Biology subjects

Jyoti, P.

Publications and source records attributed to Jyoti, P..

4 recordsLinked to original sources

bioRxiv2025

Persistent fatty acid catabolism during plant oil synthesis

Plant lipids are an essential energy source for diets and are a sustainable alternative to petroleum-based fuels and feed stocks. Fatty acid breakdown during seed germination is crucial for seedling establishment but unexpected during seed filling. Here, we demonstrate that the simultaneous biosynthesis and degradation of fatty acids begins early and continues across all phases of oil filling and throughout the photoperiod. Tests in camelina, rapeseed and engineered high-oil tobacco line confirmed that concomitant synthesis and breakdown in oil-producing tissues over development is the rule rather than the exception. We show that transgenics, designed for significantly higher fatty acid biosynthesis, fail to achieve a proportional increase in storage lipid levels due to increasing degradation, potentially explaining the underperformance of engineered lines compared to expectations.

plant biology↗

bioRxiv2021

Mutant strains of Escherichia coli lacking global regulators, arcA and fis, demonstrate better growth fitness by pathway reprogramming under acetate metabolism

Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A systems-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the substrates available in a range of nutrient niches such as the mammalian gut and high-fat diet. Therefore, investigating the study on acetate metabolism is highly significant. It is well known that the global regulators arcA and fis regulate acetate uptake genes in E. coli under glucose condition. In this study, we deciphered the growth and flux distribution of E.coli transcription regulatory knockout mutants {Delta}arcA, {Delta}fis and double deletion mutant, {Delta}arcAfis under acetate using 13C-Metabolic Flux Analysis which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~1.2-1.6 fold) with a proportionate increase in acetate uptake rates compared to the wild-type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes, which conferred an advantage of faster growth with better carbon usage in all the mutants. Under acetate metabolism, the mutants exhibited higher fluxes in the TCA cycle (~18-90%) and lower gluconeogenesis flux (~15-35%) with the proportional increase in growth rate. This study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate to acetyl-CoA and therefore are potential candidates that can serve as a precursor for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products. ImportanceUnravelling the role of global regulatory genes on microbial metabolism of substrates available in various growth niche is important. Studies have shown that the global transcriptional regulators arcA and fis, under glucose availability, suppress the acetate uptake genes indicating a link between nutrient source and gene regulatory control. This work is focused on deciphering the influence of these regulators on acetate metabolism in E.coli. Growth studies using knockout strains ({Delta}arcA, {Delta}fis and {Delta}arcAfis) and 13C Metabolic flux analysis defined precise metabolic phenotypes under acetate metabolism. Interestingly, the mutants showed metabolic readjustment to facilitate optimal biomass requirements and a better balance between energy and precursor synthesis, resulting in better growth, which lacked in the wild-type strain. The outcomes of this study will be leveraged in understanding the regulatory control under various nutrient shifts.

microbiology↗

bioRxiv2021

Oleate metabolism using kinetic 13C dilution strategy deciphered the potential role of global transcription regulator arcA in Escherichia coli

Microbial metabolism of long-chain fatty acids (LCFA; > C12) is of relevance owing to their presence in various nutrient niches. Microbes have evolved to metabolize LCFA by expressing relevant genes coordinated by various transcriptional regulators. Among the global transcriptional regulators, the metabolic control conferred by arcA (aerobic respiration control) under a LCFA medium is lacking. This work is targeted to unravel the metabolic features of E.coli MG1655 and its knockout strain {Delta}arcA under oleate (C18:1) as a sole carbon source, providing novel insights into the flexibility of the global regulators in maintaining the cellular physiology. Owing to the availability and cost of stable isotope LCFA tracers, we adopted a novel kinetic 13C dilution strategy. This allowed us to quantify the 13C dilution rates in the amino acids that retro-biosynthetically shed light on the central metabolic pathways in actively growing cells. Our data comprehensively mapped oleate oxidization in E.coli via the pathways of {beta}-oxidation, TCA cycle, anaplerotic and gluconeogenesis. Interestingly, arcA knockout showed expeditious growth (~60%) along with an increased oleate utilization rate (~55%) relative to the wild-type. {Delta}arcA also exhibited higher 13C dilution rates (> 20%) in proteinogenic amino acids than the wild-type. Overall, the study established the de-repression effect conferred by {Delta}arcA in E.coli, which resulted in a phenotype with reprogrammed metabolism favouring higher oleate assimilation. The outcomes suggest rational metabolic engineering of regulators as a strategy to develop smart cells for enhanced biotransformation of LCFA. This study also opens an avenue for adopting a kinetic 13C dilution strategy to decipher the cellular metabolism of a plethora of substrates, including other LCFA in microbes.

systems biology↗

bioRxiv2020

Entner-Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP in Ralstonia solanacearum

In Ralstonia solanacearum, a devastating phytopathogen whose metabolism is poorly understood, we observed that Entner-Doudoroff (ED) pathway and NonOxidative pentose phosphate pathway (OxPPP) bypasses glycolysis and OxPPP under glucose oxidation. Evidences derived from 13C stable isotopes feeding and genome annotation based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available 53 annotated R. solanacearum strains also including the recently reported strain (F1C1), representing the four phylotypes confirmed the lack of key genes coding for phosphofructokinase (pfk-1) and phosphogluconate dehydrogenase (gnd) enzymes that are relevant for glycolysis and OxPPP respectively. R. solanacearum F1C1 cells fed with 13C Glucose (99%[1-13C]- or 99%[1,2-13C]- or 40%[13C6]-glucose) followed by GC-MS based labelling analysis of fragments from amino acids, glycerol and ribose provided clear evidence that rather than Glycolysis and OxPPP, ED pathway and NonOxPPP are the main routes sustaining metabolism in R. solanacearum. The 13C incorporation in the mass ions of alanine (m/z 260, m/z 232); valine (m/z 288, m/z 260), glycine (m/z 218), serine (m/z 390, m/z 362), histidine (m/z 440, m/z 412), tyrosine (m/z 466, m/z 438), phenylalanine (m/z 336, m/z 308), glycerol (m/z 377) and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. ImportanceUnderstanding the metabolic versatility of Ralstonia solanacearum is important as it regulates the tradeoff between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on potential roles of Glycolysis and Oxidative pentose phosphate pathways (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotopes feeding and genome annotation based comparative metabolic network analysis that Entner-Doudoroff pathway and Non-OxPPP bypasses glycolysis and OxPPP during the oxidation of Glucose, one of the host xylem pool that serves as a potential carbon source (5). The outcomes help better defining the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.

systems biology↗