Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase

Xu, Yifan; Amador‐Noguez, Daniel; Reaves, Marshall Louis; Xiao, Feng; Rabinowitz, Joshua D.

doi:10.1038/nchembio.941

Cited by 72 publications

(75 citation statements)

References 52 publications

(52 reference statements)

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“…3C). This finding is consistent with the magnified effects of allosteric activators on anaplerotic PEPC from Escherichia coli in the presence of inhibitors (Xu et al, 2012) and may further contribute to PEPC's in vivo activation during proteoid root maturation.…”

Section: Kinetic Properties Of Proteoid Root Pepcsupporting

confidence: 77%

Reciprocal Control of Anaplerotic Phosphoenolpyruvate Carboxylase by in Vivo Monoubiquitination and Phosphorylation in Developing Proteoid Roots of Phosphate-Deficient Harsh Hakea

2013

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Accumulating evidence indicates important functions for phosphoenolpyruvate (PEP) carboxylase (PEPC) in inorganic phosphate (Pi)-starved plants. This includes controlling the production of organic acid anions (malate, citrate) that are excreted in copious amounts by proteoid roots of nonmycorrhizal species such as harsh hakea (Hakea prostrata). This, in turn, enhances the bioavailability of mineral-bound Pi by solubilizing Al 3+ , Fe 3+ , and Ca 2+ phosphates in the rhizosphere. Harsh hakea thrives in the nutrient-impoverished, ancient soils of southwestern Australia. Proteoid roots from Pi-starved harsh hakea were analyzed over 20 d of development to correlate changes in malate and citrate exudation with PEPC activity, posttranslational modifications (inhibitory monoubiquitination versus activatory phosphorylation), and kinetic/allosteric properties. Immature proteoid roots contained an equivalent ratio of monoubiquitinated 110-kD and phosphorylated 107-kD PEPC polypeptides (p110 and p107, respectively). PEPC purification, immunoblotting, and mass spectrometry indicated that p110 and p107 are subunits of a 430-kD heterotetramer and that they both originate from the same plant-type PEPC gene. Incubation with a deubiquitinating enzyme converted the p110:p107 PEPC heterotetramer of immature proteoid roots into a p107 homotetramer while significantly increasing the enzyme's activity under suboptimal but physiologically relevant assay conditions. Proteoid root maturation was paralleled by PEPC activation (e.g. reduced K m [PEP] coupled with elevated I 50 [malate and Asp] values) via in vivo deubiquitination of p110 to p107, and subsequent phosphorylation of the deubiquitinated subunits. This novel mechanism of posttranslational control is hypothesized to contribute to the massive synthesis and excretion of organic acid anions that dominates the carbon metabolism of the mature proteoid roots.

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Section: Kinetic Properties Of Proteoid Root Pepcsupporting

confidence: 77%

Reciprocal Control of Anaplerotic Phosphoenolpyruvate Carboxylase by in Vivo Monoubiquitination and Phosphorylation in Developing Proteoid Roots of Phosphate-Deficient Harsh Hakea

2013

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“…We initially found that feedback inhibition alone is sufficient to enable both intracellular metabolite concentration homeostasis and optimal steady-state fluxes (Goyal et al, 2010). More recently, we demonstrated that feed forward regulation is important in oscillating conditions (Xu et al, 2012a;Xu et al, 2012b). In general, our experimental and computational results support a primary paradigm for nutrient integration: Limitation for a nutrient other than carbon leads to build-up of the most closely related product of carbon metabolism, which in turn feedback inhibits further carbon utilization.…”

Section: Aim 3: Gain Insight Into the Key Principles Underlying The Csupporting

confidence: 50%

“…These point mutants which lack positive regulation of anaplerosis by fructose-1,6-bisphosphate, a key metabolite indicating high sugar availability. Such mutants grow normally in steady glucose but are strikingly deficient in an oscillating glucose environment (Xu et al, 2012a;Xu et al, 2012b). Related work investigates additional nutrients and stresses, and the robustness of biological responses to them (Goodarzi et al, 2010;Hart et al, 2011;Peterson et al, 2012;Reaves and Rabinowitz, 2011a, b).…”

Section: Aims Summary Aim 1: Reveal the Interplay Between Different Nmentioning

confidence: 99%

Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli

Rabinowitz¹,

Wingreen²,

Rabitz³

et al. 2012

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. REPORT DATE (DD-MM-YYYY PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)Princeton University, Princeton NJ 08544 PERFORMING ORGANIZATION REPORT NUMBER SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES)Air Force Office of Scientific Research SPONSOR/MONITOR'S ACRONYM(S) AFOSR SPONSOR/MONITOR'S REPORT NUMBER(S) DISTRIBUTION / AVAILABILITY STATEMENT SUPPLEMENTARY NOTES ABSTRACTA key challenge for living systems is balancing utilization of multiple elemental nutrients, such as carbon, nitrogen, and oxygen, whose availability is subject to environmental fluctuations. As growth can be limited by the scarcity of any one nutrient, the rate at which each nutrient is assimilated must be sensitive not only to its own availability, but also to that of other nutrients. Remarkably, across diverse nutrient conditions, E. coli grows nearly optimally, balancing effectively the conversion of carbon into energy versus biomass. To investigate the link between the metabolism of different nutrients, we quantified metabolic responses to nutrient perturbations using LC-MS based metabolomics and built differential equation models that bridge multiple nutrient systems. We discovered that the carbonaceous substrate of nitrogen assimilation, α-ketoglutarate, directly inhibits glucose uptake and that the upstream glycolytic metabolite, fructose-1,6-bisphosphate, ultrasensitively regulates anaplerosis to allow rapid adaptation to changing carbon availability. We also showed that NADH controls the metabolic response to changing oxygen levels. Our findings support a general mechanism for nutrient integration: limitation for a nutrient other than carbon leads to build-up of the most closely related product of carbon metabolism, which in turn feedback inhibits further carbon uptake. SUBJECT TERMS

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“…As a result, PKI activity remains fairly low consistent with the physiological needs of the cell. However, when glucose becomes available again, it is rapidly imported by consuming the accumulated PEP triggering rapid accumulation of FBP and an increase in the ATP/ADP ratio, which activates key glycolytic enzymes [68]. This response is responsible for the rapid adaptation of E. coli to …”

Section: Accepted M Manuscriptmentioning

confidence: 99%

A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis

Saa

Nielsen

2016

Biochimica et Biophysica Acta (BBA) - General Subjects

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BackgroundAnalysis of limiting steps within enzyme-catalyzed reactions is fundamental to understand their behavior and regulation. Methods capable of unravelling control properties and exploring kinetic capabilities of enzymatic reactions would be particularly useful for protein and metabolic engineering. While single-enzyme control analysis formalism has previously been applied to well-studied enzymatic mechanisms, broader application of formalism is limited in practice by the limited amount of kinetic data and the difficulty of describing complex allosteric mechanisms. MethodsTo overcome these limitations, we present here a probabilistic framework enabling control analysis of previously unexplored mechanisms under uncertainty. By combining a thermodynamically consistent parameterization with an efficient Sequential Monte Carlosampler embedded in a Bayesian setting, this framework yields insights into the capabilities of enzyme-catalyzed reactions with modest kinetic information, provided that the catalytic mechanism and a thermodynamic reference point are defined. ResultsThe framework was used to unravel the impact of thermodynamic affinity, substrate saturation levels and effector concentrations on the flux control and response coefficients of a diverse set of enzymatic reactions. ConclusionsOur results highlight the importance of the metabolic context in the control analysis of isolated enzymes as well as the use of statistically sound methods for their interpretation. General SignificanceThis framework significantly expands our current capabilities for unravelling the control properties of general reaction kinetics with limited amount of information. This framework will be useful for both theoreticians and experimentalists in the field.

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Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase

Cited by 72 publications

References 52 publications

Reciprocal Control of Anaplerotic Phosphoenolpyruvate Carboxylase by in Vivo Monoubiquitination and Phosphorylation in Developing Proteoid Roots of Phosphate-Deficient Harsh Hakea

Reciprocal Control of Anaplerotic Phosphoenolpyruvate Carboxylase by in Vivo Monoubiquitination and Phosphorylation in Developing Proteoid Roots of Phosphate-Deficient Harsh Hakea

Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli

A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis

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