Biology subjects

Vengayil, V.

Publications and source records attributed to Vengayil, V..

6 recordsLinked to original sources

bioRxiv2026

Rad53/Chk2 couples mitochondrial outputs and ROS with G2/M cell cycle progression

Cell-cycle progression requires coordination with cellular metabolism, yet how checkpoint kinases contribute to this coordination during normal growth remains poorly understood. Here, we uncover an unexpected role for the checkpoint kinase Rad53/Chk2 in coupling mitochondrial and redox homeostasis to G2/M progression. In prototrophic S. cerevisiae, Rad53 loss (rad53{Delta}) disrupts cell-cycle progression and causes cells to accumulate in G2/M, alongside extensive metabolic remodelling with increased tricarboxylic acid (TCA) cycle flux. Mitochondrial proteomics reveals altered relative abundances of individual electron transport chain proteins, and mitochondrial membrane potential increases without increased oxygen consumption or ATP generation. This altered mitochondrial state is associated with elevated reactive oxygen species (ROS) and oxidative stress. Genetic analyses establish that mitochondrial phenotypes require Rad53 kinase activity and are distinct from the loss of SML1. Antioxidant treatment rescues cell-division, budding defects and the accumulation of abnormally sized cells, establishing ROS as a primary cause of cell-cycle defects. Thus, Rad53 couples mitochondrial and redox homeostasis to G2/M progression during normal growth.

cell biology↗

bioRxiv2026

Metabolomics of in vivo inflammation identifies soluble sialic acid as a conserved myeloid-cell metabolite

During an immune response, metabolism changes dramatically. Metabolites are oxidized to power immune cell functions, serve as building blocks for proliferation, and act as effectors to regulate pathogen or host cells. Though metabolic changes in cultured cells have been studied extensively, metabolism changes in vivo are less understood. Here, we measured metabolomic changes across six mouse tissues in three models of immune activation: CpG-DNA cytokine storm, lymphocytic choriomeningitis virus infection, and polyI:C viral mimetic injection; and carried out metabolomics in cultured macrophages activated with different stimuli. We found most metabolomic changes were exclusive to either inflamed tissues or cultured macrophages, although itaconate was strongly induced in both contexts. We then mechanistically dissected the role of the soluble sialic acid N-glycolylneuraminic acid, which is highly induced in inflamed tissues yet only modestly in cultured macrophages. This metabolite rises in tissues in different models of inflammation, and the analogous human metabolite, N-acetylneuraminic acid, is increased in human patients experiencing inflammation. We found that N-glycolylneuraminic acid is produced in CD11b+ myeloid cells by cleavage of protein-bound sialic acid. However, blocking its production did not affect CpG-DNA liver inflammation or LCMV infection in mice. Therefore, these experiments identify soluble sialic acid as a conserved biomarker of inflammation in mice and humans and highlight the differences in metabolism between in vitro and in vivo models of inflammation.

biochemistry↗

bioRxiv2025

Gcn4 mediates SAM allocations and methylation balance between phospholipids and histones

Methionine availability alters the methylation status of various cellular molecules, and thereby controls metabolic state, via its metabolite S-adenosyl methionine (SAM). In yeast cells, supplementing excess methionine drives cell growth and proliferation, as well as phospholipid biogenesis. High methionine stabilizes the transcription factor Gcn4 (Atf4), which drives an anabolic transcription program to sustain high growth. Here, we investigated whether Gcn4 regulates the allocation of SAM towards distinct methylation outputs, during this methionine-dependent anabolic program. We find that methionine induced Gcn4 increases the expression of phospholipid methyltransferases during methionine supplementation. In{Delta} gcn4 cells, the expression of these methyltransferases significantly decreases, and results in reduced SAM allocations towards phospholipid methylation, alongside increased intracellular SAM, disrupting the balance in the SAM/SAH ratio in these cells. Excess SAM pools are re-allocated to histones, resulting in their hyper-methylation. Collectively, we uncover that Gcn4 modulates SAM allocations towards phospholipid methyltransferases, and the overall methyl allocation between phospholipids and histones. Our study reveals a novel role for Gcn4 in SAM dependent phospholipid biosynthesis in cells growing in methionine sufficiency.

cell biology↗

bioRxiv2024

Active control of mitochondrial network morphology by metabolism driven redox state

Mitochondria are dynamic organelles that constantly change morphology. What controls mitochondrial morphology however remains unresolved. Using actively respiring yeast cells growing in distinct carbon sources, we find that mitochondrial morphology and activity are unrelated. Cells can exhibit fragmented or networked mitochondrial morphology in different nutrient environments independent of mitochondrial activity. Instead, mitochondrial morphology is controlled by the intracellular redox state, which itself depends on the nature of electron entry into the Electron Transport Chain (ETC)-- through complex I/II, or directly to coenzyme Q/cytochrome c. In metabolic conditions where direct electron entry is high, reactive oxygen species (ROS) increase, resulting in an oxidized cytosolic environment and rapid mitochondrial fragmentation. Decreasing direct electron entry into the ETC genetically or chemically, or reducing the cytosolic environment rapidly restores networked morphologies. Using controlled disruptions of electron flow to alter ROS and redox state, we demonstrate minute-scale, reversible control between networked and fragmented forms in an activity independent manner. Mechanistically, the fission machinery through Dnm1 responds in minute-scale to redox state changes, preceding the change in mitochondrial form. Thus, the metabolic state of the cell and its consequent cellular redox state actively controls mitochondrial form.

cell 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↗

bioRxiv2019

The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown in S. cerevisiae.

Cells use multiple mechanisms to regulate their metabolic states depending on changes in their nutrient environment. A well-known example is the response of cells to glucose availability. In S. cerevisiae cells growing in glucose-limited medium, the re-availability of glucose leads to the downregulation of gluconeogenesis, the activation of glycolysis, and robust glucose repression. However, our knowledge of the initial mechanisms mediating this glucose-dependent downregulation of the gluconeogenic transcription factors is incomplete. We used the gluconeogenic transcription factor Rds2 as a candidate with which to discover regulators of early events leading to glucose repression. Here, we identify a novel role for the E3 ubiquitin ligase Pib1 in regulating the stability and degradation of Rds2. Glucose addition to glucose-limited cells results in rapid ubiquitination of Rds2, followed by its proteasomal degradation. Through in vivo and in vitro experiments, we establish Pib1 as a ubiquitin E3 ligase that regulates Rds2 ubiquitination and stability. Notably, this Pib1 mediated Rds2 ubiquitination, followed by proteasomal degradation, is specific to the presence of glucose. Pib1 is required for complete glucose repression, and enables cells to optimally grow in competitive environments when glucose becomes re-available. Our results reveal the existence of a Pib1 E3-ubiquitin ligase mediated regulatory program that mediates glucose-repression when glucose availability is restored.

biochemistry↗