Biology subjects

Rao, C. V.

Publications and source records attributed to Rao, C. V..

6 recordsLinked to original sources

bioRxiv2026

Metabolic engineering of Yarrowia lipolytica for higher fatty alcohol production

Fatty alcohols are versatile chemicals with growing demand across a broad range of industries, yet conventional production methods pose environmental challenges. Microbial biosynthesis offers a promising alternative, if hosts can be engineered to achieve high product titers. The industrially relevant oleaginous yeast Yarrowia lipolytica is well suited to this challenge because of its natural capacity for lipid metabolism. Here, we engineered Y. lipolytica W29 for fatty alcohol production by disrupting pathways involved in lipogenesis and fatty alcohol oxidation, identifying fatty alcohol oxidation as a major constraint on product accumulation. Initial engineering yielded fatty alcohol titers of 2.5 g/L from 40 g/L glucose. Subsequent optimization of media supplements and nutrient concentrations, combined with deletion of the citrate transporter CEX1 and addition of 1% Tergitol to the extractive culture medium, increased titers to 10.9 g/L in shake flasks with 80 g/L glucose and a carbon-to-nitrogen ratio of 60. Scaling the process to fed-batch bioreactor cultivation further increased titers to 19.4 g/L. These results demonstrate that combining metabolic engineering with medium and process optimization enables high-titer fatty alcohol production in Y. lipolytica.

synthetic biology↗

bioRxiv2025

Hepatocyte MLKL Drives Obesity-Driven Hepatocellular Carcinoma Progression via Mitochondrial Dysfunction Independent of Necroptosis in MASLD

Background and AimsMetabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of hepatocellular carcinoma (HCC), particularly in obesity, yet mechanisms linking hepatocyte dysfunction to tumorigenesis remain unclear. Mixed lineage kinase domain-like protein (MLKL), the effector of necroptosis, is elevated in MASLD, but its hepatocyte-intrinsic role in obesity-driven MASLD-HCC is unknown. Approach and ResultsUsing a long-term Western diet (WD)-induced MASLD-HCC model in hepatocyte-specific MLKL knockout (MlklHepKO) mice, we defined MLKLs hepatocyte-intrinsic function. WD increased hepatocyte MLKL protein expression without detectable necroptosis activation, indicating a necroptosis-independent role. MLKL deficiency did not alter WD-induced inflammation, fibrosis, or liver injury but increased hepatic lipid accumulation while reducing lipotoxic lipid species and preserving mitochondrial function. WD-fed MlklHepKO mice developed fewer and smaller tumors with reduced incidence, multiplicity, proliferation, and stemness. Transcriptomic analysis revealed upregulation of mitochondrial oxidative phosphorylation pathways in MlklHepKO livers. WD suppressed the mitochondrial fusion protein and tumor suppressor MFN2, whereas MLKL deficiency restored MFN2 expression post-translationally. In HCC cells, MLKL deletion reduced proliferation, improved mitochondrial respiration, and decreased glycolysis; these effects were reversed by MFN2 deletion. MLKL localized to nuclear and mitochondrial compartments, consistent with organelle-intrinsic functions. The human MLKL inhibitor necrosulfonamide (NSA) suppressed HepG2 xenograft growth, and elevated MLKL expression in human HCC correlated with poorer overall survival. ConclusionsHepatocyte MLKL promotes MASLD-associated HCC through a non-necroptotic mechanism involving MFN2 suppression, impaired mitochondrial function, and increased tumor proliferation and stemness. These findings identify MLKL as a potential therapeutic target in MASLD-associated HCC.

cancer biology↗

bioRxiv2024

The MET growth signaling complex drives Alzheimers Disease-associated brain pathology in aged Shugoshin 1 mouse cohesinopathy model

The understanding on molecular processes toward Late-onset Alzheimers Disease (LOAD) has been insufficient to design LOAD intervention drugs. Previously, we discovered transgenic genomic instability model mice Sgo1-/+ accumulate cerebral amyloid-beta in old age. We proposed the "amyloid-beta accumulation cycle" hypothesis, in which cytotoxic, mitogenic and aneuploidgenic amyloid can create an autonomous mitotic cycle leading to accumulation of itself. However, the nature of the growth signaling that drives cells toward pathogenic mitotic cycle remained unidentified. In this study, we hypothesized that the aged Sgo1-/+ mice brains would show signs of mitogenic signaling activation, and searched for growth signaling activated in the vicinity of amyloid-beta, with spatial analysis on the cortex and hippocampus of Sgo1-/+ mice in middle-age and old-age. The analysis indicated activations of kinase signaling p42/44 MAPK ERK1/2, AMPK, JNK, Wnt signaling via GSK3 inactivation, as well as increases of p-TAU and other AD biomarkers, PLCG1, EGFR, MET, Neurofibromin and RAS. Immune activation markers CD45 and CD31 were also elevated in the microenvironment. A majority of activated growth signaling components are of the oncogenic MET signaling complex. The discovery supports repurposing of cancer drugs targeting the MET signaling complex and EGFR-RAS-MAPK axis for intervention and/or treatment of genomic instability-driven AD.

neuroscience↗

bioRxiv2019

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

BackgroundRhodosporidium toruloides is a basidiomycetes yeast that can accumulate large amount of lipids and natively produce carotenoids. To better assess this non-model yeasts metabolic capabilities, we reconstruct a genome-scale model of R. toruloides IFO0880s metabolic network (iRhto1108) using recent functional genomics and phenotypic data in literature or generated herein.\n\nResultsThe model iRhto1108 accounts for 2,203 reactions, 1,985 metabolites and 1,108 genes. In this work, we integrate and supplement the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organisms metabolic capabilities. Phenotype-genotype relationship predictions were improved through manual curation of gene-protein-reaction rules for 543 reactions and validations with gene essentiality data leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificity of 53.8%). Organism-specific macromolecular composition and ATP maintenance requirements were experimentally measured for two separate growth conditions: (i) carbon and (ii) nitrogen limitations. Overall, iRhto1108 reproduced R. toruloidess utilization capabilities for 18 alternate substrates, matched measured wild-type growth yield, and recapitulated the viability of 772 out of 819 deletion mutants. As a demonstration to the models fidelity in guiding engineering interventions, the OptForce procedure was applied on iRhto1108 for the overproduction of triacylglycerol. Suggested interventions recapitulated many of the previously successfully implemented genetic modifications and put forth a few new ones.\n\nConclusioniRhto1108 offers a highly curated model for a non-model yeast supported by multiple layers of experimental data that can be used to inform genetic interventions.

systems biology↗

bioRxiv2019

Targeted sequencing of candidate genes of dyslipidemia in Punjabi Sikhs: Population-specific rare variants in GCKR promote ectopic fat deposition

Dyslipidemia is a well-established risk factor for cardiovascular diseases. Although, advances in genome-wide technologies have enabled the discovery of hundreds of genes associated with blood lipid phenotypes, most of the heritability remains unexplained. Here we performed targeted resequencing of 13 bona fide candidate genes of dyslipidemia to identify the underlying biological functions. We sequenced 940 Sikh subjects with extreme serum levels of hypertriglyceridemia (HTG) and 2,355 subjects were used for replication studies; all 3,295 participants were part of the Asian Indians Diabetic Heart Study. Gene-centric analysis revealed a burden of variants for increasing HTG risk in GCKR (p=2.1x10-5), LPL (p=1.6x10-3) and MLXIPL (p=1.6x10-2) genes. Of these, three missense and damaging variants within GCKR were further examined for functional consequences in vivo using a transgenic zebrafish model. All three mutations were South Asian population-specific and were largely absent in other multiethnic populations of the Exome Aggregation Consortium. We built different transgenic models of human GCKR with and without mutations and analyzed the effects of dietary changes in vivo. Despite the short-term feeding, profound phenotypic changes were apparent in hepatocyte histology and fat deposition associated with increased expression of GCKR in response to a high fat diet (HFD). Liver histology of the GCKRmut showed severe fatty metamorphosis which correlated with ~7 fold increase in the mRNA expression in the GCKRmut fish even in the absence of a high fat diet. These findings suggest that functionally disruptive GCKR variants not only increase the risk of HTG but may enhance ectopic lipid/fat storage defects in the absence of obesity and HFD. To our knowledge, this is the first transgenic zebrafish model of a putative human disease gene built to accurately assess the influence of rare genetic changes and their phenotypic consequences in vivo.

genetics↗

bioRxiv2018

Driving the expression of the Salmonella enterica sv Typhimurium flagellum using flhDC from Escherichia coli results in key regulatory and cellular differences.

The flagellar systems of Escherichia coli and Salmonella enterica exhibit a significant level of genetic and functional synteny. Both systems are controlled by the flagellar specific master regulator FlhD4C2. Since the early days of genetic analyses of flagellar systems it has been known that E. coli flhDC can complement a {Delta}flhDC mutant in S. enterica. The genomic revolution has identified how genetic changes to transcription factors and / or DNA binding sites can impact the phenotypic outcome across related species. We were therefore interested in asking: using modern tools to interrogate flagellar gene expression and assembly, what would the impact be of replacing the flhDC coding sequences in S. enterica for the E. coli genes at the flhDC S. entercia chromosomal locus? We show that even though all strains created are motile, flagellar gene expression is measurably lower when flhDCEC are present. These changes can be attributed to the impact of FlhD4C2 DNA recognition and the protein-protein interactions required to generate a stable FlhD4C2 complex. Furthermore, our data suggests that in E. coli the internal flagellar FliT regulatory feedback loop has a marked difference with respect to output of the flagellar systems. We argue due diligence is required in making assumptions based on heterologous expression of regulators and that even systems showing significant synteny may not behave in exactly the same manner.

microbiology↗