Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli

Zhu, Manlu; Dai, Xiongfeng

doi:10.1093/nar/gkz211

Cited by 77 publications

(94 citation statements)

References 60 publications

(118 reference statements)

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“…We suggest that a higher R-sector might represent a compensatory countermeasure against the lowered growth of the mutants. Notably, previous study have experimentally validated the correlation of high ribosome content with lowered ppGpp levels (28). Interestingly, our analysis supports this notion in case of Δihf mutant,…”

Section: Global Regulators Control the Translation And Metabolic Effisupporting

confidence: 86%

“…To explain the underlying mechanism as to how perturbations in core metabolic genes due to the loss of regulator resulted in reduction in growth rate and subsequent glucose uptake, we recalled a proteome allocation model that quantitatively relates the cellular ribosome content to the growth of E. coli (27)(28)(29)(30). As explicitly outlined in the model (27), proteome sectors (∅) are comprised of: R-sector defining the growth-rate dependent ribosomal protein sector, Msector defining the metabolic protein sector and Q-sector defining the growth-rate independent core proteome sector ( Figure 3A).…”

Section: Global Regulators Control the Translation And Metabolic Effimentioning

confidence: 99%

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Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Iyer

Pal

Srinivasan

et al. 2020

Preprint

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Complex regulatory interactions between genetic and metabolic networks together confer robustness against external and internal perturbations in an organism such as Escherichia coli. This robustness comprises of cost-effective metabolism contemplating the benefit in resource investment coordinated by the interplay between growth-rate dependent machinery and global transcriptional regulators. Here, we reappraise the role of global transcriptional regulators FNR, ArcA and IHF fundamental for optimal growth of E. coli, under energetically less favourable albeit proteome-efficient anaerobic fermentative conditions. We reveal at the transcriptome and metabolome level, that absence of these global regulators ensued a disruption of nitrogen homeostasis, overexpression of otherwise unnecessary or hedging genes and impairment in core bottleneck steps and amino acid metabolism. Notably, our findings emphasize their importance in optimizing the metabolic proteome resources essential for rapid growth. Consequentially, the perturbations in the metabolic proteome as a result of deletion of global regulators unbalances the ribosomal proteome share imposing a high translation program at the expense of lowered efficiency. We illustrate that disruption of this inherent trade-off between metabolic and ribosomal proteomic investment eventually culminate to lowered growth rate. Despite no changes in gene expression related to reduced glucose import, our findings elucidate that the changes in intracellular metabolites directly modulated by growth rate, in turn feedback regulates the glucose uptake. Our results employing the proteome allocation theory and quantitative experimental measurements, suffices to explain the physiological consequences of altered translational and metabolic efficiency in the cell, driven by the loss of these global regulators.

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Section: Global Regulators Control the Translation And Metabolic Effisupporting

confidence: 86%

Section: Global Regulators Control the Translation And Metabolic Effimentioning

confidence: 99%

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Iyer

Pal

Srinivasan

et al. 2020

Preprint

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“…Stationary-phase entry and the stringent response are, in part, regulated by the production of the alarmone guanosine 3’,5’-bispyrophosphate (ppGpp) (32, 33). Overexpression of the N-terminal domain of the ppGpp synthetase RelA results in the constitutive production of ppGpp and decreased growth rate in E. coli (34). To test whether stationary phase entry was necessary for stalk elongation in C. crescentus , we overexpressed truncated RelA in the manA * cells; overproduction of ppGpp resulted in a significant increase in stalk length (Fig.…”

Section: Resultsmentioning

confidence: 99%

Sugar-phosphate metabolism regulates stationary phase entry and stalk elongation inCaulobacter crescentus

Young

Stankeviciute

Klein

2019

Preprint

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Bacteria have a variety of mechanisms for adapting to environmental perturbations. Changes in oxygen availability result in a switch between aerobic and anaerobic respiration, whereas iron limitation may lead to siderophore secretion. In addition to metabolic adaptations, many organisms respond by altering their cell shape. Caulobacter crescentus, when grown under phosphate limiting conditions, dramatically elongates its polar stalk appendage. The stalk is hypothesized to facilitate phosphate uptake; however, the mechanistic details of stalk synthesis are not well characterized. We used a chemical mutagenesis approach to isolate and characterize stalk-deficient mutants, one of which had two mutations in the phosphomannose isomerase gene (manA) that were necessary and sufficient to inhibit stalk elongation. Transcription of the pho regulon was unaffected in the manA mutant; therefore, ManA plays a unique regulatory role in stalk synthesis. The mutant ManA had reduced enzymatic activity resulting in a 5-fold increase in the intracellular fructose 6-phosphate: mannose 6-phosphate ratio. This metabolic imbalance impaired the synthesis of cellular envelope components derived from mannose 6-phosphate, namely lipopolysaccharide O-antigen and exopolysaccharide. Furthermore, the manA mutations prevented C. crescentus cells from efficiently entering stationary phase. Deletion of the stationary-phase response regulator spdR inhibited stalk elongation in wild-type cells while overproduction of the alarmone ppGpp, which triggers growth arrest and stationary phase entry, increased stalk length in the manA mutant strain. These results demonstrate that sugar-phosphate metabolism regulates stalk elongation independently of phosphate starvation.ImportanceBacteria have various mechanisms for adapting to environmental perturbations including morphological alterations. During phosphate limitation, Caulobacter crescentus dramatically elongates its polar stalk appendage. The stalk is hypothesized to facilitate phosphate uptake; however, the mechanism of stalk synthesis is not well characterized. We isolated stalk-deficient mutants, one of which had mutations in the phosphomannose isomerase gene (manA) that blocked stalk elongation, despite normal activation of the phosphate-starvation response. The mutant ManA produced an imbalance in sugar-phosphate concentrations that impaired the synthesis of cellular envelope components and prevented entry into stationary phase. Overproduction of the alarmone ppGpp, which promotes stationary phase entry, increased stalk length in the manA mutant demonstrating that sugar-phosphate metabolism regulates stalk elongation independently of phosphate starvation.

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“…1A). Mesh1 hydrolyzes ppGpp in vitro with comparable efficiency to bacterial RSHs (21,22). The Drosophila Mesh1 loss-of-function mutant (Mesh1 lof) exhibits retarded growth, especially during…”

mentioning

confidence: 99%

“…Mesh1 expressed in E. coli exhibits ppGpp hydrolase activity (21,22). However, Mesh1 activity in vivo has never been measured because ppGpp has not been detected in metazoa (21).…”

mentioning

confidence: 99%

ppGpp functions as an alarmone in metazoa

Ito

Kawamura

Oikawa

et al. 2019

Preprint

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Guanosine 3',5'-bis(pyrophosphate) (ppGpp) functions as a second messenger in bacteria to adjust their physiology in response to environmental changes. In recent years, the ppGpp-specific hydrolase, metazoan SpoT homolog-1 (Mesh1), was shown to have important roles for growth under nutrient deficiency in Drosophila melanogaster.Curiously, however, ppGpp has never been detected in animal cells, and therefore the physiological relevance of this molecule, if any, in metazoans has not been established.Here, we report the detection of ppGpp in Drosophila and human cells and demonstrate that ppGpp accumulation induces metabolic changes, cell death, and eventually lethality 2 in Drosophila. Our results provide the first evidence of the existence and function of the ppGpp-dependent stringent response in animals. Main Text:Organisms must adjust their physiology in response to environmental changes. The stringent response is one of the most important starvation/metabolic control responses in bacteria and is controlled by the hyper-phosphorylated nucleotide, ppGpp (1, 2). ppGpp accumulates in bacterial cells upon exposure to various stresses, and the accumulated ppGpp functions as an alarmone that can alter transcription (3-6), translation (7, 8) and certain enzymatic activities (6,9,10) to overcome a stress (3). In Escherichia coli, ppGpp level is regulated by two distinct enzymes, namely RelA and SpoT (11). Both RelA and SpoT catalyze pyrophosphorylation of GDP (or GTP) by using ATP to produce ppGpp (12), and SpoT, but not RelA, hydrolyzes ppGpp (13). The RelA/SpoT homologs (RSHs) are universally conserved in bacteria (14) and have pivotal roles in various aspects of bacterial physiology, including the starvation response (1, 2), growthrate control (15), antibiotic tolerance (16), and darkness response (17). RSHs are also found in eukaryotes, including the green algae Chlamydomonas reinhardtii (18) and land plant Arabidopsis thaliana (19) as well as metazoa, including humans and Drosophila melanogaster (14, 20). Metazoan SpoT homolog-1 (Mesh1) is one class of RSHs found in metazoa. Although most RSHs have both ppGpp synthase and hydrolase domains, Mesh1 has only a ppGpp hydrolase domain (Fig. 1A). Mesh1 hydrolyzes ppGpp in vitro with comparable efficiency to bacterial RSHs (21,22). The Drosophila Mesh1 loss-of-function mutant (Mesh1 lof) exhibits retarded growth, especially during

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Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli

Cited by 77 publications

References 60 publications

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Sugar-phosphate metabolism regulates stationary phase entry and stalk elongation inCaulobacter crescentus

ppGpp functions as an alarmone in metazoa

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