scholarly journals Specialization in a nitrogen-fixing symbiosis: proteome differences between Sinorhizobium medicae bacteria and bacteroids

2021 ◽  
Author(s):  
Svetlana N Yurgel ◽  
Yi Qu ◽  
Jennifer Rice ◽  
Nivethika Ajeethan ◽  
Erika Zink ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sinorhizobium Meliloti ◽  
Genomic Sequence ◽  
Tca Cycle ◽  
Living Cells ◽  
Pentose Phosphate ◽  
Free Living ◽  
Sinorhizobium Medicae ◽  
Amino Acid Degradation ◽  
Low Levels

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. 3215 proteins were identified, over half of the ORFs predicted from the genomic sequence. The abundance of 1361 proteins displayed strong lifestyle bias. 1131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised ~12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis/gluconeogenesis and the pentose phosphate pathway, but several amino acid degradation pathways were repressed. This suggests bacteroids maintain a relatively independent anabolic metabolism. TCA cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in Sinorhizobium meliloti Rm1021 were detected and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.

The transport and metabolism of glucose in cowpea rhizobia

1983 ◽  
Vol 29 (4) ◽  
pp. 398-406 ◽  
Author(s):  
Mark D. Stowers ◽  
Gerald H. Elkan
Keyword(s):  
Potassium Cyanide ◽  
Tca Cycle ◽  
Pentose Phosphate ◽  
Free Living ◽  
Phosphogluconate Dehydrogenase ◽  
Metabolism Enzymes ◽  
Carbonyl Cyanide ◽  
Cowpea Rhizobia ◽  
Enzymes Of Carbohydrate Metabolism ◽  
Free Living Conditions

Cell-free extracts of several strains of cowpea rhizobia grown under free-living conditions were surveyed for key enzymes of carbohydrate metabolism. Enzymes of the Entner–Doudoroff (ED) and Embden–Meyerhof–Parnas (EMP) pathways were detected while 6-phosphogluconate dehydrogenase was not detected, indicating the apparent absence of the pentose phosphate (PP) pathway. Transketolase and transaldolase reactions were present, indicating a pathway for the synthesis of pyrimidines and purines from fructose-6-phosphate and glyceraldehyde-3-phosphate. Radiorespirometric analysis with specifically labelled glucose indicated that the ED pathway with the hexose cycle was the primary pathway of glucose dissimilation. The presence of isocitrate and malate dehydrogenases and results of radiorespirometric analysis with pyruvate and succinate demonstrates an operational tricarboxylic acid (TCA) cycle in glucose-grown cowpea rhizobia. The transport of glucose was inhibited by carbonyl cyanide m-chlorphenylhydrazone (CCCP), dinitrophenol, and potassium cyanide indicating that the process was active, probably using an energized membrane state. The transport of glucose was glucose specific. A lower rate of glucose uptake was seen when cells were cultured on hexoses other than glucose.

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

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.

scholarly journals Comparative proteomic analysis reveals the regulatory network of the veA gene during asexual and sexual spore development of Aspergillus cristatus

2018 ◽  
Vol 38 (4) ◽  
Author(s):  
Hui Liu ◽  
Shilei Sang ◽  
Hui Wang ◽  
Xiyi Ren ◽  
Yumei Tan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Tca Cycle ◽  
Pentose Phosphate ◽  
2D Electrophoresis ◽  
Hypertonic Medium ◽  
Spore Development ◽  
Associated Proteins ◽  
Hsp 90 ◽  
Aspergillus Cristatus

Aspergillus cristatus is the predominant fungal population during fermentation of Chinese Fuzhuan brick tea, and belongs to the homothallic fungal group that undergoes a sexual stage without asexual conidiation under hypotonic conditions, while hypertonic medium induces initiation of the asexual stage and completely blocks sexual development. However, the veA deletion mutant only produces conidia in hypotonic medium after a 24-h culture, but both asexual and sexual spores are observed after 72 h. The veA gene is one of the key genes that positively regulates sexual and negatively regulates asexual development in A. cristatus. To elucidate the molecular mechanism of how VeA regulates asexual and sexual spore development in A. cristatus, 2D electrophoresis (2-DE) combined with MALDI-tandem ToF MS analysis were applied to identify 173 differentially expressed proteins (DEPs) by comparing the agamotype (24 h) and teleomorph (72 h) with wild-type (WT) A. cristatus strains. Further analysis revealed that the changed expression pattern of Pmk1-MAPK and Ser/Thr phosphatase signaling, heat shock protein (Hsp) 90 (HSP90), protein degradation associated, sulphur-containing amino acid biosynthesis associated, valine, leucine, isoleucine, and arginine biosynthesis involved, CYP450 and cytoskeletal formation associated proteins were involved in the production of conidia in agamotype of A. cristatus. Furthermore, the deletion of veA in A. cristatus resulted in disturbed process of transcription, translation, protein folding, amino acid metabolism, and secondary metabolism. The carbohydrate and energy metabolism were also greatly changed, which lied in the suppression of anabolism through pentose phosphate pathway (PPP) but promotion of catabolism through glycolysis and tricarboxylic acid (TCA) cycle. The energy compounds produced in the agamotype were mainly ATP and NADH, whereas they were NADPH and FAD in the teleomorph. These results will contribute to the existing knowledge on the complex role of VeA in the regulation of spore development in Aspergillus and provide a framework for functional investigations on the identified proteins.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

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

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.

scholarly journals Itaconate Alters Succinate and Coenzyme A Metabolism via Inhibition of Mitochondrial Complex II and Methylmalonyl-CoA Mutase

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 117
Author(s):  
Thekla Cordes ◽  
Christian M. Metallo
Keyword(s):  
Amino Acid ◽  
Metabolic Pathways ◽  
Mammalian Cells ◽  
Coenzyme A ◽  
Cultured Cells ◽  
Tca Cycle ◽  
Regulatory Function ◽  
Reversible Inhibitor ◽  
Complex Ii ◽  
Branched Chain

Itaconate is a small molecule metabolite that is endogenously produced by cis-aconitate decarboxylase-1 (ACOD1) in mammalian cells and influences numerous cellular processes. The metabolic consequences of itaconate in cells are diverse and contribute to its regulatory function. Here, we have applied isotope tracing and mass spectrometry approaches to explore how itaconate impacts various metabolic pathways in cultured cells. Itaconate is a competitive and reversible inhibitor of Complex II/succinate dehydrogenase (SDH) that alters tricarboxylic acid (TCA) cycle metabolism leading to succinate accumulation. Upon activation with coenzyme A (CoA), itaconyl-CoA inhibits adenosylcobalamin-mediated methylmalonyl-CoA (MUT) activity and, thus, indirectly impacts branched-chain amino acid (BCAA) metabolism and fatty acid diversity. Itaconate, therefore, alters the balance of CoA species in mitochondria through its impacts on TCA, amino acid, vitamin B12, and CoA metabolism. Our results highlight the diverse metabolic pathways regulated by itaconate and provide a roadmap to link these metabolites to potential downstream biological functions.

scholarly journals Characterization of Trypsin Inhibitor in Florunner Peanut Seeds (Arachis hypogaea L.)1

1988 ◽  
Vol 15 (2) ◽  
pp. 81-84 ◽  
Author(s):  
E. M. Ahmed ◽  
J. A. Applewhite
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Arachis Hypogaea ◽  
Trypsin Inhibitor ◽  
Low Molecular Weight ◽  
Arachis Hypogaea L ◽  
Amino Acid Profiles ◽  
Low Levels

Abstract Florunner peanut seeds contained five trypsin isoinhibitors. Amino acid profiles of the trypsin inhibitors fraction showed high levels of aspartic acid, half-cystine and serine and low levels of histidine and tyrosine. The molecular weight of the inhibitor was 8.3 KDa. The presence of multiforms of this inhibitor, its low molecular weight and the high amount of half-cystine indicate that peanut trypsin inhibitor is of the Bowman-Birk type.

scholarly journals Characterization of Gmhsp26-A, a stress gene encoding a divergent heat shock protein of soybean: heavy-metal-induced inhibition of intron processing.

1988 ◽  
Vol 8 (3) ◽  
pp. 1113-1122 ◽  
Author(s):  
E Czarnecka ◽  
R T Nagao ◽  
J L Key ◽  
W B Gurley
Keyword(s):  
Amino Acid ◽  
Heat Shock ◽  
Amino Acid Sequence ◽  
Genomic Sequence ◽  
Stress Protein ◽  
Initiation Site ◽  
Gene Encoding ◽  
S1 Nuclease ◽  
Soybean Seedlings ◽  
Nuclease Mapping

We determined the DNA sequence and mapped the corresponding transcripts of a genomic clone containing the Gmhsp26-A gene of soybean. This gene is homologous to the previously characterized cDNA clone pCE54 (E. Czarnecka, L. Edelman, F. Schöffl, and J. L. Key, Plant Mol. Biol. 3:45-58, 1984) and is expressed in response to a wide variety of physiological stresses including heat shock (HS). S1 nuclease mapping of transcripts and a comparison of the cDNA sequence with the genomic sequence indicated the presence of a soybean seedlings with either CdCl2 or CuSO4. Analysis of the 5' termini of transcripts indicated the presence of one major and at least two minor start sites. In each case, initiation occurred 27 to 30 base pairs downstream from a TATA-like motif, and thus each initiation site appears to be promoted by the activity of a separate subpromoter. The three subpromoters are all associated with sequences showing low homology to the HS consensus element of Drosophila melanogaster HS genes and are differentially induced in response to various stresses. Within the carboxyl-terminal half of the protein, hydropathy analysis of the deduced amino acid sequence indicated a high degree of relatedness to the small HS proteins. A comparison of the primary amino acid sequence of hsp26-A with sequences of the small HS proteins suggested that this stress protein is highly diverged and may therefore be specialized for stress adaptation in soybean.

scholarly journals The effect of amino-acid-supplemented wheat gluten on cholesterol metabolism in the rat

1985 ◽  
Vol 53 (1) ◽  
pp. 25-30 ◽  
Author(s):  
M. Bassat ◽  
S. Mokady
Keyword(s):  
Amino Acid ◽  
Cholesterol Metabolism ◽  
Cholesterol Biosynthesis ◽  
Wheat Gluten ◽  
Blood Cholesterol ◽  
Amino Acid Supplementation ◽  
Faecal Excretion ◽  
Weanling Rats ◽  
Low Levels

1. The effect of lysine- and threonine-supplemented wheat gluten on cholesterol metabolism was studied using male weanling rats. Animals were fed on cholesterol-free diets containing 100 or 200 g gluten/kg with or without amino acid supplementation, and compared with animals given 50, 100 and 200 g casein/kg diets, for 3 weeks.2. A hypocholesterolaemic effect observed with the wheat gluten-fed rats, compared with the animals given 100 and 200 g casein/kg diets, was accompanied by increased turnover of cholesterol as expressed by enhanced cholesterol biosynthesis and increased faecal excretion of cholesterol and bile acids. This effect was not abolished by lysine and threonine supplementation.3. Low levels of blood cholesterol were also observed in the rats fed on the 50 g casein/kg diet. However, a different mechanism, related to impairment of cholesterol transport from the liver, was most likely responsible for the hypocholesterolaemia found in these protein-malnourished animals.4. The effect on cholesterol metabolism produced by dietary wheat gluten was independent of the low quality of the protein and of its specific deficiency in lysine and threonine.

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