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

Lin, Wei‐Hsiang; Jacobs‐Wagner, Christine

doi:10.1016/j.cub.2022.07.035

Cited by 45 publications

(34 citation statements)

References 58 publications

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“…A key clue to the potential significance of the fork-velocity oscillations comes from their observation, not only in E. coli, but also in B. subtilis and V. cholerae, three highly divergent species, as well as their observation under multiple growth conditions. Although it has long been assumed that homeostatic regulation keeps key cellular metabolites in a relatively narrow range, our observations, as well as the recent reports of oscillations in other key nucleotides in bacteria (e.g., ATP in E. coli 43 ), suggest that key metabolites are in fact subject to significant temporal oscillations even in the context of steady-state log-phase growth. These observations, if their ubiquity is supported by future work, may require a significant revision of our understanding of the metabolic environment of the cell.…”

Section: Discussionmentioning

confidence: 45%

The in vivo measurement of replication fork velocity and pausing by lag-time analysis

et al. 2023

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An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.

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Section: Discussionmentioning

confidence: 45%

The in vivo measurement of replication fork velocity and pausing by lag-time analysis

et al. 2023

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“…In addition to these rapid fluctuations, recent studies have demonstrated slow metabolic fluctuations correlated with the cell cycle, both in eukaryotic and prokaryotic cells, possibly related to the cell-cycle variations in protein levels [41][42][43] . Moreover, metabolic diversification on the cell-cycle timescale can emerge within clonal bacterial populations due to stochastic, and sometimes regulated, variability in expression of metabolic genes and its effects on growth 7,[44][45][46][47][48][49] .…”

mentioning

confidence: 99%

Dynamic fluctuations in a bacterial metabolic network

Kargeti

Colin

et al. 2023

Nat Commun

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The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.

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“…Single-cell ATP measurements ATP level was estimated in living E. coli MG1655 and E. coli 536 cells at different time points during growth in LB medium. Overnight cultures carrying the previously described QUEEN-2M ATP biosensor plasmid pWL2 (35) were diluted 1:1000 in fresh LB medium supplemented with 60 mM IPTG to induce the synthesis of the QUEEN-2M biosensor and incubated at 25°C with agitation until OD 600nm reached 0.2 (considered as early exponential phase) and OD 600nm reached 0.5 (considered as middle exponential phase). For each time point, cultures were sampled and a minimum of 50,000 cells was analyzed using Beckman Coulter Gallios flow cytometer with a maximum of 2000 events counted per second.…”

Section: Lc-ms Measurements Of Atp- Adp- Amp Gtp- and Ppgpp-relative ...mentioning

confidence: 99%

The protein carboxymethyltransferase–dependent aspartate salvage pathway plays a crucial role in the intricate metabolic network of Escherichia coli

Micaletto,

Fleurier,

Dion

et al. 2024

Sci. Adv.

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Protein carboxymethyltransferase (Pcm) is a highly evolutionarily conserved enzyme that initiates the conversion of abnormal isoaspartate to aspartate residues. While it is commonly believed that Pcm facilitates the repair of damaged proteins, a number of observations suggest that it may have another role in cell functioning. We investigated whether Pcm provides a means for Escherichia coli to recycle aspartate, which is essential for protein synthesis and other cellular processes. We showed that Pcm is required for the energy production, the maintenance of cellular redox potential and of S -adenosylmethionine synthesis, which are critical for the proper functioning of many metabolic pathways. Pcm contributes to the full growth capacity both under aerobic and anaerobic conditions. Last, we showed that Pcm enhances the robustness of bacteria when exposed to sublethal antibiotic treatments and improves their fitness in the mammalian urinary tract. We propose that Pcm plays a crucial role in E. coli metabolism by ensuring a steady supply of aspartate.

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

Cited by 45 publications

References 58 publications

The in vivo measurement of replication fork velocity and pausing by lag-time analysis

The in vivo measurement of replication fork velocity and pausing by lag-time analysis

Dynamic fluctuations in a bacterial metabolic network

The protein carboxymethyltransferase–dependent aspartate salvage pathway plays a crucial role in the intricate metabolic network of Escherichia coli

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