Amino acid synthesis pathway in plants -
The contents of main amino acids derived from Glu pathway Glu, Gln, Arg, Pro, and Thea , Asp pathway Asp, Ile, Thr, Lys , pyruvate pathway Ala and Leu , aromatic amino acid pathway Phe and Tyr and 3-phosphoglycerate pathway Ser and Gly were measured under the treated conditions.
Among these amino acids examined, theanine content was the highest and reached over 1. Contents of Ile, Asp, Ser, and Pro were similar, and the contents of Ala, Leu, Thr, Lys, Gly and Phe were low in tea plant roots under the treated conditions. Effects of N forms and 0N on accumulation of amino acids in tea plant roots.
Ala: Alanine; Ser: Serine; Gln: Glutamine; Pro: Proline; His: Histidine; Gly: Glycine; Arg: Arginine; Thr: Threonine; Lys: Lysine; Tyr: Tyrosine; Thea: Theanine; Leu: Leucine; Phe: Phenylalanine; Asp: Aspartic acid; Ile: Isoleucine; Glu: Glutamic acid.
Conversely, the contents of Glu-derived amino acids including Gln, Arg, Pro and Thea changed significantly under the different conditions. These results indicate that Glu pathway is not only the main flux of amino acid metabolism, but it is also most responsive to N deficiency and N forms.
Thea is synthesized from Glu and EA. EA is the product of Ala decarboxylation. Contrastingly to the Glu contents, Ala contents significantly changed in accordance with Thea contents.
This correlation suggested that formation of EA from Ala may comprise the main regulatory step of Thea synthesis. Surprisingly, a direct supply of equimolar EA 1. This implied, when low level of EA as the sole nitrogen source, EA is not used in priority as precursor to synthesize Thea but rather used for the synthesis of all amino acids.
The contents of Asp-derived Thr and Lys both changed ~1. Meanwhile, the accumulation of 3-phosphoglycerate pathway-derived Ser and Gly also showed similar response patterns.
In addition, branched-chain amino acids Leu and Ile and aromatic amino acids Phe and Tyr showed similar and slight changes Figs. These results demonstrated that metabolism of amino acids in the same pathway is likely regulated as a module, and may be controlled by genes encoding key enzymes catalyzing the common steps.
The total RNA was used to prepare cDNA libraries for transcriptomic analysis. Four biological replicates were performed.
Therefore, 20 cDNA libraries were sequenced using the Illumina HiSeq platform. In total, The clean reads were mapped to the reference genome A total of genes were identified and their expression levels in the roots under the different treatments were measured Table S3.
The comparisons found , , and DGEs for these comparisons, respectively Fig. A Venn diagram was constructed to investigate the numbers of co-expressed and uniquely expressed DEGs in response to different N forms Fig.
A total of co-expressed DEGs were obtained under treatment of all four N forms. An overview on differentially expressed genes responsive to different forms of N in tea plant root. DEGs, differentially expressed genes. adj FPKM, adjusted Fragment Per Kilo base of exon model per Million mapped reads.
Red indicates a gene up-regulated at that treatment, while green indicates down-regulated expression. D The OPLS-DA analysis of amino acids in tea plant roots under treatments with different forms of N. OPLS-DA analysis was performed by SIMCA F Hierarchical clustering representing relative expression levels of DEGs related to amino acids metabolism.
To examine the effect of different N forms on amino acid accumulation, an OPLS-DA analysis was performed to analyze 15 amino acids in tea roots under those treatments. Amino acid profiling showed that treatments of different N forms and N deficiency affected amino acids accumulation in tea roots Fig.
Subsequently, the DEGs encoding enzymes in amino acid biosynthesis and the first step of amino acid degradation were also identified. A total of genes encoding 75 enzymes were identified and their expression levels were presented in Table S6.
As shown in Fig. The two precursors of Thea synthesis are EA and Glu which are produced by CsAlaDC, CsGDHs and CsGOGATs, respectively Fig.
EA and Glu are catalyzed by CsCsTSI or CsGSs to synthesize Thea. Under this treatment, within the amino acid biosynthetic genes, CsAlaDC , CsCsTSI , CsGS TEA Impressively, total FPKM of these 3 genes accounted for Furthermore, total FPKM of CsAlaDC , CsGDHs , CsGOGATs , CsCsTSI and CsGSs accounted for as high as Therefore, the high expression of these Thea-related genes provide strong basis for the highly abundant accumulation of Thea in tea plant roots.
Identification of DEGs encoding enzymes related to Glu pathway. A The DEGs encoding enzymes related to synthesis and first step degradation of the Glu pathway. C Quantitative real-time PCR validation for potential candidate genes.
The relative expression levels and FPKM values are shown. CsAlaDC was not only the 1 st most highly expressed amino acid synthetic gene Table S6 , it was also the 5 th most highly expression genes within all genes in tea plant roots under EA-N condition Table S3.
Although CsTSI and CsGS TEA These results suggested CsAlaDC plays more regulatory role in Thea biosynthesis. Glu is the initial product of ammonia assimilation and provides α-amino group for all other amino acid biosynthesis.
It also provides carbon skeleton for Pro abd Arg biosynthesis. Therefore, Glu plays a central role in amino acid metabolism in plants Arg can be hydrolyzed by arginase into urea and ornithine Orn and was finally degraded into ammonium and carbon dioxide.
Alternatively, Arg can also be decarboxlated by Arginine decarboxylase CsADC and was further metabolized into polyamines. These results suggested CsADC regulates Arg catabolism into polyamines under N sufficient condition, and CsARG mediates Arg catabolism to ammonium under N deficient condition.
To validate the expression profiles of DEGs obtained from RNA-seq dataset, five DEGs related to the Glu pathway were selected for qRT-PCR, including CsGDH TEA The results of qRT-PCR in each treatment closely corresponded to the transcript levels of the RNA-seq dataset Fig.
Asp is synthesized from 2-oxaloacetate and Glu under the catalysis of aspartate aminotransferase AspAT Fig. Asp can then act as precursor to produce Thr, Met, Lys and Ile which are essential for mammals In this pathway, some genes encoding 25 amino acid metabolic enzymes were identified from transcriptome datasets Fig.
Identification of DEGs encoding enzymes related to Asp and pyruvate pathway. A The DEGs encoding enzymes related to synthesis and first step degradation pathway of Asp and pyruvate-derived amino acids.
In this study, we observed that Asp contents in tea plant roots were generally stable under the treatments Fig.
In addition, CsAK catalyses the first step in the conversion of Asp to Lys, Thr, Ile and Met Fig. Threonine synthase THS catalyzes Thr synthesis Fig. CsTHS TEA These results suggested CsTHS expression is probably feedback regulated by Thr accumulation in tea plant roots. Although Ile and Leu are derived from Asp and pyruvate, respectively, they are both branched-chain amino acids and share common metabolic enzymes including acetolactate synthase AHAS , ketol-acid reductoisomerase KARI , dihydroxy-acid dehydratase DHAD and branched-chain amino acid aminotransferase BCAT Fig.
Consistently, within 40 genes encoding 8 enzymes in Ile and Leu metabolism, only CsAHAS TEA Ala is synthesized from pyruvate by Alanine aminotransferase AlaT Fig. CsAlaT TEA These results suggested an importantly role of CsAlaT in Ala biosynthesis. Four representative genes CsAspAT , CsTHS , CsAK , CsAlaT were selected for qRT-PCR analysis.
Transcript levels determined by qRT-PCR were perfectly matched with those of the RNA-seq dataset Fig. The aromatic amino acids AAA Phe, Tyr, and Trp are not only essential components of protein synthesis, but also provide the precursors for the synthesis of a wide range of secondary metabolites in plants The aromatic amino acids are synthesized via the shikimate pathway, which initiates from phosphoenolpyruvate PEP and erythrose 4-phosphate E-4P.
The regulation of AAA biosynthesis via the shikimate pathways has been largely unknown in tea plant. In total, 92 annotated genes encoding 19 major enzymes in the shikimate pathway were identified Fig.
The initial step of shikimate pathway is the formation of 3-dehydroquaianate from PEP and E-4P and this reaction is catalyzed by 3-deoxy-d-arabino-heptulosonate phosphate synthase DAHPS. Within 5 genes encoding CsDAHPS, one gene TEA However, EA-N did not induce the expression of genes encoding biosynthetic enzymes in shikimate pathways Fig.
Characteristically, EA-N significantly repressed the expression of 6 genes encoding Phenylalanine ammonia-lyase PAL. Phe is a precursor for a large number of important secondary metabolites, including phenylpropanoids, flavonoids, lignin, anthocyanins, catechins, and many other metabolites The first step of Phe catabolism towards these metabolites is catalyzed by PAL.
These results suggested N, especially EA-N, represses Phe catabolism through regulating the expression of CsPALs. Shikimate is a critical precursor for aromatic amino acid synthesis. Arogenate also serves as a common substrate for both Phe and Tyr synthesis.
TAT catalyzes the first step of Tyr degradation. To further validate our results, three important genes CsPAL , CsTAT and CsTPS were chosen for qRT-PCR analysis.
The expression levels of these genes using qRT-PCR were in good accordance with corresponding transcript levels of the RNA-seq dataset Fig. It was documented that Gly, Cys, and Ser are derived from 3-phosphoglycerate in plants, and are synthesized through 6 reactions catalyzed by 6 enzymes.
Genes encoding biosynthetic and catabolic enzymes involved in 3-Phosphoglycerate pathway were screened. In total, 77 annotated genes encoding 10 major enzymes in 3-phosphoglycerate pathways were identified Fig.
Notably, only three DEGs encoding dphosphoglycerate dehydrogenase CsPGDH , Serine hydroxymethyltransferase CsSHMT and Serine O-acetyltransferase CsSOA were observed under various forms of N treatments.
Importantly, both CsSHMT and CsSOA have two members in tea plant, and these showed differential responses to N treatments. The gene expression of CsSHMT TEA Likewise, the gene expression of CsSOA TEA While, a significant decrease of transcript levels of CsSOA TEA Identification of DEGs encoding enzymes related to 3-phosphoglycerate pathway.
A The DEGs encoding enzymes related to synthesis and first step degradation pathway of amino acids from 3-phosphoglycerate pathway. To further validate our results, three important genes CsPGDH , CsSHMT and CsSOA were chosen for qRT-PCR analysis. The expression levels of these genes using qRT-PCR were consistent with corresponding transcript levels of the RNA-seq dataset Fig.
In general, the contents of secondary metabolites significantly affect the quality of tea products Among the various metabolic products, amino acids greatly contribute to the quality of green tea. Previous studies showed that N forms and N level significantly affect amino acid metabolism, thereby modulating amino acid levels in tea roots and shoots.
It is important to achieve a comprehensive understanding of the underlying molecular basis of how amino acid biosynthesis and catabolism are regulated at molecular level by N forms in tea plant root.
Several studies have explored amino acid contents and corresponding molecular changes that occur in tea plants in response to nutritional and environmental conditions 26 , 27 , 30 , 43 , 54 , 55 , 56 , Glu-derived pathway amino acids are most abundant and most dynamic in roots of tea plants.
Metabolism of amino acids derived from same precursors may be regulated in modules Figs. Notably, a direct supply of EA in the culture medium did not increase Thea synthesis, suggesting that Thea might be as a form of nitrogen storage only when N nutrition is sufficient.
In present study, we used same amount N concentration as normal nutritional solution. In this condition, the tea plants prefer to utilize EA-N to meet their need for N Fig.
S2 , but not directly providing the substrate for Thea synthesis. Bioavailability of N correlates closely to both tea yield and quality of processed tea 26 , 27 , Nutrient supplementation level is a critical factor greatly influencing both yield and quality of tea 7 , In addition, Ruan et al.
In summary, these findings are consistent with those of this study of amino acids contents in tea roots under various N forms treatments Fig. Increasing evidences showed that N forms and levels relate closely to changes of amino acids content of tea roots and leaves 26 , 27 , 30 , However, a comprehensive investigation into the molecular basis underlying amino acids metabolism in tea roots is still absent.
For example, Huang et al. Actually, previous studies reported that many amino acids are mainly synthesized in tea root, and are then transported from root to shoot 41 , 44 , Yang et al. Thus, the tissue-specific response of gene expression could not be elucidated Recently, Liu et al.
Deep RNA-sequence technology is a powerful tool to systemically identify key gene candidates in many plants, such as Poplar 60 , Arabidopsis 61 , Camellia sinensis 30 , 62 , This suggested that the genes involved in N absorption, assimilation and metabolism were remarkably affected by the forms of N.
Combined with the RNA-seq data, we identified the genes encoding enzymes involved in five main amino acid metabolism pathways. Notably, FPKM of CsAlaDC , CsGDHs , CsGOGATs , CsCsTSI and CsGSs of Thea-related amino acid biosynthetic genes accounted for as high as We speculate that high expression of these genes conferred the highly specific synthesis and accumulation of Thea in tea plant root.
In Asp and pyruvate pathway, aspartate aminotransferase AspAT catalyzed 2-oxaloacetate and Glu to synthesize Asp. Asp can be hydrolyzed by asparate kinase CsAK. In addition, Phe is a precursor for many tea secondary metabolites.
The first step of Phe catabolism is catalyzed by PAL. Our results showed EA-N significantly represses Phe catabolism by down-regulated of CsPALs , suggesting that less metabolism of Phe occurred in this treatment of shikimate pathway. Moreover, due to the significant variation of Ser and Gly contents under different forms of N and levels, we also found a key regulatory DEG CsSHMT in the 3-Phosphoglycerate pathway, which was significantly responsive to N forms treatment.
We have identified some key regulatory genes in the five main pathways of amino acid metabolism, which provided a vital and useful clue to comprehensively understand the changes of amino acid accumulation in tea roots.
However, the molecular mechanism related to how these potential genes control amino acid metabolic flux in tea roots remains unclear. Future studies of these regulatory genes will be needed to further determine the mechanistic effects.
In this study, integrated transcriptome and metabolites amino acids analyses provide new insights into amino acid metabolism of tea roots. The results showed that Glu-derived pathway amino acids are the most abundant and most dynamic in tea roots.
Metabolism of amino acids derived from same precursors may be regulated as modules. Moreover, the amino acid composition in tea roots is significantly regulated in response to different forms of N and N deficiency.
This study first systematically identified the key potential genes encoding biosynthetic enzymes as well as enzymes catalyzing the initial catabolic steps of amino acids, which can be used for providing a reference and guidance for further research on the role of these potential genes in amino acid metabolism of tea plant roots.
Two-year-old tea cutting seedings Camellia sinensis L. shuchazao were collected from Dechang Tea Fabrication Base at Shucheng County in Anhui province, China, and used for the hydroponic culture experiments in this study. In the hydroponic experiment, roots of the seedlings collected were washed in tap water to remove the soil on the root surface, and then tea cutting seedlings of similar size with 10—12 leaves were selected and transplanted into plastic pots containing 10 liters of tap water.
After 3 days, seedlings were transferred to 5-litre plastic bucket 5 plants per bucket for hydroponic culture. Afterwards, the complete basal nutrient solution was supplied for one month. The composition of the nutrient solution was used as described 50 : 0.
The pH of the nutrient solution was adjusted to 4. HCl 1. The determination of free amino acids in tea plant roots was performed as described 64 , 65 with minor modifications. Briefly, a HPLC system Waters coupled to a fluorescence detector Waters and an ultraviolet-visible detector Waters was used in this study.
Thea standard was purchased from Sigma Chemical Company St. Louis, MO, USA , and other amino acid standards were purchased from Waters Corporation Milford, Massachusetts, U. Total contents of free amino acids content were calculated as the sum of each individual free amino acid. Total RNA was extracted from root samples using the RNA pure plant Kit Tiangen, Beijing, China combined with the improved CTAB method described previously Agarose gel electrophoresis and NanoDrop spectrophotometer Thermo were used to determine the quality of samples.
Libraries were then constructed and sequenced using the Illumina Genome Analyzer Solexa. All samples for Digital Gene Expression were run in four biological replicates, and each replicate was a mixture of roots from 5 individual tea seedlings. Unique mapped reads were used for further analysis.
The fragments per kilobase of transcript sequence per millions of base pairs sequenced FPKM presented the normalized gene expression NR annotation and Gene ontology GO analysis were used to predict gene function, and identify the functional category distribution frequency GO classifications were obtained according to molecular function, biological process, and cellular component.
KEGG annotation http:www. To validate the genes expression patterns displayed by RNA-seq results, a total of 16 DEGs were randomly selected and analyzed using quantitative real-time reverse transcription PCR qRT-PCR.
qRT-PCR amplification was performed using primers designed by Primer 6. Three biological replicates were included. The expression levels of targeted genes were normalized based on the expression levels of CsACTIN in different root samples All the primers for genes amplification using qRT-PCR were listed in the Supplemental Table S The datasets analyzed during the current study are available from the corresponding author on reasonable request.
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Download references. You can also search for this author in PubMed Google Scholar. University of Wisconsin, A Bacteriology Building, Madison 6, Wisconsin, USA.
Ethel K. Institut für Kulturpflanzenforschung, Deutschen Akademie der Wissenschaften zu Berlin, Gatersleben Krs. Aschersleben , Deutschland. Institut für Zellforschung und Genetik, Medizinisches Nobelinstitut, Karolinska Institutet, Stockholm, Schweden.
Georges Dillemann Maître de Conférences Maître de Conférences. Staatsinstitut für allgemeine Botanik, Hamburg 36, Jungiusstraße 6, Deutschland. Botanisches Institut der Universität, Bonn, Meckenheimer Allee , Deutschland.
Paul Haas Formerly Reader in Plant Biochemistry Formerly Reader in Plant Biochemistry. Department of Chemistry, Indiana University, Bloomington, Indiana, USA. Felix Haurowitz Professor of Chemistry Professor of Chemistry. Department of Chemistry, Oregon State College, Corvallis, Oregon, USA.
Loomis Assistant Professor Assistant Professor. Staatsinstitut für Allgemeine Botanik, Hamburg 36, Jungiusstraße 6, Deutschland. Ernst Manshard Abteilungsvorsteher Abteilungsvorsteher. Plant Physiology Unit, Department of Botany, University of Sydney, N.
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Walter Mevius ordentl. Professor der Universität und Direktor ordentl. Professor der Universität und Direktor. Forschungsabteilung, AB Kabi, Stockholm 30, Schweden. Department of Botany, University of the Witwatersrand, Johannesburg, South-Africa.
Niilo Rautanen Lecturer in Biochemistry Lecturer in Biochemistry. Institut für Kulturpflanzenforschung, Gatersleben Krs. Agrikulturchemischen und Bodenkundlichen Institutes der Universität, Göttingen, Nikolausberger Weg 7, Deutschland. Scheffer Direktor Direktor. Karl Schmalfuss Direktor Direktor.
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University College of Swansea, Swansea, Wales, Great Britain. Street D. London Professor of Botany Professor of Botany. Department of Agric. Biochemistry, Biochem-Virus Building, University of California, Berkeley 4, California, USA. Stumpf Professor of Plant Biochemistry Professor of Plant Biochemistry.
Instituts für Ernährung Potsdam-Rehbrücke, Deutschen Akademie der Wissenschaften zu Berlin, Potsdam-Rehbrücke, In den Gehren 20, Deutschland. Kurt Täufel 1.
Direktor 1. Meirion Thomas Professor of Botany Professor of Botany. Institut für Organische Chemie, Technischen Hochschule, München, Arcisstraße 21, Deutschland. Nuffield Laboratory of Ophthalmology, University of Oxford, Great Britain.
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Abstract Amino acids, both in the free form and as constituents of protein, occupy a central position in the metabolism of all organisms, and the pathways of amino acid metabolism, as far as they are known, are for the most part quite similar from one organism to another.
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Article CAS Google Scholar Towers , G. For example, the carboxylation of glutamate allows for better binding of calcium cations.
The hydroxylation of proline is critical for maintaining connective tissues. Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.
Such modifications can also determine the localization of the protein, e. Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid.
Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism. Search site Search Search. Go back to previous article. Sign in. Learning Objectives Recognize the factors involved in amino acid synthesis.
Key Points All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Of the 22 amino acids naturally incorporated into proteins, 20 are encoded by the universal genetic code and the remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms.
Key Terms pyrrolysine : An amino acid found in methanogenic bacteria.
The core Acic is acd KEGG module for conversion of psthway compounds from glyceraldehyde-3P to Ethically harvested caffeine [MD: M on, together with the pathways around synthessis and glycine. This KEGG module is Amino acid synthesis pathway in plants Anino conserved one Amimo the KEGG MODULE database and is found in almost Hormonal balance and healthy fats the Amiho sequenced genomes. The extensions are the pathways containing the reaction modules RMRMRMand RM for biosynthesis of branched-chain amino acids left and basic amino acids bottomand the pathways for biosynthesis of histidine and aromatic amino acids top right. It is interesting to note that the so-called essential amino acids that cannot be synthesized in human and other organisms generally appear in these extensions. Furthermore, the bottom extension of basic amino acids appears to be most divergent containing multiple pathways for lysine biosynthesis and multiple gene sets for arginine biosynthesis. Image resolution: High. Link: Normal Module.
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