Homeostasis of the biosynthetic E. coli metabolome

Radoš, Dušica; Donati, Stefano; Lempp, Martin; Rapp, Johanna; Link, Hannes

doi:10.1016/j.isci.2022.104503

Cited by 19 publications

(21 citation statements)

References 33 publications

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“…The average growth rate during the cell cycle was, as expected, considerably reduced in M9Glu, M9Xyl, and M9Gly compared with the nutrient-richer medium M9GlcCAA (Figure 4B). We also found that consistent with the literature, 5,6,8 the mean ATP level remains similar across these growth conditions (Figure 4C). In contrast, the ATP fluctuations were markedly reduced in cell lineages growing in M9Glc, M9Xyl, or M9Gly compared with M9GlcCAA (Figure 4A), with differences in SD of R ATP of about 40% (Figure 4D).…”

Section: The Amplitude Of Atp Fluctuations Changes With the Quality O...supporting

confidence: 91%

“…Previous population measurements have shown that although the type of carbon source can drastically affect the growth rate of E. coli, the (mean) ATP level remains similar at the population level. 5,6,8 Therefore, to examine the potential origin of the ATP fluctuations, we performed additional microfluidic experiments and recorded the R ATP over time in cells growing in M9 media containing different carbon sources, including glucose (M9Glc), xylose (M9Xyl), or glycerol (M9Gly), instead of M9GlcCAA (Figure 4A). The average growth rate during the cell cycle was, as expected, considerably reduced in M9Glu, M9Xyl, and M9Gly compared with the nutrient-richer medium M9GlcCAA (Figure 4B).…”

Section: The Amplitude Of Atp Fluctuations Changes With the Quality O...mentioning

confidence: 99%

“…Although these ideas remain speculative, our study highlights the importance of time-resolved single-cell studies, even for metabolites as remarkably stable in concentration at the population level as ATP. 53 ATP may not be the only metabolite whose levels fluctuate in bacteria at the single-cell level. A recent single-cell study has proposed that the redox cofactors nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) oscillate during the cell cycle in E. coli based on cellular autofluorescence measurements.…”

Section: Articlementioning

confidence: 99%

“…[4][5][6][7] A recent metabolic study revealed that ATP is one of the most stable metabolites across 17 conditions that supported growth, with only 12% variability in concentration across nutrient-poor and -rich media. 8 Only when cultures exhaust essential nutrients and transition to stationary phase do average ATP levels drop to submillimolar concentrations. 9 In the aforementioned growth studies, the ATP measurements were performed using analytical methods on cell populations.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli

Lin

Jacobs‐Wagner

2022

Current Biology

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Section: The Amplitude Of Atp Fluctuations Changes With the Quality O...supporting

confidence: 91%

Section: The Amplitude Of Atp Fluctuations Changes With the Quality O...mentioning

confidence: 99%

Section: Articlementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli

Lin

Jacobs‐Wagner

2022

Current Biology

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“…UTP of PRdnBP was strongly robust to tolerate perturbations changes in environmental conditions . To produce cytidine, we analyzed the robustness of PRdnBP prior to strain design by using a kinetic model, which could faithfully represent the dynamic changes in the intracellular pyrimidine pool .…”

Section: Resultsmentioning

confidence: 99%

Computer-Based Design of a Cell Factory for High-Yield Cytidine Production

Bin

Dai

2022

ACS Synth. Biol.

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Pyrimidine ribonucleotide de novo biosynthesis pathway (PRdnBP) is an important pathway to produce pyrimidine nucleosides. We attempted to systematically investigate PRdnBP in Escherichia coli with genome-scale metabolic models and utilized the models to guide strain design. The balance of central carbon metabolism and PRdnBP affected the production of cytidine from glucose. Using Bayesian metabolic flux analysis, the effect of modified PRdnBP on the metabolic network was analyzed. The acetate overflow became coupled with PRdnBP flux, while they were originally independent under oxygen-sufficient conditions. The coupling between cytidine production and acetate secretion in the modified strain was weakened by arcA deletion, which resulted in further improving the efficient accumulation of cytidine. In total, 1.28 g/L of cytidine with a yield of 0.26 g/g glucose was produced. The yield of cytidine produced by E. coli is higher than previous reports. Our strategy provides an effective attempt to find metabolic bottlenecks in genetically engineered bacteria by using flux coupling analysis.

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Engineering an Escherichia coli based in vivo mRNA manufacturing platform

Curry,

Muir,

et al. 2024

Biotech & Bioengineering

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Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one‐size‐fits‐all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product‐related impurity profiles, and limited design options for molecule‐specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40‐fold compared to standard “unengineered” E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host‐cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.

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Homeostasis of the biosynthetic E. coli metabolome

Cited by 19 publications

References 33 publications

Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli

Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli

Computer-Based Design of a Cell Factory for High-Yield Cytidine Production

Engineering an Escherichia coli based in vivo mRNA manufacturing platform

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