vivo Cytotoxicity ◽  
Better Than

In this work, two complexes of ruthenium(III) ([Ru(phen)2Cl2]Cl·2H2O and [Ru(phen)2(G)Cl]2Cl·H2O) were synthesized from 1,10-phenanthroline alone as well as from both 1,10-phenanthroline and guanide. The synthesis was checked using halide test, conductance measurement, and spectroscopic (ICP-OES, FTIR, and UV/Vis) analysis. Their in vitro antibacterial activities were also investigated on two Gram-positive (Staphylococcus aureus (S. aureus) and methicillin resistant Staphylococcus aureus (MRSA)) and two Gram-negative (Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae)) bacteria. These complexes showed wide-range better activities than the commercially available controls (Chloramphenicol and Ciprofloxacin) against even the most drug resistant K. pneumoniae. [Ru(phen)2(G)Cl]2Cl·H2O inhibited S. aureus, MRSA, E. coli, and K. pneumoniae by 17.5%, 27.4%, 16%, and 52%, respectively, better than Chloramphenicol. It also inhibited these pathogens by 5.9%, 5.1%, 2.3%, and 17.2%, respectively, better than Ciprofloxacin. Similarly, [Ru(Phen)2(Cl)2]Cl·2H2O inhibited these pathogens by 11%, 8.7%, 0.1%, and 31.2%, respectively, better than Chloramphenicol. Therefore, after in vivo cytotoxicity investigations, these compounds can be considered as potential antibiotic drugs.

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