Biology subjects

Niphadkar, S.

Publications and source records attributed to Niphadkar, S..

3 recordsLinked to original sources

bioRxiv2023

Metabolic adaptation pilots the differentiation of human hematopoietic cells

A continuous supply of energy and metabolic intermediates is an essential prerequisite for survival and the highest priority for the cell. We hypothesize that cell differentiation is a process of optimization of energy flow in a changing environment through phenotypic adaptation. A mechanistic basis of this hypothesis is provided by the established link between core energy metabolism and epigenetic covalent modifications of chromatin. This hypothesis predicts that early metabolic perturbations impact subsequent differentiation. To test this, we induced transient metabolic perturbations in undifferentiated human hematopoietic cells using pharmacological inhibitors targeting key metabolic reactions. We recorded changes in chromatin structure and gene expression, as well as phenotypic alterations by single-cell ATAC and RNA sequencing, time-lapse microscopy and flow cytometry. Our observations suggest that these metabolic perturbations are shortly followed by alterations in chromatin structure, leading to changes in gene expression. We also show that these transient fluctuations alter the differentiation potential of the cells.

cell biology↗

bioRxiv2023

The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and adapt to glucose depletion

To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the requirement of PP2A-like phosphatase Ppg1 for appropriate carbon allocations towards gluconeogenic outputs - trehalose, glycogen, UDP-glucose, UDP-GlcNAc - specifically after glucose depletion. This homeostatic Ppg1 function is mediated via regulation of the assembly of the Far complex - a multi-subunit complex that tethers to the ER and mitochondrial outer membranes as localized signaling hubs. We show that the Far complex assembly is Ppg1 catalytic activity-dependent. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex abundance. This Ppg1-mediated Far complex assembly, and dependent control of gluconeogenic outputs enhances adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby enable cells metabolically adapt to nutrient fluctuations.

systems biology↗

bioRxiv2022

Phosphate budgeting to mitochondria controls glucose-mediated mitochondrial repression

Many cells in high glucose repress mitochondrial respiration, as observed in the Crabtree and Warburg effects. Our understanding of biochemical constraints for mitochondrial activation is limited. Using a Saccharomyces cerevisiae screen, we identified the conserved deubiquitinase Ubp3 (Usp10), as necessary for mitochondrial repression. Ubp3 mutants have increased mitochondrial activity despite abundant glucose, along with decreased glycolytic enzymes, and a rewired glucose metabolic network with increased trehalose production. Utilizing{Delta} ubp3 cells, along with orthogonal approaches, we establish that the high glycolytic flux in glucose continuously consumes free Pi. This restricts mitochondrial access to inorganic phosphate (Pi), and prevents mitochondrial activation. Contrastingly, rewired glucose metabolism with enhanced trehalose production and reduced GAPDH (as in{Delta} ubp3 cells) restores Pi. This collectively results in increased mitochondrial Pi and derepression, while restricting mitochondrial Pi transport prevents activation. We therefore suggest that glycolytic-flux dependent intracellular Pi budgeting is a key constraint for mitochondrial repression.

biochemistry↗