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Natural tricarboxylic acid (TCA) cycle variants The classical TCA cycle is represented by the unbroken black line. (1) The citramalate shunt, yellow broken arrows; (2) the glyoxylate shunt, green broken arrows; (3) the TCA cycle variant newly discovered in cyanobacteria, blue broken arrows; (4) the GABA shunt, red broken arrows; (5) the closing reaction (without glyoxylate shunt) of the previously thought to be incomplete cyanobacterial TCA cycle, grey broken arrows; and (6) the acetate shunt, broken violet arrows. For clarity, cofactors have been omitted. AlaAT, alanine aminotransferase; AspAT, aspartate aminotransferase; GABA-T, g-aminobutyric acid aminotransferase; GAD, glutamate decarboxylase; ICL, isocitratelyase; MS, malate synthase; OGDC, 2-oxoglutarate decarboxylase; SSADH, succinic semialdehydedehydrogenase; CMS, citramalate synthase; ASCT, acetate:succinate CoA-transferase.
Source publication
The tricarboxylic acid (TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were r...
Context in source publication
Context 1
... promising strategy in plants would thus likely do the same as described earler for bacteria; as mentioned earlier, a wide range of variant TCA cycles are known in nature, and the major variants are summarized in Figure 6. Introduction of some of these may prove a more effective furture strategy at improving plant performance, as these may well be less subject to (2) the glyoxylate shunt, green broken arrows; (3) the TCA cycle variant newly discovered in cyanobacteria, blue broken arrows; (4) the GABA shunt, red broken arrows; (5) the closing reaction (without glyoxylate shunt) of the previously thought to be incomplete cyanobacterial TCA cycle, grey broken arrows; and (6) the acetate shunt, broken violet arrows. ...
Citations
... These processes require both ATP and UTP and take place across the chloroplast and cytosol (McClain and Sharkey 2019). The TCA cycle provides precursors for respiration, amino acid biosynthesis, and nitrogen metabolism and ultimately produces some ATP and NADH in the mitochondria (Zhang and Fernie 2018). The OPPP produces NADPH and pentose phosphates. ...
Balancing the ATP: NADPH demand from plant metabolism with supply from photosynthesis is essential for preventing photodamage and operating efficiently, so understanding its drivers is important for integrating metabolism with the light reactions of photosynthesis and for bioengineering efforts that may radically change this demand. It is often assumed that the C3 cycle and photorespiration consume the largest amount of ATP and reductant in illuminated leaves and as a result mostly determine the ATP: NADPH demand. However, the quantitative extent to which other energy consuming metabolic processes contribute in large ways to overall ATP: NADPH demand remains unknown. Here, we used the metabolic flux networks of numerous recently published isotopically non-stationary metabolic flux analyses (INST-MFA) to evaluate flux through the C3 cycle, photorespiration, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and starch/sucrose synthesis and characterize broad trends in the demand of energy across different pathways and compartments as well as in the overall ATP:NADPH demand. These data sets include a variety of species including Arabidopsis thaliana, Nicotiana tabacum, and Camelina sativa as well as varying environmental factors including high/low light, day length, and photorespiratory levels. Examining these datasets in aggregate reveals that ultimately the bulk of the energy flux occurred in the C3 cycle and photorespiration, however, the energy demand from these pathways did not determine the ATP: NADPH demand alone. Instead, a notable contribution was revealed from starch and sucrose synthesis which might counterbalance photorespiratory demand and result in fewer adjustments in mechanisms which balance the ATP deficit.
... Similar outcomes are observed in cluster roots, with a higher proportion in white lupin under Fe-P treatment (Shane et al., 2008). On the other hand, Fe was crucial for the electron transport components essential for photosynthesis and respiration, as well as the synthesis of enzymes essential for the tricarboxylic acid cycle, such as aconitase (de Vos et al., 1986;Zhang and Fernie, 2018). Through these ways, Fe stimulates chlorophyll production and influences the accumulation of photosynthetic products, thereby ensuring plant growth status and enhancing the accumulation of aboveground biomass (Chu et al., 2018;Marastoni et al., 2020). ...
Background
Phosphorus in the soil is mostly too insoluble for plants to utilize, resulting in inhibited aboveground biomass, while Carex can maintain their aboveground biomass through the presence of dauciform roots. However, dauciform roots lead to both morphological and physiological changes in the root system, making their primary mechanism unclear.
Methods
A greenhouse experiment was conducted on three Carex species, in which Al-P, Ca-P, Fe-P, and K-P were employed as sole phosphorus sources. The plants were harvested and assessed after 30, 60 and 90 days.
Results
(1) The density of dauciform roots was positively correlated with root length and specific root length, positively influencing aboveground biomass at all three stages. (2) The aboveground phosphorus concentration showed a negative correlation with both dauciform root density and aboveground biomass in the first two stages, which became positive in the third stage. (3) Aboveground biomass correlated negatively with the aboveground Al concentration, and positively with Ca and Fe concentration (except Al-P). (4) Root morphological traits emerged as critical factors in dauciform roots’ promotion of aboveground biomass accumulation.
Conclusion
Despite the difference among insoluble phosphorus, dauciform roots have a contributing effect on aboveground growth status over time, mainly by regulating root morphological traits. This study contributes to our understanding of short-term variation in dauciform roots and their regulatory mechanisms that enhance Carex aboveground biomass under low available phosphorus conditions.
... The TCA pathway is vital for plant energy production, C metabolism, and macromolecule biosynthesis. The alteration of the TCA pathway may hinder the photosynthesis process (Zhang and Fernie, 2018). The TCA cycle is associated with the Calvin cycle, which converts CO2 into glucose during photosynthesis (Sweetlove et al., 2010). ...
Assessing the allelopathic effect of Chrysopogon zizanioides (L.) Roberty root methanolic extract on Brassica rapa subsp. chinensis var. parachinensis using an untargeted metabolomic approach ABSTRACT Chrysopogon zizanioides (L.) Roberty, or vetiver grass, is a deep-rooted perennial grass. An examination of allelopathy using a metabolomic approach offers valuable insights into vetiver extract's mechanism of action and phytotoxicity. This study utilised an untargeted metabolomics approach through the use of choisum (Brassica rapa L. subsp. chinensis (L.) Hanelt var. parachinensis (L.H. Bailey) Hanelt) as target plant because it is easier to cultivate and susceptible to the extract. Vetiver root methanolic extracts at various concentrations (0, 0.1, 1, 10, 50, and 100 mg mL-1) were sprayed at 100 mL m-2 on choisum seedlings at the 2 to 3 leaves stage. After 21 d, the Soil Plant Analysis Development (SPAD) and chlorophyll content of exposed choisum were measured, and their metabolites were subjected to gas chromatography-mass spectrometer (GC-MS)-based metabolomics analysis. The result demonstrated that the 100 mg mL-1 methanolic extract significantly decreased SPAD reading by 57.29% and reduced chlorophyll content by 66.38% (chl a) and 73.49% (chl b) of choisum compared to the control. Furthermore, considerably reduced stomatal length of exposed choisum, up to 34.31%, was observed when exposed to maximum concentration (100 mg mL-1). In total, nine metabolites with variable importance in projection (VIP) > 1 and P < 0.05 were found and identified as amino acids and carbohydrates. The highest concentration of extract enriched pathways of propanoate, Se-compound, cysteine, and methionine metabolism in choisum, suggesting the extract induced plant stress. The findings confirm the allelopathic potential of vetiver root and provide insight into the response of choisum to the allelopathic activity of vetiver grass root methanolic extract.
... Most genes from both pathways were up-regulated in MC-BL fibers at 8 DPA and down-regulated at 20 DPA. Genes encoding three enzymes from TCA pathway were significantly differentially expressed between fibers of MC-BL and MC-WL NILs, including aconitase (ACO), isocitrate dehydrogenase (IDH), and malate dehydrogenase (MDH); among them, the MDH was shown to control flux of TCA cycle (Zhang and Fernie, 2018). Glycerol-3-P and detected organic acids from TCA, including citrate, 2ketoglutarate, succinate, and malate, were significantly (FDR < 0.05) increased in MC-BL compared to MC-WL fibers. ...
Naturally-colored brown cotton (NBC) fiber is an environmentally friendly raw source of fiber for textile applications. The fiber of some NBC cultivars exhibits flame-retardant properties, which can be used in textiles that require flame resistance. Proanthocyanidins or their derivatives are responsible for the brown pigment in NBC; however, how flame retardancy is related to pigmentation in NBC is poorly understood. To gain insight into brown pigment biosynthesis, we conducted comparative transcripts and metabolites profiling analysis of developing cotton fibers between the brown (MC-BL) and white (MC-WL) cotton near-isogenic lines (NILs), genetically different only in the Lc1 locus. In this study, mass spectrometry was used to detect metabolites in BL and WL developing fibers at 8, 12, 16, 20, 24, 36, and 40 days post anthesis (DPA) and mature fibers. Transcripts analysis was performed at two critical fiber developmental points, 8 DPA (fiber elongation) and 20 DPA (secondary cell wall deposition). We found 5836 (ESI MS positive mode) and 4541 (ESI MS negative mode) metabolites significantly different accumulated between BL and WL. Among them, 142 were known non-redundant metabolites, including organic acids, amino acids, and derivatives of the phenylpropanoid pathway. Transcript analysis determined 1691 (8 DPA) and 5073 (20 DPA) differentially expressed genes (DEGs) between BL and WL, with the majority of DEGs down-regulated at 20 DPA. Organic acids of the citric acid cycle were induced, while most of the detected amino acids were reduced in the MC-BL line. Both cis- and trans-stereoisomers of flavan-3-ols were detected in developing MC-WL and MC-BL fibers; however, the gallocatechin and catechin accumulated multiple times higher. Gas chromatography-mass spectrometry (GC-MS) analysis of fatty acids determined that palmitic acid long-chain alcohols were the main constituents of waxes of mature fibers. Energy-dispersive X-ray spectrometry (EDS) analysis of mature fibers revealed that potassium accumulated three times greater in MC-BL than in MC-WL mature fibers. This study provides novel insights into the biosynthesis of pigments and its association with flame retardancy in NBC fibers.
... Phytogenic product has significantly increased PWY-5913 (obligate autotrophs) (Fig. 4C), PWY-6969 (2-oxoglutarate synthase) (Supplementary Fig. 4a), P105 PWY TCA cycle IV (2-oxoglutarate decarboxylase) ( Supplementary Fig. 4b) and P23-PWY reductive TCA cycle I ( Supplementary Fig. 4c). The more active PWY-5913 pathway in the soil microbial community makes higher TCA cycle flux, resulting in increased ATP production (Zhang and Fernie 2018). This process can promote energy availability to support plant growth. ...
Background and aims
Phytogenic bioactive plant products have shown promise in mitigating Australian pasture dieback (PDB) syndrome, a complex condition that adversely affects pasture productivity and sustainability. PDB is characterised by the progressive decline of grass, resulting in reduced soil organic matter. Recent studies have indicated that soil microbial communities play a crucial role in the remediation of affected pastures. In our previous research, the application of a phytogenic secondary metabolic product demonstrated a positive impact on soil microbial diversity, and it significantly increased pasture biomass. Building upon our previous study, we aimed to further investigate the mechanisms underlying pasture improvement through phytogenic treatment by spraying.
Methods
Here, we conducted a shotgun metagenomic investigation of the soil microbiome functional pathways affected by the phytogenic treatment.
Results
The application of phytogenic treatment to the PDB-affected soil resulted in a notable increase in soil microbial functional richness and diversity and showed alterations in beta diversity. Among the 65 significantly altered functional pathways, 54 showed an increase, while 11 decreased in response to the phytogenic treatment. The treatment altered the soil’s functional capacity towards increased production of biomolecules, including amino acids, lipids, and cofactors, thus enhancing the soil’s nutritional value. Furthermore, the phytogenic treatment significantly increased pathways involved in soil detoxification and carbon sequestration, suggesting its potential to promote soil health and carbon storage.
Conclusion
Our findings contribute to a better understanding of the mechanisms involved in improving the soils affected by pasture dieback. These insights will help develop sustainable strategies for pasture production.
... Previous studies have shown that stress reduced TCAC activity, which led to the reduction of TCAC intermediates [42,43]. As is known to all, TCAC is a metabolic hub necessary for ATP production, and its intermediates are necessary for providing precursors used in many biosynthetic pathways involved in carbohydrates, fatty acids and amino acids metabolism [44,45]. Therefore, we speculated that the significant down-regulation of proteins involved in TCAC in HC is one of the main reasons for the low cold-tolerance of HC during overwintering, compared to GL. ...
Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.
... However, in our study, the expression of ACO, IDH, ODGH, SDH, FUM, MDH, and CS genes was mostly down-regulated during aging (Figure 5), causing a severe reduction in seed energy supply. Among them, FUM, MDH, and ODGH may be targeted for TCA pathway regulation [46]. Furthermore, the PPP is a supplemental source of energy metabolism that directly oxidizes sugar and complements glycolysis to provide cells with NADPH and material to sustain seed germination, as well as providing pentose phosphate for nucleotide metabolism [47], the expression of its key genes was also down-regulated (Table S1). ...
Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.
... In our results, we observed that the sensitive inbred line showed down-accumulated proteins involved in carbohydrate metabolism and the citrate cycle (TCA cycle), whereas the tolerant inbred line had upaccumulation of proteins in these pathways. The TCA cycle consists of eight enzymes (Zhang and Fernie, 2018), and our results showed a differential accumulation of proteins from this pathway. We observed succinate-CoA ligase (A0A1D6IHT2), succinate dehydrogenase (A0A1D6LEN6), and malate dehydrogenase (B4FFV3) as up-accumulated in the tolerant inbred line. ...
Highlights
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Changes in proteomic profiles occur in response to water limitation in popcorn.
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1838 proteins were identified, with 169 differentially accumulated proteins (DAPs) in the tolerant line and 386 DAPs in the sensitive line.
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The pathways of energy metabolism, photosynthesis, oxidative stress response, and protein synthesis represented the main differences between genotypes.
... The downregulation of ribosomal protein-related genes and GDH2 involved in ammonia assimilation in Symbiodiniaceae. Photosynthates are important for the tricarboxylic acid (TCA) cycle, a process that provides energy and substrates for nitrogen metabolism (Zhang and Fernie, 2018). Protein synthesis and ammonia assimilation are important processes in nitrogen metabolism (Zhang and Fernie, 2018). ...
... Photosynthates are important for the tricarboxylic acid (TCA) cycle, a process that provides energy and substrates for nitrogen metabolism (Zhang and Fernie, 2018). Protein synthesis and ammonia assimilation are important processes in nitrogen metabolism (Zhang and Fernie, 2018). Ribosomes are the main site of protein synthesis (Cassaignau et al., 2020). ...
Relatively high-latitude coral reefs could be potential “refuges” for corals under climate change. One of the most important aspects limiting their availability as refuges is low-temperature stress. However, the mechanisms underlying the response of coral holobionts to low-temperature stress is unclear. In this study, we aimed to explore the underlying mechanisms by recording the maximum quantum yields of photosystem II (Fv/Fm) and transcriptome responses of Porites lutea under acute (1–2 weeks) and chronic (6–12 weeks) low-temperature stress at 20°C and 14°C. The P. lutea samples were collected from a relatively high-latitude coral reef in the South China Sea (109°00′–109°15′E and 21°00′–21°10′ N). The study suggested that: (1) Under acute low-temperature stress, the Fv/Fm of Symbiodiniaceae dropped by 64%, which was significantly higher than the 49% observed under chronic stress. Low-temperature stress inhibited photosystem II(PSII) functioning, with greater inhibition under acute stress. (2) Downregulation of sugar metabolism-related genes under low-temperature stress implied that the decrease in energy was due to obstruction of PSII. (3) Under low-temperature stress, calcification-related genes were downregulated in coral hosts, possibly because of energy deprivation caused by inhibited photosynthesis, Symbiodiniaceae expulsion, and oxidative phosphorylation uncoupling in mitochondria. (4) Acute low-temperature stress induced the upregulation of genes related to the TNF signaling pathway and endoplasmic reticulum stress, promoting apoptosis and coral bleaching. However, these phenomena were not observed during chronic stress, suggesting acclimation to chronic low-temperature stress and a greater survival pressure of acute low-temperature stress on coral holobionts. In conclusion, low-temperature stress inhibits Symbiodiniaceae PSII functioning, reducing energy production and affecting calcification in coral holobionts. Acute low-temperature stress is more threatening to coral holobionts than chronic stress.
... The citrate cycle is a common metabolic pathway for the complete oxidation of the three main types of organic matter in the body: sugar, fat and protein (Fernie et al., 2004). The citrate cycle is a catabolic pathway that provides precursor molecules for the biosynthesis of several substances (Zhang and Fernie, 2018). For example, sugar and glycerol are metabolized in the body to produce a-ketoglutaric acid, oxaloacetic acid and other intermediate products of the tricarboxylic acid cycle; oxaloacetic acid is a precursor for the synthesis of aspartic acid; and aketoglutaric acid is a precursor for the synthesis of glutamic acid (Zhang and Fernie, 2023). ...
Introduction
Wheat is a food crop with a large global cultivation area, and the content and quality of wheat glutenin accumulation are important indicators of the quality of wheat flour.
Methods
To elucidate the gene expression regulation and metabolic characteristics related to the gluten content during wheat grain formation, transcriptomic and metabolomic analyses were performed for the high gluten content of the Xinchun 26 cultivar and the low proteins content of the Xinchun 34 cultivar at three periods (7 d, 14 d and 21 d) after flowering.
Results
Transcriptomic analysis revealed that 5573 unique differentially expressed genes (DEGs) were divided into two categories according to their expression patterns during the three periods. The metabolites detected were mainly divided into 12 classes. Lipid and lipid-like molecule levels and phenylpropanoid and polyketide levels were the highest, and the difference analysis revealed a total of 10 differentially regulated metabolites (DRMs) over the three periods. Joint analysis revealed that the DEGs and DRMs were significantly enriched in starch and sucrose metabolism; the citrate cycle; carbon fixation in photosynthetic organisms; and alanine, aspartate and glutamate metabolism pathways. The genes and contents of the sucrose and gluten synthesis pathways were analysed, and the correlation between gluten content and its related genes was calculated. Based on weighted correlation network analysis (WGCNA), by constructing a coexpression network, a total of 5 specific modules and 8 candidate genes that were strongly correlated with the three developmental stages of wheat grain were identified.
Discussion
This study provides new insights into the role of glutenin content in wheat grain formation and reveals potential regulatory pathways and candidate genes involved in this developmental process.
