Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(8)

Published: Feb. 18, 2021

Significance When several sugars are at its disposition, the bacterium Escherichia coli consumes them in a specific order—a behavior called diauxie. We developed framework combining dynamic methods and models of metabolism gene expression to show that diauxie associated lag cell growth can be explained simply as an optimal under constraints on protein amount renewal cell. validate our model by reproducing experimental results successfully predict diauxic medium containing two types sugar, glucose lactose. Finally, we claim regulation mechanism inducing (the lac operon) is control system implement optimality cellular level.

Language: Английский

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Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

International Journal of Environmental Research and Public Health, Journal Year: 2021, Volume and Issue: 18(19), P. 10093 - 10093

Published: Sept. 26, 2021

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body theory, which has partially been experimentally tested by mimicking evolutionary processes laboratory. In first part this perspective, we outline what model systems used for experimental testing eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities spontaneous fermented foods promising system study They combine complexity community with extensive knowledge about members and ease manipulating laboratory setup. Due rapidly developing sequencing techniques meta-omics approaches incorporating data building models, diversity these can be analysed relative while hypotheses developed tested. Here, highlight several questions that addressed using foods. These relate analysing species frequencies space time, diversity-stability relationship, niche coalescence. We provide influence factors on evolution specifying setup studies where food used.

Language: Английский

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Digital Insights Into Nucleotide Metabolism and Antibiotic Treatment Failure

Frontiers in Digital Health, Journal Year: 2021, Volume and Issue: 3

Published: March 3, 2021

Nucleotide metabolism plays a central role in bacterial physiology, producing the nucleic acids necessary for DNA replication and RNA transcription. Recent studies demonstrate that nucleotide also proactively contributes to antibiotic-induced lethality pathogens disruptions antibiotic treatment failure clinic. As antimicrobial resistance continues grow unchecked, new approaches are needed study molecular mechanisms responsible efficacy. Here we review emerging technologies poised transform understanding into why antibiotics may fail We discuss how these led discovery regulates drug responses relevant human infections. highlight opportunities enhance of mechanisms.

Language: Английский

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Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(12)

Published: March 15, 2021

Metal ions are vital to metabolism, as they can act cofactors on enzymes and thus modulate individual enzymatic reactions. Although many have been reported interact with metal ions, the quantitative relationships between metabolism lacking. Here, we reconstructed a genome-scale metabolic model of yeast Saccharomyces cerevisiae account for proteome constraints enzyme such named CofactorYeast. The is able estimate abundances binding in cells under various conditions, which comparable measured ion contents biomass. In addition, predicts distinct flux distributions response reduced levels medium. Specifically, reproduces changes upon iron deficiency gene expression levels, could be interpreted by optimization principles (i.e., optimizes utilization based network kinetics rather than preferentially targeting specific or pathways). At last, show potential using understanding cell factories that harbor heterologous iron-containing synthesize high-value compounds p-coumaric acid. Overall, demonstrates dependence links genome scale.

Language: Английский

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The mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions

Evolution, Journal Year: 2022, Volume and Issue: 76(S1), P. 37 - 48

Published: Jan. 6, 2022

Since the modern synthesis, fitness effects of mutations and epistasis have been central yet provocative concepts in evolutionary population genetics. Studies how interactions between parcels genetic information can change as a function environmental context added layer complexity to these discussions. Here, I introduce "mutation effect reaction norm" (Mu-RN), new instrument through which one analyze phenotypic consequences across contexts. It embodies fusion measurements with norm, classic depiction performance genotypes environments. demonstrate utility Mu-RN case study: signature "compensatory ratchet" mutation that undermines reverse evolution antimicrobial resistance. In closing, argue norm may help us resolve dynamism unpredictability evolution, implications for theoretical biology, biotechnology, public health.

Language: Английский

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