CsrA Regulates Swarming Motility and Carbohydrate and Amino Acid Metabolism in Vibrio alginolyticus

Vibrio alginolyticus, like other vibrio species, is a widely distributed marine bacterium that is able to outcompete other species in variable niches where diverse organic matters are supplied. However, it remains unclear how these cells sense and adjust metabolic flux in response to the changing environment. CsrA is a conserved RNA-binding protein that modulates critical cellular processes such as growth ability, central metabolism, virulence, and the stress response in gamma-proteobacteria. Here, we first characterize the csrA homolog in V. alginolyticus. The results show that CsrA activates swarming but not swimming motility, possibly by enhancing the expression of lateral flagellar associated genes. It is also revealed that CsrA modulates the carbon and nitrogen metabolism of V. alginolyticus, as evidenced by a change in the growth kinetics of various carbon and nitrogen sources when CsrA is altered. Quantitative RT-PCR shows that the transcripts of the genes encoding key enzymes involved in the TCA cycle and amino acid metabolism change significantly, which is probably due to the variation in mRNA stability given by CsrA binding. This may suggest that CsrA plays an important role in sensing and responding to environmental changes.

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Effect of Huangqin Tang on Urine Metabolic Profile in Rats with Ulcerative Colitis Based on UPLC-Q-Exactive Orbitrap MS

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/1874065 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Dunfang Wang ◽

Xuran Ma ◽

Shanshan Guo ◽

Yanli Wang ◽

Tao Li ◽

...

Keyword(s):

Ulcerative Colitis ◽

Fatty Acids ◽

Amino Acid ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Unsaturated Fatty Acids ◽

Tricarboxylic Acid Cycle ◽

Tca Cycle ◽

Q Exactive ◽

Therapeutic Mechanisms

As a classic prescription, Huangqin Tang (HQT) has been widely applied to treat ulcerative colitis (UC), although its pharmacological mechanisms are not clear. In this study, urine metabolomics was first analysed to explore the therapeutic mechanisms of HQT in UC rats induced by TNBS. We identified 28 potential biomarkers affected by HQT that might cause changes in urine metabolism in UC rats, mapped the network of metabolic pathways, and revealed how HQT affects metabolism of UC rats. The results showed that UC affects amino acid metabolism and biosynthesis of unsaturated fatty acids and impairs the tricarboxylic acid cycle (TCA cycle). UC induced inflammatory and gastrointestinal reactions by inhibiting the transport of fatty acids and disrupting amino acid metabolism. HQT plays key roles via regulating the level of biomarkers in the metabolism of amino acids, lipids, and so on, normalizing metabolic disorders. In addition, histopathology and other bioinformatics analysis further confirm that HQT altered UC rat physiology and pathology, ultimately affecting metabolic function of UC rats.

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

eLife ◽

10.7554/elife.72593 ◽

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.

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

10.1101/2021.07.27.453996 ◽

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.

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Genetically encoded biosensors for branched-chain amino acid metabolism to monitor mitochondrial and cytosolic production of isobutanol and isopentanol in yeast

10.1101/2020.03.08.982801 ◽

2020 ◽

Cited By ~ 1

Author(s):

Yanfei Zhang ◽

Sarah K. Hammer ◽

Cesar Carrasco-Lopez ◽

Sergio A. Garcia Echauri ◽

José L. Avalos

Keyword(s):

Amino Acid ◽

Amino Acid Metabolism ◽

Metabolic Flux ◽

Acid Metabolism ◽

Transcriptional Regulator ◽

Higher Alcohol ◽

Alcohol Production ◽

Branched Chain Amino Acid ◽

Branched Chain ◽

Genetically Encoded Biosensor

AbstractBranched-chain amino acid (BCAA) metabolism can be harnessed to produce many valuable chemicals. Among these, isobutanol, which is derived from valine degradation, has received substantial attention due to its promise as an advanced biofuel. While Saccharomyces cerevisiae is the preferred organism for isobutanol production, the lack of isobutanol biosensors in this organism has limited the ability to screen strains at high throughput. Here, we use a transcriptional regulator of BCAA biosynthesis, Leu3p, to develop the first genetically encoded biosensor for isobutanol production in yeast. Small modifications allowed us to redeploy Leu3p in a second biosensor for isopentanol, another BCAA-derived product of interest. Each biosensor is highly specific to isobutanol or isopentanol, respectively, and was used to engineer metabolic enzymes to increase titers. The isobutanol biosensor was additionally employed to isolate high-producing strains, and guide the construction and enhancement of mitochondrial and cytosolic isobutanol biosynthetic pathways, including in combination with optogenetic actuators to enhance metabolic flux. These biosensors promise to accelerate the development of enzymes and strains for branched-chain higher alcohol production, and offer a blueprint to develop biosensors for other products derived from BCAA metabolism.

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Metabolomics reveals the defense mechanism of different rice under space flight stress

10.21203/rs.3.rs-148667/v1 ◽

2021 ◽

Author(s):

Deyong Zeng ◽

Jie Cui ◽

Yishu Yin ◽

Yi Xiong ◽

Mengyao Liu ◽

...

Keyword(s):

Amino Acid ◽

Stress Response ◽

Space Flight ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Tca Cycle ◽

Mutation Breeding ◽

Space Environment ◽

Cycle Rate ◽

The Tca Cycle

Abstract BackgroundSpace flight is a special abiotic stress condition. Due to the development of space technology, its potential value has received widespread attention. Space mutation breeding is one of the important methods for human beings to solve food security. However, the molecular mechanism of space mutagenesis is still not very clear.ResultIn this study, two kinds of rice, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the SJ-10 retractable satellite for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the space environment caused the stress response of rice. The TLP and TS of DN3 identified 113 and 58 different metabolites, respectively. The TLP and TS of DN6 identified 107 and 77 different metabolites, respectively. These metabolites include amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the TCA cycle and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggest that the space environment has different stress response mechanisms to the two rice varieties, and these differences may be reflected in energy consumption and compound biosynthesis.ConclusionsThis research uses metabolomics for the first time to explore the effects of space flight team rice. This research provides new insights for further exploring the effects of space biology and space mutation breeding.

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Involvement of enzymes of amino acid metabolism and tricarboxylic acid cycle in bovine oocyte maturation in vitro

Reproduction ◽

10.1530/rep.0.1260753 ◽

2003 ◽

pp. 753-763 ◽

Cited By ~ 40

Author(s):

P Cetica ◽

L Pintos ◽

G Dalvit ◽

M Beconi

Keyword(s):

Amino Acid ◽

Isocitrate Dehydrogenase ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Tricarboxylic Acid Cycle ◽

Tca Cycle ◽

Cumulus Cells ◽

Tricarboxylic Acid ◽

Maturation In Vitro

Few studies demonstrate at a biochemical level the metabolic profile of both cumulus cells and the oocyte during maturation. The aim of the present study was to investigate the differential participation of enzymatic activity in cumulus cells and in the oocyte during in vitro maturation (IVM) by studying the activity of enzymes involved in the control of amino acid metabolism, alanine aminotransferase (ALT) and aspartate aminotransferase (AST); and the tricarboxylic acid (TCA) cycle, isocitrate dehydrogenase (IDH) and malate dehydrogenase (MDH). No NAD-dependent isocitrate dehydrogenase (NAD-IDH) activity was recorded in cumulus-oocyte complexes (COCs). ALT, AST, NADP-dependent isocitrate dehydrogenase (NADP-IDH) and MDH enzymatic units remained constant in cumulus cells and oocytes during IVM. Specific activities increased in oocytes and decreased in cumulus cells as a result of IVM (P<0.05). Similar activity of both transaminases was detected in cumulus cells, unlike in the oocyte, in which activity of AST was 4.4 times greater than that of ALT (P<0.05). High NADP-IDH and MDH activity was detected in the oocyte. Addition of alanine, aspartate, isocitrate + NADP, oxaloacetate or malate + NAD to maturation media increased the percentage of denuded oocytes reaching maturation (P<0.05), in contrast to COCs in which differences were not observed by addition of these substrates and co-enzymes. The activity of studied enzymes and the use of oxidative substrates denotes a major participation of transaminations and the TCA cycle in the process of gamete maturation. The oocyte thus seems versatile in the use of several oxidative substrates depending on the redox state.

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Metabolomics Analysis in Different Development Stages on SP0 Generation of Rice Seeds After Spaceflight

Frontiers in Plant Science ◽

10.3389/fpls.2021.700267 ◽

2021 ◽

Vol 12 ◽

Author(s):

Deyong Zeng ◽

Jie Cui ◽

YiShu Yin ◽

Yi Xiong ◽

Mengyao Liu ◽

...

Keyword(s):

Amino Acid ◽

Stress Response ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Tricarboxylic Acid Cycle ◽

Tca Cycle ◽

Cycle Rate ◽

Development Stages ◽

The Tca Cycle ◽

Rice Seeds

Spaceflight is a special abiotic stress condition. In recent years, it has been confirmed that the spaceflight caused the stress response of rice seeds, and the protein level, transcription level, and methylation level will change during the planting process after returning to the ground. However, the changes at the metabolome level are not very clear. In this study, two kinds of rice seeds, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the ShiJian-10 retractable satellite (SJ-10) for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the spaceflight caused the stress response of rice. The TLP and TS of DN3 identified 110 and 57 different metabolites, respectively, while the TLP and TS of DN6 identified 104 and 74 different metabolites, respectively. These metabolites included amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the tricarboxylic acid cycle (TCA) and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggested that the response mechanisms of the two different rice strains to spaceflight stress are different, and these differences may be reflected in energy consumption and compound biosynthesis of rice in different growth and development stages. This study provided new insights for further exploring the effects of spaceflight.

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Fungal Enzyme l-Lysine α-Oxidase Affects the Amino Acid Metabolism in the Brain and Decreases the Polyamine Level

Pharmaceuticals ◽

10.3390/ph13110398 ◽

2020 ◽

Vol 13 (11) ◽

pp. 398

Author(s):

Elena V. Lukasheva ◽

Marina G. Makletsova ◽

Alexander N. Lukashev ◽

Gulalek Babayeva ◽

Anna Yu. Arinbasarova ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Tca Cycle ◽

Polyamine Level ◽

The Brain ◽

Oxidative Species

The fungal glycoprotein l-lysine α-oxidase (LO) catalyzes the oxidative deamination of l-lysine (l-lys). LO may be internalized in the intestine and shows antitumor, antibacterial, and antiviral effects in vivo. The main mechanisms of its effects have been shown to be depletion of the essential amino acid l-lys and action of reactive oxidative species produced by the reaction. Here, we report that LO penetrates into the brain and is retained there for up to 48 h after intravenous injection, which might be explained by specific pharmacokinetics. LO actively intervenes in amino acid metabolism in the brain. The most significant impact of LO was towards amino acids, which are directly exposed to its action (l-lys, l-orn, l-arg). In addition, the enzyme significantly affected the redistribution of amino acids directly associated with the tricarboxylic acid (TCA) cycle (l-asp and l-glu). We discovered that the depletion of l-orn, the precursor of polyamines (PA), led to a significant and long-term decrease in the concentration of polyamines, which are responsible for regulation of many processes including cell proliferation. Thus, LO may be used to reduce levels of l-lys and PA in the brain.

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Key Metabolite Differences Between Korean Pine (Pinus koraiensis) Seeds With Primary Physiological Dormancy and No-Dormancy

Frontiers in Plant Science ◽

10.3389/fpls.2021.767108 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuan Song ◽

Xiaoye Gao ◽

Yunjie Wu

Keyword(s):

Amino Acid ◽

Carbohydrate Metabolism ◽

Seed Dormancy ◽

Seed Coat ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Tca Cycle ◽

Pentose Phosphate ◽

Pinus Koraiensis ◽

Physiological Dormancy

Pinus Koraiensis seeds have physiological dormancy. Cold stratification releases seed dormancy. The changes in metabolite profiles of dormant seeds and cold stratified seeds during shorter incubation time in a favorable condition for seed germination have been studied. However, a more-long-term detection of the changes in metabolites in dormant seeds can identify the real metabolic pathways responsible for dormancy. Metabolite composition was investigated in embryo and megagametophyte of primary physiological dormant seeds (DS) of P. Koraiensis collected at 0, 1, 2, 4, and 6 weeks of incubation and of non-primary physiological dormant seeds (NDS) sampled at 0 and 1 week of incubation, seed coat rupture stage, and radicle protrusion stage. Embryos contained higher levels of most metabolites than megagametophyte. Strong accumulation of most metabolites in DS occurred at 1 and 4 weeks of incubation. A larger reduction in the relative levels of most phosphorylated sugars and amino acids in NDS was found between 1-week-incubation and seed coat rupture stage. The relative levels of metabolites involved in carbohydrate metabolism, especially the pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were higher in the embryos of 4-week-incubated DS, but the relative contents of intermediate metabolites of most amino acid metabolism were lower compared to 1-week-incubated NDS. We suggested that the disturbed carbohydrate metabolism and amino acid metabolism in the embryos of DS after 4 weeks of incubation maybe related to primary dormancy. Our study provides information for a better understanding of the mechanism of seed dormancy.

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