scholarly journals The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Xujun Liu ◽  
Wenzhe Si ◽  
Lin He ◽  
Jianguo Yang ◽  
Yani Peng ◽  
...  
Keyword(s):  
Epigenetic Regulation ◽  
Citrate Synthase ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Chromatin Dynamics ◽  
Metabolic Intermediates ◽  
The Tca Cycle ◽  
Transport Chain ◽  
Outstanding Question ◽  
Aconitase 2

AbstractThe scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid (TCA) cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the nucleus. We report here the identification of a nonclassical TCA cycle in the nucleus (nTCA cycle). We found that all the TCA cycle-associated enzymes including citrate synthase (CS), aconitase 2 (ACO2), isocitrate dehydrogenase 3 (IDH3), oxoglutarate dehydrogenase (OGDH), succinyl-CoA synthetase (SCS), fumarate hydratase (FH), and malate dehydrogenase 2 (MDH2), except for succinate dehydrogenase (SDH), a component of electron transport chain for generating ATP, exist in the nucleus. We showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in cyanobacteria. We propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates, not for energy production. We demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription regulation. Together, our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.

scholarly journals Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant Staphylococcus aureus USA300

2018 ◽  
Vol 6 (4) ◽  
pp. 113 ◽  
Author(s):  
Sarah De Backer ◽  
Julia Sabirova ◽  
Ines De Pauw ◽  
Henri De Greve ◽  
Jean-Pierre Hernalsteens ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Urea Cycle ◽  
Citrate Synthase ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Matrix Composition ◽  
Methicillin Resistant ◽  
The Tca Cycle ◽  
The Matrix ◽  
Biofilm Matrix

In methicillin-sensitive Staphylococcus aureus (MSSA), the tricarboxylic acid (TCA) cycle is known to negatively regulate production of the major biofilm-matrix exopolysaccharide, PIA/PNAG. However, methicillin-resistant S. aureus (MRSA) produce a primarily proteinaceous biofilm matrix, and contribution of the TCA-cycle therein remains unclear. Utilizing USA300-JE2 Tn-mutants (NARSA) in genes encoding TCA- and urea cycle enzymes for transduction into a prolific biofilm-forming USA300 strain (UAS391-Erys), we studied the contribution of the TCA- and urea cycle and of proteins, eDNA and PIA/PNAG, to the matrix. Genes targeted in the urea cycle encoded argininosuccinate lyase and arginase (argH::Tn and rocF::Tn), and in the TCA-cycle encoded succinyl-CoA synthetase, succinate dehydrogenase, aconitase, isocitrate dehydrogenase, fumarate hydratase class II, and citrate synthase II (sucC::Tn, sdhA/B::Tn, acnA::Tn, icd::Tn, fumC::Tn and gltA::Tn). Biofilm formation was significantly decreased under no flow and flow conditions by argH::Tn, fumC::Tn, and sdhA/B::Tn (range OD492 0.374−0.667; integrated densities 2.065−4.875) compared to UAS391-EryS (OD492 0.814; integrated density 10.676) (p ≤ 0.008). Cellular and matrix stains, enzymatic treatment (Proteinase K, DNase I), and reverse-transcriptase PCR-based gene-expression analysis of fibronectin-binding proteins (fnbA/B) and the staphylococcal accessory regulator (sarA) on pre-formed UAS391-Erys and Tn-mutant biofilms showed: (i) < 1% PIA/PNAG in the proteinaceous/eDNA matrix; (ii) increased proteins under no flow and flow in the matrix of Tn mutant biofilms (on average 50 and 51 (±11)%) compared to UAS391-Erys (on average 22 and 25 (±4)%) (p < 0.001); and (iii) down- and up-regulation of fnbA/B and sarA, respectively, in Tn-mutants compared to UAS391-EryS (0.62-, 0.57-, and 2.23-fold on average). In conclusion, we show that the biofilm matrix of MRSA-USA300 and the corresponding Tn mutants is PIA/PNAG-independent and are mainly composed of proteins and eDNA. The primary impact of TCA-cycle inactivation was on the protein component of the biofilm matrix of MRSA-USA300.

scholarly journals Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Dylan Gerard Ryan ◽  
Ming Yang ◽  
Hiran A Prag ◽  
Giovanny Rodriguez Blanco ◽  
Efterpi Nikitopoulou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Metabolic Response ◽  
Tricarboxylic Acid Cycle ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Comparative Approach ◽  
Redox Biology ◽  
The Tca Cycle

The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.

Effect of thermal injury on the TCA cycle enzymes of Staphylococcus aureus MF 31 and Salmonella typhimurium 7136

1971 ◽  
Vol 17 (6) ◽  
pp. 759-765 ◽  
Author(s):  
Richard I. Tomlins ◽  
Merle D. Pierson ◽  
Z. John Ordal
Keyword(s):  
Lactate Dehydrogenase ◽  
Malate Dehydrogenase ◽  
Thermal Injury ◽  
Specific Activity ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Tca Cycle Enzymes ◽  
The Tca Cycle ◽  
Oxoglutarate Dehydrogenase ◽  
Metabolic Activities

The heating of S. aureus MF-31 and S. typhimurium 7136 at 52C and 48C respectively, produced a sublethal heat injury. When injured cells were placed in fresh growth medium they recovered. The recovery of S. aureus was not inhibited by chloramphenicol. The metabolic activities of tricarboxylic acid (TCA) cycle enzymes, as well as other selected enzymes in crude extracts of normal and heat-injured cells of both microorganisms were assayed. In extracts from S. typhimurium there was some loss of specific activity with fumarate hydratase, glutamate dehydrogenase, fructose diphosphate aldolase, lactate dehydrogenase, and the NAD(P) oxidases as a result of heating. In extracts from S. aureus oxoglutarate dehydrogenase, malate dehydrogenase and lactate dehydrogenase were severely inactivated after heating. Other enzymes in comparison were only moderately sensitive to heat. No significant increase in enzyme activity was observed in extracts from injured cells of either microorganism. Re-naturation of lactate dehydrogenase and malate dehydrogenase occurred during the recovery of S. aureus both in the presence and absence of chloramphenicol. No renaturation of oxoglutarate dehydrogenase was found under the same conditions.

scholarly journals SUN-219 Electron Transport Chain Complex 2 in Mitochondrial Pregnenolone Synthesis

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Himangshu S Bose ◽  
Brendan Marshall ◽  
Dilip Debnath ◽  
Elizabeth W Perry ◽  
Randy M Whittal
Keyword(s):  
Electron Transport ◽  
Intermediate State ◽  
Electron Transport Chain ◽  
Molten Globule ◽  
Tca Cycle ◽  
Steroid Synthesis ◽  
Aberrant Expression ◽  
Complex Ii ◽  
The Tca Cycle ◽  
Transport Chain

Abstract The mitochondrial P450 family of enzymes (SCC), which require the electron transport chain (ETC) complexes III, IV and V, initiate steroidogenesis by cleaving the sidechain of cholesterol to synthesize steroid hormones, an essential component for mammalian survival. SCC is required for full-term gestation, and aberrant expression may cause pseudohermaphroditism, breast cancer or polycystic ovary syndrome. Complex II or succinate dehydrogenase (quinone) is shared with the TCA cycle and has no proton pumping capacity and no known role in steroid synthesis. We now show that succinate is an intermediate metabolite in the TCA cycle and plays a central role physiologically. Specifically, complex II is required for SCC activation, where the proton pump facilitates an active intermediate state conformation at the matrix, so that in the presence of succinate, ATP can add phosphate. A longer intermediate equilibrium state generates a transient stabilization to enhance the binding of phosphate anions in the presence of succinate anions, resulting in higher enthalpy and activity. An inhibition of the processing at the intermediate state stops phosphate addition and activity. We further describe that phosphate circulation brings the molten globule, an intermediate, to an active folded state. This is the first report showing that an intermediate state activated by succinate facilitates ETC complex II interaction with complexes III and IV for metabolism.

Protein hyperacylation links mitochondrial dysfunction with nuclear organization

2020 ◽  
Author(s):  
John Smestad ◽  
Micah McCauley ◽  
Matthew Amato ◽  
Yuning Xiong ◽  
Juan Liu ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Metabolic Regulation ◽  
Tca Cycle ◽  
Interphase Chromatin ◽  
Histone Octamer ◽  
The Tca Cycle ◽  
Transport Chain ◽  
Topologically Associated Domains ◽  
Biophysical Effects ◽  
Liquid Liquid Phase Separation

SummaryCellular metabolism is linked to epigenetics, but the biophysical effects of metabolism on chromatin structure and implications for gene regulation remain largely unknown. Here, using a broken tricarboxylic acid (TCA) cycle and disrupted electron transport chain (ETC) exemplified by succinate dehydrogenase subunit C (SDHC) deficiency, we investigated the effects of metabolism on chromatin architecture over multiple distance scales [nucleosomes (∼102 bp), topologically-associated domains (TADs; ∼105 – 106 bp), and chromatin compartments (106 – 108 bp)]. Metabolically-driven hyperacylation of histones led to weakened nucleosome positioning in multiple types of chromatin, and we further demonstrate that lysine acylation directly destabilizes histone octamer-DNA interactions. Hyperacylation of cohesin subunits correlated with decreased mobility on interphase chromatin and increased TAD boundary strength, suggesting that cohesin is metabolically regulated. Erosion of chromatin compartment distinctions reveals metabolic regulation of chromatin liquid-liquid phase separation. The TCA cycle and ETC thus modulate chromatin structure over multiple distance scales.

scholarly journals RSM–GA Based Optimization of Bacterial PHA Production and In Silico Modulation of Citrate Synthase for Enhancing PHA Production

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 872 ◽  
Author(s):  
Apoorva Rao ◽  
Shafiul Haque ◽  
Hesham A. El-Enshasy ◽  
Vineeta Singh ◽  
Bhartendu Nath Mishra
Keyword(s):  
Molecular Docking ◽  
Nitrogen Source ◽  
In Silico ◽  
Citrate Synthase ◽  
Tca Cycle ◽  
Management Approach ◽  
Carbon And Nitrogen ◽  
The Tca Cycle ◽  
Different Types ◽  
Pha Production

The inexhaustible nature and biodegradability of bioplastics like polyhydroxyalkanoates (PHAs) make them suitable assets to replace synthetic plastics. The eventual fate of these eco-friendly and non-toxic bioplastics relies upon the endeavors towards satisfying cost and, in addition, execution necessity. In this study, we utilized and statistically optimized different food (kitchen-/agro-) waste as a sole carbon/nitrogen source for the production of PHA at a reduced cost, indicating a proficient waste administration procedure. Seven different types of kitchen-/agro-waste were used as unique carbon source and four different types of nitrogen source were used to study their impact on PHA production by Bacillus subtilis MTCC 144. Among four different studied production media, mineral salt medium (MSM) (biomass: 37.7 g/L; cell dry weight: 1.8 g/L; and PHA: 1.54 g/L) was found most suitable for PHA production. Further, carbon and nitrogen components of MSM were optimized using one-factor-at-a-time experiments, and found that watermelon rind (PHA = 12.97 g/L) and pulse peel (PHA = 13.5 g/L) were the most suitable carbon and nitrogen sources, respectively, in terms of PHA (78.60%) recovery. The concentrations of these factors (sources) were statistically optimized using response surface methodology coupled with the genetic algorithm approach. Additionally, in order to enhance microbial PHA production, the interaction of citrate synthase, a key enzyme in the TCA cycle, with different known inhibitors was studied using in silico molecular docking approach. The inhibition of citrate synthase induces the blockage of the tricarboxylic cycle (TCA), thereby increasing the concentration of acetyl-CoA that helps in enhanced PHA production. Molecular docking of citrate synthase with different inhibitors of PubChem database revealed that hesperidin (PubChem compound CID ID 10621), generally present in citrus fruits, is the most efficient inhibitor of the TCA cycle with the binding score of –11.4 and warrants experimental validation. Overall, this study provides an efficient food waste management approach by reducing the production cost and enhancing the production of PHA, thereby lessening our reliance on petroleum-based plastics.

scholarly journals Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism

2021 ◽  
Author(s):  
Dylan Gerard Ryan ◽  
Ming Yang ◽  
Hiran A Prag ◽  
Giovanny Rodriguez Blanco ◽  
Efterpi Nikitopoulou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Metabolic Response ◽  
Tricarboxylic Acid Cycle ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Comparative Approach ◽  
Redox Biology ◽  
The Tca Cycle

The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.

scholarly journals Procyclic trypanosomes recycle glucose catabolites and TCA cycle intermediates to stimulate growth in the presence of physiological amounts of proline

2021 ◽  
Vol 17 (3) ◽  
pp. e1009204
Author(s):  
Oriana Villafraz ◽  
Marc Biran ◽  
Erika Pineda ◽  
Nicolas Plazolles ◽  
Edern Cahoreau ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Tca Cycle ◽  
Central Carbon Metabolism ◽  
Tsetse Fly ◽  
Growth Defect ◽  
Insect Vector ◽  
Metabolic Intermediates ◽  
The Tca Cycle ◽  
Production And Consumption ◽  
Tca Cycle Intermediates

Trypanosoma brucei, a protist responsible for human African trypanosomiasis (sleeping sickness), is transmitted by the tsetse fly where the procyclic forms of the parasite develop in the proline-rich (1–2 mM) and glucose-depleted digestive tract. Proline is essential for the midgut colonization of the parasite in the insect vector, however other carbon sources could be available and used to feed its central metabolism. Here we show that procyclic trypanosomes can consume and metabolize metabolic intermediates, including those excreted from glucose catabolism (succinate, alanine and pyruvate), with the exception of acetate, which is the ultimate end-product excreted by the parasite. Among the tested metabolites, tricarboxylic acid (TCA) cycle intermediates (succinate, malate and α-ketoglutarate) stimulated growth of the parasite in the presence of 2 mM proline. The pathways used for their metabolism were mapped by proton-NMR metabolic profiling and phenotypic analyses of thirteen RNAi and/or null mutants affecting central carbon metabolism. We showed that (i) malate is converted to succinate by both the reducing and oxidative branches of the TCA cycle, which demonstrates that procyclic trypanosomes can use the full TCA cycle, (ii) the enormous rate of α-ketoglutarate consumption (15-times higher than glucose) is possible thanks to the balanced production and consumption of NADH at the substrate level and (iii) α-ketoglutarate is toxic for trypanosomes if not appropriately metabolized as observed for an α-ketoglutarate dehydrogenase null mutant. In addition, epimastigotes produced from procyclics upon overexpression of RBP6 showed a growth defect in the presence of 2 mM proline, which is rescued by α-ketoglutarate, suggesting that physiological amounts of proline are not sufficient per se for the development of trypanosomes in the fly. In conclusion, these data show that trypanosomes can metabolize multiple metabolites, in addition to proline, which allows them to confront challenging environments in the fly.

scholarly journals Engineering central pathways for industrial-level (3R)-acetoin biosynthesis in Corynebacterium glutamicum

2020 ◽  
Author(s):  
Lingxue Lu ◽  
Yufeng Mao ◽  
Mengyun Kou ◽  
Zhenzhen Cui ◽  
Biao Jin ◽  
...  
Keyword(s):  
Corynebacterium Glutamicum ◽  
Citrate Synthase ◽  
Optical Purity ◽  
Value Added ◽  
Tca Cycle ◽  
Product Yield ◽  
The Tca Cycle ◽  
Acetoin Production ◽  
Industrial Level ◽  
Optically Pure

Abstract Background: Acetoin, especially the optically pure (3S)- or (3R)-enantiomer, is a high-value-added bio-based platform chemical and important potential pharmaceutical intermediate. Over the past decades, intense efforts have been devoted to the production of acetoin through green biotechniques. However, efficient and economical methods for the production of optically pure acetoin enantiomers are rarely reported. Previously, we systematically engineered the GRAS microorganism Corynebacterium glutamicum to efficiently produce (3R)-acetoin from glucose. Nevertheless, its yield and average productivity were still unsatisfactory for industrial bioprocesses.Results: In this study, cellular carbon fluxes in the acetoin producer CGR6 were further redirected toward acetoin synthesis using several metabolic engineering strategies, including blocking anaplerotic pathways, attenuating key genes of the TCA cycle and integrating additional copies of the alsSD operon into the genome. Among them, the combination of attenuation of citrate synthase and inactivation of phosphoenolpyruvate carboxylase showed a significant synergistic effect on acetoin production. Finally, the optimal engineered strain CGS11 produced a titer of 102.45 g/L acetoin with a yield of 0.419 g/g glucose at a rate of 1.86 g/L/h in a 5 L fermenter. The optical purity of the resulting (3R)-acetoin surpassed 95%.Conclusion: To the best of our knowledge, this is the highest titer of highly enantiomerically enriched (3R)-acetoin, together with a competitive product yield and productivity, achieved in a simple, green processes without expensive additives or substrates. This process therefore opens the possibility to achieve easy, efficient, economical and environmentally-friendly production of (3R)-acetoin via microbial fermentation in the near future.

scholarly journals Heterogeneous adaptation of cysteine reactivity to a covalent oncometabolite

2020 ◽  
Author(s):  
Minervo Perez ◽  
Daniel W. Bak ◽  
Sarah E. Bergholtz ◽  
Daniel R. Crooks ◽  
Youfeng Yang ◽  
...  
Keyword(s):  
Cell Line ◽  
Fumarate Hydratase ◽  
Tca Cycle ◽  
Covalent Modification ◽  
Cysteine Residues ◽  
Posttranslational Regulation ◽  
Equal Proportion ◽  
Cancer Syndrome ◽  
Cycle Enzyme ◽  
The Tca Cycle

ABSTRACTMetabolism and signaling intersect in the genetic cancer syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a disease in which mutation of the TCA cycle enzyme fumarate hydratase (FH) causes hyperaccumulation of fumarate. This electrophilic oncometabolite can alter gene activity at the level of transcription, via reversible inhibition of epigenetic dioxygenases, as well as posttranslationally, via covalent modification of cysteine residues. To better understand how metabolites function as covalent signals, here we report a chemoproteomic analysis of a kidney-derived HLRCC cell line. Building on previous studies, we applied a general reactivity probe to compile a dataset of cysteine residues sensitive to rescue of cellular FH activity. This revealed a broad upregulation of cysteine reactivity upon FH rescue, caused by an approximately equal proportion of transcriptional and posttranslational regulation in the rescue cell line. Gene ontology analysis highlights new targets and pathways potentially modulated by FH mutation. Comparison of the new dataset to literature studies highlights considerable heterogeneity in the adaptive response of cysteine-containing proteins in different models of HLRCC. Our analysis provides a resource for understanding the proteomic adaptation to fumarate accumulation, and a foundation for future efforts to exploit this knowledge for cancer therapy.

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