Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast

Qin, Ning; Li, Lingyun; Ji, Xu; Pereira, Rui; Chen, Yu; Yin, Shile; Li, Chaokun; Wan, Xiaozhen; Qiu, Danye; Jiang, Junfeng; Luo, Haiyun; Zhang, Yueping; Dong, Genlai; Zhang, Yiming; Shi, Shuobo; Jessen, Henning J.; Xia, Jian; Chen, Yun; Larsson, Christer; Tan, Tianwei; Liu, Zihe; Nielsen, Jens

doi:10.1016/j.cell.2023.01.014

Cited by 18 publications

(23 citation statements)

References 77 publications

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“…Additionally, we treated strains with 10 μM carbonyl cyanide 3chlorophenylhydrazone (CCCP). CCCP is a potent uncoupler of mitochondrial oxidative phosphorylation, disrupting the proton gradient and ATP generation in the electron transport chain [28]. Both the pfk1Δ and pfk2Δ strains exhibited slower growth on plates containing CCCP (Fig.…”

Section: Effects Of the Deletion Of Pfk1 And Pfk2 On The Respire-ferm...mentioning

confidence: 97%

Mechanistic understanding of the "gatekeeper" phosphofructokinase of the glycolytic pathway on the central carbon metabolism

Li,

Qin,

Chen

et al. 2023

Preprint

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Background: Glycolysis is one of the oldest and most fundamental metabolic pathways responsible for glucose breakdown and energy production in cells. The key regulatory enzyme in glycolysis is phosphofructokinase (Pfks), which catalyzes the phosphorylation of fructose 6-phosphate (F6P) to fructose 1,6-bisphosphate. The regulation of Pfks plays a crucial role in fine-tuning glycolytic flux to meet the cellular energy demands, making it a "gatekeeper" enzyme of glycolysis. In Saccharomyces cerevisiae, Pfks has evolved into a hetero-octameric phosphofructokinase, consisting of the Alpha and Beta subunits encoded by PFK1 and PFK2, respectively. Deletion of either PFK1 or PFK2 could significantly impair the organism's fitness, whereas the underlying metabolic mechanisms remain unclear. In this study, we investigated the specific effects of PFK1 and PFK2 on the cellular metabolism of S. cerevisiae. Results: Deletion of either PFK1 or PFK2 significantly reduced the cell growth, decreased ethanol and glycerol production and increased acetate production. Furthermore, through Flux Balance Analysis (FBA) and transcriptome analysis, we observed a significant upregulation of the Tricarboxylic Acid (TCA) cycle and the electron transfer chain in the PFK2 deletion strain. This upregulation indicated a shift towards enhanced oxidative respiration and energy production under the absence of the Beta subunit of Pfks. Furthermore, we demonstrated that the deletion of PFK2 led to a 33% improvement in the free fatty acid production, indicating its effectiveness as a key factor in regulation of lipid metabolism as well as bioproduction. Conclusions: Our physiological and transcriptomic data suggested that, as an isoenzyme, Pfk1 has a relatively limited influence on the metabolism of S. cerevisiae, whereas Pfk2 plays significant and vital roles in cellular metabolism. Deletion of PFK2 has the potential to greatly enhance respiration in yeast under aerobic conditions. These observations underscore the pivotal role of PFK2 in governing cellular energy metabolism and suggest that manipulation of PFK2 expression could hold promising implications for bioproduction processes.

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Section: Effects Of the Deletion Of Pfk1 And Pfk2 On The Respire-ferm...mentioning

confidence: 97%

Mechanistic understanding of the "gatekeeper" phosphofructokinase of the glycolytic pathway on the central carbon metabolism

Li,

Qin,

Chen

et al. 2023

Preprint

Self Cite

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“…5a). Deleting HXK2 can reduce the glucose consumption rate, which could release the Crabtree effect to get a higher ATP yield 74 . Similarly, Mth1 is involved in the glucose signalling pathway, and its active form Mth1 Δ231 acts as a transcription factor to repress hexose transporters (Fig.…”

Section: The Inositol Phosphate Mechanism Application Provides More A...mentioning

confidence: 99%

“…Similarly, Mth1 is involved in the glucose signalling pathway, and its active form Mth1 Δ231 acts as a transcription factor to repress hexose transporters (Fig. 5a), that ultimately restricts the Crabtree effect and derepress respiration 74 . Meanwhile, the mutation of Med2 *432Y , which is the tail module of RNA polymerase II mediator, can decrease the expression of genes involved in glycolysis and increase the expression of genes involved in protein synthesis.…”

Section: The Inositol Phosphate Mechanism Application Provides More A...mentioning

confidence: 99%

Increased CO2 Fixation Enables High Carbon-Yield Production of the Acrylic Acid Precursor 3-Hydroxypropionic Acid in Yeast

Liu,

Qin,

et al. 2023

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CO2 fixation plays a key role to make biobased production cost competitive. Here, we used 3-hydroxypropionic acid (3-HP) to showcase how CO2 fixation enabled approaching theoretical-yield production. Using genome-scale metabolic models to calculate the production envelope, we demonstrated that the provision of bicarbonate, formed from CO2, sealed previous attempts for high yield production of 3-HP. We thus developed multiple strategies for bicarbonate uptake, including the identification of Sul1 as a bicarbonate transporter, domain swapping and engineering of malonyl-CoA reductase, identification of Esbp6 as a 3-HP exporter, and deletion of Uga1 to prevent 3-HP degradation. The combined rational engineering increased 3-HP production from 0.15 g/L to 11.25 g/L in shake-flask using 20 g/L glucose, approaching the maximum theoretical yield with concurrent biomass formation. The engineered yeast forms the basis for commercialization of bio-acrylic acid, while our CO2 fixation strategies pave the way for CO2 being used as the sole carbon source.

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“…The function of 5PP-InsP 5 has been investigated more closely, especially its role in cellular energy signaling, where the production of 5PP-InsP 5 critically depends on ATP levels and regulates glycolytic flux accordingly [ 14 , 15 ]. Notably, 5PP-InsP 5 stimulates exocytosis of insulin-containing granules from pancreatic β-cells, ostensibly by competing with the plasma membrane lipid phosphatidylinositol-4,5-bisphosphate (PIP 2 ) for binding of synaptotagmin 7 [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

One Scaffold, Two Conformations: The Ring-Flip of the Messenger InsP8 Occurs under Cytosolic Conditions

et al. 2023

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Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” conformation with five axial substituents. Using 13C-labeled InsPs/PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger 1,5(PP)2-InsP4 (also termed InsP8) readily adopts both conformations at physiological conditions. Environmental factors—such as pH, metal cation composition, and temperature—strongly influence the conformational equilibrium. Thermodynamic data revealed that the transition of InsP8 from the equatorial to the axial conformation is, in fact, an exothermic process. The speciation of InsPs and PP-InsPs also affects their interaction with protein binding partners; addition of Mg2+ decreased the binding constant Kd of InsP8 to an SPX protein domain. The results illustrate that PP-InsP speciation reacts very sensitively to solution conditions, suggesting it might act as an environment-responsive molecular switch.

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Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast

Cited by 18 publications

References 77 publications

Mechanistic understanding of the "gatekeeper" phosphofructokinase of the glycolytic pathway on the central carbon metabolism

Mechanistic understanding of the "gatekeeper" phosphofructokinase of the glycolytic pathway on the central carbon metabolism

Increased CO2 Fixation Enables High Carbon-Yield Production of the Acrylic Acid Precursor 3-Hydroxypropionic Acid in Yeast

One Scaffold, Two Conformations: The Ring-Flip of the Messenger InsP8 Occurs under Cytosolic Conditions

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