Journal articles: 'Amino acids – Biosynthesis'

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Velíšek, J., and K. Cejpek. "Biosynthesis of food constituents: Amino acids. 3. Modified proteinogenic amino acids – a review." Czech Journal of Food Sciences 24, No. 2 (November 9, 2011): 59–61. http://dx.doi.org/10.17221/3300-cjfs.

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This review article gives a survey of principal pathways that lead to the biosynthesis of the modified principal proteinogenic amino acids, i.e. cystine, 4-hydroxyproline, 5-hydroxylysine, 3-methylhistidine, and O-phosphoserine. Except the proteinogenic amino acids, peptides and proteins often contain several unusual amino acids arising by specific modifications (e.g. oxidation or esterification) of amino acid residues present in the already synthesised polypeptide chain. The post-translational products include, e.g., the oxidation of the thiol groups of two cysteine residues to form a disulfide bridge (cystine), thus allowing cross-linking of polypeptide chains; the hydroxylation of proline to 4-hydroxyproline and of lysine to 5-hydroxylysine; N-methylation of histidine to 3-methylhistidine; and the phosphorylation of serine to O-phosphoserine. There also exist several other modified proteinogenic amino acids that are of minor significance to foods.    

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Velíšek, J., R. Kubec, and K. Cejpek. "Biosynthesis of food constituents: Amino acids: 4. Non-protein amino acids – a review." Czech Journal of Food Sciences 24, No. 3 (November 12, 2011): 93–109. http://dx.doi.org/10.17221/3304-cjfs.

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This review article gives a brief survey of the principal pathways that lead to the biosynthesis of the most important non-protein amino acids occurring in foods and feeds. These amino acids have been divided into the following groups: 3-amino acids and 4-amino acids, N-substituted amino acids, alicyclic amino acids, hydroxyamino acids, sulfur-containing amino acids, basic amino acids, and taurine.  

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Hochuli, Michel, Heiko Patzelt, Dieter Oesterhelt, Kurt Wüthrich, and Thomas Szyperski. "Amino Acid Biosynthesis in the Halophilic ArchaeonHaloarcula hispanica." Journal of Bacteriology 181, no. 10 (May 15, 1999): 3226–37. http://dx.doi.org/10.1128/jb.181.10.3226-3237.1999.

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ABSTRACT Biosynthesis of proteinogenic amino acids in the extremely halophilic archaeon Haloarcula hispanica was explored by using biosynthetically directed fractional 13C labeling with a mixture of 90% unlabeled and 10% uniformly13C-labeled glycerol. The resulting13C-labeling patterns in the amino acids were analyzed by two-dimensional 13C,1H correlation spectroscopy. The experimental data provided evidence for a split pathway for isoleucine biosynthesis, with 56% of the total Ile originating from threonine and pyruvate via the threonine pathway and 44% originating from pyruvate and acetyl coenzyme A via the pyruvate pathway. In addition, the diaminopimelate pathway involving diaminopimelate dehydrogenase was shown to lead to lysine biosynthesis and an analysis of the 13C-labeling pattern in tyrosine indicated novel biosynthetic pathways that have so far not been further characterized. For the 17 other proteinogenic amino acids, the data were consistent with data for commonly found biosynthetic pathways. A comparison of our data with the amino acid metabolisms of eucarya and bacteria supports the theory that pathways for synthesis of proteinogenic amino acids were established before ancient cells diverged into archaea, bacteria, and eucarya.

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Yang, Jianchang, Yujiao Zhou, and Yi Jiang. "Amino Acids in Rice Grains and Their Regulation by Polyamines and Phytohormones." Plants 11, no. 12 (June 15, 2022): 1581. http://dx.doi.org/10.3390/plants11121581.

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Rice is one of the most important food crops in the world, and amino acids in rice grains are major nutrition sources for the people in countries where rice is the staple food. Phytohormones and plant growth regulators play vital roles in regulating the biosynthesis of amino acids in plants. This paper reviewed the content and compositions of amino acids and their distribution in different parts of ripe rice grains, and the biosynthesis and metabolism of amino acids and their regulation by polyamines (PAs) and phytohormones in filling grains, with a focus on the roles of higher PAs (spermidine and spermine), ethylene, and brassinosteroids (BRs) in this regulation. Recent studies have shown that higher PAs and BRs (24-epibrassinolide and 28-homobrassinolide) play positive roles in mediating the biosynthesis of amino acids in rice grains, mainly by enhancing the activities of the enzymes involved in amino acid biosynthesis and sucrose-to-starch conversion and maintaining redox homeostasis. In contrast, ethylene may impede amino acid biosynthesis by inhibiting the activities of the enzymes involved in amino acid biosynthesis and elevating reactive oxygen species. Further research is needed to unravel the temporal and spatial distribution characteristics of the content and compositions of amino acids in the filling grain and their relationship with the content and compositions of amino acids in different parts of a ripe grain, to elucidate the cross-talk between or among phytohormones in mediating the anabolism of amino acids, and to establish the regulation techniques for promoting the biosynthesis of amino acids in rice grains.

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Velíšek, J., and K. Cejpek. "Biosynthesis of food constituents: Amino acids: 1. The glutamic acid and aspartic acid groups – a review." Czech Journal of Food Sciences 24, No. 1 (November 9, 2011): 1–10. http://dx.doi.org/10.17221/3287-cjfs.

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This review article gives a survey of principal pathways that lead to the biosynthesis of the proteinogenic amino acids of the glutamic acid group (glutamic acid, glutamine, proline, arginine) and aspartic acid group (aspartic acid, asparagine, threonine, methionine, lysine, isoleucine) starting with oxaloacetic acid from the citric acid cycle. There is an extensive use of reaction schemes, sequences, and mechanisms with the enzymes involved and detailed explanations using sound chemical principles and mechanisms.

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FITZGERALD, Lisa M., and Alina M. SZMANT. "Biosynthesis of ‘essential’ amino acids by scleractinian corals." Biochemical Journal 322, no. 1 (February 15, 1997): 213–21. http://dx.doi.org/10.1042/bj3220213.

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Animals rely on their diet for amino acids that they are incapable either of synthesizing or of synthesizing in sufficient quantities to meet metabolic needs. These are the so-called ‘essential amino acids’. This set of amino acids is similar among the vertebrates and many of the invertebrates. Previously, no information was available for amino acid synthesis by the most primitive invertebrates, the Cnidaria. The purpose of this study was to examine amino acid synthesis by representative cnidarians within the Order Scleractinia. Three species of zooxanthellate reef coral, Montastraea faveolata, Acropora cervicornis and Porites divaricata, and two species of non-zooxanthellate coral, Tubastrea coccinea and Astrangia poculata, were incubated with 14C-labelled glucose or with the 14C-labelled amino acids glutamic acid, lysine or valine. Radiolabel tracer was followed into protein amino acids. A total of 17 amino acids, including hydroxyproline, were distinguishable by the techniques used. Of these, only threonine was not found radiolabelled in any of the samples. We could not detect tryptophan or cysteine, nor distinguish between the amino acid pairs glutamic acid and glutamine, or aspartic acid and asparagine. Eight amino acids normally considered essential for animals were made by the five corals tested, although some of them were made only in small quantities. These eight amino acids are valine, isoleucine, leucine, tyrosine, phenylalanine histidine, methionine and lysine. The ability of cnidarians to synthesize these amino acids could be yet another indicator of a separate evolutionary history of the cnidarians from the rest of the Metazoa.

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Lauzier, Annie, Claudia Goyer, Luc Ruest, Ryszard Brzezinski, Don L. Crawford, and Carole Beaulieu. "Effect of amino acids on thaxtomin A biosynthesis by Streptomyces scabies." Canadian Journal of Microbiology 48, no. 4 (April 1, 2002): 359–64. http://dx.doi.org/10.1139/w02-031.

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The regulatory effect of amino acids on the production of thaxtomin A, a phytotoxin produced by Streptomyces scabies, was investigated. Tryptophan had an important inhibitory effect on the toxin biosynthesis in all five strains of S. scabies tested. Two other aromatic amino acids (tyrosine and phenylalanine) also inhibited thaxtomin A biosynthesis, while aliphatic amino acids did not cause an important decline in thaxtomin A production. Methylation of tryptophan prevented or reduced the inhibitory effect on thaxtomin A biosynthesis. In spite of the inhibitory action of tryptophan and phenylalanine on thaxtomin A production, incorporation of these radiolabeled molecules into thaxtomin A confirmed that they are metabolic precursors for the biosynthesis of the phytotoxin.Key words: thaxtomin A, phytotoxin, Streptomyces scabies, common scab, nitroaromatic compounds, amino acids.

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Bröer, Stefan, and Angelika Bröer. "Amino acid homeostasis and signalling in mammalian cells and organisms." Biochemical Journal 474, no. 12 (May 25, 2017): 1935–63. http://dx.doi.org/10.1042/bcj20160822.

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Cells have a constant turnover of proteins that recycle most amino acids over time. Net loss is mainly due to amino acid oxidation. Homeostasis is achieved through exchange of essential amino acids with non-essential amino acids and the transfer of amino groups from oxidised amino acids to amino acid biosynthesis. This homeostatic condition is maintained through an active mTORC1 complex. Under amino acid depletion, mTORC1 is inactivated. This increases the breakdown of cellular proteins through autophagy and reduces protein biosynthesis. The general control non-derepressable 2/ATF4 pathway may be activated in addition, resulting in transcription of genes involved in amino acid transport and biosynthesis of non-essential amino acids. Metabolism is autoregulated to minimise oxidation of amino acids. Systemic amino acid levels are also tightly regulated. Food intake briefly increases plasma amino acid levels, which stimulates insulin release and mTOR-dependent protein synthesis in muscle. Excess amino acids are oxidised, resulting in increased urea production. Short-term fasting does not result in depletion of plasma amino acids due to reduced protein synthesis and the onset of autophagy. Owing to the fact that half of all amino acids are essential, reduction in protein synthesis and amino acid oxidation are the only two measures to reduce amino acid demand. Long-term malnutrition causes depletion of plasma amino acids. The CNS appears to generate a protein-specific response upon amino acid depletion, resulting in avoidance of an inadequate diet. High protein levels, in contrast, contribute together with other nutrients to a reduction in food intake.

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Cortez-Espinosa, Nancy, Judit A. Aviña-Verduzco, Enrique Ramírez-Chávez, Jorge Molina-Torres, and Patricia Ríos-Chávez. "Valine and Phenylalanine as Precursors in the Biosynthesis of Alkamides in Acmella Radicans." Natural Product Communications 6, no. 6 (June 2011): 1934578X1100600. http://dx.doi.org/10.1177/1934578x1100600625.

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Acmella radicans (Asteraceae) produces at least seven alkamides, most with either an isobutyl- or phenylethyl group as the amine moiety. These moieties suggest that the amino acids valine and phenylalanine are the biosynthetic precursors of these alkamides. On the basis of labeled feeding experiments using either L-[2H8]valine or L-[2H8]phenylalanine we present evidence for the involvement of these two amino acids in the biosynthesis of (2 E,6 Z,8 E)- N-isobutyl-2,6,8-decatrienamide (affinin) (1), (2 Z,4 E)- N-(2-phenylethyl)-2,4-octadienamide (2), (2 E)- N-(2-phenylethyl)-nona-2-en-6,8-diynamide (3), and 3-phenyl- N-(2-phenylethyl)-2-propenamide (4). Alkamides were isolated from young A. radicans plants and analyzed by gas chromatography-mass spectrometry (GC-MS). Additionally, in cell free in vitro experiments based on isobutyl and phenylethylamide biosynthesis, using a colorimetric assay and GC-MS, valine and phenylalanine decarboxylase activities were assayed in the soluble extract of A. radicans leaves.

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Sisido, Masahiko. "Biosynthesis of Proteins Containing Nonnatural Amino Acids." Kobunshi 43, no. 9 (1994): 632–33. http://dx.doi.org/10.1295/kobunshi.43.632.

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Mendel, David, Jonathan Ellman, and Peter G. Schultz. "Protein biosynthesis with conformationally restricted amino acids." Journal of the American Chemical Society 115, no. 10 (May 1993): 4359–60. http://dx.doi.org/10.1021/ja00063a063.

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Velíšek, J., and K. Cejpek. "Biosynthesis of food constituents: Amino acids: 2. The alanine-valine-leucine, serine-cysteine-glycine, and aromatic and heterocyclic amino acids groups – a review." Czech Journal of Food Sciences 24, No. 2 (November 9, 2011): 45–58. http://dx.doi.org/10.17221/3299-cjfs.

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This review article gives a survey of principal pathways that lead to the biosynthesis of the proteinogenic amino acids of the alanine-valine-leucine group starting with pyruvic acid from the glycolytic pathway and serine-cysteine-glycine group starting with 3-phospho-d-glyceric acid from the glycolytic pathway. A survey is further given to the aromatic and heterocyclic amino acids (phenylalanine, tyrosine, tryptophan, histidine) starting with 3-phosphoenolpyruvic acid from the glycolytic pathway and d-erythrose 4-phosphate, an intermediate in the pentose phosphate cycle and Calvin cycle.  

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Kuo, Macus, Helen Chen, Lynn Feun, and Niramol Savaraj. "Targeting the Proline–Glutamine–Asparagine–Arginine Metabolic Axis in Amino Acid Starvation Cancer Therapy." Pharmaceuticals 14, no. 1 (January 18, 2021): 72. http://dx.doi.org/10.3390/ph14010072.

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Proline, glutamine, asparagine, and arginine are conditionally non-essential amino acids that can be produced in our body. However, they are essential for the growth of highly proliferative cells such as cancers. Many cancers express reduced levels of these amino acids and thus require import from the environment. Meanwhile, the biosynthesis of these amino acids is inter-connected but can be intervened individually through the inhibition of key enzymes of the biosynthesis of these amino acids, resulting in amino acid starvation and cell death. Amino acid starvation strategies have been in various stages of clinical applications. Targeting asparagine using asparaginase has been approved for treating acute lymphoblastic leukemia. Targeting glutamine and arginine starvations are in various stages of clinical trials, and targeting proline starvation is in preclinical development. The most important obstacle of these therapies is drug resistance, which is mostly due to reactivation of the key enzymes involved in biosynthesis of the targeted amino acids and reprogramming of compensatory survival pathways via transcriptional, epigenetic, and post-translational mechanisms. Here, we review the interactive regulatory mechanisms that control cellular levels of these amino acids for amino acid starvation therapy and how drug resistance is evolved underlying treatment failure.

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Henard, Calvin A., and Andrés Vázquez-Torres. "DksA-Dependent Resistance of Salmonella enterica Serovar Typhimurium against the Antimicrobial Activity of Inducible Nitric Oxide Synthase." Infection and Immunity 80, no. 4 (February 6, 2012): 1373–80. http://dx.doi.org/10.1128/iai.06316-11.

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ABSTRACTIn coordination with the ppGpp alarmone, the RNA polymerase regulatory protein DksA controls the stringent response of eubacteria, negatively regulating transcription of translational machinery and directly activating amino acid promoters andde novoamino acid biosynthesis. Given the effects of nitric oxide (NO) on amino acid biosynthetic pathways and the intimate relationship of DksA with amino acid synthesis and transport, we tested whether DksA contributes to the resistance ofSalmonellato reactive nitrogen species (RNS). Our studies show that the zinc finger predicted to position DksA in the secondary channel of the RNA polymerase is essential for the resistance ofSalmonella entericaserovar Typhimurium to RNS in a murine model of systemic salmonellosis. Despite exhibiting auxotrophies for various amino acids, ΔdksAmutantSalmonellastrains regain virulence in mice lacking inducible NO synthase (iNOS). DksA is also important for growth of this intracellular pathogen in the presence of NO congeners generated by iNOS during the innate response of murine macrophages. Accordingly,dksAmutantSalmonellastrains are hypersusceptible to chemically generated NO, a phenotype that can be prevented by adding amino acids. The DksA-dependent antinitrosative defenses do not rely on the Hmp flavohemoprotein that detoxifies NO to NO3−and appear to operate independently of the ppGpp alarmone. Our investigations are consistent with a model by which NO produced in the innate response toSalmonellaexerts considerable pressure on amino acid biosynthesis. The cytotoxicity of NO againstSalmonellaamino acid biosynthetic pathways is antagonized in great part by the DksA-dependent regulation of amino acid biosynthesis and transport.

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Yu, Zhiliang, Chenglin Guo, and Juanping Qiu. "Precursor Amino Acids Inhibit Polymyxin E Biosynthesis inPaenibacillus polymyxa, Probably by Affecting the Expression of Polymyxin E Biosynthesis-Associated Genes." BioMed Research International 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/690830.

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Polymyxin E belongs to cationic polypeptide antibiotic bearing four types of direct precursor amino acids including L-2,4-diaminobutyric acid (L-Dab), L-Leu, D-Leu, and L-Thr. The objective of this study is to evaluate the effect of addition of precursor amino acids during fermentation on polymyxin E biosynthesis inPaenibacillus polymyxa. The results showed that, after 35 h fermentation, addition of direct precursor amino acids to certain concentration significantly inhibited polymyxin E production and affected the expression of genes involved in its biosynthesis. L-Dab repressed the expression of polymyxin synthetase genespmxAandpmxE, as well as 2,4-diaminobutyrate aminotransferase geneectB; both L-Leu and D-Leu repressed thepmxAexpression. In addition, L-Thr affected the expression of not onlypmxA, but also regulatory genesspo0AandabrB. As L-Dab precursor, L-Asp repressed the expression ofectB,pmxA, andpmxE. Moreover, it affected the expression ofspo0AandabrB. In contrast, L-Phe, a nonprecursor amino acid, had no obvious effect on polymyxin E biosynthesis and those biosynthesis-related genes expression. Taken together, our data demonstrated that addition of precursor amino acids during fermentation will inhibit polymyxin E production probably by affecting the expression of its biosynthesis-related genes.

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Rijnen, Liesbeth, Sophie Bonneau, and Mireille Yvon. "Genetic Characterization of the Major Lactococcal Aromatic Aminotransferase and Its Involvement in Conversion of Amino Acids to Aroma Compounds." Applied and Environmental Microbiology 65, no. 11 (November 1, 1999): 4873–80. http://dx.doi.org/10.1128/aem.65.11.4873-4880.1999.

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ABSTRACT In lactococci, transamination is the first step of the enzymatic conversion of aromatic and branched-chain amino acids to aroma compounds. In previous work we purified and biochemically characterized the major aromatic aminotransferase (AraT) of a Lactococcus lactis subsp. cremoris strain. Here we characterized the corresponding gene and evaluated the role of AraT in the biosynthesis of amino acids and in the conversion of amino acids to aroma compounds. Amino acid sequence homologies with other aminotransferases showed that the enzyme belongs to a new subclass of the aminotransferase I subfamily γ; AraT is the best-characterized representative of this new aromatic-amino-acid-specific subclass. We demonstrated that AraT plays a major role in the conversion of aromatic amino acids to aroma compounds, since gene inactivation almost completely prevented the degradation of these amino acids. It is also highly involved in methionine and leucine conversion. AraT also has a major physiological role in the biosynthesis of phenylalanine and tyrosine, since gene inactivation weakly slowed down growth on medium without phenylalanine and highly affected growth on every medium without tyrosine. However, another biosynthesis aromatic aminotransferase is induced in the absence of phenylalanine in the culture medium.

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Keeney, Kristie, Lisa Colosi, Walter Weber, and Mary O'Riordan. "Generation of Branched-Chain Fatty Acids through Lipoate-Dependent Metabolism Facilitates Intracellular Growth of Listeria monocytogenes." Journal of Bacteriology 191, no. 7 (January 30, 2009): 2187–96. http://dx.doi.org/10.1128/jb.01179-08.

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ABSTRACT The gram-positive bacterial pathogen Listeria monocytogenes has evolved mechanisms to rapidly replicate in the host cytosol, implying efficient utilization of host-derived nutrients. However, the contribution of host nutrient scavenging versus that of bacterial biosynthesis toward rapid intracellular growth remains unclear. Nutrients that contribute to growth of L. monocytogenes include branched-chain fatty acids (BCFAs), amino acids, and other metabolic intermediates generated from acyl-coenzyme A, which is synthesized using lipoylated metabolic enzyme complexes. To characterize which biosynthetic pathways support replication of L. monocytogenes inside the host cytosol, we impaired lipoate-dependent metabolism by disrupting two lipoate ligase genes that are responsible for bacterial protein lipoylation. Interrupting lipoate-dependent metabolism modestly impaired replication in rich broth medium but strongly inhibited growth in defined medium and host cells and impaired the generation of BCFAs. Addition of short BCFAs and amino acids restored growth of the A1A2-deficient (A1A2−) mutant in minimal medium, implying that lipoate-dependent metabolism generates amino acids and BCFAs. BCFAs alone rescued intracellular growth and spread in L2 fibroblasts of the A1A2− mutant. Lipoate-dependent metabolism was also required in vivo, as a wild-type strain robustly outcompeted the lipoylation-deficient mutant in a murine model of listeriosis. The results of this study suggest that lipoate-dependent metabolism contributes to both amino acid and BCFA biosynthesis and that BCFA biosynthesis is preferentially required for intracellular growth of L. monocytogenes.

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Cornick, Nancy A., Bin Yan, Shelton Bank, and Milton J. Allison. "Biosynthesis of amino acids byOxalobacter formigenes: analysis using13C-NMR." Canadian Journal of Microbiology 42, no. 12 (December 1, 1996): 1219–24. http://dx.doi.org/10.1139/m96-157.

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The gram-negative anaerobe Oxalobacter formigenes, grows on oxalate as the principal carbon and energy source, but a small amount of acetate is also required for growth. Experiments were conducted to determine the distribution and the position of label in cellular amino acids from cells grown on [13C]oxalate, [13C]acetate (1-13C, 2-13C, and U-13C), and13CCO3. The labeling pattern (determined with NMR spectroscopy) of amino acids was consistent with their formation through common biosynthetic pathways. The majority of the carbons in the amino acids that are usually derived from pyruvate, oxaloacetate, α-ketoglutarate, 3-phosphoglycerate, and carbon in the aromatic amino acids were labeled by oxalate. Carbon from13CO3was assimilated primarily into amino acids expected to be derived from oxaloacetate and α-ketoglutarate. Approximately 60% of the acetate that was assimilated into amino acids was incorporated as a C2unit into proline, arginine, glutamate, and leucine. The pattern of labeling from acetate in glutamate, arginine, and proline was consistent with acetate incorporation via citrate (si)-synthase and subsequent formation of α-ketoglutarate via the first third of the tricarboxylic acid pathway. Acetate was also assimilated into amino acids derived from pyruvate and oxaloacetate, but results indicated that this incorporation was as single carbon atoms. Based on these findings, cell-free extracts were assayed for several key biosynthetic enzymes. Enzymatic activities found included glutamate dehydrogenase, phosphoenolpyruvate carboxylase, and pyruvate carboxylase. These findings are consistent with proposed biosynthetic mechanisms.Key words: oxalate, carbon flow, carbon assimilation.

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Kuratsu, Masahiro, Yoshimitsu Hamano, and Tohru Dairi. "Analysis of the Lactobacillus Metabolic Pathway." Applied and Environmental Microbiology 76, no. 21 (September 3, 2010): 7299–301. http://dx.doi.org/10.1128/aem.01514-10.

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ABSTRACT We performed analyses of the phenotypic and genotypic relationships focusing on biosyntheses of amino acids, purine/pyrimidines, and cofactors in three Lactobacillus strains. We found that Lactobacillus fermentum IFO 3956 perhaps synthesized para-aminobenzoate (PABA), an intermediate of folic acid biosynthesis, by an alternative pathway.

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Qin, Shuang Lin, Lin Jun Tang, Li Ping Wang, Gao Peng Wang, Fei Fei Huang, Xiao Ji Wang, and Shuang Ping Huang. "Study on Synthesis of (R)-Methyl 2-((Tert-Butoxycarbonyl)Amino)-3-((Tert-Butyldimethylsilyl)Thio)Propanoate." Advanced Materials Research 1033-1034 (October 2014): 596–98. http://dx.doi.org/10.4028/www.scientific.net/amr.1033-1034.596.

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(R)-methyl 2-((tert-butoxycarbonyl) amino)-3-((tert-butyldimethylsilyl) thio) propanoate, an key intermediate of the natural product Biotin which is a water-soluble vitamin, involved in an essential part of the metabolic cycle causing catalytic fixation of carbon dioxide in the biosynthesis of fatty acids, sugars, and α-amino acids, was synthesized from L-cystine in overall yield 67% through three steps, which synthesis included esterification, protection of amine and thiol.

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Zha, Xiliang, Francis T. Jay, and Patrick C. Choy. "Effects of amino acids and ethanolamine on choline uptake and phosphatidylcholine biosynthesis in baby hamster kidney-21 cells." Biochemistry and Cell Biology 70, no. 12 (December 1, 1992): 1319–24. http://dx.doi.org/10.1139/o92-179.

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The effects of amino acids and ethanolamine on choline uptake and phosphatidylcholine biosynthesis in baby hamster kidney (BHK-21) cells were investigated. The cells were incubated with labelled choline in the presence of an amino acid or ethanolamine. The uptake of labelled choline was noncompetitively inhibited by amino acids. Glycine, L-alanine, L-serine, L-leucine, L-aspartate, and L-arginine were effective inhibitors and a maximum of 22% inhibition of choline uptake was obtained with 5 mM glycine. Analyses of the labellings in the choline-containing metabolites revealed that the conversion of choline to CDP-choline and subsequently phosphatidylcholine was not affected by the presence of amino acids. The uptake of choline was also inhibited by ethanolamine in a concentration-dependent manner. Kinetic studies on the uptake of choline indicated that the inhibition by ethanolamine was competitive in nature. Although ethanolamine is a potent inhibitor of choline kinase, analyses of the labellings in the choline-containing metabolites indicated that the conversion of choline to phosphocholine was not affected in the cells incubated with ethanolamine. Ethanolamine did not change the pool sizes of phosphocholine and CDP-choline. Based on the specific radioactivity of CDP-choline and the labelling of phosphatidylcholine, the rates of phosphatidylcholine biosynthesis were not significantly different between the control and the ethanolamine-treated cells. In view of the concentrations of amino acids (millimolar) and ethanolamine (micromolar) in most cell culture media, it appeared that only amino acids were important metabolites for the regulation of choline uptake in BHK-21 cells. We conclude that both amino acids and ethanolamine have no direct effect on the biosynthesis of phosphatidylcholine.Key words: choline uptake, phosphatidylcholine biosynthesis, amino acids, ethanolamine, BHK-21 cells.

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Ma, Qingping, Mengyao Qin, Laichao Song, Haiwei Sun, Hong Zhang, Huanhuan Wu, Zhihong Ren, et al. "Molecular Link in Flavonoid and Amino Acid Biosynthesis Contributes to the Flavor of Changqing Tea in Different Seasons." Foods 11, no. 15 (July 31, 2022): 2289. http://dx.doi.org/10.3390/foods11152289.

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The present study was aimed to elucidate the flavor formation mechanism of Changqing tea. High-performance liquid chromatography (HPLC) analysis showed that the total catechins of Changqing tea was 65–160 mg/g, with 16–34 mg/g non-galloyated catechins and 49–126 mg/g galloylated catechins. Tea polyphenols and free amino acids account for 286–312 mg/g and 35–89 mg/g, respectively. Transcriptome of Changqing tea during different seasons revealed 316, 130 and 12 DEGs in comparisons of spring vs. autumn, spring vs. summer, and summer vs. autumn, respectively. Compared to spring, the genes involved in flavonoid biosynthesis and bitter imparted amino acids were up-regulated in summer and autumn. Metabolome analysis was conducted by using HPLC-MS; the result indicated that umami and kokumi contributing amino acids were decreased in summer and autumn compared with spring. It could be concluded that the coordination of flavonoid biosynthesis and amino acids biosynthesis resulted in the special flavor of Changqing tea.

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Kudo, Fumitaka, Akimasa Miyanaga, and Tadashi Eguchi. "Biosynthesis of natural products containing β-amino acids." Nat. Prod. Rep. 31, no. 8 (2014): 1056–73. http://dx.doi.org/10.1039/c4np00007b.

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β-Amino acids are unique components involved in a wide variety of natural products such as anticancer agents taxol, bleomycin, cytotoxic microcystin, enediyne compound C-1027 chromophore, nucleoside antibiotic blasticidin S, and macrolactam antibiotic vicenistatin. The biosynthesis and incorporation mechanisms are reviewed.

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Nakamura, Kazuhiro, Yasuhiro Goto, Naoko Yoshie, and Yoshio Inoue. "Biosynthesis of poly(3-hydroxyalkanoate) from amino acids." International Journal of Biological Macromolecules 14, no. 6 (December 1992): 321–25. http://dx.doi.org/10.1016/s0141-8130(05)80072-8.

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Jastrzębowska, Kamila, and Iwona Gabriel. "Inhibitors of amino acids biosynthesis as antifungal agents." Amino Acids 47, no. 2 (November 20, 2014): 227–49. http://dx.doi.org/10.1007/s00726-014-1873-1.

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Christiansen, Jason K., Joanne E. Hughes, Dennis L. Welker, Beatriz T. Rodríguez, James L. Steele, and Jeff R. Broadbent. "Phenotypic and Genotypic Analysis of Amino Acid Auxotrophy in Lactobacillus helveticus CNRZ 32." Applied and Environmental Microbiology 74, no. 2 (November 9, 2007): 416–23. http://dx.doi.org/10.1128/aem.01174-07.

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ABSTRACT The conversion of amino acids into volatile and nonvolatile compounds by lactic acid bacteria in cheese is thought to represent the rate-limiting step in the development of mature flavor and aroma. Because amino acid breakdown by microbes often entails the reversible action of enzymes involved in biosynthetic pathways, our group investigated the genetics of amino acid biosynthesis in Lactobacillus helveticus CNRZ 32, a commercial cheese flavor adjunct that reduces bitterness and intensifies flavor notes. Most lactic acid bacteria are auxotrophic for several amino acids, and L. helveticus CNRZ 32 requires 14 amino acids. The reconstruction of amino acid biosynthetic pathways from a draft-quality genome sequence for L. helveticus CNRZ 32 revealed that amino acid auxotrophy in this species was due primarily to gene absence rather than point mutations, insertions, or small deletions, with good agreement between gene content and phenotypic amino acid requirements. One exception involved the phenotypic requirement for Asp (or Asn), which genome predictions suggested could be alleviated by citrate catabolism. This prediction was confirmed by the growth of L. helveticus CNRZ 32 after the addition of citrate to a chemically defined medium that lacked Asp and Asn. Genome analysis also predicted that L. helveticus CNRZ 32 possessed ornithine decarboxylase activity and would therefore catalyze the conversion of ornithine to putrescine, a volatile biogenic amine. However, experiments to confirm ornithine decarboxylase activity in L. helveticus CNRZ 32 by the use of several methods were unsuccessful, which indicated that this bacterium likely does not contribute to putrescine production in cheese.

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Thomas, D., and Y. Surdin-Kerjan. "Metabolism of sulfur amino acids in Saccharomyces cerevisiae." Microbiology and Molecular Biology Reviews 61, no. 4 (December 1997): 503–32. http://dx.doi.org/10.1128/mmbr.61.4.503-532.1997.

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Sulfur amino acid biosynthesis in Saccharomyces cerevisiae involves a large number of enzymes required for the de novo biosynthesis of methionine and cysteine and the recycling of organic sulfur metabolites. This review summarizes the details of these processes and analyzes the molecular data which have been acquired in this metabolic area. Sulfur biochemistry appears not to be unique through terrestrial life, and S. cerevisiae is one of the species of sulfate-assimilatory organisms possessing a larger set of enzymes for sulfur metabolism. The review also deals with several enzyme deficiencies that lead to a nutritional requirement for organic sulfur, although they do not correspond to defects within the biosynthetic pathway. In S. cerevisiae, the sulfur amino acid biosynthetic pathway is tightly controlled: in response to an increase in the amount of intracellular S-adenosylmethionine (AdoMet), transcription of the coregulated genes is turned off. The second part of the review is devoted to the molecular mechanisms underlying this regulation. The coordinated response to AdoMet requires two cis-acting promoter elements. One centers on the sequence TCACGTG, which also constitutes a component of all S. cerevisiae centromeres. Situated upstream of the sulfur genes, this element is the binding site of a transcription activation complex consisting of a basic helix-loop-helix factor, Cbf1p, and two basic leucine zipper factors, Met4p and Met28p. Molecular studies have unraveled the specific functions for each subunit of the Cbf1p-Met4p-Met28p complex as well as the modalities of its assembly on the DNA. The Cbf1p-Met4p-Met28p complex contains only one transcription activation module, the Met4p subunit. Detailed mutational analysis of Met4p has elucidated its functional organization. In addition to its activation and bZIP domains, Met4p contains two regulatory domains, called the inhibitory region and the auxiliary domain. When the level of intracellular AdoMet increases, the transcription activation function of Met4 is prevented by Met30p, which binds to the Met4 inhibitory region. In addition to the Cbf1p-Met4p-Met28p complex, transcriptional regulation involves two zinc finger-containing proteins, Met31p and Met32p. The AdoMet-mediated control of the sulfur amino acid pathway illustrates the molecular strategies used by eucaryotic cells to couple gene expression to metabolic changes.

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Ross-Inta, Catherine, Chern-Yi Tsai, and Cecilia Giulivi. "The mitochondrial pool of free amino acids reflects the composition of mitochondrial DNA-encoded proteins: indication of a post- translational quality control for protein synthesis." Bioscience Reports 28, no. 5 (September 11, 2008): 239–49. http://dx.doi.org/10.1042/bsr20080090.

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Mitochondria can synthesize a limited number of proteins encoded by mtDNA (mitochondrial DNA) by using their own biosynthetic machinery, whereas most of the proteins in mitochondria are imported from the cytosol. It could be hypothesized that the mitochondrial pool of amino acids follows the frequency of amino acids in mtDNA-encoded proteins or, alternatively, that the profile is the result of the participation of amino acids in pathways other than protein synthesis (e.g. haem biosynthesis and aminotransferase reactions). These hypotheses were tested by evaluating the pool of free amino acids and derivatives in highly-coupled purified liver mitochondria obtained from rats fed on a nutritionally adequate diet for growth. Our results indicated that the pool mainly reflects the amino acid composition of mtDNA-encoded proteins, suggesting that there is a post-translational control of protein synthesis. This conclusion was supported by the following findings: (i) correlation between the concentration of free amino acids in the matrix and the frequency of abundance of amino acids in mtDNA-encoded proteins; (ii) the similar ratios of essential-to-non-essential amino acids in mtDNA-encoded proteins and the mitochondrial pool of amino acids; and (iii), lack of a correlation between codon usage or tRNA levels and amino-acid concentrations. Quantitative information on the mammalian mitochondrial content of amino acids, such as that presented in the present study, along with functional studies, will help us to better understand the pathogenesis of mitochondrial diseases or the biochemical implications in mitochondrial metabolism.

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Ting, Chi P., Michael A. Funk, Steve L. Halaby, Zhengan Zhang, Tamir Gonen, and Wilfred A. van der Donk. "Use of a scaffold peptide in the biosynthesis of amino acid–derived natural products." Science 365, no. 6450 (July 18, 2019): 280–84. http://dx.doi.org/10.1126/science.aau6232.

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Genome sequencing of environmental bacteria allows identification of biosynthetic gene clusters encoding unusual combinations of enzymes that produce unknown natural products. We identified a pathway in which a ribosomally synthesized small peptide serves as a scaffold for nonribosomal peptide extension and chemical modification. Amino acids are transferred to the carboxyl terminus of the peptide through adenosine triphosphate and amino acyl-tRNA–dependent chemistry that is independent of the ribosome. Oxidative rearrangement, carboxymethylation, and proteolysis of a terminal cysteine yields an amino acid–derived small molecule. Microcrystal electron diffraction demonstrates that the resulting product is isosteric to glutamate. We show that a similar peptide extension is used during the biosynthesis of the ammosamides, which are cytotoxic pyrroloquinoline alkaloids. These results suggest an alternative paradigm for biosynthesis of amino acid–derived natural products.

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BESSON, F., and M. L. HOURDOU. "Effect of amino acids on the biosynthesis of .BETA.-amino acids, constituents of bacillomycins F." Journal of Antibiotics 40, no. 2 (1987): 221–23. http://dx.doi.org/10.7164/antibiotics.40.221.

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Hatch, Grant M., Willem K. Stevens, and Patrick C. Choy. "Effect of amino acids on choline uptake and phosphatidylcholine biosynthesis in the isolated hamster heart." Biochemistry and Cell Biology 66, no. 5 (May 1, 1988): 418–24. http://dx.doi.org/10.1139/o88-050.

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Choline uptake by the hamster heart has been shown to be enhanced by exogenous glycine. In this study, the effect of neutral, basic, and acidic amino acids on choline uptake was assessed. Hamster hearts were perfused with labelled choline, and in the presence of L-alanine, L-serine, or L-phenylalanine (≥0.1 mM), choline uptake was enhanced 20–38%. L-Arginine, L-lysine, L-aspartate, and L-glutamate did not influence choline uptake. The rate of phosphatidylcholine biosynthesis was unaffected by all amino acids tested. Enhancement of choline uptake by neutral amino acids was not additive or dose dependent but required a concentration threshold. The enhancement of choline uptake by neutral amino acids was not influenced by preperfusion with the same amino acid. Exogenous choline had no effect on the uptake of amino acids. We postulate that choline and the neutral amino acids are not cotransported and modulation of choline uptake is facilitated by direct interaction of the neutral amino acids with the choline transport system.

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Caballero-Molada, Marcos, María D. Planes, Helena Benlloch, Sergio Atares, Miguel A. Naranjo, and Ramón Serrano. "The Gcn2–eIF2α pathway connects iron and amino acid homeostasis in Saccharomyces cerevisiae." Biochemical Journal 475, no. 8 (April 30, 2018): 1523–34. http://dx.doi.org/10.1042/bcj20170871.

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In eukaryotic cells, amino acid biosynthesis is feedback-inhibited by amino acids through inhibition of the conserved protein kinase Gcn2. This decreases phosphorylation of initiation factor eIF2α, resulting in general activation of translation but inhibition of translation of mRNA for transcription factor (TF) Gcn4 in yeast or ATF4 in mammals. These TFs are positive regulators of amino acid biosynthetic genes. As several enzymes of amino acid biosynthesis contain iron–sulfur clusters (ISCs) and iron excess is toxic, iron and amino acid homeostasis should be co-ordinated. Working with the yeast Saccharomyces cerevisiae, we found that amino acid supplementation down-regulates expression of genes for iron uptake and decreases intracellular iron content. This cross-regulation requires Aft1, the major TF activated by iron scarcity, as well as Gcn2 and phosphorylatable eIF2α but not Gcn4. A mutant with constitutive activity of Gcn2 (GCN2c) shows less repression of iron transport genes by amino acids and increased nuclear localization of Aft1 in an iron-poor medium, and increases iron content in this medium. As Aft1 is activated by depletion of mitochondrial ISCs, it is plausible that the Gcn2–eIF2α pathway inhibits the formation of these complexes. Accordingly, the GCN2c mutant has strongly reduced activity of succinate dehydrogenase, an iron–sulfur mitochondrial enzyme, and is unable to grow in media with very low iron or with galactose instead of glucose, conditions where formation of ISCs is specially needed. This mechanism adjusts the uptake of iron to the needs of amino acid biosynthesis and expands the list of Gcn4-independent activities of the Gcn2–eIF2α regulatory system.

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Rao, Muhammad Junaid, Mingzheng Duan, Jihong Wang, Shijian Han, Li Ma, Xinyi Mo, Min Li, Lihua Hu, and Lingqiang Wang. "Transcriptomic and Widely Targeted Metabolomic Approach Identified Diverse Group of Bioactive Compounds, Antiradical Activities, and Their Associated Genes in Six Sugarcane Varieties." Antioxidants 11, no. 7 (July 4, 2022): 1319. http://dx.doi.org/10.3390/antiox11071319.

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Sugarcane is cultivated mainly for its high sucrose content but it can also produce many metabolites with promising antioxidant potential. However, very few studies have been reported on the biosynthesis of metabolites in sugarcane to date. In this study, we have identified a wide range of amino acids and organic acids in the rind of six sugarcane varieties by the LC-MS/MS method. A total number of 72 amino acids and 55 organic acid compounds were characterized; among these, 100 were reported for the first time. Moreover, 13 amino acids and seven organic acids were abundantly distributed in all varieties tested and considered major amino acids and organic acids in sugarcane. The variety Taitang134 (F134) showed the highest content of total amino acids, whereas the varieties ROC16 and Yuetang93/159 (YT93/159) had maximum content of organic acids. The amino acids of the rind extract presented higher antioxidant capacity than the organic acids of the rind extract. In addition, the transcriptomic and metabolic integrated analysis highlighted some candidate genes associated with amino acid biosynthesis in sugarcane. We selected a transcription factor gene, MYB(t), and over-expressed it in Arabidopsis. The transgenic plants showed a higher accumulation of amino acids with higher antiradical activity compared with the wild-type Arabidopsis plants. Thus, we characterize a wide range of amino acids and organic acids and their antiradical activities in different sugarcane varieties and present candidate genes that can be potentially valuable for the genetic improvement of metabolites in sugarcane bagasse

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Zhou, Tianxiao, Kaige Yang, Yinjie Ma, Jin Huang, Wenchang Fu, Chao Yan, Xinyan Li, and Yan Wang. "GC/MS-Based Analysis of Fatty Acids and Amino Acids in H460 Cells Treated with Short-Chain and Polyunsaturated Fatty Acids: A Highly Sensitive Approach." Nutrients 15, no. 10 (May 17, 2023): 2342. http://dx.doi.org/10.3390/nu15102342.

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The important metabolic characteristics of cancer cells include increased fat production and changes in amino acid metabolism. Based on the category of tumor, tumor cells are capable of synthesizing as much as 95% of saturated and monounsaturated fatty acids through de novo synthesis, even in the presence of sufficient dietary lipid intake. This fat transformation starts early when cell cancerization and further spread along with the tumor cells grow more malignant. In addition, local catabolism of tryptophan, a common feature, can weaken anti-tumor immunity in primary tumor lesions and TDLN. Arginine catabolism is likewise related with the inhibition of anti-tumor immunity. Due to the crucial role of amino acids in tumor growth, increasing tryptophan along with arginine catabolism will promote tumor growth. However, immune cells also require amino acids to expand and distinguish into effector cells that can kill tumor cells. Therefore, it is necessary to have a deeper understanding of the metabolism of amino acids and fatty acids within cells. In this study, we established a method for the simultaneous analysis of 64 metabolites consisting of fatty acids and amino acids, covering biosynthesis of unsaturated fatty acids, aminoacyl-tRNA biosynthesis, and fatty acid biosynthesis using the Agilent GC-MS system. We selected linoleic acid, linolenic acid, sodium acetate, and sodium butyrate to treat H460 cells to validate the current method. The differential metabolites observed in the four fatty acid groups in comparison with the control group indicate the metabolic effects of various fatty acids on H460 cells. These differential metabolites could potentially become biomarkers for the early diagnosis of lung cancer.

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Jim, Susan, Vicky Jones, Stanley H. Ambrose, and Richard P. Evershed. "Quantifying dietary macronutrient sources of carbon for bone collagen biosynthesis using natural abundance stable carbon isotope analysis." British Journal of Nutrition 95, no. 6 (June 2006): 1055–62. http://dx.doi.org/10.1079/bjn20051685.

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The diets of laboratory rats were isotopically and nutritionally manipulated using purifiedC3 and/or C4 macronutrients to investigate the routing of dietary carbonto bone collagen biosynthesis. Diets were formulated with purified proteins, carbohydrates andlipids of defined composition and natural abundance stable isotope ratios. Bulk protein and constituent amino acid δ13C values determined for whole diet and bone collagen provided the basis for assessing isotopic fractionation and estimating the degree of routing versus synthesis de novo of essential, non-essential and conditionally indispensable amino acids. Essential and conditionally indispensable amino acids were shown to be routed from diet to collagen with little isotopic fractionation whereas non-essential amino acids differed by up to 20‰. Mathematical modelling of the relationships between macronutrient and tissue δ13C values provided qualitative and quantitative insights into the metabolic and energetic controls on bone collagen biosynthesis. Essential amino acids comprise 21·7% of the carbon in collagen, defining the minimum amount of dietary carbon routing. Estimates of 42 and 28% routing were shown for the non-essential amino acids, glycine and aspartate, respectively. In total, the routing of non-essential and conditionally indispensable amino acids was estimated to equal 29·6% of the carbon in collagen. When the contribution of carbon from the essential amino acids is also considered, we arrive at an overall minimum estimate of 51·3% routing of dietary amino acid carbon into bone collagen.

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Sun, D. Y., X. T. Cheng, D. K. Gao, P. P. Xu, Q. Q. Guo, Z. L. Zhu, M. L. Zhu, X. Y. Wang, H. M. Qin, and F. P. Lu. "Properties, biosynthesis, and catalytic mechanisms of hydroxy-amino-acids." IOP Conference Series: Earth and Environmental Science 188 (October 30, 2018): 012084. http://dx.doi.org/10.1088/1755-1315/188/1/012084.

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Lau, Raymond C. M., and Kenneth L. Rinehart. "Biosynthesis of berninamycin: Incorporation of 13C-labeled amino acids." Journal of the American Chemical Society 117, no. 29 (July 1995): 7606–10. http://dx.doi.org/10.1021/ja00134a004.

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Zhang, Xingang, Weijuan Ni, and Wilfred A. van der Donk. "Synthesis of Nonproteinogenic Amino Acids To Probe Lantibiotic Biosynthesis." Journal of Organic Chemistry 70, no. 17 (August 2005): 6685–92. http://dx.doi.org/10.1021/jo051182o.

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Shiobara, Takuya, Yuichi Nakajima, Kazuyuki Maeda, Manami Akasaka, Yoshiyuki Kitou, Kyoko Kanamaru, Shuichi Ohsato, Tetsuo Kobayashi, Takumi Nishiuchi, and Makoto Kimura. "Identification of amino acids negatively affecting Fusarium trichothecene biosynthesis." Antonie van Leeuwenhoek 112, no. 3 (September 28, 2018): 471–78. http://dx.doi.org/10.1007/s10482-018-1172-z.

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Ibrahim Khayatt, Barzan. "Automated Reconstruction and Manual Curation of Amino Acid Biosynthesis Pathways in Sulfolobus solfataricus P2." Ibn AL-Haitham Journal For Pure and Applied Sciences 32, no. 3 (September 11, 2019): 1–18. http://dx.doi.org/10.30526/32.3.2271.

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The efficient sequencing techniques have significantly increased the number of genomes that are now available, including the Crenarchaeon Sulfolobus solfataricus P2 genome. The genome-scale metabolic pathways in Sulfolobus solfataricus P2 were predicted by implementing the â€œPathway Toolsâ€ software using MetaCyc database as reference knowledge base. A Pathway/Genome Data Base (PGDB) specific for Sulfolobus solfataricus P2 was created. A curation approach was carried out regarding all the amino acids biosynthetic pathways. Experimental literatures as well as homology-, orthology- and context-based protein function prediction methods were followed for the curation process. The â€œPathoLogicâ€ component of the â€œPathway Toolsâ€ programme was able to predict many amino acid biosynthetic metabolic pathways. The total number of the metabolic pathways was modified to 168 pathways by adding extra pathways that have not been detected by the â€œPathoLogicâ€. Amino acid biosynthetic pathways such as alpha-aminoadipic acid (AAA) pathway of Lysine biosynthesis and Alanine biosynthesis as well as the super-pathway of Phenylalanine, Tyrosine and Tryptophan biosynthesis variation II were added to the Pathway/Genome data base of Sulfolobus solfataricus P2. Discovery of the missing enzymes that have to fill in the metabolic holes in the pathways under study was the main curation task. This approach and the curated amino acid biosynthetic pathways in the PGDB of Sulfolobus solfataricus P2 can be used for genomic annotations and metabolic pathway reconstructions of closely related Bacteria and Archaea.

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Li, Nanyu, Lanlan Jiang, Yiyi Liu, Shimei Zou, Min Lu, and Huaming An. "Metabolomics Combined with Transcriptomics Analysis Revealed the Amino Acids, Phenolic Acids, and Flavonol Derivatives Biosynthesis Network in Developing Rosa roxburghii Fruit." Foods 11, no. 11 (June 1, 2022): 1639. http://dx.doi.org/10.3390/foods11111639.

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Rosa roxburghii Tratt. is a specific fruit with high nutritional value and antioxidative activities. However, the key metabolites and their biosynthesis are still unknown. Herein, a main cultivated variety, ‘Guinong 5’ (Rr5), was chosen to analyze the metabolomics of the three developmental stages of R. roxburghii fruit by liquid chromatography–tandem mass spectrometry (LC-MS/MS). A total of 533 metabolites were identified, of which 339 were significantly altered. Total phenols, flavonoids, and amino acids were significantly correlated to at least one in vitro antioxidant activity. The conjoint Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis of metabolome and transcriptome was focused on amino acid, phenylpropanoid, and flavonoid biosynthesis pathways. The amino acid, phenolic acid, and flavonol biosynthesis networks were constructed with 32 structural genes, 48 RrMYBs, and 23 metabolites. Of these, six RrMYBs correlated to 9–15 metabolites in the network were selected to detect the gene expression in six different R. roxburghii genotypes fruits. Subsequently, 21 key metabolites were identified in the in vitro antioxidant activities in the fruits at various developmental stages or in fruits of different R. roxburghii genotypes. We found that four key RrMYBs were related to the significantly varied amino acids, phenolic acids, and flavonol derivatives in the network during fruit development and the key metabolites in the in vitro antioxidative activities in the fruits of six R. roxburghii genotypes. This finding provided novel insights into the flavonoid, polyphenol, and amino acid synthesis in R. roxburghii.

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Du, Zhaokui, Weida Lin, Jinxing Zhu, and Junmin Li. "Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus." PeerJ 10 (July 5, 2022): e13689. http://dx.doi.org/10.7717/peerj.13689.

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Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).

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Bajguz, Andrzej, and Alicja Piotrowska-Niczyporuk. "Biosynthetic Pathways of Hormones in Plants." Metabolites 13, no. 8 (July 25, 2023): 884. http://dx.doi.org/10.3390/metabo13080884.

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Phytohormones exhibit a wide range of chemical structures, though they primarily originate from three key metabolic precursors: amino acids, isoprenoids, and lipids. Specific amino acids, such as tryptophan, methionine, phenylalanine, and arginine, contribute to the production of various phytohormones, including auxins, melatonin, ethylene, salicylic acid, and polyamines. Isoprenoids are the foundation of five phytohormone categories: cytokinins, brassinosteroids, gibberellins, abscisic acid, and strigolactones. Furthermore, lipids, i.e., α-linolenic acid, function as a precursor for jasmonic acid. The biosynthesis routes of these different plant hormones are intricately complex. Understanding of these processes can greatly enhance our knowledge of how these hormones regulate plant growth, development, and physiology. This review focuses on detailing the biosynthetic pathways of phytohormones.

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Jakeman, David L., Stephanie N. Dupuis, and Cathy L. Graham. "Isolation and characterization of jadomycin L from Streptomyces venezuelae ISP5230 for solid tumor efficacy studies." Pure and Applied Chemistry 81, no. 6 (May 5, 2009): 1041–49. http://dx.doi.org/10.1351/pac-con-08-11-08.

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Precursor-directed biosynthesis offers opportunities to modify natural products and obtain structurally complex metabolites without the need for chemical synthesis. However, such opportunities are limited owing to the inherent substrate specificity of biosynthetic enzymes. The jadomycins are a family of natural products produced by the soil microbe Streptomyces venezuelae ISP5230. Their biosynthesis contains one step that is potentially non-enzymatic, namely, the condensation of a biosynthetic aldehyde and an amino acid that leads to a uniquely substituted oxazolone ring. Variation of amino acids in the culture media enables the production of a wide array of substituted oxazolones. These analogs have been shown to have a variety of biological activities against cancer cell lines and also against Gram-positive bacteria. Herein, we report the first isolation and characterization of jadomycin L and jadomycin L aglycone from 8 L of bacterial culture for solid tumor efficacy studies.

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Bell, E. Arthur, Alison A. Watson, and Robert J. Nash. "Non-Protein Amino Acids: A Review of the Biosynthesis and Taxonomic Significance." Natural Product Communications 3, no. 1 (January 2008): 1934578X0800300. http://dx.doi.org/10.1177/1934578x0800300117.

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The non-protein amino acids, with which we are concerned here, are not incorporated into the proteins of the organisms that synthesize them nor are their residues formed by the post-translational modification of protein amino acid residues. Non-protein amino acids are of value in the study of relationships between species and higher taxa of organisms because most of them are of restricted distribution. If a particular non-protein amino acid is only known to occur in a limited group of species which are related in other respects then it is probable that these species have all arisen from a common ancestral form in which the biosynthetic pathway to that particular non-protein amino acid already existed.

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Cornick, N. A., and M. J. Allison. "Assimilation of oxalate, acetate, and CO2byOxalobacter formigenes." Canadian Journal of Microbiology 42, no. 11 (November 1, 1996): 1081–86. http://dx.doi.org/10.1139/m96-138.

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Oxalobacterformigenes is the only well-documented oxalate-degrading bacterium isolated from the gastrointestinal tract of animals. The production of ATP by Oxalobacter formigenes is centered around oxalate metabolism and oxalate is required for growth. A small amount of acetate (0.5 mM) is also required. Oxalate is decarboxylated to formate plus CO2in nearly equimolar amounts. Experiments were conducted to determine which potential carbon sources (oxalate, acetate, formate, CO2) were assimilated by Oxalobacter formigenes and which metabolic pathways were operative in carbon assimilation. Measurements of the specific activities of total cell carbon after growth with different14C-labeled precursors indicated that at least 54% of the total cell carbon was derived from oxalate and at least 7% was derived from acetate. Carbonate was also assimilated, but formate was not a significant source of cell carbon. Labeling patterns in amino acids from cells grown in [14C]oxalate or14CO3were different; however, in both cases14C was widely distributed into most cellular amino acids. Carbon from [14C]acetate was less widely distributed and detected mainly in those amino acids known to be derived from α-ketoglutarate, oxaloacetate, and pyruvate. Cell-free extracts contained citrate synthase, isocitrate dehydrogenase, and malate dehydrogenase activities. The labeling observed in amino acids derived from acetate is in agreement with the function of these enzymes in biosynthesis and indicates that the majority of acetate carbon entered into amino acid biosynthesis via well-known pathways.Key words: biosynthesis, carbon assimilation, metabolism.

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Bergh, Katharina Then, and Axel A. Brakhage. "Regulation of the Aspergillus nidulansPenicillin Biosynthesis Gene acvA (pcbAB) by Amino Acids: Implication for Involvement of Transcription Factor PACC." Applied and Environmental Microbiology 64, no. 3 (1998): 843–49. http://dx.doi.org/10.1128/aem.64.3.843-849.1998.

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The β-lactam antibiotic penicillin is produced as an end product by some filamentous fungi only. It is synthesized from the amino acid precursors l-α-aminoadipic acid, l-cysteine, and l-valine. Previous data suggested that certain amino acids play a role in the regulation of its biosynthesis. Therefore, in this study the effects of externally added amino acids on bothAspergillus (Emericella) nidulanspenicillin production and expression of the bidirectionally oriented biosynthesis genes acvA (pcbAB) andipnA (pcbC) were comprehensively investigated. Different effects caused by amino acids on the expression of penicillin biosynthesis genes and penicillin production were observed. Amino acids with a major negative effect on the expression of acvA-uidAand ipnA-lacZ gene fusions, i.e., histidine, valine, lysine, and methionine, led to a decreased ambient pH during cultivation of the fungus. An analysis of deletion clones lacking binding sites for the pH-dependent transcriptional factor PACC in the intergenic regions between acvA-uidA andipnA-lacZ gene fusions and in a pacC5 mutant (PacC5-5) suggested that the negative effects of histidine and valine on acvA-uidA expression were due to reduced activation by PACC under acidic conditions. These data also implied that PACC regulates the expression of acvA, predominantly through PACC binding site ipnA3. The repressing effect caused by lysine and methionine on acvA expression, however, was even enhanced in one of the deletion clones and the pacC5 mutant strain, suggesting that regulators other than PACC are also involved.

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Bennett, John. "From Amino Acids to Biotechnology Amino Acids: Biosynthesis and Genetic Regulation Klaus M. Herrman Ronald L. Somerville." BioScience 35, no. 3 (March 1985): 187. http://dx.doi.org/10.2307/1309874.

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Liu, Ziyu, Junjie Tian, Zhengang Miao, Wenxing Liang, and Guangyuan Wang. "Metabolome and Transcriptome Profiling Reveal Carbon Metabolic Flux Changes in Yarrowia lipolytica Cells to Rapamycin." Journal of Fungi 8, no. 9 (September 6, 2022): 939. http://dx.doi.org/10.3390/jof8090939.

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Yarrowia lipolytica is an oleaginous yeast for the production of oleochemicals and biofuels. Nitrogen deficiency is beneficial to lipids biosynthesis in Y. lipolytica. Target of rapamycin (TOR) regulates the utilization of nutrients, which is inhibited in nitrogen starvation or by rapamycin treatment. However, under nitrogen-rich conditions, the lipids biosynthesis in Y. lipolytica after inhibition of TOR by rapamycin is elusive. Combining metabolomics and transcriptomics analysis, we found that rapamycin altered multiple metabolic processes of Y. lipolytica grown in nitrogen-rich medium, especially the metabolisms of amino acids and lipids. A total of 176 differentially accumulated metabolites were identified after rapamycin treatment. Rapamycin increased the levels of tryptophan, isoleucine, proline, serine, glutamine, histidine, lysine, arginine and glutamic acid, and decreased the levels of threonine, tyrosine and aspartic acid. Two fatty acids in lipid droplets, stearic acid (down-regulated) and stearidonic acid (up-regulated), were identified. The expression of 2224 genes changed significantly after rapamycin treatment. Further analysis revealed that rapamycin reduced carbon flux through lipids biosynthesis, accompanied by increased carbon flux through fatty acids degradation and amino acid (especially glutamic acid, glutamine, proline and arginine) biosynthesis. The dataset provided here is valuable for understanding the molecular mechanisms of amino acid and lipids metabolisms in oleaginous yeast.

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Gong, Xuejiao, Lanying Li, Lin Qin, Yingbo Huang, Yulong Ye, Min Wang, Yingchun Wang, Yaqiong Xu, Fan Luo, and Huiling Mei. "Targeted Metabolomics Reveals Impact of N Application on Accumulation of Amino Acids, Flavonoids and Phytohormones in Tea Shoots under Soil Nutrition Deficiency Stress." Forests 13, no. 10 (October 4, 2022): 1629. http://dx.doi.org/10.3390/f13101629.

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Abstract:

The abundant amino acids and flavonoids in tea crucially contribute to its particular flavor and many health benefits. The biosynthesis of these compounds is significantly affected by carbon and nitrogen metabolism, which is regulated by the nitrogen conditions in the soil. However, exactly how N-starved tea plants use N absorbed from the soil for the biosynthesis of amino acids, flavonoids, and phytohormones is still little known. Here, tea plants that were deficient in nitrogen owing to long-term non-fertilization were subjected to a higher N application (300 kg/ha) or lower N application rate (150 kg/ha) as well as organic or inorganic N. The levels of 30 amino acids, 26 flavonoids, and 15 phytohormone compounds were analyzed using ultra-high-performance liquid chromatography quadrupole mass spectrometry (UPLC-Q-MS/MS). It was found that a continuous lack of fertilization generated a minimal availability of soil N; as a result, the yield and the theanine and soluble sugar contents were greatly decreased, while the accumulation of seven flavonoid compounds (e.g., epigallocatechin, vitexin, and genistein) increased notably. The levels of theanine, glutamate, and aspartate significantly increased with the supply of N, whereas multiple amino acids, such as alanine, phenylalanine, valine, etc., decreased, indicating that the absorption of nitrogen is preferentially used for the biosynthesis of theanine and glutamate-derived amino acids by a N-starved tea plant. Meanwhile, the changes in the accumulation of flavonoids in tea shoots with various N supplies clarified that a lower N application rate has a negative influence while higher N has a positive effect on the synthesis of flavonoids in a N-starved tea plant. In addition, following N supply, the N-deficient tea plant accumulated ABA (Abscisic acid), SA (Salicylic acid), JA (Jasmonic acid), CKs (Cytokinins), and ACC (1-Aminocyclopropanecarboxylic acid), at 2.03, 1.14, 1.97, 1.34, and 1.26 times, respectively, as high as those in a tea plant with normal fertilization. Furthermore, we performed the correlation network analysis among amino acids, flavonoids, and phytohormones. Its result confirmed that glutamate, aspartate, and hydroxyproline showed a significantly positive correlation with 8, 11, and 8 flavonoid compounds, respectively. Cis-OPDA (cis-12-oxo-phytodienoic acid) was also significantly negatively correlated with eight flavonoid compounds (e.g., naringenin, myricetin, and quercetin). Collectively, our tests suggested that a lower N application promotes the biosynthesis of the theanine and amino acids involved in theanine synthesis, thus inhibiting the accumulation of other amino acids, while greater N application promotes flavonoids in a N-starved tea plant.

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Journal articles on the topic 'Amino acids – Biosynthesis'

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